Neural Query System NQS Data-Mining From Within the NEURON Simulator (Lytton 2006)

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Accession:97874
NQS is a databasing program with a query command modeled loosely on the SQL select command. Please see the manual NQS.pdf for details of use. An NQS database must be populated with data to be used. This package includes MFP (model fingerprint) which provides an example of NQS use with the model provided in the modeldb folder (see readme for usage).
Reference:
1 . Lytton WW (2006) Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics 4:163-76 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Lytton, William [bill.lytton at downstate.edu];
// $Id: declist.hoc,v 1.81 2005/01/31 20:56:53 billl Exp $

strdef mchnms
objref tmplist,tmplist2,tmpobj,stack,SO,aa,XO,YO
if (! name_declared("datestr")) load_file("setup.hoc")
tmplist = new List()
stack = new List()
proc declist() {}

//* Declarations

begintemplate String2
public s,t,x,append,prepend,exec
strdef s,t
proc init() {
  if (numarg() == 1) { s=$s1 }
  if (numarg() == 2) { s=$s1 t=$s2 }
  if (numarg() == 3) { s=$s1 t=$s2 x=$3 }
}
proc append () { local i
  if (argtype(1)==2) sprint(t,"%s%s",s,$s1)
  for i=2,numarg() sprint(t,"%s%s",t,$si)
}
proc prepend () { local i
  if (argtype(1)==2) sprint(t,"%s%s",$s1,s)
  for i=2,numarg() sprint(t,"%s%s",$si,t)
}
proc exec () {
  if (numarg()==1) sprint(t,"%s%s",$s1,s)
  execute(t)
}
endtemplate String2

// template Union
// USAGE: XO=new Union(val) where val can be a number string or object
//        XO=new Union(list,index) will pick up a string or object from list
//        XO=new Union(vec,index)  will pick up a number from vector
//        XO=new Union(&dbl,index) will pick up a number from double array
// Union allows storage of a double, string or object
// It is useful as a localobj in an obfunc since it will permit returning anything
// It also makes it easy to pick up any kind of value out of a list, vector or array
begintemplate Union
public ty,x,s,o
strdef s
objref o[2]
double x[2]
external sfunc,tstr
// 1arg -- store a num, string or obj
// 2arg -- pick up type out of list
proc init() { local ii
  x=x[1]=0 ty=-1
  if (numarg() == 1) {
    ty = argtype(1)
    if (ty==0) { x=$1
    } else if (ty==2) { s=$s1 
    } else if (ty==1) { o=$o1 
    } else printf("Union ERR: argtype not recognized %d\n",ty)
  } else if (numarg()==2) {
    ii=$2
    if (argtype(1)==1) {
      if (isobj($o1,"Vector")) { 
        if (ii<0 || ii>=$o1.size) {
          printf("Union ERR: vec index (%d) out of bounds for %s\n",ii,$o1)
          return }
        ty=0 x=$o1.x[ii] o=$o1
      } else if (isobj($o1,"List")) {
        if (ii<0 || ii>=$o1.count) {
          printf("Union ERR: list index (%d) out of bounds for %s\n",ii,$o1)
          return }
        if (isobj($o1.object(ii),"String")) { // will handle String2
          ty=2 s=$o1.object(ii).s o=$o1.object(ii) x=ii
        } else { ty=1 o=$o1.object(ii) x=ii }
      }
    } else if (argtype(1)==3) {
      ty=0 x=$&1[ii] // could check - but no + bound checking possible
    }
  }
}

func isobj () {
  sprint(tstr,"%s",$o1)
  if (sfunc.substr(tstr,$s2)==0) return 1 else return 0
}
endtemplate Union

