test_suite/fit_anyrows_time.m,348
tic;3,23
tic; for i=1:100; anyRows(a_model_dball2(:, 'ItemIndex'), [(1:50)']); end;3,23
tic; for i=1:1000; rows & rows & rows & rows;31,969
tic; for i=1:1000; rows & rows & rows & rows; end;31,969
tic;32,1024
tic; for i=1:1000; rows2 & rows2 32,1024
tic; for i=1:1000; rows2 & rows2 ; end;32,1024
logic_nm_time 34,1069
logic_error 37,1184

test_suite/tests_db/joinRowsUT.m,76
function failed 1,0
order 23,371
b_db 24,390
j_db 26,451
failed 28,481

classes/@plot_superpose/set.m,125
function b 1,0
    a.(attr)15,499
    b 16,519
    errstr 18,538
    a.plot_abstract plot_abstract
19,562
    b 20,617

classes/@plot_superpose/display.m,16
function s 1,0

classes/@plot_superpose/superposePlots.m,158
function a_plot 1,0
a_plot 39,1296
a_props 40,1315
num_plots 55,1655
    a_legend 59,1792
    w_legend 60,1830
    a_plot 61,1877
    a_props 62,1942

classes/@plot_superpose/get.m,33
function b 1,0
  errstr 14,468

classes/@plot_superpose/plot.m,224
function handles 1,0
%  axes('position', layout_axis)35,925
num_plots 38,964
all_handles 40,999
    hold all;45,1166
    to_plot 46,1180
    to_plot 49,1278
  handles 52,1418
  all_handles 53,1459
hold off;55,1503

classes/@plot_superpose/plot_superpose.m,564
function obj 1,0
% >> a_p2 45,1900
% See also: plot_abstract/superpose,superpose
49,2016
% Copyright 55,2193
  obj 65,2599
  obj 67,2708
   plot_command 87,3082
   superposable 88,3104
   plot_array 90,3184
	 break;96,3332
	 superposable 105,3591
	 break;106,3615
	 plot_command = plots{plot_num}.command;command
115,3840
	   superposable 119,4014
	   break;120,4040
  obj.plots plots
132,4215
  legend 134,4237
	axis_labels{axis_labels
141,4491
	axis_labels{axis_labels
144,4579
    plot_legend 148,4637
      legend 152,4771
  obj 161,4926

classes/@plot_superpose/axis.m,36
function ranges 1,0
ranges 30,799

classes/@plot_superpose/decorate.m,38
function handles 1,0
handles 32,901

classes/@results_profile/subsref.m,99
function b 1,0
  b 12,434
      % Generalized get method,19,581
      b 21,675
      b 24,753

classes/@results_profile/display.m,16
function s 1,0

classes/@results_profile/get.m,16
function b 1,0

classes/@results_profile/plot.m,26
function h 1,0
h 34,878

classes/@results_profile/results_profile.m,190
function obj 1,0
  obj.id id
43,1395
  obj.props props
44,1410
  obj 45,1436
  obj 47,1534
  obj.results results
53,1616
  obj.id id
54,1641
  obj.props props
55,1656
  obj 58,1700

classes/@results_profile/getResults.m,22
function results 1,0

classes/@cip_traceset_dataset/display.m,16
function s 1,0

classes/@cip_traceset_dataset/readDBItems.m,247
function 1,0
rows 34,1179
first_item 37,1284
param_names 38,1314
param_names 39,1352
test_names 40,1398
params 43,1503
tests 44,1552
start_time 47,1626
rows 51,1692
  item 58,1840
  num_traces 63,1982
  rows 68,2179
end_time 71,2212

classes/@cip_traceset_dataset/get.m,33
function b 1,0
  errstr 14,468

classes/@cip_traceset_dataset/cip_traceset_dataset.m,207
function obj 1,0
  obj.props props
46,1779
  obj 47,1805
  obj 49,1931
  obj.cip_mags cip_mags
60,2061
  obj.props props
61,2088
  listlength=64,2166
      ct 70,2306
  params_tests_dataset(77,2416

classes/@cip_traceset_dataset/loadItemProfile.m,43
function a_profile 1,0
a_profile 32,1124

classes/@doc_multi/set.m,54
function a 1,0
  a.doc_generate doc_generate
14,455

classes/@doc_multi/get.m,45
function b 1,0
  b 23,638
  errstr 25,677

classes/@doc_multi/getTeXString.m,61
function tex_string 1,0
tex_string 40,1261
  docs 44,1338

classes/@doc_multi/doc_multi.m,98
function a_doc 1,0
  a_doc 45,1392
  a_doc 47,1493
  a_doc.docs docs
53,1574
  a_doc 55,1596

classes/@cluster_db/display.m,16
function s 1,0

classes/@cluster_db/cluster_db.m,410
function a_cluster_db 1,0
   a_cluster_db.cluster_idx cluster_idx
51,1981
   %a_cluster_db.props props
52,2015
   %a_cluster_db.props = struct([]); props removed,52,2015
   a_cluster_db 55,2209
   a_cluster_db.orig_db orig_db
62,2325
   a_cluster_db.cluster_idx cluster_idx
63,2360
   %a_cluster_db.props props
64,2403
   a_cluster_db 67,2472
		       tests_db(data, col_names, {}, id, props)68,2528

classes/@cluster_db/plotQuality.m,86
function a_plot 1,0
  distance_measure 34,1005
  title_str 44,1212
a_plot 47,1288

classes/@cluster_db/get.m,33
function b 1,0
  errstr 14,468

classes/@cluster_db/plot_abstract.m,157
function a_plot 1,0
a_cluster_db 33,941
    pc2 40,1150
    score_plots{score_plots
41,1172
  cluster_props 47,1428
  a_plot 48,1474
  a_plot 57,1799

classes/@cluster_db/plotHist.m,111
function a_plot 1,0
tests_props 33,918
  title_str 37,1068
bins 40,1143
a_hist_db 43,1227
a_plot 46,1328

classes/@chans_db/plotAllVars.m,233
function a_plot 1,0
chan_props 35,1035
chan_names 37,1075
all_names 38,1111
db_id 39,1148
chan_num 44,1248
  inf_gates 50,1394
  tau_gates 51,1492
    %   create plot with act-inact curves superposed,59,1858
a_plot 67,2038

classes/@chans_db/chans_db.m,211
function a_chans_db 1,0
   a_chans_db 42,1338
   a_chans_db 44,1445
   a_chans_db.channel_info channel_info
51,1559
     a_tests_db.id id
55,1655
     a_tests_db.props props
56,1680
   a_chans_db 61,1809

classes/@chans_db/set.m,46
function a 1,0
  a.tests_db tests_db
14,455

classes/@chans_db/display.m,32
function s 1,0
display(22,564

classes/@chans_db/get.m,33
function b 1,0
  errstr 14,451

classes/@chans_db/plotInf.m,183
function a_subplot 1,0
  inf_name 38,1190
  db_id 39,1225
    powers 51,1566
  % recalculate channel conductance by inf values,54,1636
  a_chans_db 55,1703
  a_subplot 61,2007

classes/@chans_db/plotGateVars.m,198
function a_subplot 1,0
  subplots 39,1252
  db_id 40,1269
        a_chans_db 56,1683
        gate_subname 63,2041
      gate_subname_label 66,2093
      subplots 67,2152
  a_subplot 75,2398

classes/@chans_db/plotAllInf.m,167
function a_plot 1,0
chan_props 35,940
chan_names 37,980
all_names 38,1016
db_id 39,1053
all_plots 44,1185
chan_num 46,1213
  inf_gates 52,1361
a_plot 64,1654

classes/@mesh_amira/private/loadAmiraMesh.m,700
function obj 1,0
amcontents 37,1127
obj 39,1161
% Read beginning of file to parse nVertices,41,1176
obj.nVertices nVertices
44,1290
obj.nEdges nEdges
45,1328
obj.nOrigins nOrigins
46,1360
% Read vertices and edge definitions,48,1396
sec_Coordinates 54,1572
sec_NeighbourCount 55,1621
sec_Radii 56,1676
sec_NeighbourList 57,1713
sec_Origins 58,1766
blankrows 61,1822
obj.vertices vertices
67,1996
obj.neighborCount neighborCount
68,2043
obj.radii radii
69,2098
obj.neighborList neighborList
70,2136
obj.origins origins
71,2189
    val 85,2540
    val 88,2634
function num 92,2660
    num 100,3012
    num 103,3110
function data 107,3136
  end_index 110,3258
  data 112,3316

classes/@mesh_amira/plot_abstract.m,58
function a_p 1,0
title_str 37,1118
  all_title 42,1235

classes/@mesh_amira/mesh_amira.m,585
function a_mesh 1,0
  a_mesh.nVertices nVertices
49,1657
  a_mesh.nEdges nEdges
50,1681
  a_mesh.nOrigins nOrigins
51,1702
  a_mesh.vertices vertices
52,1725
  a_mesh.neighborCount neighborCount
53,1749
  a_mesh.radii radii
54,1778
  a_mesh.neighborList neighborList
55,1799
  a_mesh.origins origins
56,1827
  a_mesh.origFilename origFilename
57,1850
  a_mesh.id id
58,1880
  a_mesh.props props
59,1898
  a_mesh 60,1923
  a_mesh 62,2018
  a_mesh 68,2100
  a_mesh.origFilename origFilename
71,2189
  a_mesh.id id
72,2223
  a_mesh.props props
73,2241
  a_mesh 75,2266

classes/@mesh_amira/exportMorphML.m,551
function a_dom 1,0
% $$$   <morphml xmlns=39,1083
  docRootNode 46,1538
  cells 54,2092
  cell 57,2169
  cell.setAttribute('name', a_mesh.origFilename)origFilename
58,2207
  note 61,2285
  parents 72,2656
  edge_num 78,2818
  output_num 79,2834
      % skip backwards edges;85,3099
      output_num 98,3431
      segment 101,3496
      % two types of "cables": Regular 107,3843
    edge_num 127,4626
  cables 133,4833
  cable 136,4906
  cable 143,5158
    segment 154,5561
    prox 166,5893
    % prox=169,5973
    dist 175,6260

classes/@params_tests_db/addParams.m,92
function obj 1,0
num_params 52,1845
a_param_db 55,1920
a_test_db 59,2054
  obj 64,2275

classes/@params_tests_db/plotParamsHists.m,130
function a_ps 1,0
    barAxisProps 46,1373
axis_limits 53,1552
% with tight_limits,61,1788
y_ticks_pos 62,1843
a_ps 67,1914

classes/@params_tests_db/crossProd.m,261
function cross_db 1,0
b_num_params 31,925
a_params_db 34,1004
b_params_db 35,1060
both_params_db 36,1116
a_tests_db 39,1226
b_tests_db 40,1301
both_tests_db 41,1376
a_db.tests_db tests_db
44,1461
a_db.num_params num_params
45,1493
  cross_db 49,1623

classes/@params_tests_db/paramsHists.m,175
function p_hists 1,0
colnames 37,1153
itemsFound 39,1199
itemIndices 41,1241
colnames 49,1434
cols 52,1560
reduced_db 55,1628
num_params 56,1673
  param_vals 62,1914

classes/@params_tests_db/varyParams.m,528
function a_params_db 1,0
% with each value in levels. Thus,25,830
% pruned. Then,27,972
% See also: makeGenesisParFile,30,1091
% See also: makeGenesisParFile, ranked_db/blockedDistances,blockedDistances
30,1091
% v. 3.0. To view a copy of this license,38,1412
props 42,1575
levels=49,1682
a_params_db 52,1722
new_params 55,1794
  index 59,1975
  new_params 61,2095
a_params_db 64,2145
param_names 67,2245
% expand db using fake column(71,2378
a_params_expand_db 77,2687
a_params_db 80,2775
a_params_db 85,2942

classes/@params_tests_db/matchingRow.m,102
function crit_db 1,0
params_cols 38,1110
tests_cols 39,1143
no_params_db 48,1413
crit_db 55,1658

classes/@params_tests_db/subsref.m,165
function b 1,0
  b 26,949
	b 33,1091
% $$$ 	b(1) = tmp;			% meaningless,42,1399
% $$$ 44,1492
	% Ground case: only one DB,51,1669
	b 52,1713
      b 59,1858

classes/@params_tests_db/set.m,46
function a 1,0
  a.tests_db tests_db
14,455

classes/@params_tests_db/display.m,16
function s 1,0

classes/@params_tests_db/getProfile.m,632
function a_pt_profile 1,0
num_params 53,1812
num_tests 54,1842
col_names 57,1937
results.idx.NaN NaN
60,2031
  results.idx = setfield(results.idx, col_names{param_num}, param_num)62,2081
  results.idx = setfield(results.idx, col_names{num_params + test_num}, test_num)65,2182
very_start_time 68,2270
start_time 71,2322
results.t_hists t_hists
73,2382
start_time 77,2511
results.p_t3ds p_t3ds
79,2602
start_time 83,2745
start_time 89,3047
results.p_coefs p_coefs
91,3159
start_time 95,3313
results.pt_coefs_hists pt_coefs_hists
98,3451
start_time 102,3617
results.pp_coefs pp_coefs
105,3792
a_pt_profile 111,4038

classes/@params_tests_db/getParamNames.m,24
function col_names 1,0

classes/@params_tests_db/rankVsDB.m,143
function a_ranked_db 1,0
dist_db 41,1389
min_distance 43,1429
avg_distance 44,1478
max_distance 45,1528
a_ranked_db 49,1712
% a=51,1750

classes/@params_tests_db/joinRows.m,191
function a_db 1,0
joined_db 42,1330
% afterwards,45,1390
joined_col_names 55,1698
output_param_names 56,1741
rest_col_names 57,1808
num_params 58,1872
joined_db 61,1952
a_db 65,2112

classes/@params_tests_db/onlyRowsTests.m,134
function obj 1,0
  cols 39,1309
  param_col_idx 42,1380
  varargin{varargin
45,1465
  obj 48,1560
obj.tests_db tests_db
50,1616

classes/@params_tests_db/invarParam.m,332
function a_3D_db 1,0
num_params 47,1877
props 48,1913
col_name_cell 49,1952
  no_trial_cols 56,2267
  % before everything,60,2391
  % before everything, make sure database has no redundant parameter sets60,2391
    db 65,2649
col 69,2707
cols 72,2784
db_props 75,2857
db_props(1).invarName invarName
76,2886
db 77,2934

classes/@params_tests_db/get.m,87
function b 1,0
  b 14,474
% $$$   b 18,518
% $$$   errstr 20,552
% $$$   b 23,623

classes/@params_tests_db/delColumns.m,82
function obj 1,0
obj.tests_db tests_db
32,893
obj.num_params num_params
33,941

classes/@params_tests_db/paramsCoefs.m,83
function p_coefs 1,0
num_tests 31,886
p_coefs 33,959
  p_coefs{p_coefs
38,1169

classes/@params_tests_db/scanParamAllRows.m,467
function a_params_db 1,0
% See also: makeGenesisParFile,32,1420
% See also: makeGenesisParFile, scaleParamsOneRow,32,1420
% See also: makeGenesisParFile, scaleParamsOneRow, ranked_db/blockedDistances,blockedDistances
32,1420
% See also: makeGenesisParFile, scaleParamsOneRow, ranked_db/blockedDistances, getParamRowIndices,32,1420
% v. 3.0. To view a copy of this license,40,1777
  levels 52,2119
a_params_db 58,2308
a_params_db 62,2460
a_params_db 65,2547

classes/@params_tests_db/plotVarBoxMatrix.m,298
function a_plot_stack 1,0
num_params 35,960
num_tests 36,990
plot_rows 43,1191
  ranges 47,1282
      ranges 56,1548
    plots{plots
58,1606
    rprops 65,1774
  % fixed y-axis bounds,72,1949
  % fixed y-axis bounds, but flexible x-axis axis
72,1949
vprops 77,2156
a_plot_stack 81,2287

classes/@params_tests_db/rankVsAllDB.m,238
function tex_string 1,0
% Generate a tests list without the ItemIndex column 38,1268
rows_per_page 43,1475
    page_props 49,1676
  tex_string 52,1708
stats_db 57,1844
tex_string 58,1892
tex_string 62,2087
    tex_string 75,2603

classes/@params_tests_db/paramsTestsCoefsHists.m,120
function pt_coefs_hists 1,0
num_tests 32,986
pt_coefs_hists 34,1059
	histogram(p_coefs{param_num}, test_num)38,1205

classes/@params_tests_db/paramsParamsCoefs.m,179
function pp_coefs 1,0
num_tests 33,1075
pp_coefs 35,1148
  a_coef_db 38,1247
  all_test_cols 40,1319
  all_test_cols 46,1634
  j2_db 49,1772
    pp_coefs{pp_coefs
54,2018

classes/@params_tests_db/params_tests_db.m,327
function obj 1,0
  obj 58,2016
  obj 60,2123
  obj.num_params num_params
63,2187
    props 67,2285
  %obj.props props
69,2315
  obj 70,2362
  data 99,3460
  col_names 100,3495
  obj.num_params num_params
102,3539
  obj 103,3579
  obj = class(obj, 'params_tests_db', tests_db(data, col_names, {}, id, props)103,3579

classes/@params_tests_db/invarParams.m,76
function p_t3ds 1,0
num_tests 30,806
% no need,32,850
%a_db a_db
33,889

classes/@params_tests_db/mergeMultipleCIPsInOne.m,307
function cip_fold_db 1,0
% Fold into multiple pages,71,2727
cip_fold_db 72,2779
  db_cip_levels 77,2932
  num_cip_levels 81,3062
  new_cip_fold_data 82,3106
  cip_fold_db 91,3447
page_suffixes 95,3562
tests_cell 96,3607
num_pages 105,3911
cip_fold_db 112,4166
% Get the parameters back 119,4344

classes/@params_tests_db/displayRankingsTeX.m,1347
function tex_string 1,0
tex_string 46,1643
ranked_db 48,1661
joined_db 49,1702
ranked_num_rows 50,1739
a_db_id 53,1810
crit_db_id 54,1863
    num_best 61,2060
  top_ranks 63,2085
  short_caption 64,2169
  caption 65,2233
  tex_string 67,2328
  num_best 72,2526
  top_ranks 73,2543
  all_param_cols 74,2627
  p_hists 76,2743
  filename 83,3061
  filename 85,3184
  filename 86,3225
  filename 87,3266
  short_caption 92,3459
  caption 93,3550
  tex_string 96,3672
    crit_trace_d100 112,4376
    crit_trace_h100 116,4554
    crit_trace_id 120,4733
    num_plots 122,4804
    trace_d100_plots 123,4823
    trace_h100_plots 124,4866
      trial_num 128,4981
	crit_traces 131,5117
	sup_props 133,5146
	crit_traces 134,5167
      plot_matching_d100 136,5197
      trace_d100_plots{trace_d100_plots
138,5299
			 'plot', sup_props)142,5497
      plot_matching_h100 143,5521
      trace_h100_plots{trace_h100_plots
145,5624
			 'plot', sup_props)148,5764
    best_filename 156,6063
    best_filename 161,6288
    orient tall;162,6341
    horiz_props 164,6403
    d100_row_plot 165,6493
    h100_row_plot 167,6667
    filename 174,6995
    filename 179,7201
    short_caption 183,7331
    caption 185,7428
    tex_string 187,7536
    short_caption 197,7925
    caption 199,8032
    tex_string 203,8253

classes/@params_tests_db/meanDuplicateParams.m,59
function a_params_tests_db 1,0
a_params_tests_db 34,1141

classes/@params_tests_db/testsHists.m,231
function t_hists 1,0
  % reduced_tests_db 38,1175
  reduced_tests_db 40,1252
  hist_pars 46,1370
t_hists 49,1409
function reduced_db 53,1468
  itemIndices 55,1550
  tests 58,1664
  % Preserve original column order 60,1725

classes/@params_tests_db/getParamRowIndices.m,186
function row_indices 1,0
data 34,995
row_indices 35,1021
  lrows 38,1082
    lrows 41,1204
  found_num 43,1301
    found_num 46,1428
    found_num 50,1553
  row_indices 52,1580

classes/@params_tests_db/unionCat.m,133
function a_db=1,0
  with_db = unionCat(varargin{1}, varargin{varargin
26,839
elseif isempty(27,891
  with_db 31,944
a_db 34,974

classes/@params_tests_db/fillMissingParams.m,36
function db 1,0
dif_names 34,1067

classes/@params_tests_db/makeGenesisParFile.m,301
%   For each a_db row,9,219
% See also: scanParamAllRows,27,821
% Copyright 33,991
  trial_col 52,1602
    a_db = addParams(a_db, {'trial'}, trial_col)54,1675
    lerr 56,1733
    % If column already exists,57,1755
  param_names 69,2120
first_row 76,2370
data_rows 79,2515
data_str 82,2648

classes/@params_tests_db/getDualCIPdb.m,75
function a_db 1,0
  merged_db 42,1537
% Get the parameters back 46,1647

classes/@params_tests_db/unionCatTwo.m,483
function a_db=1,0
with_params 35,1116
with_names 36,1154
params 37,1211
names 38,1239
combined_params 41,1329
combined_cols 42,1375
with_db 45,1444
db 46,1502
with_db 48,1551
db 49,1610
  with_db 58,1982
props=70,2351
with_props=71,2374
commonfield=72,2407
        props.(field{field
75,2534
        props.(field{1})=mergeStructs(props.(field{1}),with_props.(field{field
75,2534
    elseif iscell(props.(field{1})) || isnumeric(76,2613
props=80,2760
a_db 82,2826

classes/@params_tests_db/reIndexNeurons.m,231
function a_db 1,0
colName 32,1039
data 34,1081
col_name_cell 35,1107
colIdx 36,1157
old_idx 37,1200
new_sort_idx 39,1261
new_idx 40,1328
a_db 43,1417
props=45,1450
        props.neuron_idx.(k{k
49,1584
    a_db 51,1660

classes/@plot_stack/set.m,97
function a 1,0
    a.(attr)15,496
    errstr 17,524
    a.plot_abstract plot_abstract
18,548

classes/@plot_stack/display.m,28
function s 1,0
  s 19,544

classes/@plot_stack/superposePlots.m,78
function a_plot 1,0
num_plot_stacks 39,1326
a_plot 56,1876
a_plot 57,1895

classes/@plot_stack/get.m,33
function b 1,0
  errstr 14,468

classes/@plot_stack/plot_stack.m,345
function a_plot 1,0
  a_plot.axis_limits axis_limits
54,2182
  a_plot.orient orient
55,2209
  a_plot 56,2232
   a_plot 58,2340
   a_plot.plots plots
83,2761
   a_plot.axis_limits axis_limits
84,2786
   a_plot.orient orient
85,2823
   % By default,90,2988
   a_plot 91,3040
	     plot_abstract([], {}, title_str, {}, '', props)93,3095

classes/@plot_stack/plot.m,1594
function handles 1,0
verbose 36,1003
a_plot_props 38,1038
minwidth 40,1076
minheight 41,1094
  border 48,1309
plot_stack_id 51,1328
left_side 66,1695
bottom_side 67,1723
width 68,1753
height 69,1777
% Hide the axis,71,1803
  set(77,2008
num_plots 101,2715
decosize_x 107,2922
decosize_y 108,2944
tickwidth 115,3246
labelheight 116,3261
labelwidth 117,3278
titleheight 118,3294
% If only topmost plot has title,140,3872
  relative_sizes 155,4454
  tileheight 160,4622
elseif strcmp(161,4645
      one_plot 175,5041
    maximal_ranges 177,5090
  bottom_space 185,5273
  title_space 186,5293
    % invert the sequence,191,5377
    plot_seq 192,5448
    one_plot 197,5567
  its_props 206,5861
        its_props(1).YTickLabel YTickLabel
216,6227
      % Then,219,6284
      %its_props(1).YTickLabel YTickLabel
221,6369
        its_props(1).noYLabel noYLabel
234,6821
      % Then,237,6875
      its_props(1).XTickLabel XTickLabel
255,7494
    bottom_space 258,7545
    %its_props(1).XTickLabel XTickLabel
262,7673
      its_props(1).noXLabel noXLabel
271,7994
    bottom_space 275,8099
        its_props(1).noTitle noTitle
289,8656
        its_props(1).noTitle noTitle
291,8701
      title_space 294,8754
        its_props(1).noTitle noTitle
299,8919
        its_props(1).noTitle noTitle
301,8964
  one_plot 307,9072
  x_offset 310,9155
  y_offset 312,9308
    this_height 316,9558
    this_width 318,9595
    this_height 319,9623
  position 321,9686
    current_axis 333,10105
    axis_height 338,10339
handles 350,10721
hold off;352,10736

classes/@plot_stack/decorate.m,51
function handles 1,0
%handles.title title
31,783

classes/@dataset_db_bundle/dataset_db_bundle.m,315
function a_bundle 1,0
  a_bundle.db db
50,2034
  a_bundle.joined_db joined_db
51,2060
  a_bundle.props props
52,2093
  a_bundle 53,2124
  a_bundle 55,2238
  a_bundle.dataset dataset
61,2327
  a_bundle.db db
62,2359
  a_bundle.joined_db joined_db
63,2381
  a_bundle.props props
64,2417
  a_bundle 66,2444

classes/@dataset_db_bundle/matchingRow.m,39
function crit_db 1,0
crit_db 42,1265

classes/@dataset_db_bundle/subsref.m,63
function b 1,0
  b 43,1161
      b 49,1277
      b 51,1322

classes/@dataset_db_bundle/set.m,16
function a 1,0

classes/@dataset_db_bundle/plotfICurve.m,315
function a_plot 1,0
% See also: plot_abstract,27,806
% Copyright 33,965
neuron_name 43,1305
  short_caption 48,1433
  caption 56,1607
% Get unique current values 59,1643
      curve_tests 71,2015
      curve_tests 73,2102
      curve_tests 75,2190
curve_labels 81,2354
joined_db 83,2414
a_plot 85,2455

classes/@dataset_db_bundle/display.m,16
function s 1,0

classes/@dataset_db_bundle/reportNeuron.m,1918
function a_doc 1,0
  num_items 66,2687
% If input is an array,69,2724
db_id 97,3404
      a_doc 106,3736
      % Get raw data traces from bundles110,3847
      a_doc 114,4045
      % Get raw data traces from bundles120,4290
      a_doc 124,4494
      plot_title 133,4921
      a_doc 137,5066
      plot_title 152,5754
	fI_axis_limits 159,5988
      fIcurve_plot 162,6032
      a_doc 165,6155
      a_trace_rate_plot 179,6825
      short_caption 180,6908
      caption 182,7037
      a_doc 183,7068
      a_trace_rate_plot 191,7479
      short_caption 192,7562
      caption 194,7691
      a_doc 195,7722
      short_caption 203,8138
      caption 205,8272
      a_doc 206,8303
      trace_plot_quad 220,8966
	fI_axis_limits 231,9464
      fIcurve_plot 234,9508
      sshape_ratecurve_plot 243,9801
      short_caption 247,9939
      caption 251,10194
      a_doc 252,10225
  % The following are nested functions,269,10802
function sshape_doc 272,10891
  caption 275,10991
  sshape_doc 277,11025
function 286,11331
    trace_axis_limits 290,11506
    a_d100_plot 300,11781
    a_h100_plot 310,12050
  a_d100_plot.legend legend
314,12111
  a_h100_plot.legend legend
315,12138
  plot_title 317,12166
  trace_plot 318,12196
function 325,12426
  trace_h100 327,12565
  trace_id 328,12625
  short_caption 330,12677
  % If specified,332,12730
  % Mostly to allow showing only one trace,333,12806
      trace_h100 338,13052
      caption 339,13103
      trace_d100 344,13358
      trace_h100 345,13441
      caption 346,13524
    caption 352,13734
function 361,13903
    sshape_axis_limits 366,14125
  pulse_sshape_plot 378,14500
  both_sshape_plots 381,14683
function a_plot_doc 387,14874
function sshape 396,15278
  num_spikes 398,15346
    sshape 403,15539
function a_trace_rate_plot 407,15576
    rate_axis_limits 413,15785
  a_trace_rate_plot 416,15828

classes/@dataset_db_bundle/getNeuronRowIndex.m,26
function a_row_index 1,0

classes/@dataset_db_bundle/get.m,16
function b 1,0

classes/@dataset_db_bundle/profileFromRows.m,109
function a_prof 1,0
fs_db 34,1051
col_names 35,1080
index_col 36,1111
  indices 45,1435
a_prof 51,1569

classes/@dataset_db_bundle/constrainedMeasuresPreset.m,1919
function 1,0
p1_test_names 38,1074
p2_test_names 107,5945
test_weights 138,7235
    % Same tests as in 144,7386
    test_names 145,7431
    test_weights.PulsePotAvg_H100pA PulsePotAvg_H100pA
146,7463
    % Same tests as in 148,7514
    test_names 149,7559
    test_weights.PulsePotAvg_H100pA PulsePotAvg_H100pA
150,7591
    % Same tests as in 152,7643
    test_names 154,7752
    test_weights.PulsePotAvg_H100pA PulsePotAvg_H100pA
155,7784
    test_weights.RecIniSpontPotRatio_D100pA RecIniSpontPotRatio_D100pA
156,7826
    test_weights.RecIniSpontRateRatio_D100pA RecIniSpontRateRatio_D100pA
157,7877
    test_names 160,7963
    % Same as 162,8004
    test_names 163,8049
    test_weights.PulsePotAvg_H100pA PulsePotAvg_H100pA
164,8081
    test_weights.PulsePotSag_H100pA PulsePotSag_H100pA
165,8123
    test_weights.PulseSpikeAmplitude_D100pA PulseSpikeAmplitude_D100pA
166,8165
    % Same as 168,8224
    test_names 169,8266
    test_weights.PulsePotAvg_H100pA PulsePotAvg_H100pA
170,8298
    test_weights.PulsePotSag_H100pA PulsePotSag_H100pA
171,8340
    test_weights.PulseSpikeAmplitude_D100pA PulseSpikeAmplitude_D100pA
172,8382
    rate_factor 173,8432
    test_weights.IniSpontSpikeRateISI_0pA IniSpontSpikeRateISI_0pA
174,8455
    test_weights.PulseIni100msSpikeRateISI_D40pA PulseIni100msSpikeRateISI_D40pA
175,8512
    test_weights.PulseIni100msRest2SpikeRateISI_D40pA PulseIni100msRest2SpikeRateISI_D40pA
176,8576
    test_weights.PulseIni100msSpikeRateISI_D100pA PulseIni100msSpikeRateISI_D100pA
177,8645
    test_weights.PulseIni100msRest2SpikeRateISI_D100pA PulseIni100msRest2SpikeRateISI_D100pA
178,8710
    test_weights.PulseIni100msSpikeRateISI_D200pA PulseIni100msSpikeRateISI_D200pA
179,8780
    test_weights.PulseIni100msRest2SpikeRateISI_D200pA PulseIni100msRest2SpikeRateISI_D200pA
180,8845
j_db 185,8993
test_names 188,9058
j_db 190,9118
a_bundle 196,9276

classes/@dataset_db_bundle/ctFromRows.m,26
function a_cip_trace 1,0

classes/@dataset_db_bundle/subsasgn.m,44
function a 1,0
  a 18,590
      a 31,895

classes/@dataset_db_bundle/simNewParams.m,28
function 1,0
fs_db 33,993

classes/@dataset_db_bundle/rankingReportTeX.m,1372
function tex_string 1,0
tex_string 44,1695
a_ranked_db 46,1713
joined_db 47,1770
ranked_num_rows 48,1809
a_db_id 51,1882
crit_db_id 52,1949
  crit_trace_h100 63,2333
  crit_trace_id 69,2551
  num_plots 71,2620
  trace_d100_plots 72,2637
  trace_h100_plots 73,2678
    trial_num 77,2787
      crit_traces 80,2924
      sup_props 82,2956
      crit_traces 83,2982
    trace_d100_plots{trace_d100_plots
85,3015
		       'plot', sup_props)89,3240
    trace_h100_plots{trace_h100_plots
90,3269
		       'plot', sup_props)93,3432
  best_filename 101,3726
  orient tall;102,3818
  horiz_props 104,3879
  d100_row_plot 105,3967
  h100_row_plot 107,4139
  filename 114,4459
  short_caption 118,4630
  caption 120,4725
  tex_string 122,4829
  short_caption 131,5166
  caption 133,5269
  tex_string 137,5482
    num_best 150,5888
  top_ranks 152,5913
  short_caption 153,5999
  caption 154,6063
  tex_string 156,6158
  num_best 161,6344
  filename 165,6464
  orient tall;167,6599
  short_caption 171,6741
  caption 173,6897
  tex_string 177,7113
  filename 188,7501
  orient tall;190,7643
  short_caption 194,7785
  caption 196,7948
  tex_string 200,8209
  num_best 208,8496
  top_ranks 209,8513
  all_param_cols 210,8597
  p_hists 212,8713
  filename 219,9031
  short_caption 225,9275
  caption 226,9366
  tex_string 229,9488

classes/@voltage_clamp/periodWhole.m,27
function whole_period 1,0

classes/@voltage_clamp/plotAllIVs.m,88
function a_p 1,0
title_str 30,831
  all_title 35,932
skip_step 39,1065
a_p 42,1160

classes/@voltage_clamp/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,650

classes/@voltage_clamp/voltage_clamp.m,443
function a_vc 1,0
  a_vc.i i
53,1761
  a_vc.v v
54,1779
  a_vc.time_steps time_steps
55,1797
  a_vc.v_steps v_steps
56,1821
  a_vc.i_steps i_steps
57,1842
  a_vc 58,1863
  a_vc 60,1965
  % find time and values of voltage steps and steady-state currents66,2043
  a_vc 70,2203
  a_vc.i i
71,2220
  a_vc.v v
73,2368
  a_vc.time_steps time_steps
74,2423
  a_vc.v_steps v_steps
75,2455
  a_vc.i_steps i_steps
76,2481
  a_vc 78,2508

classes/@voltage_clamp/set.m,70
function b 1,0
    b 21,583
    b 24,632
    b.trace trace
25,643

classes/@voltage_clamp/getTimeRelStep.m,40
function rel_time 1,0
rel_time 33,837

classes/@voltage_clamp/private/findSteps.m,266
function 1,0
  data_t 49,1347
time 52,1371
num_mags 53,1406
step_dur 57,1544
thr 59,1607
time_steps2 65,1868
num_steps 72,2024
i_steps 78,2203
  step_range 81,2317
data_len 90,2575
step_range 91,2603
function time_steps 98,2783
    time_steps 102,2988

classes/@voltage_clamp/private/findChange.m,141
function t_change 1,0
  first_ms 4,118
  t_begin 5,134
  v_start 6,159
  %v_start_sd v_start_sd
7,221
  % find beginning of step 9,289

classes/@voltage_clamp/get.m,45
function b 1,0
  b 23,638
  errstr 25,677

classes/@voltage_clamp/withinPeriod.m,119
function 1,0
end34,1073
num_samples 39,1197
a_vc.time_steps time_steps
42,1254
a_vc.time_steps time_steps
45,1352

classes/@voltage_clamp/scale_sub_cap_leak.m,1049
function 1,0
% See also: param_I_v,47,2041
title_str 61,2564
dt 63,2608
cell_name 64,2664
time 66,2694
range_rel 69,2801
  range_rel 73,2923
  step_num 75,2960
range_maxima 77,2980
range_cap_resp 81,3153
use_levels 84,3254
  f_capleak 93,3515
extra_text 96,3554
  all_title 105,3836
props 124,4345
  line_colors 128,4429
  function stop 130,4496
    stop 137,4843
  fig_props 140,4868
  function stop 142,4893
      Im 146,5106
      fig_handle 147,5195
            fig_props)170,6597
      fig_props 171,6621
    stop 173,6708
  v_legend 178,6804
  params 182,6934
  %select_params select_params
186,7021
  %select_params select_params
187,7062
  %f_capleak f_capleak
188,7094
  f_capleak_orig 191,7191
  f_capleak 194,7237
  extra_text 201,7496
    all_title 210,7786
  params 219,8086
  Im 221,8126
  line_colors 251,9484
  period_range 254,9569
% $$$   period_range 255,9639
  range_steps 262,9946
  model_vc 264,9984
  sub_vc 267,10077
  Re 270,10152
  sub_vc.v v
276,10487
    all_title 281,10610

classes/@voltage_clamp/plot_abstract.m,531
function a_p 1,0
title_str 41,1354
cur_unit 43,1398
    cur_scale 49,1512
v_steps 56,1687
v_legend 58,1751
  cur_label 65,1946
  plot_label 68,2039
  cur_label 69,2062
dt 73,2131
data_i 75,2188
data_v 76,2230
cell_name 77,2260
time 78,2289
  all_title 83,2398
vcolor_func 87,2468
line_colors 90,2554
axis_limits 93,2630
plot_props 100,2841
% $$$ plot_i 106,3044
% $$$                   plot_props)109,3193
plot_i 110,3230
% $$$ plot_v 113,3322
% $$$                     plot_props)117,3503
plot_v 118,3542

classes/@voltage_clamp/updateSteps.m,141
function a_vc 1,0
% recalculate values of step steady-state currents30,541
a_vc.time_steps time_steps
35,753
a_vc.v_steps v_steps
36,783

classes/@voltage_clamp/saveDataTxt.m,120
dt 35,725
data_i 37,782
cell_name 38,812
time 39,841
vc_props 45,952
% extract cell name and path from file47,984

classes/@voltage_clamp/plotSimCurrent.m,186
function a_p 1,0
dt 35,818
data_i 37,875
data_v 38,905
cell_name 39,935
time 40,964
period_range 43,1019
range_steps 45,1142
line_colors 55,1493
% $$$ a_p 58,1575
a_p 71,2371

classes/@voltage_clamp/setLevels.m,140
function a_vc 1,0
a_vc.v.data data
34,743
a_vc.i.data data
35,781
a_vc.i_steps i_steps
38,847
a_vc.v_steps v_steps
39,887
a_vc 41,928

classes/@voltage_clamp/getResults.m,484
function a_prof 1,0
% >> a_db 20,540
skip_step 32,925
params 35,990
% add peak current,37,1009
% add peak current, persistent component,37,1009
act_vc 38,1056
act_props 43,1237
results.peakITrans peakITrans
47,1333
results.peakVTrans peakVTrans
49,1396
halfITrans 53,1511
half_act_idx 54,1548
results.actVhalfobs actVhalfobs
66,1931
inact_vc 69,2035
inact_props 73,2218
half_inact_idx 75,2257
results.inactVhalfobs inactVhalfobs
78,2340
% persistent current 81,2425

classes/@voltage_clamp/plotSteadyIV.m,423
function a_p 1,0
% TODO: make this part a private function;44,1416
cur_unit 46,1505
    cur_scale 52,1619
plot_label 62,1812
dt 64,1867
data_i 66,1924
data_v 67,1954
cell_name 68,1984
time 69,2013
vc_props 70,2048
  all_title 75,2153
elseif isfield(81,2297
    props.stepRange stepRange
84,2404
    cur_step_num 86,2455
  props.stepRange stepRange
88,2490
  i_steps 90,2581
  i_steps 93,2669
a_p 96,2713

classes/@voltage_clamp/calcCurPeaks.m,488
function a_vc 1,0
step_num 38,1184
num_vsteps 39,1224
dt 40,1260
% by default,44,1306
rel_start 47,1427
  rel_start 51,1553
  start_step_num 53,1586
rel_end 56,1624
  rel_end 60,1739
  end_step_num 62,1768
  start_time 68,1845
  end_time 74,1980
range_maxima 77,2029
range_vc 83,2277
i_peaks 87,2407
% $$$     f 94,2634
  % compare magnitude of min and max peaks;97,2667
    val = min_val; idx 105,2964
    val 107,3005
    val = max_val; idx 107,3005
a_vc 121,3473

classes/@voltage_clamp/simModel.m,273
function model_vc 1,0
dt 49,1397
data_v 51,1454
cell_name 52,1484
time 53,1513
nA_scale 56,1580
period_range 59,1629
% set and update the period63,1807
range_steps 67,1927
model_vc 76,2098
  model_vc.v v
82,2305
  Im 86,2444
model_vc 95,2701
model_vc 98,2814

classes/@voltage_clamp/minus.m,186
function sub_vc 1,0
% plot the subtracted voltage trace,26,674
sub_vc 39,934
sub_vc 40,986
% recalculate values of step steady-state currents43,1097
sub_vc.i_steps i_steps
47,1263

classes/@voltage_clamp/scale_IClCa_NaP_sub_IClCa.m,996
function params 1,0
dt 46,1435
data_i 48,1492
data_v 49,1522
cell_name 50,1552
time 51,1581
t_step_start 54,1635
t_step_end 57,1703
range_prepulse 60,1807
v_prepulse 61,1876
i_prepulse 63,1932
v_steps 68,2115
i_steps 71,2169
  % INaP 99,3239
  % minf 100,3276
  ENa 101,3317
  %minf_ClCa minf_ClCa
106,3436
  mtau_ClCa 107,3487
  EClCa 108,3510
  Vpre 112,3614
  m0_ClCa 113,3638
  v_delay 114,3675
  v_delay = 2; % ms,114,3675
  f_INaP_minf_v 122,3947
  % and IClCa parameters,125,4155
  %f_INaP_minf_v f_INaP_minf_v
129,4401
  %m_inf_ClCa m_inf_ClCa
130,4460
  f_steady 131,4492
  f_steady 145,5073
  %  MSE of 148,5204
  m_NaP_steps 202,7278
  minf_nap 205,7366
  V=206,7432
f_IClCa_v 248,8942
f_IClCa_v 249,9001
f_IClCa_v.f.m m
250,9046
range_steps 253,9129
data_sub_ClCa 263,9415
line_colors 275,9859
function t_change 305,11242
  t_begin 308,11340
  v_start 309,11365
  %v_start_sd v_start_sd
310,11422
  t_change 313,11512
  t_change 314,11590

classes/@trace/periodWhole.m,27
function whole_period 1,0

classes/@trace/analyzeSpikesInPeriod.m,647
function 1,0
  verbose 38,1546
  ms_factor 40,1583
  period_trace 42,1624
  period_spikes 43,1672
  num_spikes 44,1722
  empty_results 47,1820
  empty_results.Index Index
48,1863
  empty_results.Time Time
49,1892
  % Collect spike shape analysis results,52,1987
	a_results 61,2315
	a_results.Index Index
62,2343
	spike_time 63,2373
	period_spikes_new 64,2419
	a_results.Time Time
65,2482
	err 68,2575
	  warning('trace:info', 'Rethrowing error in %s spikes:', prefix_str)76,2893
    period_spikes_new 83,3055
  test_names 86,3101
  num_tests 87,3143
  % find mean,96,3534
  % find mean, std 96,3534
  period_spikes 121,4575

classes/@trace/power.m,62
function res_tr 1,0
% See also: trace,24,463
res_tr 34,649

classes/@trace/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,651

classes/@trace/set.m,49
function b 1,0
    b 20,582
    errstr 22,601

classes/@trace/saveAsNeuronVecAscii.m,30
%   filename:filename
10,226

classes/@trace/getSpike.m,344
function obj 1,0
num_traces 41,1237
num_spikes 42,1261
trace_props 67,1849
copy_from_trace 70,1925
    props.(copy_from_trace{copy_from_trace
75,2141
spike_idx 84,2419
  max_left 90,2537
% Points from left side of peak,93,2623
left 94,2688
  max_right 99,2834
right 104,2980
  spike_id_prefix 110,3156
data 113,3185
obj 114,3208

classes/@trace/display.m,28
function s 1,0
  s 19,544

classes/@trace/plotData.m,498
function a_plot 1,0
% If input is an array,42,1123
time 57,1457
    time 62,1576
    xlabel 63,1607
scale_y 67,1649
unit_y 68,1667
        curunit 76,1820
        curunit 78,1861
        scale_y 79,1885
        curunit 81,1925
        curunit 83,1970
        scale_y 84,1994
    ylabel 86,2025
    ylabel 89,2097
% Remove all '_' characters,101,2347
the_legend 103,2424
    the_title 108,2552
    the_legend 109,2579
  class_name 112,2618
  the_title 113,2661
a_plot 116,2731

classes/@trace/avgTraces.m,115
function 1,0
% TODO: implement separately as the sum(40,1191
  avg_tr 47,1393
  sd_tr 59,1667
  sd_tr 63,1769

classes/@trace/medianfilt.m,16
function t 1,0

classes/@trace/private/loadABF.m,233
function 1,0
  % read ABF file37,1069
  dt 41,1156
  chan 44,1232
  y_units 45,1274
  dy 46,1291
    y_units 50,1367
    dy 51,1386
    dy 57,1502
    y_units 58,1517
      dy 62,1608
        chan 65,1665
  data 76,1878

classes/@trace/private/ns_GetLastErrorMsg.m,14
function 1,0

classes/@trace/private/ns_OpenFile.m,14
function 1,0

classes/@trace/private/ns_GetEventInfo.m,14
function 1,0

classes/@trace/private/ns_GetLibraryInfo.m,14
function 1,0

classes/@trace/private/trace_loadns.m,1199
function 1,0
verbose 36,1235
  file_ext 45,1514
    case '.smr' % PC spike2,50,1652
      DLLName 51,1714
    case '.son' % Mac spike2,52,1746
      DLLName 53,1809
      DLLName 55,1876
      %         DLLName 58,2009
    case '.nex' % Nex Technologies 59,2048
      DLLName 68,2435
  sep 76,2731
  DLLName 78,2798
  % Open data file85,2962
  % Gives you EntityCount,95,3206
  SegmentList 105,3497
  cSegment 106,3549
  AnalogList 110,3676
  cAnalog 111,3727
          props.nsType nsType
122,4017
      props.channel channel
129,4211
      props.traces traces
135,4383
  EntityInfo 139,4471
          ChannelList 144,4656
          ChannelList 147,4802
      ChannelIDs 154,5045
  trace_id 158,5130
          % Load the waveform data and do the analysis170,5532
          % Load the requested traces on the selected channel174,5755
          trace_dt 178,5960
          clear nsSegmentInfo nsSegmentSourceInfo sampleCount UnitIDs;180,6012
          % Load the waveform data and do the analysis183,6104
          % Load all traces on the selected channel198,6830
          trace_dt 202,6999
          clear nsAnalogInfo contCount;204,7050
clear mexprog;211,7200

classes/@trace/private/ns_GetEntityInfo.m,14
function 1,0

classes/@trace/private/ns_SetLibrary.m,14
function 1,0

classes/@trace/private/ns_GetAnalogData.m,14
function 1,0

classes/@trace/private/ns_GetAnalogInfo.m,14
function 1,0

classes/@trace/private/ns_GetEventData.m,14
function 1,0

classes/@trace/private/ns_GetFileInfo.m,14
function 1,0

classes/@trace/private/ns_GetNeuralInfo.m,141
function 1,0
SourceEntityID 36,1358
SourceUnitID 37,1410
ind 39,1455
ind 42,1512
    nsNeuralInfo(i).SourceUnitID SourceUnitID
47,1700

classes/@trace/private/ns_CloseFile.m,47
function ns_RESULT 1,0
%      ns_RESULT 6,98

classes/@trace/private/ns_GetSegmentInfo.m,14
function 1,0

classes/@trace/private/ns_GetIndexByTime.m,29
function 1,0
Index 51,2354

classes/@trace/private/ns_GetTimeByIndex.m,14
function 1,0

classes/@trace/private/ns_GetSegmentSourceInfo.m,14
function 1,0

classes/@trace/private/ns_GetNeuralData.m,14
function 1,0

classes/@trace/private/ns_GetSegmentData.m,54
function 1,0
Data 49,2120
ind 54,2190
ind 57,2235

classes/@trace/lowpassfilt.m,39
function t 1,0
data 34,883
t 40,995

classes/@trace/calcMax.m,47
function 1,0
elseif nargin 33,859
end35,908

classes/@trace/get.m,28
function b 1,0
  b 23,638

classes/@trace/withinPeriod.m,65
function 1,0
  t.data data
47,1301
  err 49,1368
obj 60,1723

classes/@trace/calcAvg.m,62
function avg_val 1,0
elseif nargin 29,761
  avg_val 36,935

classes/@trace/binary_op.m,149
function result_tr 1,0
end31,792
result_tr 36,905
result_tr 37,975
function 41,1061
  name 45,1188
elseif isnumeric(46,1212
    name 51,1305

classes/@trace/getDy.m,28
function dy 1,0
dy 32,659

classes/@trace/plus.m,62
function sub_tr 1,0
% See also: trace,24,482
sub_tr 34,664

classes/@trace/plot.m,63
function h 1,0
s 38,858
    orientation 45,993
  h 52,1189

classes/@trace/unary_op.m,86
function result_tr 1,0
data 33,771
name 34,797
result_tr 36,822
result_tr 37,875

classes/@trace/calcMin.m,72
function 1,0
elseif nargin 33,863
 min_idx 40,1047
 min_val 41,1063

classes/@trace/plot_abstract.m,56
function a_plot 1,0
title_str 37,1062
a_plot 39,1106

classes/@trace/mtimes.m,62
function res_tr 1,0
% See also: trace,24,465
res_tr 34,651

classes/@trace/spike_shape.m,161
function obj 1,0
    spike_time 46,1212
  min_isi 48,1240
% Points from left side of peak,51,1321
left 52,1386
right 56,1499
  obj 61,1660
  obj 65,1819

classes/@trace/getRateResults.m,93
function results 1,0
results.SpikeRateISI SpikeRateISI
34,980
results.ISICV ISICV
38,1068

classes/@trace/rdivide.m,62
function res_tr 1,0
% See also: trace,24,464
res_tr 34,654

classes/@trace/sqrt.m,36
function res_tr 1,0
res_tr 32,533

classes/@trace/uminus.m,62
function res_tr 1,0
% See also: trace,24,380
res_tr 34,568

classes/@trace/runAvg.m,47
function avg_t 1,0
data 29,709
avg_t 30,732

classes/@trace/subsasgn.m,77
function a 1,0
  a 18,590
      a 29,889
      a 31,948
      a 34,1064

classes/@trace/spikes.m,240
function obj 1,0
    minamp 52,1433
  if plotit > 0, plot_str = {'plot'}; else plot_str 77,2117
      t.props.spike_finder spike_finder
85,2482
    [times, peimes, p
91,2676
  % Assume spike_finder 95,2825
obj 101,2988
obj 105,3044

classes/@trace/times.m,62
function res_tr 1,0
% See also: trace,24,462
res_tr 34,646

classes/@trace/findFilteredSpikes.m,869
function 1,0
s 50,1877
fields 51,1924
fd 52,1948
dn_threshold = getFieldDefault(props, 'downThreshold', -2)ownThreshold', -2
53,2013
prepend_size 65,2311
period_len 66,2361
  data 68,2419
  err 74,2734
  b 87,3183
  a 88,3213
  filtered 89,3243
  b 90,3276
  a 91,3305
  filtered=92,3334
  filtered 99,3595
    up_threshold 107,3830
  up_threshold 110,3907
filtered 119,4092
data 120,4148
% run findspikes by passing 1KHz sampling rate to get results in dt122,4197
newtimes 133,4526
newpeaks 134,4541
newn 135,4556
lasttime 137,4594
  old_time 144,4819
  period_before 155,5170
  period_after 156,5208
  min1 157,5246
  min2 158,5315
    real_time 165,5587
    real_time 169,5734
      continue;177,6045
    newtimes 181,6096
    newpeaks 182,6134
    newn 183,6172
    lasttime 184,6193
times 200,6564
peaks 201,6608
n 202,6626

classes/@trace/getProfileAllSpikes.m,90
function profile_obj 1,0
whole_period 35,1146
results_obj 40,1349
profile_obj 44,1478

classes/@trace/getResults.m,22
function results 1,0

classes/@trace/setProp.m,97
function obj 1,0
    val 40,1059
      a 42,1098
      a(1).(attr)43,1119
      obj 44,1144

classes/@trace/getPotResults.m,111
function results 1,0
  results.avg avg
42,1165
  results.max max
43,1186
% convert all to ms/mV(mV
47,1222

classes/@trace/minus.m,62
function sub_tr 1,0
% See also: trace,24,486
sub_tr 34,670

classes/@trace/trace.m,1330
function obj 1,0
verbose 127,6526
   obj.dt dt
131,6618
   obj.dy dy
132,6633
   obj.id id
133,6648
   obj.props props
134,6664
   obj 135,6691
   obj 137,6770
     ext 150,6991
       props.file_endian file_endian
155,7188
         props.file_type file_type
163,7463
           data 182,8096
           data 183,8165
           data 192,8501
           data 193,8570
       channel 199,8764
       data 203,8878
       data 204,8915
       channel 212,9232
       data 216,9348
       dt 220,9491
       data 221,9570
       id 222,9596
       data 227,9747
       s 231,9916
       fields 232,9943
       data 233,9974
       props.file_type file_type
239,10198
       s1 240,10231
          data 245,10418
       % abf2load260,11242
       props.unit_y unit_y
263,11338
     elseif strcmpi(ext, '.txt') || strcmpi(267,11448
       data 278,11947
   elseif isnumeric(286,12148
       id 294,12432
     data 308,12862
         data 321,13383
     data 337,13863
       hpf 345,14094
       lpf 350,14200
     butterWorth.highPass highPass
358,14534
     butterWorth.lowPass lowPass
360,14625
     props.butterWorth butterWorth
361,14676
   obj.data data
363,14721
   obj.dt dt
364,14741
   obj.dy dy
365,14757
   obj.id id
366,14773
   obj.props props
367,14789
   obj 368,14811

classes/@ranked_db/joinOriginal.m,173
function a_db 1,0
crit_cols 40,1236
% Remove the RowIndex and ItemIndex columns,41,1297
crit_cols 55,1872
crit_cols 58,1939
orig_cols 60,2000
  elseif ischar(69,2302

classes/@ranked_db/subsref.m,60
function b 1,0
  b 12,434
      b 18,565
      b 20,610

classes/@ranked_db/set.m,46
function a 1,0
  a.tests_db tests_db
14,455

classes/@ranked_db/renameColumns.m,68
function a_db 1,0
%endend
39,1260
  a_db.crit_db crit_db
46,1445

classes/@ranked_db/getDistMatrix.m,86
function 1,0
joined_db 39,1260
joined_db 45,1373
%displayRows(displayRows
47,1406

classes/@ranked_db/ranked_db.m,276
function a_ranked_db 1,0
   a_ranked_db.crit_db crit_db
47,1755
   a_ranked_db 48,1790
   a_ranked_db 50,1901
   a_ranked_db.orig_db orig_db
57,2016
   a_ranked_db.crit_db crit_db
58,2050
   a_ranked_db 60,2085
		       tests_db(data, col_names, {}, id, props)61,2138