//* SNO: generic template to store strings numbers and objects
begintemplate SNO
public s,t,u,n,o,set
public ov,ol,set,get,pr,init
strdef s,t,u,tstr
objref o[3],this
double n[3]

proc init() {
  if (numarg() >= 2) {s=$s1 n[0]=$2}
  if (numarg() >= 4) {t=$s3 n[1]=$4}
  if (numarg() == 6) {u=$s5 n[2]=$6}
}

proc ov () { local a,sz
  if (numarg()>=1) a=$1 else a=0
  if (numarg()==1) sz=$2 else sz=100
  o[a]=new Vector(sz)
}
proc ol () { 
  if (numarg()==1) a=$1 else a=0
  o[a]=new List() 
}
proc set () { local ii
  if (numarg()==1) ii=$1 else ii=0
  if (ii==0) tstr=s else if (ii==1) tstr=t else if (ii==2) tstr=u else {
    printf("ERROR: only 3 items in SNO: %s\n",this) return } 
  sprint(tstr,"%s = %s.n[%d]",tstr,this,ii)
  execute(tstr)
}
proc get () { local ii
  if (numarg()==1) ii=$1 else ii=0
  if (ii==0) {
    sprint(tstr,"%s.n[%d] = %s",this,ii,this.s)
  } else   if (ii==1) {
    sprint(tstr,"%s.n[%d] = %s",this,ii,this.t)
  } else   if (ii==2) {
    sprint(tstr,"%s.n[%d] = %s",this,ii,this.u)
  } else { printf("ERROR: only 3 items in SNO: %s\n",this) return } 
  execute(tstr)
}
proc pr () { local ii
  if (numarg()==1) ii=$1 else ii=0
  if (ii==0) {
    sprint(tstr,"print %s.s,\" \",%s,\" \",%s.n[%d]",this,s,this,ii)
  } else   if (ii==1) {
    sprint(tstr,"print %s.t,\" \",%s,\" \",%s.n[%d]",this,t,this,ii)
  } else   if (ii==2) {
    sprint(tstr,"print %s.u,\" \",%s,\" \",%s.n[%d]",this,u,this,ii)
  } else { printf("ERROR: only 3 items in SNO: %s\n",this) return } 
  execute(tstr)
}
endtemplate SNO

//* list iterator ltr
// usage 'for ltr(tmplist) { print XO }' :: 1 arg, assumes XO as dummy
// usage 'for ltr(YO, tmplist) { print YO }' 2 arg, specify dummy
// usage 'for ltr(XO, tmplist, &x) { print XO,x }' :: 3 args, define counter (else i1 default)
//                        :: note that x, i1 must be globally defined
// usage 'for ltr(XO, tmplist, 5) { print XO,x }' :: 3 args, only print out 0-5
iterator ltr () { local i,max,ifl
  max=-1 ifl=0 // iterator flag
  if (numarg()==3) {
    if (argtype(3)==3) {ifl=1 $&3=0}
    if (argtype(3)==0) max=$3
  }
  if (! ifl) i1=0
  if (numarg()==1) {
    if (max==-1) max=$o1.count()-1
    for i = 0, max {
      XO = $o1.object(i)
      iterator_statement
      i1+=1
    }
    tmpobj=$o1
    XO=nil
  } else {
    if (max==-1) max=$o2.count()-1
    for i = 0, max {
      $o1 = $o2.object(i)
      iterator_statement
      if (ifl) { $&3+=1 } else { i1+=1 }
    }
    tmpobj=$o2
    $o1 = nil
  }
}

//* list iterator ltrb -- backwards list iterator
// usage 'for ltrb(tmplist) { print XO }' :: 1 arg, assumes XO as dummy
// usage 'for ltrb(YO, tmplist) { print YO }' 2 arg, specify dummy
// usage 'for ltrb(XO, tmplist, &x) { print XO,x }' :: 3 args, define counter (else i1 default)
//                                                 :: note that x, i1 must be defined
iterator ltrb () { local i
  if (numarg()==1) {
    i1=$o1.count-1
    for (i=$o1.count()-1;i>=0;i-=1) {
      XO = $o1.object(i)
      iterator_statement
      i1-=1
    }
    tmpobj=$o1 XO=nil
  } else {
    if (numarg()==3) $&3=$o2.count-1 else i1=$o2.count-1
    for (i=$o2.count()-1;i>=0;i-=1) {
      $o1 = $o2.object(i)
      iterator_statement
      if (numarg()==3) { $&3-=1 } else { i1-=1 }
    }
    tmpobj=$o2
    $o1 = nil
  }
}