classes/@ranked_db/get.m,33
function b 1,0
  errstr 14,451

classes/@ranked_db/plotCompareDistMatx.m,714
function a_plot 1,0
dmatx2 48,1871
num_plot_rows 50,1926
plot_props 53,1986
plot_props.YTick YTick
56,2061
plot_props.YTickLabel YTickLabel
61,2289
plot_props.XTick XTick
63,2326
plot_props.XTickLabel XTickLabel
69,2534
num_colors 76,2681
dsub 79,2721
  row_vector 90,3060
plot_props.XTick XTick
97,3324
plot_props.XTickLabel XTickLabel
102,3551
dcorr2 110,3830
plot_props.YTick YTick
116,4069
plot_props.YTickLabel YTickLabel
121,4306
  num_rows 138,4880
function unbias_matx 142,4990
  diff_cols 144,5114
  num_rows 145,5156
  num_cols 146,5204
  counter 147,5252
  countert 148,5296
  quart 149,5341
% Make colormap with num_colors,154,5522
function colors 155,5599
  colors 157,5681

classes/@ranked_db/blockedDistances.m,350
function 1,0
joined_db 48,1651
data 50,1691
row_names 51,1743
ranked_dbs 52,1778
out_row 55,1855
  row_indices 63,2082
  this_blocked 66,2187
  this_ranked 69,2283
  this_ranked 72,2384
  ranked_dbs{ranked_dbs
73,2435
  this_dists 76,2495
  %dbsize(dbsize
80,2627
  out_row 87,2785
col_names 94,2910
orig_names 95,2949
a_db 102,3167

classes/@ranked_db/plotRowErrors.m,358
function a_plot 1,0
joined_db 51,1542
joined_data 52,1587
crit_cols 55,1637
num_std_colors 67,2163
only_ranked_rows_db 76,2368
distmatx 77,2443
  distmatx 84,2682
  common_cols 85,2720
  row_steps 91,2831
plot_props 93,2852
plot_props.YTickLabel YTickLabel
94,2960
  the_title 101,3152
  row_name 108,3331
a_plot 111,3358
  num_rows 144,4854

classes/@ranked_db/displayRows.m,406
function s 1,0
joined_db 34,854
joined_data 35,890
crit_cols 38,940
crit_cols 49,1346
crit_cols 52,1413
cols = tests2cols(joists2cols(jo
55,1509
cells = num2cell(db.crit_db.data(1:2, tests2cols(db.crit_db, crit_cols, crit_col
57,1623
[critcol{cols, 1}] = deal(cells{1, :}); % Fill available values from crit_db58,1698
s 62,1892
names 63,1952
    distcol{distcol
77,2604
  s 80,2730
s 85,2868

classes/@ranked_db/plotDistMatrix.m,427
function a_plot 1,0
% See also: ranked_db,33,1422
% See also: ranked_db, plot_abstract,33,1422
% See also: ranked_db, plot_abstract, getDistMatrix,33,1422
% Copyright 39,1615
num_colors 49,1951
num_plot_rows 52,2035
plot_props 54,2071
plot_props.YTick YTick
56,2108
plot_props.YTickLabel YTickLabel
61,2336
plot_props.XTick XTick
63,2373
plot_props.XTickLabel XTickLabel
69,2581
a_plot 75,2745
  num_rows 88,3238

classes/@corrcoefs_db/corrcoefs_db.m,247
function a_coef_db 1,0
  a_coef_db 45,1535
  a_coef_db 47,1653
  col_names 56,1817
  page_names 57,1863
  a_coef_db.col_name col_name
59,1906
  a_coef_db 61,1940
		    tests_3D_db(test_results, col_names, {}, page_names, id, props)62,1991

classes/@plot_simple/set.m,125
function b 1,0
    a.(attr)15,499
    b 16,519
    errstr 18,538
    b 19,562
    b.plot_abstract plot_abstract
20,573

classes/@plot_simple/get.m,33
function b 1,0
  errstr 14,468

classes/@plot_simple/plot_simple.m,104
function a_plot 1,0
   a_plot 50,1626
   a_plot 60,1778
				title, {legend}, command, props)62,1883

classes/@tests_3D_db/set.m,70
function b 1,0
  b 13,462
  a.tests_db tests_db
15,477
  b 16,520

classes/@tests_3D_db/mergePages.m,340
function a_db 1,0
%dbs dbs
36,1136
row_index_col 38,1179
num_tests 44,1328
tests_list 45,1343
  num_tests 57,1778
  tests_list{tests_list
58,1819
data 62,1874
num_tests 65,1940
all_tests 66,1955
orig_tests 67,1971
  %these_tests these_tests
70,2073
  these_tests 71,2133
  all_tests 75,2292
  num_tests 78,2466
a_db 82,2538

classes/@tests_3D_db/display.m,35
function s 1,0
page_names 21,534

classes/@tests_3D_db/diff2D.m,182
function a_tests_db 1,0
test_names 44,1392
col_names 46,1440
a_db_props 51,1555
db_id 53,1589
a_tests_db 56,1700
             { col_names{:}, 'PageIndex' }, {}, db_id)58,1828

classes/@tests_3D_db/get.m,33
function b 1,0
  errstr 14,468

classes/@tests_3D_db/tests_3D_db.m,258
function a_3D_db 1,0
  a_3D_db 50,1729
  a_3D_db 52,1834
  a_3D_db.page_idx page_idx
54,1905
    a_3D_db 58,2035
   row_names 66,2161
   col_names 67,2207
   page_names 68,2253
   id 69,2301
   a_3D_db.page_idx page_idx
71,2337
   a_3D_db 73,2381

classes/@tests_3D_db/plotScatter.m,31
function a_p 1,0
a_p 47,1668

classes/@tests_3D_db/corrCoefs.m,353
function a_coefs_db 1,0
  skipCoefs 52,1955
% Obsolete,55,1977
  excludeNaNs 59,2082
col1 63,2144
cols 64,2173
num_pages 66,2203
pages=67,2230
      data 82,2661
	continue;87,2820
      end88,2831
% Cannot strip all the NaNs out,100,3047
nanrows 102,3137
col_name_cell 111,3352
col1_name 112,3400
col_names 113,3433
a_coefs_db 123,3674

classes/@tests_3D_db/paramsTestsHistsStats.m,74
function 1,0
num_tests 39,1383
  stats_func 48,1582
  ass_t3d 60,1916

classes/@tests_3D_db/flattenPages.m,19
function a_db 1,0

classes/@tests_3D_db/swapRowsPages.m,56
function a_3D_db 1,0
a_3D_db 36,1134
a_3D_db 37,1190

classes/@tests_3D_db/plotParamPairImage.m,530
function a_plot 1,0
% See also: params_tests_db/invarParam,invarParam
31,1308
% See also: params_tests_db/invarParam, plotImage,31,1308
% Copyright 37,1498
page_db 48,1865
% Enumerate the first two columns 50,1910
num_colors 67,2412
col_names 69,2430
  mult_factor 79,2800
  skip_steps 85,2897
page_data 88,2920
plot_props.YTick YTick
89,2954
unique_vals 90,2998
plot_props.YTickLabel YTickLabel
91,3084
plot_props.XTick XTick
93,3141
unique_vals 94,3185
plot_props.XTickLabel XTickLabel
95,3271
a_plot 102,3429

classes/@tests_3D_db/histograms.m,285
function a_histogram_db 1,0
% For all pages,37,1081
num_pages 38,1112
pages=39,1148
col 47,1387
col_name_cell 50,1461
col_name 51,1509
props 52,1540
db_props 54,1561
    page_names{page_names
60,1784
  props 63,1878
  title 64,1923
  title 66,2003
a_histogram_db 69,2053

classes/@tests_3D_db/joinPages.m,304
function a_db 1,0
verbose 35,1058
data 37,1093
w_data 38,1117
page_col 39,1148
pages 40,1193
size_db 41,1222
size_wdb 42,1244
cols 44,1273
w_cols 45,1301
%log_cols log_cols
46,1336
page_size 49,1408
new_data 53,1541
ones_vector 55,1576
cols_cell1 66,1935
cols_cell2 67,1980
a_db 76,2127

classes/@tests_3D_db/plotVarBox.m,392
function a_plot 1,0
  num_test2s 57,1504
				   notch, sym, vert, whis, props)64,1735
col1 69,1787
col2 70,1819
col_names 73,1874
data 74,1920
col1data 78,2017
col2data 79,2075
% Flatten into a single dimension,81,2114
bicoldata 84,2275
bicoldata 88,2461
col1name 90,2543
col2name 91,2589
  all_title 96,2686
a_plot 99,2749
		       all_title, {}, 'boxplotp', props)102,2903

classes/@plot_image/plot_image.m,812
function a_plot 1,0
% See also: plot_abstract,47,1859
% Copyright 53,2019
  a_plot 65,2554
    num_colors 74,2712
    a_colormap 80,2812
    max_val 87,2912
    min_val 93,3029
  image_data 96,3077
  is_symmetric 97,3152
    num_grads 102,3267
  image_props 105,3295
  image_props.colorbarLabel colorbarLabel
106,3319
  image_props.maxValue maxValue
107,3365
    image_props.colorbarProps colorbarProps
118,3708
    image_props.colorbarProps.YTick YTick
119,3748
      image_props.colorbarProps.YTickLabel YTickLabel
126,4034
    image_props.colorbarProps colorbarProps
134,4250
    image_props.colorbarProps.YTick YTick
135,4290
    image_props.colorbarProps.YTickLabel YTickLabel
137,4377
  a_plot 141,4519
                          axis_labels, title_str, {}, @plotImage, props)146,4726

classes/@plot_image/get.m,45
function b 1,0
  errstr 14,468
  b 15,490

classes/@plot_image/axis.m,36
function ranges 1,0
ranges 30,820

classes/@trace_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@trace_profile/trace_profile.m,386
function obj 1,0
  props 61,1981
  obj.spikes spikes
66,2091
  obj.spike_shape spike_shape
67,2114
  obj.props props
68,2147
  obj 69,2173
  obj 71,2288
  obj.trace trace
74,2435
  obj.spikes spikes
75,2471
  obj.spike_shape spike_shape
76,2505
  trace_results 79,2594
  rate_results 80,2647
  shape_results 81,2699
  obj 84,2769
  obj.props props
92,3069
  obj 94,3112

classes/@plot_errorbars/plot_errorbars.m,265
function a_plot 1,0
   a_plot 47,1640
   a_plot 49,1755
     %props.XTickLabel XTickLabel
53,1851
   a_plot.labels labels
60,1964
   num_plots 62,1992
   num_rows 63,2026
		       {labels{plot_num}, ''}, '', {}, 'errorbar', props)70,2317
   a_plot 73,2386

classes/@script_factory/script_factory.m,264
function obj 1,0
  obj.out_name out_name
45,1527
  obj.id id
46,1550
  obj.props props
47,1565
  obj 48,1587
  obj 50,1687
  obj.num_scripts num_scripts
56,1769
  obj.out_name out_name
57,1802
  obj.id id
58,1829
  obj.props props
59,1844
  obj 62,1888

classes/@script_factory/get.m,16
function b 1,0

classes/@model_data_vcs/plotDataCompare.m,537
function a_p 1,0
skip_step 48,1451
label_zoom 49,1502
  all_title 54,1577
    label_zoom 61,1826
  elseif strcmp(62,1858
      a_p 83,2854
    axis_limits 89,3066
color_num_levels 92,3109
line_colors 94,3199
  a_md.data_vc data_vc
98,3320
  a_md.model_vc model_vc
99,3374
data_props 102,3435
model_props 110,3719
  model_props 120,4063
plot_props 124,4147
a_p 129,4254
plots 137,4618
sizes 138,4635
  sizes 148,5172
  h 152,5289
  time 153,5326
  plots 154,5378
  sizes 169,6276
  sizes 186,7188
  a_p 188,7216

classes/@model_data_vcs/subsref.m,46
function b 1,0
  b 43,1184
      b 52,1358

classes/@model_data_vcs/set.m,16
function a 1,0

classes/@model_data_vcs/selectFitParams.m,494
function a_md 1,0
      a_m.I I
40,1022
    a_m.I I
43,1099
    a_m.I.m.inf inf
44,1128
    a_m.I.h.inf inf
45,1169
    a_m.I.h2.inf inf
46,1210
    a_m.I.m.tau tau
47,1257
    a_m.I.h.tau tau
48,1298
    a_m.I.h2.tau tau
49,1339
    a_m.I.m.tau tau
51,1396
    a_m.I.h.tau tau
52,1437
        a_m.I.m.inf inf
54,1494
    a_m.I.h.inf inf
55,1539
%     a_m.I.h2.inf inf
56,1580
a_md.model_f model_f
61,1693
function m 64,1733
  m 68,1805
function m 72,1835
function m 78,1955

classes/@model_data_vcs/display.m,39
function str 1,0
%props props
30,459

classes/@model_data_vcs/updateModel.m,79
function a_md 1,0
a_md.model_f model_f
33,886
a_md.model_vc model_vc
34,940

classes/@model_data_vcs/plotDataModelSub.m,253
function a_p 1,0
skip_step 45,1322
label_zoom 48,1411
    label_zoom 52,1587
  elseif strcmp(53,1619
  all_title 67,2057
color_num_levels 70,2115
line_colors 72,2205
  a_md.data_vc data_vc
76,2326
  a_md.model_vc model_vc
77,2380
a_p 80,2441

classes/@model_data_vcs/get.m,16
function b 1,0

classes/@model_data_vcs/plotPeaksCompare.m,71
function a_p 1,0
  all_title 40,1034
skip_step 44,1182
a_p 47,1277

classes/@model_data_vcs/plot.m,26
function h 1,0
h 39,991

classes/@model_data_vcs/convertTauFromSpline.m,94
function a_md 1,0
v_range 31,731
model_f 33,784
model_f 36,856
model_f.h.tau tau
43,1119

classes/@model_data_vcs/fit.m,1050
function 1,0
% See also: param_I_v,54,2473
% See also: param_I_v, param_func,54,2473
title_str 70,3058
data_vc 72,3102
dt 73,3126
cell_name 74,3185
time 76,3215
range_rel 79,3330
    range_rel 84,3473
    step_num 86,3514
  range_maxima 93,3687
range_cap_resp 101,3837
    plot_zoom 111,4256
% $$$   plot_zoom 115,4408
  plot_zoom 118,4586
num_iter_label 121,4667
    num_iter 126,4815
    save_model_file 131,4983
    num_iter_label 135,5160
use_levels 140,5260
f_model 143,5345
out_fcns 145,5370
props 154,5563
props 160,5742
  function stop 167,5883
    stop 173,6128
  function dispParams(176,6155
  function stop 186,6529
    stop 193,6842
  fig_handle 196,6867
    fig_props 201,7015
  function a_plot 204,7048
    extra_text 210,7196
      all_title 219,7462
    a_plot 224,7613
    fig_handle 232,7944
    fig_props 235,8011
  params 243,8235
  f_model_orig 249,8350
  % TODO: models are unitless,251,8377
  nA_scale 254,8493
  f_model 257,8541
  % show all parameters 263,8769
    a_doc 278,9292

classes/@model_data_vcs/plot_abstract.m,190
function a_p 1,0
  all_title 54,1758
  data_p 61,1996
  data_ps 73,2734
  data_p 82,3231
  data_p 85,3358
v_props 92,3653
v_limits 94,3724
    v_limits 98,3837
if isfield(106,4063

classes/@model_data_vcs/plotModelTaus.m,127
function a_p 1,0
  all_title 40,903
% find the current 43,988
elseif isfield(46,1076
a_p 62,1362
a_p.props props
65,1398

classes/@model_data_vcs/subsasgn.m,28
function a 1,0
  a 18,590

classes/@model_data_vcs/model_data_vcs.m,257
function a_md 1,0
  a_md.model_f model_f
44,1492
  a_md.model_vc model_vc
45,1521
  a_md.data_vc data_vc
46,1554
  a_md.id id
47,1586
  a_md.props props
48,1602
  a_md 49,1625
  a_md 51,1723
    elseif strcmpi(68,2268
      elseif strcmpi(82,2728

classes/@model_data_vcs/plotModelInfs.m,220
function a_p 1,0
% find the current 37,837
elseif isfield(40,927
  a_m_label 55,1300
  a_m_p 57,1346
  a_m_label 58,1396
  a_h_label 63,1489
  a_h_p 65,1524
  a_h_label 66,1549
  all_title 72,1629
a_p 75,1728

classes/@cip_traces_dataset/getItemParams.m,56
function params_row 1,0
%params_row params_row
30,856

classes/@cip_traces_dataset/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,650

classes/@cip_traces_dataset/set.m,70
function a 1,0
  a.params_tests_dataset params_tests_dataset
14,455

classes/@cip_traces_dataset/display.m,16
function s 1,0

classes/@cip_traces_dataset/cip_traces_dataset.m,192
function obj 1,0
  obj.props props
51,1902
  obj 52,1928
  obj 54,2049
  obj.cipmag cipmag
61,2127
  obj.props props
62,2150
    dt = ts{1}.dt;dt
66,2221
    dt 68,2247
  obj 72,2296

classes/@cip_traces_dataset/get.m,33
function b 1,0
  errstr 14,468

classes/@cip_traces_dataset/cip_trace_profile.m,78
function a_cip_trace_profile 1,0
magidx 34,958
a_cip_trace_profile 41,1165

classes/@cip_traces_dataset/loadItemProfile.m,24
function a_profile 1,0

classes/@cip_traces_dataset/paramNames.m,26
function param_names 1,0

classes/@script_array_loaddb/runJob.m,82
function a_db_piece 1,0
num_items 34,1036
num_runs 35,1063
a_db_piece 37,1097

classes/@script_array_loaddb/runLast.m,186
function a_db 1,0
  num_rows 35,1042
  a_db.data data
42,1193
  a_db 43,1211
  % fill it by addressing rows 45,1251
        job_results{i}.data;data
50,1457
    start_row 51,1486

classes/@script_array_loaddb/script_array_loaddb.m,135
function a_s 1,0
  a_s 56,2374
  a_s 58,2495
  % by default,64,2576
  props 65,2613
  a_s.dataset dataset
69,2701
  a_s 72,2751

classes/@params_cip_trace_fileset/set.m,70
function a 1,0
  a.params_tests_fileset params_tests_fileset
14,455

classes/@params_cip_trace_fileset/display.m,16
function s 1,0

classes/@params_cip_trace_fileset/get.m,33
function b 1,0
  errstr 14,468

classes/@params_cip_trace_fileset/cip_trace_profile.m,122
function a_cip_trace_profile 1,0
filename 32,916
fullname 33,957
  a_cip_trace 50,1623
  a_cip_trace_profile 55,1878

classes/@params_cip_trace_fileset/ctFromRows.m,93
function a_cip_trace 1,0
    index_vals 44,1663
  index_vals 51,1878
a_cip_trace 54,1904

classes/@params_cip_trace_fileset/params_cip_trace_fileset.m,210
function obj 1,0
  obj.pulse_time_width pulse_time_width
64,2491
  obj 65,2519
  obj 67,2662
  obj.pulse_time_start pulse_time_start
78,2882
  obj.pulse_time_width pulse_time_width
79,2925
  obj 82,2992

classes/@params_cip_trace_fileset/cip_trace.m,254
function a_cip_trace 1,0
  col_data 38,1110
  a_cip_trace 40,1187
  num_indices 42,1245
    fullname 46,1409
    f_props 48,1467
	num_params 56,1804
      str_index 61,1944
      trial_num 68,2244
      trace_id 69,2288
      trace_id 71,2342

classes/@params_cip_trace_fileset/loadItemProfile.m,24
function a_profile 1,0

classes/@period/period.m,191
function obj 1,0
   obj.end_time end_time
43,1297
   obj 44,1318
   obj 46,1401
  start_time 50,1514
  obj.start_time start_time
52,1550
  obj.end_time end_time
53,1581
  obj 54,1608

classes/@period/subsref.m,60
function b 1,0
  b 12,434
      b 18,550
      b 20,599

classes/@period/set.m,16
function a 1,0

classes/@period/SpikeTimesinPeriod.m,50
function SpkTimes 1,0
i=35,952
SpkTimes=39,999

classes/@period/display.m,16
function s 1,0

classes/@period/get.m,16
function b 1,0

classes/@period/char.m,16
function s 1,0

classes/@period/array.m,23
function an_array 1,0

classes/@cip_trace_allspikes_profile/set.m,28
function b 1,0
  b 13,462

classes/@cip_trace_allspikes_profile/display.m,16
function s 1,0

classes/@cip_trace_allspikes_profile/plotRowSpontSpikeAnal.m,256
function a_plot 1,0
% If input is an array,33,1025
% Remove all '_' characters,44,1305
class_name 45,1381
quiet_trace 47,1426
  a_spike 51,1509
  comparison_plots 52,1560
  err 54,1633
    comparison_plots 59,1862
top_row 64,1966
a_plot 66,2004

classes/@cip_trace_allspikes_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@cip_trace_allspikes_profile/cip_trace_allspikes_profile.m,528
function obj 1,0
  obj.spikes spikes
54,1945
  obj.spont_spikes_db spont_spikes_db
55,1968
  obj.pulse_spikes_db pulse_spikes_db
56,2002
  obj.recov_spikes_db recov_spikes_db
57,2036
  obj.props props
58,2070
  obj 59,2096
  obj 61,2239
  % Create object with custom data 63,2266
  obj.trace trace
68,2384
  obj.spikes spikes
69,2411
  obj.spont_spikes_db spont_spikes_db
70,2436
  obj.pulse_spikes_db pulse_spikes_db
71,2477
  obj.recov_spikes_db recov_spikes_db
72,2518
  obj.props props
73,2559
  obj 76,2603

classes/@params_tests_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@params_tests_profile/params_tests_profile.m,201
function a_pt_profile 1,0
  a_pt_profile.props props
44,1498
  a_pt_profile 45,1533
  a_pt_profile 47,1676
  a_pt_profile.db db
53,1768
  a_pt_profile.props props
54,1794
  a_pt_profile 57,1847

classes/@script_array_for_cluster/set.m,54
function a 1,0
  a.script_array script_array
15,483

classes/@script_array_for_cluster/get.m,16
function b 1,0

classes/@script_array_for_cluster/script_array_for_cluster.m,181
function a_script_cluster 1,0
  a_script_cluster 52,2237
  a_script_cluster 54,2394
  a_script_cluster.sge_wrapper_script sge_wrapper_script
60,2486
  a_script_cluster 63,2569

classes/@script_array_for_cluster/runFirst.m,179
function job_results 1,0
% Copyright 28,824
array_job_command 41,1334
  array_job_number 50,1660
  array_job_number 51,1710
    sge_opts 61,2044
  last_job_command 65,2129

classes/@plot_inset/set.m,125
function b 1,0
    a.(attr)15,499
    b 16,519
    errstr 18,538
    b 19,562
    b.plot_abstract plot_abstract
20,573

classes/@plot_inset/get.m,33
function b 1,0
  errstr 14,451

classes/@plot_inset/plot.m,272
function handles 1,0
num_plots 34,869
all_handles 36,904
this_layout_axis 37,922
a_plot_props 39,955
      layout_axis 52,1372
    this_layout_axis 59,1642
  handles 63,1695
  handles = plot(a_plot.plots{plot_num}, this_layout_axis)63,1695
  all_handles 64,1756

classes/@plot_inset/plot_inset.m,274
function a_plot 1,0
  a_plot.axis_locations axis_locations
46,1674
  a_plot 47,1704
   a_plot 49,1812
   a_plot.plots plots
67,2159
   a_plot.axis_locations axis_locations
68,2184
   a_plot 78,2460
                           props)81,2566
   % mergeStructs(83,2657

classes/@spikes_db/plot_abstract.m,136
function a_pm 1,0
trace_plot 41,1108
num_spikes 43,1162
% Then superpose all spike measures45,1193
  results 49,1373
a_pm 53,1527

classes/@spikes_db/spikes_db.m,268
function a_spikes_db 1,0
   a_spikes_db.period period
44,1496
   a_spikes_db 45,1528
   a_spikes_db 47,1639
   a_spikes_db.trace trace
54,1754
   a_spikes_db.period period
55,1786
   a_spikes_db 58,1849
		       tests_db(data, col_names, {}, id, props)59,1902

classes/@current_clamp/set.m,86
function b 1,0
    b 21,583
    b 24,632
    b.voltage_clamp voltage_clamp
25,643

classes/@current_clamp/current_clamp.m,131
function a_cc 1,0
  a_cc 55,1798
  a_cc 57,1908
  a_cc 59,1983
  a_cc 60,2000
  a_cc 61,2047
  a_cc 63,2102
  a_cc 64,2119

classes/@current_clamp/get.m,45
function b 1,0
  b 23,638
  errstr 25,677

classes/@current_clamp/params_tests_db.m,380
function 1,0
%   profs:profs
21,788
a_db 43,1542
  param_names 47,1630
  num_params 48,1678
  a_db 50,1741
                                    num_rows, 1), param_names, {}, ''), a_db)51,1825
  num_params 53,1909
  num_params 58,2010
  all_vals 60,2083
  param_vals 62,2147
  a_db 66,2272
                             param_names, {}, ''), a_db)67,2330
a_db 71,2421

classes/@current_clamp/cip_trace.m,113
function 1,0
step_num 36,1047
a_vc 38,1097
istep_num = cip_num;;
42,1225
a_ct 43,1246
cip_level_pA 54,1627

classes/@current_clamp/getResults.m,186
function 1,0
step_num 35,1044
a_vc 38,1145
num_isteps 45,1320
profs 46,1356
  % make current step a parameter49,1438
  profs{profs
53,1552
  a_results 54,1600
  results 57,1702

classes/@tests_db/end.m,16
function s 1,0

classes/@tests_db/meanDuplicateRows.m,368
function a_tests_db 1,0
rest_cols 41,1748
wo_cols 44,1821
% Sort rows46,1855
% Find unique rows49,1902
sorted 53,2000
sorted_db 54,2046
%sorted(sorted
56,2106
    rows 71,2472
  rows_db 74,2527
  no_mean_rows_db 77,2656
  new_vals 78,2732
  new_row 79,2775
  new_std 80,2859
col_names 88,3076
a_tests_db 92,3258
a_tests_db 93,3301
a_tests_db 94,3362

classes/@tests_db/le.m,32
function rows 1,0
rows 31,833

classes/@tests_db/plotrows.m,297
function a_plot 1,0
num_rows 48,1277
plots 49,1311
%border border
50,1338
    %border border
58,1641
    row_plot 61,1789
props(1).xLabelsPos xLabelsPos
66,1925
%props.xTicksPos xTicksPos
67,1957
props.titlesPos titlesPos
68,1986
tests_props 70,2013
  title_str 74,2140
a_plot 77,2182

classes/@tests_db/assignRowsTests.m,87
function obj 1,0
cols 39,1207
val_size 52,1385
num_dims 53,1407
addr_size 54,1436

classes/@tests_db/crossProd.m,201
function cross_db 1,0
b_size 32,1006
a_expand_vector 34,1030
a_expand_vector 35,1063
a_expand_vector 36,1121
b_expand_vector 39,1199
a_expand_db 42,1331
b_expand_db 43,1388
  cross_db 50,1569

classes/@tests_db/plotTestsHistsMatrix.m,354
function a_pm 1,0
stack_props 48,1519
  hist_pars 53,1653
num_tests 56,1680
  all_title 61,1820
num_dbs 64,1850
    hists 74,2294
    max_val 75,2331
      extra_props 82,2507
      axis_limits 101,3312
  a_pm 110,3563
  plots 115,3866
    extra_props 121,4117
    a_pm 129,4405
    a_pm = matrixPlots(plots, {}, all_title, props)129,4405

classes/@tests_db/uop.m,59
function a_db 1,0
a_db 35,979
a_db 36,996
a_db 37,1027

classes/@tests_db/plotYTests.m,253
function a_p 1,0
% Copyright 40,1531
cols_db 62,2053
test_names 64,2097
  all_title 69,2243
  line_style 75,2343
  props.LineStyleOrder LineStyleOrder
76,2362
c_data 79,2430
		      axis_labels, all_title, {short_title}, command, props)86,2692

classes/@tests_db/matchingRow.m,276
function crit_db 1,0
tests 42,1315
cols 45,1360
crit_db 46,1390
crit_tests 47,1431
  dist_db 53,1545
crit_db 65,1968
crit_db 68,2032
crit_db = addColumns(crit_db, {'RowIndex'}, row)68,2032
% Add the STD row,70,2083
crit_db 71,2126
crit_db 74,2221
crit_db 75,2284

classes/@tests_db/subsref.m,63
function b 1,0
  b 43,1184
      b 60,1709
      b 62,1754

classes/@tests_db/set.m,16
function a 1,0

classes/@tests_db/unique.m,32
function a_db 1,0
a_db 33,779

classes/@tests_db/abs.m,19
function a_db 1,0

classes/@tests_db/approxMappingNNet.m,462
function 1,0
orig_inputs 90,3118
orig_outputs 91,3147
% first,93,3179
num_samples 94,3230
train_logic 95,3268
  num_test 98,3418
  a_perm 104,3611
  a_nnet_inputs 106,3692
  a_nnet_outputs 107,3741
  orig_outputs 110,3862
% balance inputs,113,3915
    num_passes 128,4385
  goal_mse 130,4412
  cell_ins 131,4431
  cell_outs 132,4472
  last_conditions 133,4513
    nn_mse 137,4682
      break;141,4832
new_data 147,4918
an_approx_db 153,5168

classes/@tests_db/display.m,69
function s 1,0
colnames 25,719
colnums 26,753
numnamecell 28,805

classes/@tests_db/tests2cols.m,19
function cols 1,0

classes/@tests_db/statsMeanStd.m,209
function a_stats_db 1,0
a_db 38,981
test_results 40,1052
row_names 41,1114
cols 44,1173
col_name_cell 45,1203
col_names 46,1243
a_stats_db 48,1277
		      [ 'Mean and STDs of ' db.id ], props)49,1343

classes/@tests_db/physiol_bundle.m,1084
function a_pbundle 1,0
%       	others), default is an empty array,25,1179
% 	biasLimit: Limit in pA,26,1251
% 		eliminated. (default=27,1315
  verbose 47,2096
  bias_limit 61,2394
phys_db 63,2417
    weed_cols 73,2755
  phys_db 75,2837
    phys_db 86,3172
  CIPList 112,4088
    phys_db 124,4440
    pulse_spike_tests 168,6052
    recov_spike_tests 203,7378
    ini_spont_tests 238,8704
    pulse_rate_tests 244,8860
    pulse_hyper_pot_tests 260,9406
    recov_rate_tests 267,9586
merge_args 287,10208
phys_2_join_db 297,10753
% get the main values 302,10950
    phys_joined_added_db 305,11125
    phys_joined_control_db 306,11168
    phys_joined_db 308,11218
    phys_joined_std_db 312,11335
    num_params 323,11881
      phys_joined_added_db1 330,12164
    phys_joined_added_db 359,13408
      drug_cols 366,13636
    phys_joined_control_db 368,13721
    phys_joined_control_db 378,14050
phys_db 383,14240
a_pbundle 386,14335
    physiol_bundle({phys_dataset, phys_db, phys_joined_added_db}, struct('controlDB', phys_joined_control_db)387,14351

classes/@tests_db/renameColumns.m,389
function a_db 1,0
% >> new_db 22,763
% >> new_db 24,849
% the regular expression renaming,29,1000
    a_db = renameColumns(a_db, test_names{col_num}, new_names{new_names
54,2037
  test_names = test_names{1}; new_names 59,2175
  all_names 70,2553
  all_new_names 71,2588
col_idx 83,2926
col_idx.(new_names)84,2950
col_idx 85,2994
% Reorder 87,3035
a_db.col_idx col_idx
89,3104

classes/@tests_db/histogram.m,440
function a_histogram_db 1,0
% See also: histogram_db,27,815
% See also: histogram_db, tests_db,27,815
% Copyright 33,971
num_dbs 47,1381
  max_val 51,1510
    col_db 54,1601
    bounds_data 55,1685
    min_val 56,1737
    max_val 57,1781
  % If a scalar,60,1832
  [a_hi_h
66,2034
col_db 74,2212
col_db 77,2279
%col_db col_db
78,2359
  hist_results 94,2765
col_name_cell 101,2925
col_name 102,2969
a_histogram_db 104,2999

classes/@tests_db/dbsize.m,28
function s 1,0
  s 31,692

classes/@tests_db/tests_db.m,718
function obj 1,0
%     csvReadColNames: If 19,800
%   row_idx,24,1041
%   id,25,1114
   obj.col_idx col_idx
88,3916
   obj.row_idx row_idx
89,3945
   obj.id id
90,3974
   obj.props props
91,3990
   obj 92,4017
   obj 94,4107
     %strcmpi(strcmpi
105,4364
     delim 109,4464
       oneline 117,4746
       col_names 118,4775
         col_names 120,4876
       col_names 123,4973
         rc 131,5208
         csv_args{csv_args
133,5267
       props 137,5375
     test_results 140,5440
     col_names 156,5934
     col_names 157,5972
   obj.data data
168,6336
   obj.col_idx col_idx
172,6385
   obj.row_idx row_idx
173,6422
   obj.id id
174,6459
   obj.props props
175,6475
   obj 177,6498

classes/@tests_db/setRows.m,40
function obj 1,0
obj.data data
35,965

classes/@tests_db/ne.m,19
function rows 1,0

classes/@tests_db/private/findRegExpIdx.m,52
function idx 1,0
    idx 33,1020
    idx 36,1127

classes/@tests_db/private/processRecurseRowsNonNaNInf.m,153
function 1,0
    n 41,1540
    else46,1691
      dims{dims
53,1855
          processRecurseRowsNonNaNInf(data(dims{:}), dim_num - 1, a_func)55,1929

classes/@tests_db/joinRows.m,507
function a_db 1,0
%	  multipleIndices: If 25,973
verbose 46,1700
num_pages 52,1785
  index_col_name 61,2035
wd_db 64,2071
w_data 69,2203
cols_cell1 71,2233
cols_cell2 72,2265
a_db 75,2338
data 78,2485
num_pages 81,2539
  size_db 87,2734
  size_wdb 88,2760
  new_data 91,2814
    row_index_cols 108,3309
    all_non_nans 112,3520
  non_nan_joins 123,3792
    %a_db a_db
130,4068
    new_data 133,4235
cols_cell1 140,4378
cols_cell2 141,4425
a_db 142,4473
a_db 143,4509
a_db 144,4581

classes/@tests_db/tests2idx.m,154
function idx 1,0
dim_names 44,1362
dim_name 45,1398
% $$$   dim_num 49,1491
idx 61,1834
  ind_struct 81,2416
  all_names 82,2456
    idx 101,2946

classes/@tests_db/displayRowsTeX.m,59
function tex_string 1,0
def_props 45,1361
props 53,1604

classes/@tests_db/anyRows.m,119
function 1,0
num_db_rows 52,1509
ones_matx 53,1541
idx 54,1575
rows_idx 55,1604
db_data 57,1645
    idx 76,2323

classes/@tests_db/rankMatching.m,621
function a_ranked_db 1,0
% >> a_ranked_db 29,1122
  %row_db row_db
61,2311
  %row_index row_index
62,2359
row_index 65,2392
itemIndices 73,2626
% Strip out the NeuronId,75,2676
% Strip out the NeuronId, RowIndex,75,2676
crit_tests 76,2752
crit_row_db 79,2891
nonnans 80,2944
crit_tests 81,2981
first_row 87,3099
second_row 90,3191
second_row_data 91,3243
elseif isfield(95,3349
    weights_tests 104,3662
ss_data 147,5273
  ss_data 152,5418
clear second_row_matx;156,5545
ss_data 170,6048
row_index 171,6074
wghd_data 172,6104
a_ranked_db 184,6497
			 lower(get(crit_db, 'id')) ], props)187,6641

classes/@tests_db/onlyRowsTests.m,109
function obj 1,0
cols 40,1221
rows 41,1254
  obj.data data
52,1455
col_names 56,1503
row_names 62,1639

classes/@tests_db/plotUniquesStatsStacked3D.m,664
function a_stacked_plot 1,0
a_db 41,1285
sorted_unique_vals1 45,1434
sorted_unique_vals2 48,1601
sorted_unique_vals3 51,1768
num_stack_uniques 55,1936
stack_var_name 57,1986
stack_var_name 58,2056
  stats_func 64,2200
  stats_row 71,2323
default_image_props 74,2350
default_image_props.uniqueVals1 uniqueVals1
75,2379
default_image_props.uniqueVals2 uniqueVals2
76,2434
      default_image_props.popDev popDev
86,2861
    elseif strcmp(88,2972
s_plots 106,3460
  image_props 112,3629
  an_image_plot 118,3826
  axis_labels 122,4025
  s_plots 123,4076
  all_title 135,4436
  props.relativeSizes relativeSizes
143,4716
a_stacked_plot 147,4797

classes/@tests_db/plotBox.m,210
function a_plot 1,0
% See also: plot_abstract,21,573
% See also: plot_abstract, plotFigure,21,573
% Copyright 27,732
   notch 44,1178
  whis 58,1334
col_name 65,1460
  all_title 70,1570
a_plot 74,1680

classes/@tests_db/get.m,16
function b 1,0

classes/@tests_db/eq.m,19
function rows 1,0

classes/@tests_db/isinf.m,59
function rows 1,0
col 33,761
col_db 35,789
rows 37,828

classes/@tests_db/delColumns.m,123
function obj 1,0
mask 37,1230
col_idx 43,1335
test_names 44,1366
test_names 48,1440
new_col_idx 51,1493
obj 52,1528

classes/@tests_db/mean.m,188
function 1,0
order 37,1043
  data 41,1123
  data 43,1164
db_size 47,1214
s 48,1236
a_db 57,1401
a_db 58,1457
nout 60,1487
    n 70,1716
      s 76,1876
      dims{dims
82,2010

classes/@tests_db/corrcoef.m,211
function a_coefs_db 1,0
  skipCoefs 40,1096
% Obsolete,43,1118
  excludeNaNs 47,1230
  alpha 53,1309
col_names 67,1600
a_coefs_db 74,1758
                  properTeXLabel(get(db, 'id')) ], props)78,1937

classes/@tests_db/groupBy.m,122
function a_tests_3D_db 1,0
verbose 41,1401
col_ids 43,1436
all_col_names 44,1468
col_names 45,1501
all_cols 48,1570

classes/@tests_db/rows2Struct.m,44
function s 1,0
col_names 39,892
s 40,928

classes/@tests_db/sortrows.m,211
function 1,0
db_size 43,1180
  num_pages 47,1259
pages=49,1280
cols 51,1300
%idx idx
52,1329
    idx 60,1535
  % Sort all68,1705
    idx 73,1831
sorted_db 83,1996
sorted_db 84,2012
%  sorted 92,2353

classes/@tests_db/max.m,51
function 1,0
  varargout 37,1076
  nout 42,1187

classes/@tests_db/plus.m,19
function a_db 1,0

classes/@tests_db/tests2log.m,45
function a_log 1,0
% >> stripped_db 24,681

classes/@tests_db/plot.m,27
function h 1,0
h 39,1018

classes/@tests_db/gt.m,32
function rows 1,0
rows 31,822

classes/@tests_db/plot_abstract.m,33
function a_pm 1,0
a_pm 44,1256

classes/@tests_db/mtimes.m,19
function a_db 1,0

classes/@tests_db/processDimNonNaNInf.m,196
function 1,0
% >> b_db 28,1035
    elseif ischar(52,1899
    data 65,2192
    data 67,2237
  db_size 71,2293
  s 72,2317
  a_db 82,2575
  a_db 83,2641
      a_db 90,2794
  nout 97,2977

classes/@tests_db/plotScatter3D.m,403
function a_p 1,0
col1 43,1280
col2 44,1312
col3 45,1344
col1_db 47,1377
col2_db 48,1419
col3_db 49,1461
non_nans_rows 52,1526
col1_db 53,1578
col2_db 54,1632
col3_db 55,1686
test_names 57,1741
  all_title 68,2112
  line_style 75,2213
  props.LineStyleOrder LineStyleOrder
76,2232
  all_title 86,2557
col_labels 89,2631
a_p 90,2694
		    props)93,2877
  y_lims 97,2988
  a_p 99,3080

classes/@tests_db/isnanrows.m,33
function rows 1,0
rows 38,1125

classes/@tests_db/enumerateColumns.m,294
function a_db 1,0
% Copyright 32,919
cols 42,1259
data 43,1291
    col_vals 49,1425
    col_vals 51,1500
a_db 56,1598
function col_vector 60,1636
  % Sort rows63,1733
  % Find unique rows66,1787
  num_uniques 68,1865
  % For each unique row to next,70,1906
      page_rows 75,2113

classes/@tests_db/addLastRow.m,18
function obj 1,0

classes/@tests_db/addColumns.m,164
function obj 1,0
  test_names 42,1454
  test_columns 43,1504
existing_cols 59,2073
new_col_id 66,2291
obj.data data
67,2324
new_col_idx 70,2391
obj 78,2585

classes/@tests_db/diff.m,46
function a_db 1,0
a_db 38,945
a_db 39,1000

classes/@tests_db/min.m,51
function 1,0
  varargout 37,1081
  nout 42,1192

classes/@tests_db/fillMissingColumns.m,36
function db 1,0
dif_names 34,1055

classes/@tests_db/rdivide.m,19
function a_db 1,0

classes/@tests_db/statsBounds.m,323
function a_stats_db 1,0
cols 39,1073
num_pages 41,1106
pages=42,1135
data 43,1154
                        max(get(a_page_db, 'data'), [], 1); n]n
50,1463
row_names 54,1538
col_name_cell 57,1604
col_names 58,1646
a_stats_db 60,1680
		      [ 'Mean value and min-max bounds from ' get(a_db, 'id') ], props)61,1738

classes/@tests_db/statsAll.m,222
function a_stats_db 1,0
a_db 38,952
stds 40,1022
test_results 41,1046
row_names 42,1130
cols 45,1201
col_name_cell 46,1231
col_names 47,1271
a_stats_db 49,1305
		      [ 'Statistics from ' db.id ], props)50,1371

classes/@tests_db/sqrt.m,32
function a_db 1,0
a_db 30,702

classes/@tests_db/plotUniquesStats2D.m,983
function an_image_plot 1,0
a_db 55,1915
  sorted_unique_vals1 61,2108
  sorted_unique_vals2 69,2367
  stats_func 78,2636
  stats_row 85,2759
      pop_dev 96,3131
    elseif strcmp(98,3223
  pop_dev 117,3706
num_left_uniques 122,3809
num_right_uniques 123,3857
stats_matx 125,3907
left_var_name 149,4605
left_var_name 150,4654
right_var_name 151,4688
right_var_name 152,4738
  all_title 158,4856
num_colors 163,4956
plot_props.XTick XTick
166,4995
plot_props.XTickLabel XTickLabel
167,5035
plot_props.YTick YTick
168,5080
plot_props.YTickLabel YTickLabel
169,5119
plot_props.minValue minValue
170,5164
plot_props.maxValue maxValue
171,5196
% $$$ plot_props.colorbarProps colorbarProps
172,5238
% $$$ plot_props.colorbarProps.YTickLabel YTickLabel
173,5279
plot_props.truncateDecDigits truncateDecDigits
175,5374
image_props 178,5426
image_props.colorbarProps colorbarProps
179,5448
image_props.colorbarProps.YTick YTick
180,5484
an_image_plot 183,5562

classes/@tests_db/plotScatter.m,406
function a_p 1,0
verbose 38,1341
col1 48,1480
col2 49,1512
col1_db 51,1545
col2_db 52,1587
non_nans_rows 55,1652
col1_db 56,1704
col2_db 57,1758
test_names 59,1813
  all_title 69,2127
  line_style 76,2228
  props.LineStyleOrder LineStyleOrder
77,2247
  all_title 90,2737
col_labels 93,2811
a_p 94,2869
		    props)97,3029
  x_lims 104,3170
  regress_props_props 105,3236
  a_p 108,3349

classes/@tests_db/invarValues.m,678
function a_tests_3D_db 1,0
verbose 68,3286
props 70,3321
cols 72,3361
test_names 75,3459
trial_col 76,3504
% Remove all given columns,78,3548
log_cols 79,3609
wo_cols 82,3702
    % % Sort rows87,3797
    % % Find unique rows90,3860
    num_rows 99,4208
    num_total_rows 100,4243
      in_page_unique_cols 114,4786
      unique_main_vals 117,4915
      num_uniques 118,4999
    data 129,5259
      unique_main_vals_exist 134,5446
    % For each unique row to next,137,5493
        page_rows 142,5683
      page_size 145,5750
        unique_index 151,5996
        this_page_idx 196,8105
col_name_cell 203,8271
col_names 204,8311
a_tests_3D_db 207,8385

classes/@tests_db/plotrow.m,262
function a_plot 1,0
data 40,1042
x_vals 41,1066
%props.XTickLabel XTickLabel
42,1100
props.XTick XTick
43,1160
props.grid grid
44,1182
%flatrow flatrow
52,1381
  the_title 57,1496
  data 63,1676
  row_names 70,1869
  row_names 72,1912
a_plot 75,1935

classes/@tests_db/uminus.m,19
function a_db 1,0

classes/@tests_db/factoran.m,61
function a_factors_db 1,0
end35,1105
a_factors_db 41,1217

classes/@tests_db/checkConsistentCols.m,111
function 1,0
vs 36,1090
verbose 37,1124
col_names 39,1159
with_col_names 40,1188
    common_cols 52,1711

classes/@tests_db/addRow.m,18
function obj 1,0

classes/@tests_db/noNaNRows.m,19
function a_db 1,0

classes/@tests_db/subsasgn.m,44
function a 1,0
  a 18,590
      a 30,885

classes/@tests_db/plotXRows.m,66
function a_p 1,0
    new_col_name 50,1371
col_added_db 52,1407

classes/@tests_db/sum.m,195
function a_db 1,0
order 39,913
  data 43,993
  data 45,1034
db_size 49,1084
s 50,1106
a_db 58,1228
a_db 60,1258
    a_db 65,1395
    n 73,1654
      s 79,1814
      dims{dims
85,1947

classes/@tests_db/times.m,19
function a_db 1,0

classes/@tests_db/transpose.m,100
function a_db 1,0
a_db.row_idx row_idx
30,728
a_db.col_idx col_idx
31,757
a_db.data data
34,794

classes/@tests_db/plotCovar.m,749
function a_plot 1,0
% See also: tests_db/cov,cov
27,871
% See also: tests_db/cov, plotImage,27,871
% See also: tests_db/cov, plotImage, tests_db/matchingRow,matchingRow
27,871
% Copyright 33,1056
image_data 46,1470
  data_label 50,1582
  data_label 52,1617
  image_data 58,1759
  data_label 65,1955
  log_cov_data 71,2073
  image_data 74,2222
  data_label 75,2251
  shuffle_idx 83,2456
num_colors 86,2500
plot_props 92,2625
col_names 94,2753
plot_props.YTickLabel YTickLabel
95,2784
plot_props.truncateDecDigits truncateDecDigits
97,2849
a_plot 99,2884
function 104,3025
num_rows 107,3119
idx=108,3151
  cand_row_2 111,3235
  new_image_data 113,3279
  new_entropy 119,3511
    total_entropy 124,3706
entropy_val 136,3955

classes/@tests_db/shufflerows.m,64
function a_db 1,0
cols 37,985
num_rows 38,1015
data 39,1041

classes/@tests_db/testsHists.m,100
function t_hists 1,0
num_dbs 31,857
  bin_param 36,943
t_hists 39,966
%t_hists t_hists
41,1062

classes/@tests_db/displayRows.m,115
function s 1,0
col_names 43,1073
row_nums 52,1298
    col_header 57,1424
  all_row_names 59,1451
  s 61,1545

classes/@tests_db/approxMappingLIBSVM.m,744
function 1,0
%     		of svm-train for options; default=28,1235
orig_inputs 79,2808
orig_outputs 80,2837
% first,82,2869
num_samples 83,2920
train_logic 84,2958
  num_test 87,3108
  a_perm 93,3301
  an_svm_inputs 95,3382
  an_svm_outputs 96,3431
  orig_outputs 99,3552
% balance inputs,102,3605
an_svm.model model
129,4389
% calculate predictions131,4463
% accuracy contains: accuracy,134,4606
% accuracy contains: accuracy, mean squared error,134,4606
an_svm.accuracy accuracy
135,4690
an_svm.mse mse
136,4721
an_svm.scc scc
137,4747
an_svm.prob_estimates prob_estimates
138,4773
  an_svm.cross_accuracy cross_accuracy
143,5000
col_names 157,5459
an_approx_db 158,5490
             struct('classifier', an_svm)163,5721

classes/@tests_db/cov.m,41
function a_cov_db 1,0
col_names 39,929

classes/@tests_db/isnan.m,59
function rows 1,0
col 33,761
col_db 35,789
rows 37,828

classes/@tests_db/approxMappingSVM.m,396
function 1,0
% normalize inputs75,2461
  C 83,2709
  kernel=84,2719
  kerneloption=85,2737
  verbose=86,2755
  qpsize=87,2768
  span 88,2782
  an_svm 89,2822
  an_svm.xsup xsup
93,2996
  an_svm.w w
94,3018
  an_svm.w0 w0
95,3034
  an_svm.tps tps
96,3052
  an_svm.alpha alpha
97,3072
  an_svm.kernel kernel
98,3096
  an_svm.kerneloption kerneloption
99,3122
an_approx_db 107,3298

classes/@tests_db/princomp.m,99
function a_pca_db 1,0
nanrows 34,898
  db 38,1043
  data 44,1160
end45,1186
a_pca_db 49,1243

classes/@tests_db/swapRowsPages.m,19
function a_db 1,0

classes/@tests_db/ge.m,32
function rows 1,0
rows 31,842

classes/@tests_db/kmeansCluster.m,89
function a_cluster_db 1,0
  distance_measure 42,1353
end43,1389
a_cluster_db 50,1563

classes/@tests_db/plotUniquesStatsBars.m,244
function a_bar_plot 1,0
a_db 46,1605
  stats_func 52,1756
  stats_row 59,1879
  sorted_unique_vals 66,2015
  all_title 84,2547
a_bar_plot 92,2705
    pop_mean 102,3120
  a_line_plot 106,3215
  a_bar_plot 111,3457
a_stats_db 130,4133

classes/@tests_db/vertcat.m,228
function a_db 1,0
% See also: vertcat,21,596
% Copyright 27,739
  with_db = vertcat(varargin{1}, varargin{varargin
40,1229
  with_db 45,1337
num_db_rows 61,1643
db_rows 62,1672
wdb_rows 63,1702
db 64,1738
a_db 70,2029

classes/@tests_db/lt.m,32
function rows 1,0
rows 31,816

classes/@tests_db/allocateRows.m,41
function obj 1,0
obj.data data
40,1307

classes/@tests_db/plot_bars.m,245
function a_plot 1,0
col_names 39,1028
data 40,1096
row_idx 41,1128
num_rows 42,1166
num_cols 43,1200
stats_props 45,1235
  axis_limits 49,1360
props.dispErrorbars dispErrorbars
56,1532
props.dispNvals dispNvals
57,1557
a_plot 59,1579

classes/@tests_db/displayRowsCSV.m,100
function csv_string 1,0
csv_string 37,1090
csv_string 41,1235
 function y 49,1382
   y 53,1453

classes/@tests_db/setProp.m,85
function obj 1,0
  val 33,920
    a 35,955
    a(1).(attr)36,974
    obj 37,997

classes/@tests_db/getColNames.m,73
function col_names 1,0
cols 34,860
col_names 36,891
col_names 37,935

classes/@tests_db/std.m,188
function 1,0
order 42,1142
  data 46,1222
  data 48,1263
db_size 52,1313
s 53,1335
a_db 62,1506
a_db 63,1562
nout 65,1592
    n 76,1898
      s 82,2041
      dims{dims
88,2181

classes/@tests_db/compareRows.m,176
function 1,0
db_data 48,1604
num_db_rows 58,1945
ones_matx 59,1977
idx 60,2011
  row_data 72,2453
% Thus,76,2526
compared 80,2623
idx 83,2683
idx = idxx = id
86,2771

classes/@tests_db/statsMeanSE.m,209
function a_stats_db 1,0
a_db 39,1002
test_results 41,1072
row_names 42,1145
cols 45,1203
col_name_cell 46,1233
col_names 47,1273
a_stats_db 49,1307
		      [ 'Mean and SEs of ' db.id ], props)50,1373

classes/@tests_db/minus.m,19
function a_db 1,0

classes/@tests_db/rop.m,479
function a_db 1,0
  left_data 44,1650
  right_data 46,1725
  a_db 47,1798
  an_id 48,1817
elseif isa(left_obj, 'tests_db') || isa(49,1887
    left_data 52,2002
    left_label 53,2041
    right_data 54,2079
      right_label 58,2185
    a_db 61,2238
    left_data 62,2260
      left_label 66,2361
    right_data 68,2406
    right_label 69,2447
  an_id 71,2497
  right_data 79,2786
  left_data 80,2825
  an_id 81,2911
  a_db 82,2979
a_db 85,3004
a_db 86,3035

classes/@tests_db/plotImage.m,431
function a_p 1,0
verbose 36,1196
a_db 47,1366
col_names 50,1455
par1_values 53,1502
par2_values 54,1569
image_data 60,1739
data_label 62,1817
  log_cov_data 66,1920
  image_data 69,2069
  data_label 70,2098
all_title 79,2383
axis_labels 81,2460
plot_props 83,2511
plot_props.XTickLabel XTickLabel
85,2659
plot_props.YTickLabel YTickLabel
86,2696
plot_props.truncateDecDigits truncateDecDigits
87,2733
a_p 93,2826

classes/@plot_bars/set.m,119
function b 1,0
    a.(attr)15,499
    b 16,519
    errstr 18,538
    a.plot_stack plot_stack
19,562
    b 20,611

classes/@plot_bars/plot_bars.m,656
function a_plot 1,0
   a_plot 65,2803
   a_plot 67,2910
     %props.XTickLabel XTickLabel
71,3008
           props.groupValues groupValues
89,3650
         props.groupValues groupValues
91,3740
       props.XTickLabel XTickLabel
93,3809
       props.XTick XTick
94,3854
   a_plot 102,3981
   num_plots 104,4002
   plots 105,4036
       bar_axis_props 109,4177
       plot_components 131,4841
       linestyle 136,5099
       props.dispErrorbars dispErrorbars
139,5214
       plot_components 140,5246
       linestyle 141,5275
       plot_components 149,5567
       plot_components 171,6510
     plots{plots
184,7038
   a_plot 188,7169