// lrm(LIST,STR) will remove item with string from LIST
proc lrm () { local cnt
  cnt=0
  if (argtype(2)==2) {
    for ltrb(XO,$o1) if (strm(XO.s,$s2)) { $o1.remove(i1) cnt+=1 }
    printf("%s found %d time\n",$s2,cnt)
  } else {
    $o1.remove($o1.index($o2))
  }
}

// lrepl(LIST,#,OBJ) will replace item at location # with OBJ
proc lrepl () { $o1.remove($2) $o1.insrt($2,$o3) }

// lswap(list,#1,#2) swap items on a list
proc lswap () { local a,b
  if ($2<$3) {a=$2 b=$3} else {a=$3 b=$2}
  $o1.insrt(a,$o1.object(b))
  $o1.remove(b+1)
  $o1.insrt(b+1,$o1.object(a+1))
  $o1.remove(a+1)
}

// proc shl() show a list
proc shl () { 
  if (numarg()==1) tmpobj=$o1 else tmpobj=tmplist 
  if (tmpobj.count==0) return
  if (isstring(tmpobj.object(0),tstr)) {
    for ltr(XO,tmpobj) print XO.s
  } else for ltr(XO,tmpobj) print XO
}
// lfu() = ltr follow-up, pick out a single item from the last ltr request
// lfu(list,num[,obj])
proc lfu () { 
  if (numarg()==1) { 
    if (argtype(1)==0) XO=tmpobj.object($1)
    if (argtype(1)==1) tmpobj=$o1
  }
  if (numarg()==2) {
    if (argtype(1)==1 && argtype(2)==0) {tmpobj=$o1 XO=$o1.object($2)}
    if (argtype(1)==0 && argtype(2)==1) {$o2=tmpobj.object($1)}
  }
  if (numarg()==3) {
    if (argtype(1)==1 && argtype(2)==0 && argtype(3)==1) { tmpobj=$o1 $o3=$o1.object($2) }
  }
  if (numarg()==4) {
    $o2=tmpobj.object($1)  $o4=tmpobj.object($3) 
  }
}
  
//* list iterator ltr2
// usage 'for ltr2(XO, YO, list1, list2) { print XO,YO }'
iterator ltr2() { local i,cnt
  if (numarg()==5) $&5=0 else i1=0
  if ($o3.count != $o4.count) { print "ltr2 WARNING: lists have different lengths" 
    if ($o3.count<$o4.count) cnt=$o3.count else cnt=$o4.count
  }
  for i = 0, cnt-1 {
    $o1 = $o3.object(i)
    $o2 = $o4.object(i)
    iterator_statement
    if (numarg()==5) { $&5+=1 } else { i1+=1 }
  }
  $o1=nil $o2=nil
}

//* list pairwise iterator ltrp
// usage 'for ltrp(XO, YO, list) { print XO,YO }' takes them pairwise
iterator ltrp() { local i
  if (numarg()==4) {$&4=0} else {i1 = 0}
  for (i=0;i<$o3.count()-1;i+=2) {
    $o1 = $o3.object(i) $o2 = $o3.object(i+1)
    iterator_statement
    if (numarg()==4) { $&4+=1 } else { i1+=1 }
  }
  $o1=nil $o2=nil
}

//* list iterator sltr
// usage 'for sltr(XO, string) { print XO }'
iterator sltr() { local i
  tmplist = new List($s2)
  if (numarg()==3) {$&3=0} else {i1=0}
  for i = 0, tmplist.count() - 1 {
    $o1 = tmplist.object(i)
    iterator_statement
    if (numarg()==3) { $&3+=1 } else { i1+=1 }
  }
  $o1 = nil
}

//* listedit() allows you to remove things by clicking
proc listedit () {
  if (numarg()==0) { print "listedit(list,str) gives browser(list,str) for removing items" return}
  if (numarg()==1) {
  if (! isstring($o1.object(0),temp_string_)) {print "Give name for string of object?" return }
    sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,"s")
  } else {
    sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,$s2)
  }
  execute1(temp_string_)
  $o1.browser("Double click on item to remove",temp_string_,"ledt1()")
  sprint(temp_string_,"%s.remove(hoc_ac_)",$o1)
  $o1.accept_action(temp_string_)
}