classes/@doc_plot/set.m,54
function a 1,0
  a.doc_generate doc_generate
14,455

classes/@doc_plot/get.m,45
function b 1,0
  b 23,638
  errstr 25,677

classes/@doc_plot/plot.m,46
function figure_handle 1,0
doc_props 35,976

classes/@doc_plot/plot_abstract.m,85
function a_plot 1,0
% If input is an array,40,1097
a_plot 53,1506
a_plot 61,1678

classes/@doc_plot/getTeXString.m,220
function tex_string 1,0
doc_dir 42,1432
plot_dir 43,1480
fig_num 48,1692
filename 50,1716
final_dir 53,1797
a_doc.float_props.floatType floatType
61,1969
a_doc.float_props.label label
62,2009
tex_string 65,2094

classes/@doc_plot/doc_plot.m,391
function a_doc 1,0
% See also: doc_generate,38,1442
% Copyright 44,1589
  a_doc.caption caption
52,1944
  a_doc.plot_filename plot_filename
53,1966
  a_doc.float_props float_props
54,1994
  a_doc 55,2028
  a_doc 57,2129
  a_doc.plot plot
63,2212
  a_doc.caption caption
64,2235
  a_doc.plot_filename plot_filename
65,2262
  a_doc.float_props float_props
66,2301
  a_doc 68,2337

classes/@histogram_db/calcKLhist.m,179
function kl_bits 1,0
data 46,1555
data2 47,1592
% (PDF) and make zero bins small numbers 50,1701
data2 52,1812
kl_bits 55,1885
      kl_bits 63,2071
      kl_bits 65,2131

classes/@histogram_db/subsref.m,60
function b 1,0
  b 19,544
      b 26,706
      b 28,755

classes/@histogram_db/private/calcKL.m,14
function 1,0

classes/@histogram_db/calcKLmodel.m,132
function 1,0
data 40,1297
bin_size 43,1379
norm_data 47,1489
%data_range data_range
50,1546
kl_bits 73,2215
  a_plot 77,2337

classes/@histogram_db/plotPages.m,336
function a_plot 1,0
%	  quiet: If 16,550
% See also: plotPages,21,678
% Copyright 27,828
num_pages 46,1307
pages=47,1350
ranges 50,1404
  a_hist_db_props 56,1611
    axis_labels 59,1743
    axis_labels{axis_labels
60,1789
    a_plot 61,1856
    ranges 67,2008
  subplots{subplots
69,2062
the_title 72,2098
a_plot 83,2306

classes/@histogram_db/get.m,33
function b 1,0
  errstr 14,468

classes/@histogram_db/histogram_db.m,316
function a_hist_db 1,0
% >> a_hist_db 33,1133
% See also: tests_db,36,1244
% See also: tests_db, plot_simple,36,1244
% Copyright 42,1416
   a_hist_db 50,1764
   a_hist_db 52,1881
   col_names 69,2208
   a_hist_db 71,2249
   a_hist_db 72,2272
		     tests_db(test_results, col_names, {}, id, props)73,2324

classes/@histogram_db/plotRowMatrix.m,124
function a_plot 1,0
num_rows 38,1345
num_cols 39,1375
      header_plot.axis_labels{axis_labels
51,1797
a_plot 86,2888

classes/@histogram_db/plot_abstract.m,371
function a_plot 1,0
  command 49,1429
% If input is an array,52,1453
num_dbs 54,1557
  % Create array of plots58,1665
  a_plot 64,1875
% First column is the variable,68,1928
colnames 69,1984
data 71,2035
  hist_label 78,2250
  y_label 84,2378
  x_label 86,2426
  y_label 87,2469
  all_title 93,2617
  y_label 99,2748
  line_spec 105,2852
a_plot 122,3390

classes/@histogram_db/calcMode.m,58
function 1,0
% Find heaviest bin31,847
mode_val 35,927

classes/@histogram_db/plotEqSpaced.m,410
function a_plot 1,0
% If input is an array,46,1394
% First column is the variable,57,1681
colnames 58,1737
data 60,1788
all_vals 61,1819
skip_x_num 63,1855
props(1).XTick XTick
70,2175
props(1).XTickLabel XTickLabel
71,2227
  hist_label 78,2460
  y_label 84,2588
  x_label 86,2618
  y_label 87,2643
  all_title 93,2791
a_plot 97,2871
		     properTeXLabel(colnames{1}), command, props)100,3017

classes/@model_ranked_to_physiol_bundle/plotfICurve.m,284
function a_doc 1,0
% See also: doc_generate,22,582
% Copyright 28,734
crit_db_id 39,1208
traceset_index 40,1276
crit_trace_id 41,1342
short_caption 44,1498
caption 45,1574
curve_pAvals 46,1603
curve_tests 47,1634
curve_labels 49,1797
best_trial_num 50,1856
a_doc 51,1901

classes/@model_ranked_to_physiol_bundle/model_ranked_to_physiol_bundle.m,289
function r_bundle 1,0
  r_bundle.ranked_db ranked_db
46,1870
  r_bundle.crit_bundle crit_bundle
47,1903
  r_bundle 48,1947
  r_bundle 50,2086
  r_bundle.m_bundle m_bundle
56,2174
  r_bundle.ranked_db ranked_db
57,2206
  r_bundle.crit_bundle crit_bundle
58,2242
  r_bundle 59,2282

classes/@model_ranked_to_physiol_bundle/comparisonReport.m,1301
function a_doc_multi 1,0
a_ranked_db 44,1688
crit_db_id 49,1855
  joined_db 55,2051
  crit_trace_id 58,2124
  num_plots 59,2163
  short_caption 62,2260
  caption 63,2341
  best_doc 65,2445
  short_caption 79,3128
  caption 80,3208
  crit_trace_d100 81,3239
  crit_spikes 82,3306
  crit_spont_sshape 83,3347
  crit_pulse_sshape 84,3433
  best_trace 85,3524
  best_spikes 86,3612
  best_spont_sshape 87,3648
  best_pulse_sshape 88,3729
  best_sshape_doc 89,3815
		      caption,97,4221
  short_caption 103,4528
  caption 104,4599
  best2_doc 106,4703
  % original and 5 matching data traces,117,5285
  short_caption 119,5417
  caption 120,5487
  horiz_props 125,5701
  d100_row_plot 126,5789
  h100_row_plot 128,5967
  rest_doc 131,6145
  clearpage_doc 140,6572
    num_best 146,6781
  top_ranks 148,6806
  short_caption 149,6892
  caption 150,6953
  distancetable_doc 152,7048
  num_best 158,7299
  short_caption 160,7396
  caption 162,7528
  coloredplot_doc 166,7744
  short_caption 175,8169
  caption 177,8309
  sortedcoloredplot_doc 181,8570
  short_caption 190,9050
  caption 191,9138
  num_best 194,9260
  top_ranks 195,9277
  all_param_cols 196,9361
  p_hists 198,9477
  paramshist_doc 199,9549
  a_doc_multi 210,10080
  a_doc_multi 215,10313

classes/@model_ranked_to_physiol_bundle/plotCompareRanks.m,695
function plots 1,0
% Copyright 29,817
num_plots 44,1256
a_db_id 47,1314
crit_db_id 48,1382
  plots.crit_trace_h100 crit_trace_h100
54,1605
  crit_trace_id 60,1862
  trace_d100_plots 62,1937
  trace_h100_plots 63,1978
    trial_num 67,2079
      crit_traces 70,2216
      sup_props 72,2248
      crit_traces 73,2274
    trace_d100_plots{trace_d100_plots
75,2307
		       'plot', sup_props)79,2547
    trace_h100_plots{trace_h100_plots
80,2576
		       'plot', sup_props)83,2754
  plots.crit_trace_id crit_trace_id
86,2792
  plots.joined_db joined_db
87,2831
  plots.trace_d100_plots trace_d100_plots
88,2862
  plots.trace_h100_plots trace_h100_plots
89,2907
  plots 91,2957

classes/@model_ct_bundle/reportCompareModelToPhysiolNeuron.m,1224
function a_doc_multi 1,0
phys_trace_d100 49,1897
phys_trace_h100 50,1958
phys_trace_id 51,2020
% If specified,55,2161
% Mostly to allow showing only one trace,56,2235
  phys_trace_h100 60,2449
phys_db_row 64,2562
phys_db_id 65,2657
model_trace_d100 67,2710
model_trace_h100 68,2767
model_trace_id 69,2825
mj_db 70,2906
model_db_row 71,2942
model_db_id 72,2999
a_d100_plot 74,3040
a_h100_plot 78,3165
  a_d100_plot.legend legend
86,3402
  a_h100_plot.legend legend
87,3429
  orientation 89,3461
short_caption 91,3486
caption 92,3575
plot_title 94,3678
trace_doc 96,3696
short_caption 107,4176
caption 108,4266
plot_title 109,4295
phys_spont_sshape 111,4313
phys_pulse_sshape 112,4383
model_spont_sshape 114,4451
model_pulse_sshape 115,4520
sshape_doc 117,4587
	     caption,126,5016
short_caption 133,5312
caption 134,5402
  sup_props 138,5504
fIcurve_doc 141,5531
phys_spikes_h100 153,6058
model_spikes_d100 154,6105
model_spikes_h100 155,6151
short_caption 157,6198
caption 158,6298
freq_profile_doc 159,6327
	     caption,172,6903
  a_doc_multi 181,7349
	       plot_title,190,7790
  a_doc_multi 192,7824
function sshape 199,8016
  num_spikes 201,8084
    sshape 206,8277

classes/@model_ct_bundle/set.m,64
function a 1,0
  a.dataset_db_bundle dataset_db_bundle
14,455

classes/@model_ct_bundle/plotComparefICurve.m,328
function a_plot 1,0
% See also: plot_abstract,32,1131
% Copyright 38,1297
  short_caption 51,1714
  caption 59,1969
curve_pAvals 63,2041
curve_tests 64,2072
curve_labels 66,2235
joined_db 69,2296
neuron_name 71,2337
plots_all 74,2457
plots_all 75,2473
    stats_caption 89,3076
  plots_all 92,3148
a_plot 99,3353

classes/@model_ct_bundle/rankMatching.m,47
function a_ranked_db 1,0
a_ranked_db 37,1044

classes/@model_ct_bundle/getNeuronRowIndex.m,113
function a_row_index 1,0
joined_db 38,1060
dataset_props 40,1101
  trial_name 44,1256
  a_row_index 49,1374

classes/@model_ct_bundle/getTrialNum.m,118
function trial_num 1,0
      trial_name 40,1252
      j_db 45,1389
      trial_num 48,1570
    trial_num 51,1666

classes/@model_ct_bundle/get.m,33
function b 1,0
  errstr 14,451

classes/@model_ct_bundle/collectPhysiolMatches.m,204
function row_index 1,0
num_crits 37,1079
  row_index 41,1202
    %ranked{ranked
45,1349
  %a_ranked_bundle a_ranked_bundle
48,1477
  num_best 52,1635
  a_ranked_bundle 57,1730
  row_index 58,1790

classes/@model_ct_bundle/plotCompareRanks.m,695
function plots 1,0
% Copyright 31,969
num_plots 45,1374
a_db_id 48,1432
crit_db_id 49,1500
  plots.crit_trace_h100 crit_trace_h100
55,1711
  crit_trace_id 61,1944
  trace_d100_plots 63,2019
  trace_h100_plots 64,2060
    trial_num 68,2161
      crit_traces 71,2298
      sup_props 73,2330
      crit_traces 74,2356
    trace_d100_plots{trace_d100_plots
76,2389
		       'plot', sup_props)80,2620
    trace_h100_plots{trace_h100_plots
81,2649
		       'plot', sup_props)84,2818
  plots.crit_trace_id crit_trace_id
87,2856
  plots.joined_db joined_db
88,2895
  plots.trace_d100_plots trace_d100_plots
89,2926
  plots.trace_h100_plots trace_h100_plots
90,2971
  plots 92,3021

classes/@model_ct_bundle/model_ct_bundle.m,145
function a_bundle 1,0
  a_bundle 48,1783
  a_bundle 50,1912
  col_names 57,2030
  all_names 59,2060
  a_bundle 67,2339
  a_bundle 68,2360

classes/@model_ct_bundle/ctFromRows.m,105
function a_cip_trace 1,0
trial_num 39,1245
props.neuronLabel neuronLabel
40,1294
a_cip_trace 42,1348

classes/@model_ct_bundle/addToDB.m,78
function a_mbundle 1,0
  j_db 44,1399
a_mbundle 51,1525
a_mbundle 53,1641

classes/@model_ct_bundle/reportRankingToPhysiolNeuronsTeXFile.m,1482
function tex_filename 1,0
traceset_index 43,1561
neuron_name 44,1614
tex_filename 45,1706
tex_filename 51,1865
a_ranked_db 53,1906
ranked_num_rows 54,1980
ranked_num_cols 55,2022
crit_db_id 59,2156
  joined_db 65,2375
  best_trial_num 66,2406
  num_plots 69,2495
  short_caption 72,2592
  caption 73,2673
  best_doc 75,2776
  fIcurve_doc 86,3367
  caption 98,3988
  crit_trace_d100 99,4019
  crit_spikes 100,4086
  crit_spont_sshape 101,4127
  crit_pulse_sshape 102,4213
  best_trace 103,4304
  best_spikes 104,4383
  best_spont_sshape 105,4419
  best_pulse_sshape 106,4500
  best_sshape_doc 107,4586
		      caption,115,4992
  short_caption 121,5299
  caption 122,5370
  best2_doc 124,5474
  % original and 5 matching data traces,135,6054
  short_caption 137,6186
  caption 138,6256
  horiz_props 143,6470
  d100_row_plot 144,6558
  h100_row_plot 146,6736
  rest_doc 149,6914
  clearpage_doc 158,7339
    num_best 164,7548
  top_ranks 166,7573
  short_caption 167,7659
  caption 168,7720
    aspect_props 173,7882
  distancetable_doc 175,7911
  num_best 182,8170
  short_caption 184,8267
  caption 186,8399
  coloredplot_doc 190,8615
  short_caption 199,9040
  caption 201,9180
  sortedcoloredplot_doc 205,9441
  short_caption 214,9925
  caption 215,10013
  num_best 218,10135
  top_ranks 219,10152
  all_param_cols 220,10236
  p_hists 222,10352
  paramshist_doc 223,10424
  a_doc_multi 234,10955
  a_doc_multi 239,11188

classes/@model_ct_bundle/getNeuronLabel.m,56
function a_label 1,0
trial_num 34,942
a_label 36,996

classes/@script_array/runJob.m,95
function job_result 1,0
% See also: runLast,23,648
% Copyright 29,790
  job_result 39,1233

classes/@script_array/script_array.m,192
function obj 1,0
  obj.id id
55,2005
  obj.props props
56,2020
  obj 57,2042
  obj 59,2135
  obj.num_runs num_runs
65,2214
  obj.id id
66,2241
  obj.props props
67,2256
  obj 70,2300

classes/@script_array/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,651

classes/@script_array/set.m,16
function a 1,0

classes/@script_array/runLast.m,73
function job_results 1,0
% See also: runJob,24,749
% Copyright 30,891

classes/@script_array/get.m,16
function b 1,0

classes/@script_array/subsasgn.m,32
function a 1,0
      a 19,642

classes/@script_array/runFirst.m,95
function job_results 1,0
% See also: runLast,21,541
% Copyright 27,681
job_results 48,1372

classes/@sql_portal/subsref.m,79
function b 1,0
  b 19,544
      %b b
29,796
      b 31,838
      b 33,883

classes/@sql_portal/tests_db.m,511
function a_db 1,0
verbose 37,1246
conn 55,1571
use_java_direct 56,1607
  rs 67,2056
  num_rows 74,2209
  rsm 75,2234
  num_cols 76,2259
  max_read 89,2484
  max_rows 90,2524
  elseif strfind(102,2865
    row_num 127,3442
  col_names 130,3476
  rsm 131,3494
  % get the Java object directly,143,3702
  %rs rs
144,3759
  new_data 151,3922
% $$$     start_row 157,4089
  % get names 165,4337
  new_data 177,4744
a_db 181,4819
a_db = tests_db(new_data, col_names, {}, query_id, props)181,4819

classes/@sql_portal/sql_statement.m,62
function response_str 1,0
verbose 36,1235
a_cursor 47,1394

classes/@sql_portal/get.m,16
function b 1,0

classes/@sql_portal/sql_table.m,277
% See also: tests_db/tests_db,tests_db
21,641
% See also: tests_db/tests_db, database,21,641
% Copyright 27,815
verbose 37,1221
col_names 44,1324
query_string 47,1377
comma_str 50,1437
  query_string 54,1544
  comma_str 56,1632
query_string 59,1657
a_cursor 67,1777

classes/@sql_portal/sql_portal.m,198
function obj 1,0
   obj.id id
42,1306
   obj.props props
43,1322
   obj 44,1349
   obj 46,1439
   obj.db_conn db_conn
59,1646
   obj.id id
60,1672
   obj.props props
61,1688
   obj 63,1711

classes/@spike_shape/calcMaxVm.m,14
function 1,0

classes/@spike_shape/plotCompareMethods.m,387
function a_plot 1,0
sm3 40,1133
resultsm3 41,1207
init_idx 42,1236
rise_time 43,1268
peak_time 44,1301
min_time 45,1335
% Method 47,1366
sm7 48,1413
resultsm7 49,1487
r2_plot 51,1517
r2_plot 52,1615
r_plot 57,1782
r_plot 58,1869
r3_plot 62,2019
m3_plot 64,2096
% Method 66,2172
% Method 76,2649
% Method 86,3147
% Method 96,3630
class_name 112,4253
a_plot 113,4294

classes/@spike_shape/set.m,81
function b 1,0
  b 13,462
  errstr 15,477
  a.trace trace
16,499
  b 17,536

classes/@spike_shape/calcInitVmV3hKpTinterp.m,643
function 1,0
a_plot 47,1716
%num_points num_points
52,1800
%interp_v interp_v
54,1820
d2 62,2065
d1 63,2108
d3 66,2176
d2 67,2199
d1 68,2221
low_d1_idx 71,2296
low_d1_idx 77,2481
hi_d1_idx 79,2510
hi_d1_idx 85,2694
h = (d3 .* = (d3 .*
90,2801
s_props 92,2849
  constrained_idx 98,3055
  else 103,3288
    max_h_idx 105,3348
  add_h_title 108,3403
max_h_idx 111,3457
k1 114,3509
k 115,3528
constrained_idx 118,3640
  max_k_idx 124,3981
  max_h_idx 125,4000
else 129,4153
  max_k_idx 131,4209
  max_h_idx 134,4315
  max_h_idx 135,4357
    title_str 143,4554
  a_plot 145,4631
  a_plot 172,6015
init_idx 175,6134

classes/@spike_shape/display.m,28
function s 1,0
  s 19,544

classes/@spike_shape/plotTPP.m,50
function a_plot 1,0
deriv 31,842
a_plot 33,890

classes/@spike_shape/calcMinVm.m,53
function 1,0
min_idx 34,1058
max_min_time 35,1091

classes/@spike_shape/calcInitVmV2PPLocal.m,374
function 1,0
a_plot 40,1393
d3 42,1407
d2 43,1481
d1 44,1555
d3 46,1653
d2 47,1676
d1 48,1698
h 49,1720
dh 52,1795
dh2 53,1813
hd2 54,1847
zc 55,1882
  cross_idx 64,2235
    % Then,70,2530
    idx 71,2602
    cross_idx 73,2622
    % choose maximum nearest to crossing point75,2653
    idx 77,2755
  class_name 82,2851
  t_data 83,2894
  a_plot 84,2937

classes/@spike_shape/calcInitVm.m,705
function 1,0
a_plot 48,1554
min_val 51,1580
max_val 52,1613
max_d1o 53,1646
s_props 56,1734
method 57,1761
vs 59,1795
verbose 60,1829
    accel 74,2054
    deriv 79,2168
    accel 80,2200
    idx 81,2225
    idx 88,2487
  case 91,2534
  case 96,2715
  % Point of maximum curvature: Kp 99,2795
  case 105,3022
  case 110,3211
  % Point of maximum curvature in phase-plane: Kp 114,3334
      err 132,3881
    idx 152,4505
  err 158,4615
    idx 163,4816
init_idx 170,4881
init_val 173,4912
% Find the REAL max_val175,4966
rise_time 178,5051
amplitude 179,5100
function [peak_mnction [peak_
182,5212
  interp 186,5345
  peak_idx 190,5454
  flip 205,5783
  left_idx 208,5855

classes/@spike_shape/calcInitVmMaxCurvPhasePlane.m,1821
function 1,0
a_plot 47,1782
windowsize 51,1873
smooth_data 53,1948
smooth_data 54,2017
trace_data 59,2198
%trace_data trace_data
60,2224
%d2 d2
62,2320
d1o 63,2390
%d2 d2
65,2499
d1o 66,2521
% Find max in derivative68,2545
last_pos_d 72,2664
  last_pos_d_idx 77,2814
last_neg_d 81,2899
  last_neg_d_idx 88,3155
% Find min in voltage before end91,3196
num_points 97,3472
start_idx 98,3490
dv 99,3530
voltage_points 100,3605
d1o_points 107,3918
interp_vpp 120,4276
windowsize 123,4378
filtered_vpp 124,4395
low_bound 125,4465
%figure;figure
127,4539
  voltage_points 133,4773
  d2 139,4926
  d3 140,4960
  d1 141,4994
  d2 142,5017
  d3 143,5039
  d1 145,5066
  d2 146,5091
  d3 147,5108
  d1 148,5125
  d2 149,5148
  d3 150,5170
% Find max in derivative as upper limit of region of interest153,5197
d3 156,5313
d2 157,5337
d1 158,5361
  max_d2vpp_t_idx 163,5479
    max_d3vpp_idx 170,5782
    max_d3vpp_t_idx 171,5832
  err 177,6074
    max_d2vpp_idx 180,6229
    max_d2vpp_t_idx 181,6252
    max_d3vpp_idx 182,6277
    max_d3vpp_t_idx 183,6300
k1 191,6434
k 192,6453
% Maximal curvature194,6486
% Highest maximum197,6533
    idx 213,7018
max_k_idx 217,7096
max_k_t_idx 218,7113
thr_vol 220,7201
    max_k_near_d2vpp_t_idx 236,7689
    max_k_near_d2vpp_idx 239,7948
    max_k_near_d2vpp_t_idx 240,7986
    max_k_near_d2vpp_idx 243,8039
    max_k_near_d2vpp_t_idx 244,8077
init_idx 248,8148
s_props 250,8233
  fail_cond 255,8452
  fail_cond 257,8480
  v 262,8562
  t 263,8611
  t_data 264,8651
    title_str 268,8782
  a_plot 270,8859
		     'K_p = d^2v\prime/dv^2[1 + dv\prime/dv^2]^{-3/2}, v\prime=rime
284,9759
  a_plot 294,10401
  denom 302,10745
    t_idx 308,11005
function idx 313,11143
  % Highest maximum316,11220
      idx 332,11700

classes/@spike_shape/get.m,33
function b 1,0
  errstr 14,468

classes/@spike_shape/calcInitVmSekerliV2.m,300
function 1,0
a_plot 39,1287
s_props 40,1300
d3 42,1328
d2 43,1402
d1 44,1476
d3 46,1574
d2 47,1597
d1 48,1619
h 49,1641
  constrained_idx 52,1796
  else 57,2029
    idx 59,2083
  add_title 62,2126
idx 65,2172
  class_name 68,2242
  t_data 69,2285
  a_plot 70,2328
init_idx 81,2834

classes/@spike_shape/calcWidthFall.m,1761
function 1,0
%max_val max_val
50,1896
vs 52,1931
verbose 53,1965
depol 56,2025
end_depol 59,2151
% concave66,2317
end_depol 69,2407
  base_width 76,2741
  half_width 77,2761
  half_Vm 78,2781
  fixed_Vm_width 79,2798
  fall_time 80,2822
  min_idx 81,2841
  min_val 82,2858
  max_ahp 83,2875
  ahp_decay_constant 84,2892
  dahp_mag 85,2920
  dahp_idx 86,2938
denum 92,3023
  extra_time 96,3195
fall_init_cross_time 98,3217
base_width 101,3292
fall_time 102,3338
half_Vm 105,3406
half_width 107,3454
fixed_Vm_width 108,3495
after_ahp = s.tter_ahp = s.
118,3844
%decay_constant_threshold decay_constant_threshold
124,4026
  % Find minimum after the double AHP133,4295
  recover_times 135,4379
  recover_times 139,4508
  ahp_decay_constant 146,4724
function a_width 149,4757
    a_width 159,5197
  above_half 165,5343
  some_of_the_above 175,5717
  end_of_first_hump 176,5780
      end_of_first_hump 180,5944
  some_of_the_above 184,6057
  start_of_last_ramp 185,6124
    start_of_last_ramp 190,6332
    half_start 200,6659
    half_end 210,6995
  a_width 213,7036
function 218,7078
  dahp_idx 221,7193
  %dahp_bump_rise dahp_bump_rise
236,7644
  fall_time 237,7717
  dahp_bump_fall 238,7763
  %dahp_bump_fall dahp_bump_fall
239,7847
  dahp_bump 240,7945
  nodahp_error 248,8260
    dahp_mag 252,8374
function 256,8425
  windowsize 259,8576
    after_fall 262,8723
    after_fall 264,8811
  thr_start_from 267,8865
  first_thr_crossing 268,8931
    first_thr_crossing_idx 272,9103
  next_thr_crossing 276,9216
    end_at 281,9376
  % Max AHP must be the minimal point in between284,9447
  min_idx 287,9552
  max_ahp 289,9596
  max_ahp = max(0, init_val - min_val); 	% maximal AHP amplitude289,9596

classes/@spike_shape/spike_shape.m,216
function obj 1,0
  obj 70,2777
  obj 72,2882
    %props.init_threshold init_threshold
81,3048
    % max vPP curvature,86,3259
    props.init_Vm_method init_Vm_method
87,3324
  trace_obj 95,3537
  obj 96,3583

classes/@spike_shape/calcInitVmMaxCurvature.m,250
function 1,0
a_plot 43,1423
d2 45,1437
d1 46,1508
d2 47,1578
d1 48,1599
k1 49,1620
k 50,1639
dk 52,1721
dk2 53,1735
zc 54,1769
  % Then,59,1994
  idx 60,2064
  idx 63,2105
  idx 64,2158
  t 68,2232
  t_data 69,2272
  a_plot 70,2310

classes/@spike_shape/plotResults.m,503
function a_plot 1,0
% If input is an array,41,1097
results 52,1363
init_idx 54,1389
rise_time 55,1419
peak_time 56,1450
peak_mag 57,1484
min_val 58,1511
init_val 59,1536
half_Vm 60,1564
amplitude 61,1590
max_ahp 62,1622
dahp_mag 63,1649
fall_time 64,1678
min_idx 65,1709
%results.ahp_decay_constant ahp_decay_constant
67,1763
base_width 68,1814
half_width 69,1847
approx_half_idx 72,1897
plot_data 76,2014
spsh_plot 96,2727
annot_plot 99,2824
annot_plot 100,2872
a_plot 103,2934

classes/@spike_shape/calcInitVmSlopeThresholdSupsample.m,376
function 1,0
a_plot 39,1317
smooth_data 42,1371
s 43,1412
% Supersampling factor 50,1588
  grid on;70,2421
last_pos_d 74,2495
  last_pos_d_idx 79,2653
last_neg_d 82,2694
  last_neg_d_idx 89,2968
start_idx 92,3009
deriv 94,3050
deriv2 95,3080
idx 98,3144
init_idx 107,3476
  t 111,3590
  t_data 112,3636
        threshold_estimate 116,3793
  a_plot 121,3966

classes/@spike_shape/plotCompareMethodsSimple.m,618
function a_plot 1,0
s 39,1168
th 42,1247
sm3 43,1256
resultsm3 44,1330
r3_plot 45,1359
init_idx 48,1471
rise_time 49,1503
peak_time 50,1536
min_time 51,1570
% Method 56,1681
sm7 57,1728
resultsm7 58,1802
% Method 60,1832
try 67,2234
  err 70,2328
% plot with all derivatives,79,2526
%d_plot d_plot
80,2564
r_plot 83,2682
r_plot 84,2750
points_cell 88,2884
t_points 96,3397
v_points 97,3429
annotation_plot 98,3461
r_plot 105,3728
spike_shape_time_plot 108,3861
t_plots_row 110,3937
class_name 118,4171
a_plot 119,4212
function voltage 123,4340
    voltage 128,4460
    voltage 131,4562

classes/@spike_shape/calcInitVmLtdMaxCurv.m,254
function 1,0
s_props 45,1599
a_plot 47,1627
d2 49,1641
d1 50,1715
d2 51,1785
d1 52,1806
k1 53,1827
k 54,1846
constrained_idx 56,1957
else 66,2444
  idx 68,2494
  idx 69,2524
  t 74,2599
  t_data 75,2639
  a_plot 76,2677
init_idx 88,3225

classes/@spike_shape/plotPP.m,50
function a_plot 1,0
deriv 30,759
a_plot 34,923

classes/@spike_shape/getResults.m,1476
function 1,0
ms_factor 39,1021
mV_factor 40,1051
results.PeakVm PeakVm
44,1152
results.InitVm InitVm
45,1174
results.InitVmBySlope InitVmBySlope
46,1196
results.MaxVmSlope MaxVmSlope
47,1225
results.HalfVm HalfVm
48,1251
results.Amplitude Amplitude
49,1273
results.MaxAHP MaxAHP
50,1298
results.DAHPMag DAHPMag
51,1320
results.InitTime InitTime
52,1343
results.RiseTime RiseTime
53,1367
results.FallTime FallTime
54,1391
results.MinTime MinTime
55,1415
results.BaseWidth BaseWidth
56,1438
results.HalfWidth HalfWidth
57,1463
results.FixVWidth FixVWidth
58,1488
% Run tests66,1623
end77,2036
s_props 84,2215
try 87,2328
  init_st_val 90,2444
  err 92,2512
    min_tm_amp 103,2723
    min_mm_amp 109,2831
end118,3187
% If you change any of the following names,139,3933
% make sure to change the above NaN names,140,3978
results.MinVm MinVm
141,4026
results.PeakVm PeakVm
142,4063
results.InitVm InitVm
143,4102
results.InitVmBySlope InitVmBySlope
144,4141
results.MaxVmSlope MaxVmSlope
145,4190
results.HalfVm HalfVm
146,4232
results.Amplitude Amplitude
147,4270
results.MaxAHP MaxAHP
148,4313
results.DAHPMag DAHPMag
149,4351
results.InitTime InitTime
151,4392
results.RiseTime RiseTime
152,4433
results.FallTime FallTime
153,4475
results.MinTime MinTime
154,4517
%results.ahp_decay_constant ahp_decay_constant
156,4582
results.BaseWidth BaseWidth
157,4644
results.HalfWidth HalfWidth
158,4688
results.FixVWidth FixVWidth
159,4732

classes/@spike_shape/calcInitVmSlopeThreshold.m,155
function 1,0
a_plot 39,1213
deriv 41,1227
deriv 42,1300
idx 44,1357
  idx 51,1697
init_idx 53,1712
  t 57,1789
  t_data 58,1829
  a_plot 59,1867

classes/@stats_db/plotVarMatrix.m,504
function a_plot_stack 1,0
  rotate_labels 41,1288
num_params 44,1331
num_tests 45,1361
plot_rows 48,1464
  ranges 52,1555
  relativeSizes 53,1570
      a_plot 65,2019
      a_plot.plot_stack.plots{1}.props.tightLimits tightLimits
71,2292
      axis_ranges 72,2348
      a_plot 74,2411
      axis_ranges 77,2569
      ranges 83,2672
    plots{plots
89,2854
    horiz_props 95,3091
  % fixed y-axis bounds,100,3279
  plot_rows{plot_rows
101,3324
title_str 104,3417
a_plot_stack 107,3502

classes/@stats_db/plotYTests.m,221
function a_p 1,0
% Copyright 38,1404
cols_db 60,1926
test_names 62,1976
  all_title 67,2134
  line_style 73,2234
  props.LineStyleOrder LineStyleOrder
74,2253
data 77,2321
row_idx 78,2350
elseif isfield(82,2459

classes/@stats_db/subsref.m,60
function b 1,0
  b 21,618
      b 27,749
      b 30,827

classes/@stats_db/set.m,52
function a 1,0
  a.tests_3D_db tests_3D_db
14,455

classes/@stats_db/plotColorVar.m,400
function a_plot 1,0
num_params 38,1186
num_tests 39,1216
image_data 41,1294
image_data 49,1562
num_colors 51,1652
num_plot_rows 52,1669
plot_props 54,1707
plot_props.YTick YTick
56,1745
row_labels 57,1777
plot_props.YTickLabel YTickLabel
58,1848
plot_props.XTick XTick
60,1885
  col_labels{col_labels
63,1994
plot_props.XTickLabel XTickLabel
65,2035
a_plot 71,2231
  num_rows 87,2857

classes/@stats_db/plot_bars_ax.m,298
function a_plot 1,0
col_names 42,1213
data 43,1283
row_idx 44,1315
num_cols 45,1353
num_pages 46,1387
mids 48,1423
elseif isfield(52,1519
  ns 74,2087
plot_props.groupValues groupValues
81,2187
swaprowspages 84,2246
mids 85,2271
lows 86,2308
highs 87,2345
ns 88,2384
a_plot 91,2450

classes/@stats_db/stats_db.m,91
function a_stats_db 1,0
  a_stats_db 52,1779
  a_stats_db 54,1895
  a_stats_db 61,1992

classes/@stats_db/plotVar.m,370
function a_plot 1,0
%	  quiet: If 20,789
% See also: plotVar,26,949
% Copyright 32,1095
col_names 47,1511
data 48,1579
row_idx 49,1611
col1 51,1650
col2 52,1688
elseif isfield(56,1804
a_stats_db_props 68,2095
  axis_limits 72,2235
col1name 75,2260
col2name 76,2288
props 78,2317
the_title 80,2365
			 props)97,2899
  a_plot 99,2916
			 props)103,3083

classes/@stats_db/onlyRowsTests.m,18
function obj 1,0

classes/@stats_db/get.m,33
function b 1,0
  errstr 14,451

classes/@stats_db/plot_abstract.m,245
function a_plot 1,0
col_names 44,1309
data 45,1377
row_idx 46,1409
elseif isfield(50,1511
elseif isfield(60,1790
stats_props 72,2067
  axis_limits 76,2192
swaprowspages 79,2217
mids 80,2242
lows 81,2279
highs 82,2316
a_plot 84,2356

classes/@stats_db/compareStats.m,132
function a_mult_stats_db 1,0
  with_db 46,1268
col_names 50,1320
wcol_names 51,1372
  with_db 62,1843
a_mult_stats_db 67,1989

classes/@stats_db/plot_bars.m,402
function a_plot 1,0
  props.groupValues groupValues
47,1485
  page_names 48,1518
  % Then,49,1578
  a_stats_db 50,1606
  page_names 52,1670
col_names 56,1718
data 57,1788
row_idx 58,1820
num_cols 59,1858
num_pages 60,1892
elseif isfield(66,2068
    % If there are negative elements,81,2531
    neg_data 82,2596
  ns 95,2847
stats_props 98,2863
elseif isfield(101,2983
a_plot 117,3382

classes/@spike_shape_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@spike_shape_profile/spike_shape_profile.m,147
function a_ss_profile 1,0
  a_ss_profile 44,1527
  a_ss_profile 46,1668
  a_ss_profile.spike_shape spike_shape
52,1760
  a_ss_profile 55,1827

classes/@spike_shape_profile/plot_abstract.m,501
function a_plot 1,0
results 35,965
  absolute_peak_shift 40,1126
init_idx 43,1158
rise_time 44,1209
peak_time 45,1240
peak_mag 46,1274
min_val 47,1301
init_val 48,1326
half_Vm 49,1354
amplitude 50,1380
max_ahp 51,1412
dahp_mag 52,1439
fall_time 53,1468
min_idx 54,1499
%results.ahp_decay_constant ahp_decay_constant
56,1574
base_width 57,1625
half_width 58,1658
approx_half_idx 61,1708
plot_data 65,1825
spsh_plot 85,2538
annot_plot 88,2629
annot_plot 89,2677
  a_plot 96,2863

classes/@params_tests_dataset/getItemParams.m,25
function params_row 1,0

classes/@params_tests_dataset/subsref.m,44
function b 1,0
  b 19,544
      b 25,661

classes/@params_tests_dataset/set.m,16
function a 1,0

classes/@params_tests_dataset/display.m,16
function s 1,0

classes/@params_tests_dataset/readDBItems.m,601
function 1,0
  num_items 47,1546
  err 49,1581
  test_names 59,1986
  param_names 60,2005
  params 61,2025
  tests 62,2040
tests 68,2188
docs 69,2238
start_time 72,2292
line_buffer 75,2334
  row_index 78,2358
  doc_row_index 79,2375
      line_buffer 95,2798
        est_remaining 100,3017
        line_buffer 101,3091
	line_buffer 107,3395
    end110,3466
    num_rows 114,3592
      docs{docs
118,3773
      row_index 119,3808
      docs{docs
125,4046
      row_index 126,4081
    doc_row_index 128,4122
  err 131,4173
docs 149,4815
end_time 151,4856
total_time 153,4877

classes/@params_tests_dataset/get.m,16
function b 1,0

classes/@params_tests_dataset/itemResultsRow.m,153
function 1,0
a_doc 37,1339
% get params from file 39,1352
a_profile 48,1629
% If found in profile,55,1800
  tests_row 68,2203
  tests_row 71,2309

classes/@params_tests_dataset/testNames.m,101
function 1,0
props 35,1021
% get params from file 37,1053
test_names 53,1461
test_names 54,1506

classes/@params_tests_dataset/params_tests_db.m,275
function db_obj 1,0
  args 43,1370
% in case the fileset is lost,47,1464
    props(1).neuron_idx=neuron_idx
51,1611
        props.data_src{data_src
54,1692
        ds=55,1738
        props.tracesets{tracesets
56,1781
end58,1825
props.doc doc
62,1903
db_obj 64,1923

classes/@params_tests_dataset/params_tests_dataset.m,268
function obj 1,0
  obj.dt=dt
65,2863
  obj.dy=dy
66,2875
  obj.id id
67,2887
  obj.props props
68,2902
  obj 69,2928
  obj 71,3033
  obj.list list
78,3113
  obj.dt dt
79,3132
  obj.dy dy
80,3147
  obj.id id
81,3162
  obj.props props
82,3177
  obj 85,3227

classes/@params_tests_dataset/subsasgn.m,44
function a 1,0
  a 18,590
      a 31,895

classes/@params_tests_dataset/getItem.m,34
function item 1,0
  item 32,823

classes/@params_tests_dataset/addItem.m,51
function dataset 1,0
  dataset.list list
36,1127

classes/@params_tests_dataset/setProp.m,85
function obj 1,0
  val 33,920
    a 35,955
    a(1).(attr)36,974
    obj 37,997

classes/@params_tests_dataset/loadItemProfile.m,24
function a_profile 1,0

classes/@params_results_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@params_results_profile/params_results_profile.m,124
function obj 1,0
  obj 47,1648
  obj 49,1776
  props 52,1820
  obj 54,1862
  obj.params params
55,1878
  obj 63,2035

classes/@cip_trace_profile/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,655

classes/@cip_trace_profile/set.m,28
function b 1,0
  b 13,462

classes/@cip_trace_profile/display.m,16
function s 1,0

classes/@cip_trace_profile/get.m,33
function b 1,0
  errstr 14,468

classes/@cip_trace_profile/cip_trace_profile.m,707
function obj 1,0
  obj.spikes spikes
64,2220
  obj.spont_spike_shape spont_spike_shape
65,2243
  obj.pulse_spike_shape pulse_spike_shape
66,2282
  obj.props props
67,2321
  obj 68,2347
  obj 70,2470
    props 76,2619
  obj.trace trace
80,2672
  obj.trace = cip_trace(varargin{1:6}, props)80,2672
  obj.spikes spikes
83,2736
  obj.spont_spike_shape spont_spike_shape
87,2852
  spont_sh_results 90,3014
  obj.pulse_spike_shape pulse_spike_shape
92,3094
  pulse_sh_results 95,3251
  misc_results.PulseSpontAmpRatio PulseSpontAmpRatio
98,3349
  obj.props props
101,3463
  % Create object with custom data 114,3911
    props 118,4016
  end119,4041
  obj.props props
123,4154
  obj 126,4198

classes/@cip_trace_profile/plot.m,223
function h 1,0
  ht 33,742
  % TODO: Hack,35,845
  % TODO: Hack, fix it35,845
  super_plot 39,1009
  h 43,1174
function 46,1203
    hss1 49,1315
    pp 50,1387
    hss2 51,1411
    hss1 53,1489
    hss2 54,1505

classes/@physiol_cip_traceset/getItemParams.m,341
function params_row 1,0
% 'type', type,34,1024
% 'type', type, 'on', on,34,1024
% 'type', type, 'on', on, 'off', off,34,1024
% 'type', type, 'on', on, 'off', off, 'finish', finish,34,1024
% 'type', type, 'on', on, 'off', off, 'finish', finish, 'bias', bias,34,1024
fnames 35,1108
tvec 36,1149
params_row 40,1241
params_row 41,1316

classes/@physiol_cip_traceset/set.m,70
function a 1,0
  a.params_tests_dataset params_tests_dataset
14,455

classes/@physiol_cip_traceset/get.m,33
function b 1,0
  errstr 14,468

classes/@physiol_cip_traceset/CIPform.m,1433
function 1,0
  warning off MATLAB:polyfit:PolyNotUnique;PolyNotUnique
36,1177
  traceset_props 41,1355
    cipList 46,1532
  %	cipList 48,1603
      idx 54,1776
      idx 56,1882
    pulse 58,1945
      off 61,2070
          traceset_props.Trials{trace_index}.AcquisitionData{traceset.vchan}.Samples;Samples
65,2219
      off 66,2305
    ciptype 68,2376
    bias 69,2403
    current 70,2417
    finish 71,2508
      bias 75,2599
                   AcquisitionData{traceset.ichan}.DataUnit,DataUnit
79,2771
            bias 81,2853
            bias 83,2902
            bias 85,2951
    nSD 92,3035
    current 94,3153
    % method 97,3351
    windowsize 100,3474
    filtcurr 104,3655
    filtcurr 106,3759
    dt 107,3830
    maxc 108,3860
    minc 109,3886
    stdev 110,3912
    bsln 111,3947
      off 115,4099
      ciptype 116,4128
      tmp 119,4272
      ciptype 120,4329
      tmp 123,4409
      ciptype 124,4466
    % extract pulse start & end times 127,4499
      off 130,4649
    %	figure(hfig); plot(filtcurr, '-green'); hold on;143,5185
    %	figure;144,5240
    %	figure; plot(current, '-blue'); hold on;144,5240
      pulse 148,5375
      bias=150,5401
      pulse 152,5505
      %    	pulse 153,5547
      tvec 155,5653
      pulseidx 156,5690
      elseif pulseidx 159,5793
      elseif pulseidx 161,5845
      elseif abs(tvec(pulseidx + 1) - pulse) > abs(163,5919

classes/@physiol_cip_traceset/cip_trace_profile.m,303
function a_profile 1,0
  pulse_time_start=38,1282
  pulse_time_width=39,1305
  ygain 40,1339
  props=41,1369
  trace_props 46,1602
%   dt 47,1654
%   dt = 1/trace_props.AcquisitionData{traceset.vchan}.SamplingRate;SamplingRate
47,1654
%   dy 48,1723
  a_cip_trace 59,2131
  a_profile 60,2181

classes/@physiol_cip_traceset/itemResultsRow.m,73
function 1,0
params_row 38,1267
resultCell 41,1355
tests_row 44,1436

classes/@physiol_cip_traceset/physiol_cip_traceset.m,1112
function obj 1,0
%   This is a subclass of params_tests_dataset. Each trace varies in bias,10,313
verbose 63,2620
  obj.vchan vchan
67,2715
  obj.ichan ichan
68,2732
  obj.vgain vgain
69,2749
  obj.igain igain
70,2766
  obj.treatments treatments
71,2783
  obj.neuron_id neuron_id
72,2814
  obj 73,2836
  obj 75,2968
  obj.data_src data_src
79,2994
  obj.vchan vchan
80,3021
  obj.ichan ichan
81,3048
  obj.vgain vgain
82,3075
  obj.igain igain
83,3102
  obj.treatments treatments
84,3129
  obj.neuron_id neuron_id
85,3160
  trace_list 91,3291
      trace_list 95,3384
      trace_str 96,3414
      ns_h5_info 116,3992
    props.nsHDF5 nsHDF5
119,4091
    Trials 122,4142
    Trials 124,4272
             Trials, 'uniformoutput', false)130,4493
    props.Trials Trials
131,4539
    props.cip_list cip_list
132,4566
    tr1=142,4827
    tr1=trace_list(1); ch=142,4827
      dt = 1/props.Trials{tr1}.AcquisitionData{ch}.SamplingRate;SamplingRate
144,4914
      dy = 1; %/pros.Trials{tr1}.AcquisitionData{ch}.SamplingRate;SamplingRate
148,5029
  traceset_id 156,5199
  obj 165,5434

classes/@physiol_cip_traceset/cip_trace.m,428
function a_cip_trace 1,0
% First call CIPform and get necessary parameters40,1243
pulse_time_start=42,1364
pulse_time_width=43,1385
ygain 44,1417
new_props=45,1445
  trace_id 52,1775
    num_params 59,1920
  param_names 61,1973
  param_vals 62,2011
    param_idx = strmatch(props.showParamsList{param_num}, param_names)66,2148
    trace_id 67,2220
traceset_props 76,2467
  trace_props 82,2673
a_cip_trace 85,2714

classes/@physiol_cip_traceset/setProp.m,81
function b 1,0
  val 33,918
    a 35,953
    a(1).(attr)36,972
    b 37,995

classes/@physiol_cip_traceset/loadItemProfile.m,24
function a_profile 1,0

classes/@physiol_cip_traceset/paramNames.m,46
function param_names 1,0
param_names 34,901

classes/@physiol_cip_traceset_fileset/neuronNameFromId.m,87
function name_strs 1,0
neuron_names 30,932
% sort the ids32,980
diffed_ids 36,1063

classes/@physiol_cip_traceset_fileset/set.m,70
function a 1,0
  a.params_tests_dataset params_tests_dataset
14,455

classes/@physiol_cip_traceset_fileset/display.m,16
function s 1,0

classes/@physiol_cip_traceset_fileset/readDBItems.m,402
function 1,0
rows 40,1331
    rows 45,1453
first_item 49,1566
param_names 50,1596
param_names 51,1634
test_names 52,1697
params 55,1802
tests 56,1851
start_time 59,1925
rows 63,1976
  %num_traces num_traces
70,2200
  num_traces 71,2243
  neuron_id 75,2366
    % edited by Li Su. Cannot directly put item_params into params,79,2538
    rows 90,3213
    tests 97,3408
    break;98,3438

classes/@physiol_cip_traceset_fileset/physiol_bundle.m,43
function a_pbundle 1,0
a_pbundle 36,1058

classes/@physiol_cip_traceset_fileset/private/scanNeuronsTreats.m,268
function 1,0
  neuron_idx 29,863
    neuron_id 33,967
  all_treatments 35,992
      neuron_idx.(a_ts{1}.neuron_id)neuron_id
39,1153
      neuron_id 40,1203
    all_treatments 43,1269
    all_treatments = mergeStructs(a_ts{1}.treatments, all_treatments)43,1269

classes/@physiol_cip_traceset_fileset/private/resetDefaultTreats.m,186
function traceset_list 1,0
  zero_treatments 26,855
    traceset_list{ts_num}.treatments treatments
29,1040
                                 zero_treatments), all_treatments)31,1154

classes/@physiol_cip_traceset_fileset/get.m,33
function b 1,0
  errstr 14,468

classes/@physiol_cip_traceset_fileset/physiol_cip_traceset_fileset.m,1333
function obj 1,0
  obj 78,3595
  obj 80,3748
  obj.neuron_idx neuron_idx
90,3963
    traceset_items_str 97,4213
    list 108,4725
    traceset_items_str 109,4752
    list 119,5130
      % read ASCII file,121,5214
      tcell 122,5278
      % Parse each line,123,5368
      tmtstruct 124,5424
      names 125,5495
      paths 126,5533
      traces 127,5571
      chaninfo 128,5610
      tmts 129,5651
      list 130,5688
        neuron_id 134,5822
      traceset_items_str 136,5855
        resid 140,5947
        ntok 141,5973
        pars 142,5991
        % If data file,154,6306
        % If data file, make neuron id name 154,6306
        elseif exist(158,6478
                tstr 166,6826
            dots 168,6874
                names{names
172,7023
          obj.neuron_idx.(names{names
178,7209
          neuron_id 179,7258
        paths{paths
182,7308
        traces{traces
183,7336
        chaninfo{chaninfo
185,7366
            ttm 191,7617
            if isfield(tmtstruct, ttm{m, 1}) ~=194,7704
                if isstr(ttm{m, 1}) ~=195,7754
        tmts{tmts
204,8135
        ttm 215,8437
            tempstruct = setfield(tempstruct, ttm{m,1}, ttm{ttm
217,8491
        list{list
219,8570
                           dt, dy, tempstruct, names{n}, props)220,8647
  obj 228,8910

classes/@physiol_cip_traceset_fileset/cip_trace.m,136
function a_cip_trace 1,0
  col_data 42,1404
  num_rows 43,1488
  a_cip_trace 44,1518
  num_traces 55,1896
    a_cip_trace 65,2238

classes/@physiol_cip_traceset_fileset/mergeFilesets.m,325
function 1,0
list2 34,1118
traceset_offset 37,1169
a_fileset_neuronids 40,1222
w_fileset_neuronids 41,1289
w_fileset_neuronnames 42,1356
neuron_id_offset 44,1415
w_fileset.neuron_idx neuron_idx
45,1491
a_list 49,1646
% find union of all treatments51,1681
a_fileset 55,1843
a_fileset.neuron_idx neuron_idx
58,1943

classes/@physiol_cip_traceset_fileset/vertcat.m,79
function obj 1,0
list2 33,967
obj 34,994
obj.neuron_idx neuron_idx
37,1063

classes/@physiol_cip_traceset_fileset/setProp.m,85
function obj 1,0
  val 33,920
    a 35,955
    a(1).(attr)36,974
    obj 37,997

classes/@physiol_cip_traceset_fileset/loadItemProfile.m,43
function a_profile 1,0
a_profile 33,1173

classes/@plot_errorbar/plot_errorbar.m,82
function a_plot 1,0
  a_plot 52,1882
  a_plot 58,1966
			       props)61,2125

classes/@plot_errorbar/get.m,45
function b 1,0
  errstr 14,468
  b 15,490

classes/@plot_errorbar/axis.m,36
function ranges 1,0
ranges 30,824

classes/@cip_traceset/getItemParams.m,25
function params_row 1,0

classes/@cip_traceset/display.m,49
function s 1,0
    first 17,458
  disp(19,482

classes/@cip_traceset/get.m,33
function b 1,0
  errstr 14,468

classes/@cip_traceset/cip_trace_profile.m,93
function a_cip_trace_profile 1,0
mag_idx 33,982
data 39,1152
a_cip_trace_profile 45,1330

classes/@cip_traceset/cip_traceset.m,138
function obj 1,0
  obj.props props
51,1939
  obj 52,1965
  obj 54,2074
  obj.ct ct
65,2200
  obj.props props
66,2215
  obj 69,2260

classes/@cip_traceset/loadItemProfile.m,24
function a_profile 1,0

classes/@cip_traceset/paramNames.m,26
function param_names 1,0

classes/@plot_abstract/subsref.m,79
function b 1,0
  b 19,544
      %b b
29,796
      b 31,838
      b 33,883

classes/@plot_abstract/set.m,46
function a 1,0
val 12,446
  a.(attr)16,531

classes/@plot_abstract/display.m,28
function s 1,0
  s 20,588

classes/@plot_abstract/superposePlots.m,350
function a_plot 1,0
command 39,1337
data 40,1351
legend 41,1362
a_props 42,1375
color_order 43,1393
        plot_props 51,1660
	a_plot 55,1776
    one_props 60,1932
    a_props 64,2077
        % general case 73,2384
      legend 80,2616
  data 85,2738
  legend 86,2759
  a_props 87,2784
a_plot 90,2822
a_plot 91,2860
a_plot 92,2930

classes/@plot_abstract/get.m,16
function b 1,0

classes/@plot_abstract/matrixPlots.m,821
function a_plot 1,0
verbose 47,1603
  goldratio 52,1705
    height 58,1866
  elseif isfield(59,1893
  horz_props.yLabelsPos yLabelsPos
80,2444
  horz_props.yTicksPos yTicksPos
86,2561
  axis_limits 92,2670
vert_stacks 96,2720
    horz_stacks 101,2825
    horz_props.xLabelsPos xLabelsPos
102,2880
  vert_stacks{vert_stacks
110,3065
a_plot 112,3147
function good 114,3209
  ratio 118,3399
  margin 123,3481
    good 127,3639
function 132,3797
num_max 137,3936
iter_num 139,3958
  factors 142,4019
      side2 152,4260
      break;153,4283
      num_max 155,4305
      continue;156,4334
    side1 161,4506
    side2 162,4542
    break;163,4578
	side2 170,4774
    num_max 187,5111
% TODO: If all fails,191,5149
%width width
194,5226
%height height
195,5255
width 196,5285
height 197,5300

classes/@plot_abstract/plot.m,254
function handles 1,0
verbose 32,898
% Open the axis43,1084
a_plot_props 46,1161
  ph 71,1978
  % do nothing,76,2248
  ph 77,2293
    ph 83,2447
% Add titles,92,2585
%handles handles
93,2631
handles.plot plot
96,2679
handles.axis axis
97,2698

classes/@plot_abstract/plotFigure.m,494
function handle 1,0
props 39,1053
s 41,1097
    orientation 48,1237
  handle 50,1283
    % Use same figure,54,1438
    figure(handle); clf;55,1482
    %set(handle, 'NextPlot', 'replace'); % clf;56,1507
    handle 58,1563
  title 60,1590
    old_units 78,2144
    old_pos 81,2252
  %position position
88,2482
  drawnow;118,3301
% OBSOLETE,121,3318
function position 122,3380
    titleheight 126,3479
  axis_labels 130,3511
    left_border 134,3639
    bottom_border 140,3762