//* listXO() connects stuff to XO from a list
proc listXO () {
  if (numarg()==1) {
    $o1.browser("Double click")
    sprint(temp_string_,"print hoc_ac_,\":XO -> \",%s.object(hoc_ac_) XO = %s.object(hoc_ac_)",$o1,$o1)
    $o1.accept_action(temp_string_)
  } else if (numarg()==2) {
    $o1.browser($s2)
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s",$o1,$o1,$s2)
    $o1.accept_action(temp_string_)
  } else if (numarg()==3) {
    $o1.browser($s2)
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s,%s.object(hoc_ac_).%s",$o1,$o1,$s2,$o1,$s3)
    $o1.accept_action(temp_string_)
  }
}

//* lcatstr(list,s1,s2,...) make new List("s1") new List("s2") ... in one list
proc lcatstr() { local i
  if (numarg()<3) { print "lcatstr(l1,s1,s2,...) puts new Lists into l1" return }
  $o1 = new List($s2)
  for i=3,numarg() {
    tmplist2 = new List($si)
    for ltr(XO,tmplist2) { $o1.append(XO) }  
  }
}

//* sublist() places a sublist in LIST0 from LIST1 index BEGIN to END inclusive
proc sublist () { local ii
  $o1.remove_all
  for ii=$3,$4 {
    $o1.append($o2.object(ii))
  }
}

//* catlist() concats LIST2...LISTN on end of LIST1
proc catlist () { local i
  for i = 2, numarg() {
    for ltr(YO,$oi) {
      $o1.append(YO)
    }
  }
}  

//* mechlist() creates a LIST of all this CELL type's TEMPLATE type
// list, cell, template
// make a list of mechanisms belonging to a certain template
proc mechlist () { local num,ii
//  mchnms = ""  // not a good storage since runs out of room
  if (numarg()==0) { print "mechlist(list, cell, template)" return}
  $o1 = new List($s2)
  num = $o1.count
  for ii=0,num-1 {
    sprint(temp_string_,"%s.append(%s.%s)",$o1,$o1.object(ii),$s3)
    execute(temp_string_)
    sprint(mchnms,"%s/%d/%s.%s",mchnms,ii,$o1.object(ii),$s3)
  }
  for (ii=num-1;ii>=0;ii=ii-1) { $o1.remove(ii) }
}

//* lp() loop through a list running command in object's context
// assumes list in tmplist
// with 1 args run $o1.object().obj_elem
// with 2 args run comm($o1.object().obj_elem)
proc lp () {
  for ii=0,tmplist.count-1 {
    printf("%s ",tmplist.object(ii))
    if (numarg()==2) {
      sprint(temp_string_,"%s(%s.%s)",$s2,tmplist.object(ii),$s1)
    } else {
      sprint(temp_string_,"%s.%s",tmplist.object(ii),$s1)
    }
    execute(temp_string_)
  }
}

//* prlp() loop through a list printing object name and result of command
proc prlp () {
  tmpobj=tmplist
  if (numarg()>0) if (argtype(1)==1) tmpobj=$o1
  for ltr(XO,tmpobj) {
    printf("%d %s ",i1,XO)
    if (numarg()>1) {
      sprint(temp_string_,"print %s.%s",XO,$s2)
      execute(temp_string_)
    } else { print "" }
  }
}

//** repl_str(str,stra,strb,scratch): replace stra with strb in string
// will only replace first string match
proc repl_str() {
  if (sfunc.head($s1,$s2,$s4) == -1) { print $s2," not in ",$s1  return }
  sfunc.tail($s1,$s2,$s4)
  sprint($s4,"%s%s",$s3,$s4)
  sfunc.head($s1,$s2,$s1)
  sprint($s1,"%s%s",$s1,$s4)
}

//** repl_mstr(str,stra,strb,scratch): replace stra with strb in string
// multiple replace
proc repl_mstr() {
  while (sfunc.head($s1,$s2,$s4) != -1) {
    sfunc.tail($s1,$s2,$s4)
    sprint($s4,"%s%s",$s3,$s4)
    sfunc.head($s1,$s2,$s1)
    sprint($s1,"%s%s",$s1,$s4)
  }
}