classes/@plot_abstract/plot_abstract.m,401
function obj 1,0
  obj.axis_labels axis_labels
85,3921
  obj.title title
86,3945
  obj.legend legend
87,3963
  obj.command command
88,3982
  obj.props props
89,4006
  obj 90,4032
  obj 92,4123
  obj.data data
114,4447
  obj.axis_labels axis_labels
115,4466
  obj.title title
116,4499
  obj.legend legend
117,4520
  obj.command command
118,4543
  obj.props props
119,4568
  obj 121,4590

classes/@plot_abstract/subsasgn.m,71
function a 1,0
elseif length(a) > 1 || iscell(17,569
      a 31,908

classes/@plot_abstract/openAxis.m,632
function 1,0
verbose 32,978
decosize_x 41,1228
decosize_y 42,1250
%decosize decosize
44,1273
minwidth 45,1291
minheight 46,1309
  border 51,1401
% If a new axis need to be opened,65,1657
    right_margin 70,1883
    top_margin 72,1912
    right_margin 73,1941
  % Factor in borders and special margins84,2182
  layout_axis 89,2481
a_plot_props 95,2650
    %bottom_side bottom_side
104,2954
    height 105,2996
	(~isfield(113,3217
    bottom_side 126,3666
    height 127,3707
	(~isfield(135,3935
    left_side 149,4402
    width 150,4439
  layout_axis 160,4719
  axis_handle 161,4775
  axis_handle 163,4827

classes/@plot_abstract/axis.m,43
function ranges 1,0
      ranges 37,1124

classes/@plot_abstract/setProp.m,65
function obj 1,0
  val 34,935
  a(1).(attr)35,964
obj 37,989

classes/@plot_abstract/decorate.m,267
function handles 1,0
xh 30,805
yh 31,814
% Do this first,33,824
  % Skip NaNs,36,932
    axis_limits 88,2415
    xticklist 89,2451
    xtickscell 91,2545
  xticklabels 102,2892
  %xticklist xticklist
108,3153
  lh 141,4060
  lh 143,4096
handles 151,4225

classes/@cip_trace/periodRecSpontIniPeriod.m,61
function the_period 1,0
time_end 32,914
the_period 34,948

classes/@cip_trace/periodPulseHalf1.m,61
function the_period 1,0
time_end 29,751
the_period 31,808

classes/@cip_trace/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,650

classes/@cip_trace/periodRecSpontRestPeriod.m,61
function the_period 1,0
time_end 32,915
the_period 34,949

classes/@cip_trace/set.m,70
function b 1,0
    b 21,583
    b 24,632
    b.trace trace
25,643

classes/@cip_trace/display.m,28
function s 1,0
  s 19,544

classes/@cip_trace/periodPulse.m,25
function the_period 1,0

classes/@cip_trace/plotData.m,221
function a_plot 1,0
% If input is an array,41,1139
a_plot 53,1429
% If specified,55,1476
    time 66,1700
pulse_end 69,1744
% Find top of spikes in CIP period71,1798
bar_y 75,1918
bar_top 76,1989
a_plot 79,2058

classes/@cip_trace/getBurstResults.m,130
function results 1,0
results.SlowRD_ISIdecayTime SlowRD_ISIdecayTime
36,1131
results.SlowRD_ISIchange SlowRD_ISIchange
37,1168

classes/@cip_trace/get.m,45
function b 1,0
  b 23,638
  errstr 25,677

classes/@cip_trace/periodPulseIni100ms.m,25
function the_period 1,0

classes/@cip_trace/periodPulseIni50msRest1.m,61
function the_period 1,0
time_end 30,842
the_period 32,899

classes/@cip_trace/calcPulsePotAvg.m,22
function avg_val 1,0

classes/@cip_trace/periodRecSpont1.m,61
function the_period 1,0
time_end 30,798
the_period 32,832

classes/@cip_trace/plot_abstract.m,37
function a_plot 1,0
a_plot 37,1062

classes/@cip_trace/calcRecSpontPotAvg.m,22
function avg_val 1,0

classes/@cip_trace/periodPulseIni50ms.m,25
function the_period 1,0

classes/@cip_trace/getRateResults.m,1904
function results 1,0
results.IniSpontSpikeRate IniSpontSpikeRate
33,948
results.IniSpontSpikeRateISI IniSpontSpikeRateISI
35,1034
results.PulseSpikeRate PulseSpikeRate
37,1126
results.PulseSpikeRateISI PulseSpikeRateISI
39,1206
results.RecSpontSpikeRate RecSpontSpikeRate
41,1292
results.RecSpontSpikeRateISI RecSpontSpikeRateISI
43,1378
results.PulseIni100msSpikeRateISI PulseIni100msSpikeRateISI
47,1489
results.PulseIni100msISICV PulseIni100msISICV
49,1591
results.PulseIni100msSpikeRate PulseIni100msSpikeRate
51,1679
results.PulseIni100msRest1SpikeRate PulseIni100msRest1SpikeRate
53,1775
results.PulseIni100msRest2SpikeRate PulseIni100msRest2SpikeRate
55,1881
results.PulseIni100msRest1SpikeRateISI PulseIni100msRest1SpikeRateISI
57,1987
results.PulseIni100msRest2SpikeRateISI PulseIni100msRest2SpikeRateISI
59,2099
results.RecSpont1SpikeRate RecSpont1SpikeRate
61,2211
results.RecSpont2SpikeRate RecSpont2SpikeRate
63,2299
results.RecSpont1SpikeRateISI RecSpont1SpikeRateISI
65,2387
results.RecSpont2SpikeRateISI RecSpont2SpikeRateISI
67,2481
% Add one to both num and denum to avoid Inf and NaNs,70,2576
results.RecIniSpontRateRatio RecIniSpontRateRatio
72,2669
pulse_spikes 78,2848
  pulse_ISIs 81,3014
  results.PulseFirstISI PulseFirstISI
82,3052
  results.PulseFirstSpikeTime PulseFirstSpikeTime
84,3110
  results.PulseFirstISI PulseFirstISI
85,3147
results.IniSpontISICV IniSpontISICV
89,3193
results.PulseISICV PulseISICV
90,3263
results.RecSpontISICV RecSpontISICV
91,3327
% Spike frequency accommodation 93,3398
results.PulseSpikeAmpDecayTau PulseSpikeAmpDecayTau
99,3670
results.PulseSpikeAmpDecayDelta PulseSpikeAmpDecayDelta
100,3709
recov_spikes 103,3769
  recov_ISIs 106,3941
  results.RecSpontFirstISI RecSpontFirstISI
107,3979
  results.RecSpontFirstSpikeTime RecSpontFirstSpikeTime
109,4040
  results.RecSpontFirstISI RecSpontFirstISI
110,4080

classes/@cip_trace/measureNames.m,405
function measures 1,0
measures.spont_spike_tests spont_spike_tests
32,1203
measures.pulse_spike_tests pulse_spike_tests
64,2290
measures.recov_spike_tests recov_spike_tests
96,3377
measures.ini_spont_tests ini_spont_tests
128,4464
measures.pulse_rate_tests pulse_rate_tests
134,4609
measures.pulse_hyper_pot_tests pulse_hyper_pot_tests
149,5078
measures.recov_rate_tests recov_rate_tests
155,5213

classes/@cip_trace/calcPulsePotSag.m,70
function 1,0
steady_val 36,1159
sag_val 37,1218
  sag_val 41,1341

classes/@cip_trace/getCIPResults.m,785
function results 1,0
ms_factor 31,869
results.IniSpontPotAvg IniSpontPotAvg
33,912
results.PulsePotAvg PulsePotAvg
35,1015
results.RecSpontPotAvg RecSpontPotAvg
36,1079
results.RecIniSpontPotRatio RecIniSpontPotRatio
37,1149
pulse_spikes 41,1310
  results.PulsePotMin PulsePotMin
44,1460
  results.PulsePotMinTime PulsePotMinTime
45,1505
  results.PulsePotSag PulsePotSag
46,1554
    results.PulsePotTau PulsePotTau
52,1763
  results.PulsePotMin PulsePotMin
55,1805
  results.PulsePotMinTime PulsePotMinTime
56,1834
  results.PulsePotSag PulsePotSag
57,1867
  results.PulsePotTau PulsePotTau
58,1896
function time_constant 62,1964
  %rest_val rest_val
65,2130
  drop_val 66,2159
  decay_constant_threshold 68,2193
  recover_times 70,2260
    time_constant 75,2413

classes/@cip_trace/cip_trace.m,280
function obj 1,0
  obj.pulse_time_start pulse_time_start
57,1948
  obj.pulse_time_width pulse_time_width
58,1976
  obj 59,2004
  obj 61,2101
  trace_obj 67,2191
  obj.pulse_time_start pulse_time_start
74,2403
  obj.pulse_time_width pulse_time_width
75,2446
  obj 77,2490

classes/@cip_trace/periodPulseIni100msRest1.m,61
function the_period 1,0
time_end 30,844
the_period 32,901

classes/@cip_trace/periodRecSpont2.m,61
function the_period 1,0
time_end 30,799
the_period 32,833

classes/@cip_trace/spikes.m,278
function obj 1,0
ini_period 40,1107
  ini_spikes 45,1407
  ini_spikes 48,1515
cip_period 51,1571
  cip_period 55,1843
  cip_spikes 57,1965
  cip_spikes 60,2070
rec_period 63,2126
  rec_spikes 67,2393
  rec_spikes 70,2501
% do array processing,73,2557
  obj 83,2956

classes/@cip_trace/periodPulseIni50msRest2.m,61
function the_period 1,0
time_end 30,843
the_period 32,900

classes/@cip_trace/getProfileAllSpikes.m,264
function profile_obj 1,0
spont_period 35,1166
pulse_period 40,1385
recov_period 45,1601
% TODO: rebuild the a_spikes object here,51,1829
new_spikes 52,1894
misc_results.PulseSpontAmpRatio PulseSpontAmpRatio
57,2068
results_obj 61,2214
profile_obj 67,2447

classes/@cip_trace/periodIniSpont.m,44
function the_period 1,0
the_period 30,737

classes/@cip_trace/getResults.m,22
function results 1,0

classes/@cip_trace/getRecSpontSpike.m,62
function obj 1,0
props.spike_id spike_id
33,890
obj 34,916

classes/@cip_trace/periodPulseIni100msRest2.m,61
function the_period 1,0
time_end 30,845
the_period 32,902

classes/@cip_trace/periodRecSpont.m,61
function the_period 1,0
time_end 30,776
the_period 32,810

classes/@cip_trace/getPulseSpike.m,104
function obj 1,0
num_traces 39,1160
num_spikes 40,1184
props.spike_id spike_id
65,1781
obj 66,1807

classes/@params_tests_fileset/getItemParams.m,217
function params_row 1,0
params_row 30,864
  fullname 35,1028
  names_vals 37,1078
    num_params 42,1211
  params_row 45,1256
  str_index 56,1592
  trues 58,1664
    trial_num 77,2324
    params_row 83,2603

classes/@params_tests_fileset/set.m,70
function a 1,0
  a.params_tests_dataset params_tests_dataset
14,455

classes/@params_tests_fileset/display.m,16
function s 1,0

classes/@params_tests_fileset/get.m,28
function b 1,0
  b 14,468

classes/@params_tests_fileset/params_tests_fileset.m,453
function obj 1,0
  obj 80,3582
  obj 82,3717
    % Separate filename components95,3968
    num_patterns 98,4071
    % Separate filename components100,4094
  % Loop over patterns 109,4344
      this_pattern 115,4533
    filestruct 118,4577
    entries 119,4613
      names 127,4886
    end128,4977
    total_entries 131,5049
    props.param_rows param_rows
145,5413
      param_names 155,5869
      props.param_names param_names
157,5981

classes/@params_tests_fileset/trace_profile.m,71
function a_trace_profile 1,0
fullname 30,875
a_trace_profile 33,951

classes/@params_tests_fileset/addFiles.m,386
function 1,0
  % Separate filename components44,1452
  num_patterns 47,1549
  % Separate filename components49,1572
% Loop over patterns 53,1666
    this_pattern 59,1843
  filestruct 62,1885
  entries 63,1919
  total_entries 65,2023
existing_list 69,2094
num_existing 70,2134
a_fileset 71,2172
index_list 72,2243
  props.param_rows param_rows
77,2432
  a_fileset 79,2520

classes/@params_tests_fileset/loadItemProfile.m,90
function a_profile 1,0
  a_profile 46,1692
  % old code,49,1809
    a_profile 55,2042

classes/@params_tests_fileset/trace.m,176
function a_trace 1,0
fullname 30,793
props 32,839
    num_params 41,1153
  str_index 43,1197
  trial_num 50,1434
  trace_id 51,1474
  trace_id 53,1520
a_trace 57,1581

classes/@params_tests_fileset/paramNames.m,190
function param_names 1,0
props 34,984
param_names 35,1015
  fullname 40,1179
  names_vals 42,1229
    num_params 47,1362
  param_names 50,1409
  trues 56,1618
  param_names 65,1868

classes/@physiol_bundle/bestMatchAllNeurons.m,116
function all_ranks_db 1,0
  num_neurons 45,1546
  no_rows_ranks 48,1650
  all_ranks_db 53,1826
    a_r 61,2159

classes/@physiol_bundle/matchingRow.m,157
function a_crit_db 1,0
% See also: rankMatching,27,929
% Copyright 33,1093
num_tracesets 43,1429
  j_db 52,1757
  row_num 54,1795
  a_crit_db 61,2014

classes/@physiol_bundle/mergeBundles.m,193
function p_bundle 1,0
% - count tracesets,37,972
% - count neuronids,38,1032
p_bundle 45,1318
p_bundle 51,1491
p_bundle 54,1608
p_bundle 57,1746
  function a_db 63,1944
  a_db 74,2301

classes/@physiol_bundle/set.m,64
function a 1,0
  a.dataset_db_bundle dataset_db_bundle
14,455

classes/@physiol_bundle/physiol_bundle.m,207
function a_bundle 1,0
  a_bundle 47,1816
  a_bundle 49,1940
  end53,2019
    a_bundle.joined_control_db joined_control_db
63,2326
  % TODO: do not remove anything from a_db,66,2385
  a_bundle 68,2529

classes/@physiol_bundle/private/addPostDBColumns.m,998
function an_addedcols_db 1,0
  min_name 23,569
  tau_name 24,597
  spontavg_name 25,625
  spontisi_name 26,661
  cip_levels 27,703
  sagdiv_name 28,741
  inputres_name 29,778
  inputcap_name 30,812
  recfirstisi_name 31,844
  inirec_isiratio_name 32,885
  recini_rateratio_name 33,928
  sfa_rateratio_name 34,978
  pulse_inirate_name 35,1018
  pulse_lastrate_name 36,1072
  sag_name 38,1137
  min_name 39,1172
  tau_name 40,1207
  spontavg_name 48,1412
  spontisi_name 49,1465
  cip_levels 50,1525
  sagdiv_name 51,1574
  inputres_name 52,1618
  inputcap_name 53,1656
  recfirstisi_name 54,1692
  inirec_isiratio_name 55,1740
  recini_rateratio_name 56,1790
  recini_drateratio_name 57,1847
  sfa_rateratio_name 58,1905
  pulse_inirate_name 59,1952
  pulse_lastrate_name 60,2011
input_res 64,2107
an_addedcols_db 66,2190
% Maybe add this one,75,2625
% Maybe add this one, too,75,2625
  spont_amp_data 78,2809
  spont_pot_data 79,2898
  an_addedcols_db 80,2978

classes/@physiol_bundle/private/item2TracesetIndex.m,80
function traceset_index 1,0
    common_cols 11,425
    traceset_index 21,877

classes/@physiol_bundle/getNeuronRowIndex.m,66
function a_row_index 1,0
joined_db 40,1177
a_row_index 42,1218

classes/@physiol_bundle/get.m,33
function b 1,0
  errstr 14,451

classes/@physiol_bundle/constrainedMeasuresPreset.m,122
function 1,0
end36,1127
% Fix the control DB,41,1256
jc_db 42,1282
jc_db 43,1327
j_props 45,1403
a_pbundle 50,1560

classes/@physiol_bundle/ctFromRows.m,98
function a_cip_trace 1,0
traceset_vals 38,1294
p_db 40,1350
rows 41,1379
a_cip_trace 51,1669

classes/@physiol_bundle/plotfICurveStats.m,268
function a_plot 1,0
% See also: dataset_db_bundle/plotfICurve,plotfICurve
23,563
% See also: dataset_db_bundle/plotfICurve, plot_abstract,23,563
% Copyright 29,758
  caption 46,1207
curve_pAvals 50,1322
curve_tests 51,1353
curve_labels 53,1516
a_plot 55,1576

classes/@physiol_bundle/getNeuronLabel.m,86
function a_label 1,0
traceset_index 34,954
traceset_index 35,1019
a_label 37,1076

classes/@physiol_bundle/matchingControlNeuron.m,66
function a_crit_bundle 1,0
t_idx 42,1353
a_crit_bundle 46,1525

classes/@spikes/periodWhole.m,27
function whole_period 1,0

classes/@spikes/spikeAmpSlope.m,377
function 1,0
  s 35,1075
  t 36,1091
  s 38,1111
  t 39,1151
  da_inf 44,1234
mV_factor 49,1286
ms_factor 50,1318
%hold on;53,1361
%hold off;56,1441
data 58,1453
peak_vals 59,1476
% Get linear approximation to see the slope61,1516
  da_inf 68,1717
  decay_constant_threshold 70,1775
  recover_times 72,1837
    a_tau 77,2016
  da_inf 80,2044
  a_tau 81,2060

classes/@spikes/spikeRateISI.m,45
function freq 1,0
  s 36,997
freq 39,1035

classes/@spikes/subsref.m,60
function b 1,0
  b 14,490
      b 20,606
      b 22,655

classes/@spikes/set.m,45
function b 1,0
  b 13,462
  errstr 15,477

classes/@spikes/plotISIs.m,158
function a_plot 1,0
% If input is an array,34,872
ms_factor 45,1136
% Remove all '_' characters,47,1161
class_name 48,1237
isis 49,1278
a_plot 50,1309

classes/@spikes/display.m,28
function s 1,0
  s 19,544

classes/@spikes/plotData.m,125
function a_plot 1,0
% If input is an array,34,872
% Remove all '_' characters,45,1136
class_name 46,1212
a_plot 47,1253

classes/@spikes/spikeRate.m,44
function freq 1,0
  s 35,909
freq 38,947

classes/@spikes/getISIs.m,30
function isi 1,0
isi 37,995

classes/@spikes/get.m,16
function b 1,0

classes/@spikes/withinPeriod.m,31
function obj 1,0
obj 50,1209

classes/@spikes/intoPeriod.m,31
function obj 1,0
obj 44,1274

classes/@spikes/plot.m,62
function h 1,0
s 33,726
    orientation 40,861
  h 44,989

classes/@spikes/plotFreqVsTime.m,503
function a_plot 1,0
% If input is an array,44,1325
    x_label 62,1716
    time_factor 64,1754
    x_label 65,1784
% Remove all '_' characters,68,1816
class_name 69,1892
freqs 71,1934
      stimes 83,2225
    freqs 85,2257
      num_stimes 90,2369
      new_stimes 91,2412
      stimes 96,2596
      new_freqs 99,2638
      freqs 102,2764
      stimes 105,2805
      freqs 106,2829
class_name 113,2939
the_title 114,2980
the_legend 116,3072
    the_legend 120,3171
a_plot 125,3215

classes/@spikes/withinPeriodWOffset.m,66
function obj 1,0
s.num_samples num_samples
42,1103
obj 44,1161

classes/@spikes/spikes.m,262
function obj 1,0
   obj.num_samples num_samples
54,1740
   obj.dt dt
55,1764
   obj.id id
56,1779
   obj 57,1795
   obj 59,1874
   obj.times times
61,1896
   obj.num_samples num_samples
62,1918
   obj.dt dt
63,1952
   obj.id id
64,1968
   obj 65,1984

classes/@spikes/getResults.m,130
function results 1,0
  results.spikeRateISI spikeRateISI
38,874
  results.ISICV ISICV
39,902
% convert all to ms/mV(mV
43,940

classes/@spikes/ISICV.m,43
function cv 1,0
ISIs 34,805
  cv 39,893

classes/@spikes/vertcat.m,146
function a_spikes 1,0
  with_spikes = vertcat(varargin{1}, varargin{varargin
32,1020
  with_spikes 34,1080
a_spikes 37,1114
a_spikes 38,1165

classes/@spikes/addSpikes.m,16
function s 1,0

classes/@spikes/SFA.m,32
function sfa 1,0
  sfa 36,908

classes/@doc_generate/subsref.m,79
function b 1,0
  b 19,544
      %b b
26,744
      b 28,786
      b 30,831

classes/@doc_generate/set.m,16
function a 1,0

classes/@doc_generate/display.m,16
function s 1,0

classes/@doc_generate/get.m,16
function b 1,0

classes/@doc_generate/printTeXFile.m,385
% should only be added at this point or at getTeXString,11,346
%	tex_string: A string that contains TeX commands,22,706
%	tex_string: A string that contains TeX commands, which upon writing to a file,22,706
%	>> a_doc 26,866
% See also: doc_generate,30,1058
% See also: doc_generate, doc_plot,30,1058
% See also: doc_generate, doc_plot, string2File,30,1058
% Copyright 36,1240

classes/@doc_generate/getTeXString.m,25
function tex_string 1,0

classes/@doc_generate/doc_generate.m,202
function a_doc 1,0
  a_doc.id id
46,1566
  a_doc.props props
47,1583
  a_doc 48,1611
  a_doc 50,1711
  a_doc.text text
56,1799
  a_doc.id id
57,1827
  a_doc.props props
58,1844
  a_doc 60,1868

functions/gettracelist2.m,301
% gettracelist2 - Gets a list of the form: '1 3 7-10' and returns a column vector with the traces numbers,2,1
	tidx 17,480
	rgs 19,513
	nrgs 21,544
	traces 27,644
	ntrs 29,677
	ridx 35,771
        	range 42,956
	clear tidx ntrs ridx nrgs rgs range trls;48,1139
ntrs 50,1187
ntraces 51,1208

functions/diff2T.m,92
function deriv2 1,0
  x 36,1112
x16 42,1158
x30 43,1172
deriv2 45,1187
deriv2 50,1360

functions/readNeuronVecAscii.m,112
function 1,0
% Also see: dlmread,21,515
% Copyright 25,625
  label 37,1042
  count 38,1089
  data 43,1155

functions/balanceInputProbs.m,294
function 1,0
verbose 41,1652
% find uniques in the output classifier47,1737
num_in_class 55,1958
num_classes 56,2028
  num_samples 63,2312
class_probs 67,2407
base 68,2444
count_in_class 83,2869
new_inputs 84,2908
new_outputs 85,2972
  chosen_class 88,3112
  sample_offset 89,3146

functions/readNeuronVecBin.m,123
    errmsg 22,721
 end 23,772
 precision 32,927
    errmsg 40,1125
 end 43,1213
    data 48,1355
    errmsg 52,1409

functions/logLevels.m,91
function levels 1,0
  b 29,922
a 31,935
min_pow 33,966
max_pow 34,994
levels 36,1023

functions/string2File.m,79
%	  append: If 14,307
% Copyright 23,503
    write_mode 37,949
  fp 39,977

functions/properTeXFilename.m,149
function filename 1,0
%filename filename
31,955
%filename filename
32,995
filename 33,1035
filename 34,1074
filename 35,1114
filename 36,1153

functions/abf2load.m,14
function 1,0

functions/maxima.m,66
function x_idx 1,0
dxflip 32,849
%dx2 dx2
34,887
x_idx 36,924

functions/calcGraphNormPtsRatio.m,224
function 1,0
% Copyright 26,879
      width 36,1284
      height 37,1314
      width 41,1408
      height 42,1425
old_units 49,1581
axis_pos_pt 51,1657
axis_width_pt 52,1701
axis_height_pt 53,1733
ratio_y 58,1872

functions/sortedUniqueValues.m,109
function 1,0
    nonzerorows 38,1250
    idx 40,1296
    rows 41,1325
    rows=43,1355
    idx=44,1388

functions/cell2TeX.m,256
function tex_string 1,0
% TODO: get column formatting in props,36,1043
col_align = {'|c'};
37,1120
col_align 38,1140
tex_string 39,1197
	add_string 50,1524
    elseif isempty(52,1599
    row_string 66,2086
  tex_string 71,2215
tex_string 76,2390

functions/findspikes_old.m,72
    peaksv 22,880
    peaksdy 26,965
    clear m peaks*peaks
42,1312

functions/parseGenesisFilename.m,25
function names_vals 1,0

functions/trace2cc.m,269
function a_cc 1,0
% See also: plotXPPparamRanges,35,1458
% Copyright 41,1616
  num_vals 54,2122
    num_vals 57,2238
  cip_vals 59,2290
num_traces 62,2339
num_allpts 63,2370
num_onepts 64,2403
data 73,2651
I_hold 75,2703
current_steps 77,2759
a_cc 82,2960

functions/chanTables2DB.m,388
function a_chans_db 1,0
chan_names 35,1057
channel_info 37,1108
chan_num 39,1132
  chan 44,1235
  chan_fields 45,1264
  a_db 49,1430
props.chan_names chan_names
55,1536
a_chans_db 58,1595
a_chans_db = chans_db(a_db, {}, channel_info, id, props)58,1595
  a_result 65,1867
  gate_num 68,1937
    a_result 72,2013
    gate_num 78,2160
  a_db 82,2219
  % other fields 85,2340

functions/cell2str.m,115
function a_str 1,0
a_str 32,815
	add_string 43,1081
    elseif isempty(45,1156
  a_str 57,1494
a_str 59,1544

functions/fillederrorbar.m,36
function handles 1,0
pairs 29,735

functions/defaultValue.m,92
function value 1,0
% Author: Li,21,614
% Modified: Cengiz Gunay,23,632
    value=29,834

functions/getFieldDefault.m,70
function value 1,0
% $$$       value 30,724
% $$$     value 33,781

functions/loadVclampAbf.m,486
function 1,0
% See also: abf2load,32,1106
% See also: abf2load, plotVclampAbf,32,1106
  props 42,1357
  % extract cell name from file44,1401
  fid 48,1507
    curdir 54,1649
    filename 63,1873
    fid 66,1947
  % extract cell name from file73,2038
  % read ABF file76,2122
  dt 81,2247
  time 84,2289
    v_scale 97,2694
  chan_i 105,2882
  i_scale 106,2926
    i_scale 110,3011
      data_i 123,3338
      data_i = squeeze(data(:,2));      % as TTL pulse 123,3338

functions/diff3T_h4.m,78
function deriv2 1,0
  x 34,1036
x2 39,1081
deriv2 41,1094
deriv2 46,1251

functions/findVectorInMatrix.m,18
function idx 1,0

functions/struct2DB.m,106
function a_tests_db 1,0
field_names 39,1011
cell_data 40,1047
if size(cell_data{1}, 1) > size(41,1082

functions/collectspikes.m,253
function 1,0
% Gets and returns the spikes in trace indicated by the timeidx;5,170
% left and right are how much 6,235
spksavg 33,1568
chopped 35,1583
	tright 40,1655
	% Exclude chopped off spikes,42,1686
  spksavg 60,2127
    hold off;67,2262

functions/abfload.m,14400
function 1,0
% NAME        TYPE,22,1007
% start       scalar,24,1104
% stop        scalar or char,26,1229
% sweeps      1d-array or char,29,1424
%             'a'                 read. By default,30,1498
% channels    cell array         names of channels to be read,32,1615
%              or char,33,1684
%                                 to the abf file,40,2200
% chunk       scalar,43,2399
%                                 size 44,2475
% d                     the data read,55,3174
%                    d(61,3432
%                    d{d
80,4614
stop=126,6980
sweeps=128,7001
channels=130,7023
% the size of data chunks 131,7037
machineF=135,7209
verbose=136,7229
  doLoadData=141,7472
  doLoadData=143,7497
BLOCKSIZE=149,7623
d=151,7657
si=152,7664
h=153,7671
% on the occasion,172,8224
fileSz=174,8292
sz=178,8414
fFileSignature=187,8607
% The list of header parameters created below 206,9251
Sections=243,11295
% define a few of these 244,11321
numOfParams=255,11817
clear tmp headPar;256,11840
  sz=264,12066
  % use dynamic field names265,12091
h.fFileSignature=fFileSignature
273,12315
  h.lFileStartTime=lFileStartTime
281,12707
  % little less than what it should be 284,12828
  numOfSections=300,13688
  offset=301,13722
  % this creates all sections 302,13735
    offset=305,13884
  % --- read in the StringsSection and use some fields 307,13915
  goodstart=314,14334
  BigString=322,14609
  stringends=324,14684
  h.recChNames=recChNames
328,14817
  h.recChUnits=recChUnits
329,14836
    ii=334,15051
    h.recChNames=recChNames
336,15123
    unitsIndex=337,15204
        h.recChUnits=recChUnits
341,15353
  ProtocolSec=352,15879
  h.nOperationMode=nOperationMode
353,15962
  h.fSynchTimeUnit=fSynchTimeUnit
354,16009
  h.nADCNumChannels=nADCNumChannels
356,16059
  h.lActualAcqLength=lActualAcqLength
357,16104
  h.lDataSectionPtr=lDataSectionPtr
358,16151
  h.nNumPointsIgnored=nNumPointsIgnored
359,16196
  h.fADCSampleInterval=fADCSampleInterval
365,16429
  h.fADCRange=fADCRange
366,16504
  h.lADCResolution=lADCResolution
367,16541
  h.lSynchArrayPtr=lSynchArrayPtr
371,16764
  h.lSynchArraySize=lSynchArraySize
372,16814
  TagSection.uBlockIndex=uBlockIndex
380,17229
  TagSection.uBytes=uBytes
381,17272
recChInd=394,17797
  h.recChUnits=recChUnits
401,18087
h.recChNames=recChNames
405,18210
h.recChUnits=recChUnits
406,18255
chInd=409,18342
eflag=410,18352
else418,18596
  addGain=450,19491
    precision=457,19639
    dataSz=459,19671
    precision=460,19700
headOffset=465,19794
h.si=si
467,19915
si=469,20015
  sweeps=472,20086
  nSweeps=474,20121
    h.synchArrTimeBase=synchArrTimeBase
484,20403
h.tags=tags
488,20515
      h.lSynchArrayPtrByte=lSynchArrayPtrByte
512,21657
      end522,22182
      synchArr=529,22435
      segStartInPts=533,22685
          end546,23295
          h.dataPtsPerChan=dataPtsPerChan
551,23616
          tmpd=557,23838
          tmpd=559,23946
          tmpd=560,23976
          d{d
570,24531
    elseif h.nOperationMode=nOperationMode
578,24697
    h.lSynchArrayPtrByte=lSynchArrayPtrByte
589,25134
    end599,25639
    synchArr=606,25878
    h.recTime=recTime
619,26596
    h.recTime=recTime
620,26628
    startPt=622,26808
    h.dataPts=dataPts
623,26823
    h.dataPtsPerChan=dataPtsPerChan
624,26857
    dataPtsPerSweep=630,27093
    d=635,27317
    selectedSegStartInPts=637,27447
        h.dataPtsPerChan=dataPtsPerChan
647,27935
        tmpd=653,28144
        tmpd=655,28248
        tmpd=656,28276
    startPt=674,28998
    startPt=676,29162
      h.dataPts=dataPts
681,29444
      h.dataPtsPerChan=dataPtsPerChan
683,29505
      h.dataPts=dataPts
684,29562
    tmp=694,29845
    h.recTime=recTime
703,30328
    h.recTime=recTime
704,30360
        % read, skipping h.nADCNumChannels-1 data points after each read727,31529
        chunkPts=743,32464
        nChunk=745,32555
        restPts=747,32627
        restPtsPerChan=748,32670
        dix=750,32759
          tmpd=767,33557
          tmpd=779,34052
        d=790,34501
        d=791,34558
    d=804,35059
    h.si=si
805,35069
function headPar=822,35551
function Sections=897,38249
function ProtocolInfo=918,38632
function ADCInfo=993,40953
function TagInfo=1024,41900
function Section=1032,42072
function SectionInfo=1039,42317
SectionInfo.uBlockIndex=uBlockIndex
1041,42391
SectionInfo.uBytes=uBytes
1043,42465
SectionInfo.llNumEntries=llNumEntries
1045,42534
  end;1061,43101
end;1062,43108
%    UINT  uFileSignature;1069,43145
%    UINT  uFileVersionNumber;1070,43172
%    UINT  uFileInfoSize;1073,43288
%    UINT  uActualEpisodes;1075,43317
%    UINT  uFileStartDate;1076,43345
%    UINT  uFileStartTimeMS;1077,43372
%    UINT  uStopwatchTime;1078,43401
%    short nFileType;1079,43428
%    short nDataFormat;1080,43450
%    short nSimultaneousScan;1081,43474
%    short nCRCEnable;1082,43504
%    UINT  uFileCRC;1083,43527
%    GUID  FileGUID;1084,43548
%    UINT  uCreatorVersion;1085,43569
%    UINT  uCreatorNameIndex;1086,43597
%    UINT  uModifierVersion;1087,43627
%    UINT  uModifierNameIndex;1088,43656
%    UINT  uProtocolPathIndex;1089,43687
%    ABF_Section ProtocolSection;1092,43775
%    ABF_Section ADCSection;1093,43835
%    ABF_Section DACSection;1094,43907
%    ABF_Section EpochSection;1095,43979
%    ABF_Section ADCPerDACSection;1096,44045
%    ABF_Section EpochPerDACSection;1097,44122
%    ABF_Section UserListSection;1098,44201
%    ABF_Section StatsRegionSection;1099,44271
%    ABF_Section MathSection;1100,44344
%    ABF_Section StringsSection;1101,44374
%    ABF_Section DataSection;1104,44437
%    ABF_Section TagSection;1105,44486
%    ABF_Section ScopeSection;1106,44535
%    ABF_Section DeltaSection;1107,44592
%    ABF_Section VoiceTagSection;1108,44643
%    ABF_Section SynchArraySection;1109,44698
%    ABF_Section AnnotationSection;1110,44754
%    ABF_Section StatsSection;1111,44810
%    char  sUnused[sUnused
1113,44873
%       MEMSET_CTOR;1117,44957
%       uFileSignature 1120,45037
%       uFileInfoSize 1121,45081
%    short nOperationMode;1128,45177
%    float fADCSequenceInterval;1129,45204
%    bool  bEnableFileCompression;1130,45237
%    char  sUnused1[sUnused1
1131,45272
%    UINT  uFileCompressionRatio;1132,45296
%    float fSynchTimeUnit;1134,45333
%    float fSecondsPerRun;1135,45360
%    long  lNumSamplesPerEpisode;1136,45387
%    long  lPreTriggerSamples;1137,45421
%    long  lEpisodesPerRun;1138,45452
%    long  lRunsPerTrial;1139,45480
%    long  lNumberOfTrials;1140,45506
%    short nAveragingMode;1141,45534
%    short nUndoRunCount;1142,45561
%    short nFirstEpisodeInRun;1143,45587
%    float fTriggerThreshold;1144,45618
%    short nTriggerSource;1145,45648
%    short nTriggerAction;1146,45675
%    short nTriggerPolarity;1147,45702
%    float fScopeOutputInterval;1148,45731
%    float fEpisodeStartToStart;1149,45764
%    float fRunStartToStart;1150,45797
%    long  lAverageCount;1151,45826
%    float fTrialStartToStart;1152,45852
%    short nAutoTriggerStrategy;1153,45883
%    float fFirstRunDelayS;1154,45916
%    short nChannelStatsStrategy;1156,45947
%    long  lSamplesPerTrace;1157,45981
%    long  lStartDisplayNum;1158,46010
%    long  lFinishDisplayNum;1159,46039
%    short nShowPNRawData;1160,46069
%    float fStatisticsPeriod;1161,46096
%    long  lStatisticsMeasurements;1162,46126
%    short nStatisticsSaveStrategy;1163,46162
%    float fADCRange;1165,46201
%    float fDACRange;1166,46223
%    long  lADCResolution;1167,46245
%    long  lDACResolution;1168,46272
%    short nExperimentType;1170,46305
%    short nManualInfoStrategy;1171,46333
%    short nCommentsEnable;1172,46365
%    long  lFileCommentIndex;1173,46393
%    short nAutoAnalyseEnable;1174,46435
%    short nSignalType;1175,46466
%    short nDigitalEnable;1177,46493
%    short nActiveDACChannel;1178,46520
%    short nDigitalHolding;1179,46550
%    short nDigitalInterEpisode;1180,46578
%    short nDigitalDACChannel;1181,46611
%    short nDigitalTrainActiveLogic;1182,46642
%    short nStatsEnable;1184,46682
%    short nStatisticsClearStrategy;1185,46707
%    short nLevelHysteresis;1187,46747
%    long  lTimeHysteresis;1188,46776
%    short nAllowExternalTags;1189,46804
%    short nAverageAlgorithm;1190,46835
%    float fAverageWeighting;1191,46865
%    short nUndoPromptStrategy;1192,46895
%    short nTrialTriggerSource;1193,46927
%    short nStatisticsDisplayStrategy;1194,46959
%    short nExternalTagType;1195,46998
%    short nScopeTriggerOut;1196,47027
%    short nLTPType;1198,47059
%    short nAlternateDACOutputState;1199,47080
%    short nAlternateDigitalOutputState;1200,47117
%    float fCellID[fCellID
1202,47161
%    short nDigitizerADCs;1204,47187
%    short nDigitizerDACs;1205,47214
%    short nDigitizerTotalDigitalOuts;1206,47241
%    short nDigitizerSynchDigitalOuts;1207,47280
%    short nDigitizerType;1208,47319
%    char  sUnused[sUnused
1210,47349
%       MEMSET_CTOR;1214,47437
%    short nMathEnable;1221,47560
%    short nMathExpression;1222,47584
%    UINT  uMathOperatorIndex;1223,47612
%    UINT  uMathUnitsIndex;1224,47648
%    float fMathUpperLimit;1225,47684
%    float fMathLowerLimit;1226,47712
%    short nMathADCNum[nMathADCNum
1227,47740
%    char  sUnused[sUnused
1228,47767
%    float fMathK[fMathK
1229,47791
%    char  sUnused2[sUnused2
1231,47816
%       MEMSET_CTOR;1235,47899
%    short nADCNum;1243,48060
%    short nTelegraphEnable;1245,48083
%    short nTelegraphInstrument;1246,48112
%    float fTelegraphAdditGain;1247,48145
%    float fTelegraphFilter;1248,48177
%    float fTelegraphMembraneCap;1249,48206
%    short nTelegraphMode;1250,48240
%    float fTelegraphAccessResistance;1251,48267
%    short nADCPtoLChannelMap;1253,48309
%    short nADCSamplingSeq;1254,48340
%    float fADCProgrammableGain;1256,48371
%    float fADCDisplayAmplification;1257,48404
%    float fADCDisplayOffset;1258,48441
%    float fInstrumentScaleFactor;1259,48471
%    float fInstrumentOffset;1260,48506
%    float fSignalGain;1261,48536
%    float fSignalOffset;1262,48560
%    float fSignalLowpassFilter;1263,48586
%    float fSignalHighpassFilter;1264,48619
%    char  nLowpassFilterType;1266,48656
%    char  nHighpassFilterType;1267,48687
%    float fPostProcessLowpassFilter;1268,48719
%    char  nPostProcessLowpassFilterType;1269,48757
%    bool  bEnabledDuringPN;1270,48799
%    short nStatsChannelPolarity;1272,48831
%    long  lADCChannelNameIndex;1274,48868
%    long  lADCUnitsIndex;1275,48901
%    char  sUnused[sUnused
1277,48931
%       MEMSET_CTOR;1281,49016
%    short nDACNum;1289,49176
%    short nTelegraphDACScaleFactorEnable;1291,49199
%    float fInstrumentHoldingLevel;1292,49242
%    float fDACScaleFactor;1294,49281
%    float fDACHoldingLevel;1295,49309
%    float fDACCalibrationFactor;1296,49338
%    float fDACCalibrationOffset;1297,49372
%    long  lDACChannelNameIndex;1299,49409
%    long  lDACChannelUnitsIndex;1300,49442
%    long  lDACFilePtr;1302,49479
%    long  lDACFileNumEpisodes;1303,49503
%    short nWaveformEnable;1305,49538
%    short nWaveformSource;1306,49566
%    short nInterEpisodeLevel;1307,49594
%    float fDACFileScale;1309,49628
%    float fDACFileOffset;1310,49654
%    long  lDACFileEpisodeNum;1311,49681
%    short nDACFileADCNum;1312,49712
%    short nConditEnable;1314,49742
%    long  lConditNumPulses;1315,49768
%    float fBaselineDuration;1316,49797
%    float fBaselineLevel;1317,49827
%    float fStepDuration;1318,49854
%    float fStepLevel;1319,49880
%    float fPostTrainPeriod;1320,49903
%    float fPostTrainLevel;1321,49932
%    short nMembTestEnable;1322,49960
%    short nLeakSubtractType;1324,49991
%    short nPNPolarity;1325,50021
%    float fPNHoldingLevel;1326,50045
%    short nPNNumADCChannels;1327,50073
%    short nPNPosition;1328,50103
%    short nPNNumPulses;1329,50127
%    float fPNSettlingTime;1330,50152
%    float fPNInterpulse;1331,50180
%    short nLTPUsageOfDAC;1333,50209
%    short nLTPPresynapticPulses;1334,50236
%    long  lDACFilePathIndex;1336,50273
%    float fMembTestPreSettlingTimeMS;1338,50306
%    float fMembTestPostSettlingTimeMS;1339,50345
%    short nLeakSubtractADCIndex;1341,50388
%    char  sUnused[sUnused
1343,50425
%       MEMSET_CTOR;1347,50507
%    short nEpochNum;1355,50683
%    short nDACNum;1356,50705
%    short nEpochType;1359,50801
%    float fEpochInitLevel;1360,50824
%    float fEpochLevelInc;1361,50852
%    long  lEpochInitDuration;1362,50879
%    long  lEpochDurationInc;1363,50912
%    long  lEpochPulsePeriod;1364,50942
%    long  lEpochPulseWidth;1365,50972
%    char  sUnused[sUnused
1367,51004
%       MEMSET_CTOR;1371,51093
%    short nEpochNum;1379,51264
%    short nDigitalValue;1382,51317
%    short nDigitalTrainValue;1383,51343
%    short nAlternateDigitalValue;1384,51374
%    short nAlternateDigitalTrainValue;1385,51409
%    bool  bEpochCompression;1386,51449
%    char  sUnused[sUnused
1388,51549
%       MEMSET_CTOR;1392,51632
%    short nRegionNum;1400,51811
%    short nADCNum;1401,51834
%    short nStatsActiveChannels;1403,51857
%    short nStatsSearchRegionFlags;1404,51890
%    short nStatsSelectedRegion;1405,51926
%    short nStatsSmoothing;1406,51959
%    short nStatsSmoothingEnable;1407,51987
%    short nStatsBaseline;1408,52021
%    long  lStatsBaselineStart;1409,52048
%    long  lStatsBaselineEnd;1410,52080
%    long  lStatsMeasurements;1413,52148
%    long  lStatsStart;1414,52179
%    long  lStatsEnd;1415,52203
%    short nRiseBottomPercentile;1416,52225
%    short nRiseTopPercentile;1417,52259
%    short nDecayBottomPercentile;1418,52290
%    short nDecayTopPercentile;1419,52325
%    short nStatsSearchMode;1420,52357
%    short nStatsSearchDAC;1421,52386
%    short nStatsBaselineDAC;1422,52414
%    char  sUnused[sUnused
1424,52447
%       MEMSET_CTOR;1428,52534
%    short nListNum;1436,52713
%    short nULEnable;1439,52769
%    short nULParamToVary;1440,52791
%    short nULRepeat;1441,52818
%    long  lULParamValueListIndex;1442,52840
%    char  sUnused[sUnused
1444,52878
%       MEMSET_CTOR;1448,52961

functions/diff3T.m,91
function deriv3 1,0
  x 36,1136
x8 41,1181
x13 42,1193
deriv3 44,1208
deriv3 50,1444

functions/readgenbin.m,427
function 1,0
%   start_time,10,292
% >> dat 38,1656
% >> figure;41,1795
% >> dat 43,1880
fil 65,2534
length 72,2712
act_start_time 76,2823
timestep 77,2870
freq 78,2911
adjustment_ratio 84,3247
num_cols 85,3280
  start_time 93,3665
  ev_start_time 95,3688
header_size 100,3862
read_start 101,3901
total_data_length 102,3960
  ev_end_time 109,4275
read_length 112,4351
disp(117,4574
    time_trace 132,5081

functions/boxplotp.m,1114
%   BOXPLOTP(5,115
%   If there are no data outside the whisker,34,1689
%   If there are no data outside the whisker, then,34,1689
%   bottom whisker,35,1764
%   a whisker falls inside the box,36,1835
%   it to be drawn at the right place,37,1906
%   it to be drawn at the right place, set whissw 37,1906
whissw 47,2299
end51,2398
    yy 56,2454
    n 58,2472
    xx 59,2483
    yy 60,2495
% If the 2nd arg is not a grouping variable,63,2512
nargs 64,2573
elseif 67,2614
   notch 72,2804
   g 73,2818
   nargs 75,2834
xorig 84,3082
gorig 85,3093
xvisible 86,3104
included 87,3134
      sep 94,3235
   end95,3252
   n 98,3320
   gorig 99,3342
   k 101,3360
lb 109,3475
xlims 111,3486
k 113,3510
ymin 114,3531
ymax 115,3554
dy 116,3577
ylims 117,3598
lf 119,3630
      z 141,4288
      pts 142,4312
      pts 143,4345
      ylim 151,4605
   elseif 163,5087
      pts 174,5312
   g 178,5433
   notnan 179,5465
      z 182,5536
         pts 185,5617
h 198,5950
ax 203,6045
nlines 204,6073
p 208,6208
ptop 209,6233
xl 220,6444
p 222,6495
ylim 223,6520
p2 224,6545

functions/loadtraces.m,44
    tracenums 35,1095
    ntraces 36,1122

functions/properTeXLabel.m,22
function a_label 1,0

functions/makeIdealClampV.m,98
function 1,0
pre_t 37,1172
pulse_t 38,1201
post_t 39,1240
num_steps 40,1278
trace_v 42,1308

functions/getfuzzyfield.m,102
function value=1,0
    f=18,511
    FS=19,527
    fs=20,552
      idx=24,651
      value=32,916

functions/setAxisNonNaN.m,45
function new_axis 1,0
  % Skip NaNs,32,884

functions/TeXfloat.m,301
function tex_string 1,0
% See also: cell2TeX,32,1016
% v. 3.0. To view a copy of this license,39,1298
float_type 49,1554
tex_string 54,1644
  resize 64,1934
elseif isfield(props, 'height') && ~ strcmp(65,1948
  is_rotate 76,2265
tex_string 80,2307
short_caption 93,2489
tex_string 105,2845

functions/properAlphaNum.m,39
function a_label 1,0
a_label 35,1009

functions/makeIdx.m,18
function idx 1,0

functions/mergeStructsRecursive.m,299
function results 1,0
fieldcell 35,1196
    fields 40,1267
              mergeStructsRecursive(left_struct, getfield(varargin{k}, fieldcell{fieldcell
48,1587
    % find new fields on right-hand-side argument52,1712
    fieldcell 55,1855
    val 56,1902
    valcell 57,1938
  results 65,2074

functions/colormapBlueCrossRed.m,171
function colors 1,0
h_blue_end 35,1123
h_red_start 36,1142
h_red_end 37,1161
v_max 41,1246
v_levels 42,1258
blue_levels 45,1375
red_levels 48,1537
colors 53,1732

functions/diff2T_h4.m,66
function deriv2 1,0
  x 34,1001
deriv2 39,1046
deriv2 44,1192

functions/interpValByIndex.m,73
function val 1,0
% ans 18,434
ci 36,994
  val 41,1062
  val 43,1121

functions/struct2str.m,68
function a_str 1,0
names 29,869
  a_str 33,948
  prefix 34,1010

functions/diffT.m,75
function deriv 1,0
  x 36,1053
x8 41,1098
deriv 43,1111
deriv 48,1253

functions/meanSpikeFreq.m,38
function meanFreq 1,0
elseif 28,858

functions/parseFilenameNamesVals.m,361
function 1,0
  names_first 46,1671
  skip_num 47,1728
sep_indices 51,1832
  word_num 66,2396
pre_name 69,2428
  leftstr 74,2642
    rightlimit 80,2817
  rightstr 82,2858
    val 87,2981
    param_name 89,3016
    val 90,3043
function val 97,3178
  val 101,3248
% $$$     param_name 106,3338
% $$$     errstr 109,3449
% $$$ 	param_name 123,4118

functions/subTextLabel.m,93
function handle 1,0
handle 34,898
prop_names 36,930
num_props 37,962
  prop_val 43,1098

functions/ns_CIPlist.m,440
function cipList 1,0
verbose 12,399
tr=17,506
  file 23,597
hyp_name 25,640
hyp_name = file.Trials{tr}.StimulationData{1}.VChannel;VChannel
25,640
hyp_names 26,696
hyp_idx 27,790
  hyp_name 38,1063
  hyp_idx 39,1115
hyp_data 50,1385
trans 51,1451
amp 53,1519
dur 56,1688
on 59,1854
finish 62,2020
finish = str2num(file.Trials{tr}.ExperimentControl.ParsedXML.MaxStimulusDuration)MaxStimulusDuration
62,2020
cipList=64,2104

functions/ns_load_tracesets.m,1398
function 1,0
% Author: Li, Su; Cengiz Gunay <cgunay@emory.edu>; and Jeremy Edgerton,47,2114
% Modified: Li,49,2199
% Modified: Li, Su 3/25/08 add IncludeSeq,49,2199
% Modified: Li, Su 3/25/08 add IncludeSeq, ExcludeSeq,49,2199
% Modified: Li, Su 3/25/08 add IncludeSeq, ExcludeSeq, VGain,49,2199
% Copyright 51,2269
  verbose 61,2689
  n 67,2782
  a_tss 68,2841
  h5_infos 69,2855
        a_tss 81,3317
        h5_infos 82,3350
    filename 86,3426
          ns_load_tracesets(data_src{k}, props)92,3596
      a_tss 93,3645
      h5_infos 94,3676
    filename 99,3826
  end103,3988
  h5_infos{h5_infos
106,4038
  idx 126,4966
      idx 128,5039
  excl=134,5219
  not_idx 135,5280
      not_idx 137,5356
      trials 147,5652
      atts 153,5814
              Vm_chan 161,6069
              Vm_chan 162,6148
        Vm_chan 165,6238
        Vm_chan 167,6328
      neuron_id 172,6513
          Vm_dy 176,6669
          Vm_dy 178,6711
      Vm_dt 188,7101
      Vm_dt = 1/first_trial.AcquisitionData{Vm_chan}.SamplingRate;SamplingRate
188,7101
            Im_chan 195,7333
            Im_chan 196,7410
        Im_chan 199,7498
        Im_chan 201,7588
        default_attr 212,7900
        fields 222,8162
      atts=250,9102
      n=261,9516
  function chan_num 278,10080
  function treats 290,10555
      found_name 293,10693
        treats 299,10960

functions/boxutilp.m,503
function outlier=1,0
pctiles 30,764
q1 31,797
med 32,816
q3 33,836
% find the extreme values 35,856
vlo 40,1004
loadj 41,1027
x1 44,1089
x2 45,1108
outlier 46,1136
yy 47,1167
   sym 52,1249
xx 55,1273
    lbp 56,1301
    lbm 57,1324
   loadj 61,1389
% Set up 64,1420
    yy2 67,1507
    xx3 68,1535
    n1 70,1561
    n2 71,1606
    lnm 74,1705
    lnp 75,1727
    xx2 76,1749
    yy2 77,1806
    xx3 78,1855
yy3 80,1880
if isfield(props, 'nooutliers'), xx = []; yy 83,1937

functions/mergeStructs.m,140
function results 1,0
fieldcell 32,993
    fields 37,1064
    fieldcell 39,1155
    val 40,1202
    valcell 41,1238
  results 49,1374

functions/prefixStruct.m,25
function new_struct 1,0

functions/growRange.m,47
function range 1,0
maxs 28,764
range 38,914

functions/array2str.m,181
function string 1,0
form 27,932
        string=34,1082
string=42,1230
da=44,1243
dda=45,1261
        idx=51,1429
        idx 53,1453
        string 57,1583
string=63,1710

functions/plotImage.m,80
function h 1,0
  mult_factor 56,1848
      max_val 65,1996
num_rows 93,3050

functions/uniqueValues.m,135
function 2,1
    inv_idx 39,1075
    rows 40,1112
    idx 41,1141
    rows 43,1165
    rows = zeros(0,size(data,2)); idx 43,1165

functions/writeNeuronVecAscii.m,144
%   datax:datax
10,321
elseif strcmp(unit_y, 'V'), dy 50,1694
elseif strcmp(unit_y, 's'), dy 51,1740
elseif strcmp(unit_x, 's'), dx 58,1900

functions/findspikes.m,1485
function 1,0
%  spikeTime=32,1313
%  spikeTime=33,1364
%  spikeTime=34,1414
%  spikeTime=35,1468
% Author: Li,37,1537
% Copyright 39,1603
        plotit=50,2016
    elseif isnumeric(51,2044
            win_range=55,2160
        direction=70,2387
direction=74,2437
thresh_min=81,2612
n 82,2635
    trace 89,2781
    left_edges 91,2811
    right_edges 92,2935
    timeidx=93,3061
    timeidx=[]; tips=93,3061
    timeidx=[]; tips=[]; spike_num=93,3061
    not_empty=95,3104
        spike_num=100,3324
        if spike_num==0; break;101,3388
        left_edges=102,3424
        right_edges=103,3468
            left_time=108,3645
            right_time=109,3759
            win_width=110,3878
            out_of_data_range_idx=111,3922
            spike_num=114,4134
        if spike_num==0; break;116,4214
        refractory=119,4313
        interval=120,4335
        smallInterval=121,4392
        count=122,4446
        count=0; realSmallInterval=122,4446
        spike_num=132,4870
        if spike_num==0; break;133,4934
        timeidx=135,4971
        timeidx=zeros(spike_num,1); tips=135,4971
        timeidx=138,5112
        spike_num=146,5360
%         interval=149,5435
%         smallInterval=150,5472
%         rmlist=151,5514
        tips=162,5940
        not_empty=163,5969
        spikePeak 168,6065
        spikeTime{spikeTime
170,6100
        spikePeak{spikePeak
171,6137
    n 173,6176
thres=177,6226
trace=178,6249

examples/probe_load.m,92
    a_spikes 7,244
    a_trace 10,323
    a_spikes 12,450
end13,482
  test_data38,1269

classes/Contents.m,0