//** clean_str(str,scratch,s1,s2,s3,...)
// remove serial $si from string
proc clean_str () { local i
  for i=3,numarg() {
    while (sfunc.head($s1,$si,$s2) != -1) { 
      sfunc.tail($s1,$si,$s2)
      sfunc.head($s1,$si,$s1)
      sprint($s1,"%s%s",$s1,$s2)      
    }
  }
}

// aa (or $o2) becomes a list of strings from file $s1
proc aaaa () { local flag
  if (numarg()==2) { tmpfile.ropen($s1) aa=$o2 flag=0
  } else if (numarg()==1) { tmpfile.ropen($s1) flag=1
  } else { tmpfile.ropen("aa") flag=1 }
  if (flag==1) if (isobj(aa,"List")) { aa.remove_all() } else { aa=new List() }
  while (tmpfile.gets(temp_string_)>0) {
    chop(temp_string_)
    tmpobj=new String(temp_string_)
    aa.append(tmpobj)
  }
  tmpobj=nil
}

//* objid() find information about object -- replaces var2obj, canobj, objnum
obfunc objid () { local flag localobj xo
  xo=new Union()
  if (argtype(1)==1) sprint(xo.s,"tmpobj=%s",$o1) else sprint(xo.s,"tmpobj=%s",$s1)
  execute(xo.s) // change variable name to object name
  xo.o=tmpobj
  sprint(xo.s,"%s",xo.o)
  sscanf(xo.s,"%*[^[][%d]",&xo.x)
  return xo
}

//* var2obj() and canobj() -- find true object names
// var2obj("tstr"[,"objvar"]) replaces variable name with actual name of the object
// default into XO; optional second arg allows to place somewhere else
// eg tstr="TC[0].ampa" var2obj(tstr) -> AMPA[0]
proc var2obj () { local flag
  if (numarg()==1) flag=1 else flag=0
  if (flag) sprint($s1,"XO=%s",$s1) else sprint($s1,"%s=%s",$s2,$s1)
  execute($s1) // change variable name to object name
  if (flag) sprint($s1,"%s",XO) else sprint($s1,"%s",$s2)
  printf("var2obj() PLEASE REPLACE WITH objid()\n") 
}

//** objnum(OBJ) -- find object number
func objnum () {
  if (argtype(1)==1) sprint(temp_string_,"%s",$o1) else temp_string_=$s1
  if (sscanf(temp_string_,"%*[^[][%d]",&x) != 1) x=-1
  printf("objnum() PLEASE REPLACE WITH objid()\n") 
  return x
}

//** canobj(obj[,"OBJVAR"]) -- default will assign to XO
// canonical object -- return canonical identity for an object
// eg canobj(tc,"YO") -- figure out what tc is and assign it to YO
proc canobj () { local flag
  if (numarg()==1) flag=1 else flag=0
  if (flag) sprint(tstr,"XO=%s",$o1) else sprint(tstr,"%s=%s",$s2,$o1)
  execute(tstr) // change variable name to object name
  sprint(tstr,"%s",$o1)
  printf("canobj() PLEASE REPLACE WITH objid()\n") 
}

//* push() and pop() for objects -- returns
proc push () { local i
  for i=1,numarg() stack.append($oi)
}

proc pop () { local i
  if ((numarg()>0 && stack.count<numarg()) || stack.count==0) {
    print "ERR: stack underflow" return
  } 
  if (numarg()>=1) {
    for i=1,numarg() {
      $oi=stack.object(stack.count-1)
      stack.remove(stack.count-1) 
    }
  } else { 
    SO=stack.object(stack.count-1) 
    stack.remove(stack.count-1) 
  }
}

strdef tmstr
tmstr="run()"
func time () { local tti
  prtime()
  system("date")
  if (numarg()==1) execute1($s1) else execute1(tmstr)
  tti=prtime()
  if (tti<60) print tti,"s" else print tti/60,"m"
  system("date")
  return tti
}

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