SNPDict.sc: Retabbing document.

1 files changed, 209 insertions, 209 deletions

diff --git a/SNPDict.sc b/SNPDict.sc
index 155dad7..0e4566f 100644
--- a/SNPDict.sc
+++ b/SNPDict.sc
@@ -1,223 +1,223 @@
 SNPDict{
-	const <emptyBasePair = #[\none,\none];
-	const <emptyBase = #[\none];
-	var <snpDict;
-	var <snpArr;
-	var <positionLookup;
-	var <unknownLookup;
-	var <unknownArr;
-	var <unknownToDelete;
-	var <>length;
-	var <positions = 0;
-	var <unknowns = 0;
-	var <userID;
+  const <emptyBasePair = #[\none,\none];
+  const <emptyBase = #[\none];
+  var <snpDict;
+  var <snpArr;
+  var <positionLookup;
+  var <unknownLookup;
+  var <unknownArr;
+  var <unknownToDelete;
+  var <>length;
+  var <positions = 0;
+  var <unknowns = 0;
+  var <userID;
 
-	*new{
-		arg aLength, aUserID = 0;
-		^super.new.init(aLength, aUserID);
-	}
+  *new{
+    arg aLength, aUserID = 0;
+    ^super.new.init(aLength, aUserID);
+  }
 
-	init{
-		arg aLength, aUserID;
-		userID = aUserID.asInt;
-		length = aLength.asInt;
-		snpDict = Dictionary.new(length);
-		//snpArr = Array.new(length);
-		positionLookup = Dictionary.new(length);
-		unknownLookup = Dictionary.new(length);
-		//unknownArr = Array.new(length);
-	}
-	
-	updatePositionLookup{//sort the dictionary's position lookup table when updating a new position
-		arg position, positionAdd;
-		if(positionAdd,{//add or remove a position in the lookup table
-			positionLookup.add(position.asFloat -> true);
-		},{
-			positionLookup.removeAt(position.asFloat);
-		});
-	}
+  init{
+    arg aLength, aUserID;
+    userID = aUserID.asInt;
+    length = aLength.asInt;
+    snpDict = Dictionary.new(length);
+    //snpArr = Array.new(length);
+    positionLookup = Dictionary.new(length);
+    unknownLookup = Dictionary.new(length);
+    //unknownArr = Array.new(length);
+  }
 
-	updateUnknownLookup{//sort the dictionary's unknown lookup table when updating a SNP with unknown resolver
-		arg position, positionAdd;
-		if(positionAdd,{
-			unknownLookup.add(position.asFloat -> true);
-		},{
-			unknownLookup.removeAt(position.asFloat);
-		});
-	}
+  updatePositionLookup{//sort the dictionary's position lookup table when updating a new position
+    arg position, positionAdd;
+    if(positionAdd,{//add or remove a position in the lookup table
+      positionLookup.add(position.asFloat -> true);
+    },{
+      positionLookup.removeAt(position.asFloat);
+    });
+  }
 
-	orderLookup{//order the lookup tables (position and unknown) and store them to Arrays (for sequential access)
-		arg table;
-		switch(table,
-			0,{
-				snpArr = positionLookup.order;
-				("Done sorting position lookup table. Positions: "++snpArr.size.asString).postln;
-				^true;
-			},
-			1,{
-				unknownArr = unknownLookup.order;
-				("Done sorting unknown lookup table. Unknowns: "++snpArr.size.asString).postln;
-				^true;
-			},
-			2,{
-				snpArr = positionLookup.order;
-				("Done sorting position lookup table. Positions: "++snpArr.size.asString).postln;
-				unknownArr = unknownLookup.order;
-				("Done sorting unknown lookup table. Unknowns: "++snpArr.size.asString).postln;
-				unknownLookup = nil;
-				positionLookup = nil;
-				^true;
-			},{
-				("Unknown operation on sorting lookup tables: "++table.asString).postln;
-				^false;
-			}
-		);
-	}
+  updateUnknownLookup{//sort the dictionary's unknown lookup table when updating a SNP with unknown resolver
+    arg position, positionAdd;
+    if(positionAdd,{
+      unknownLookup.add(position.asFloat -> true);
+    },{
+      unknownLookup.removeAt(position.asFloat);
+    });
+  }
 
-	storeSNP{//store a combo to the snpDict and the lookup tables when reading from opensnp.org -file
-		arg snp, position;
-		var positionHolder, new = 0;//the SNP holder in snpDict
-		if(snpDict.includesKey(position.asSymbol), {//if there is an entry already, add this one after it
-			snpDict.at(position.asSymbol).add(snp.chromosome -> snp);
-			new = -1;
-		},{//else create the first one in this slot
-			positionHolder = Dictionary.new(25);	
-			positionHolder.add(snp.chromosome -> snp);
-			snpDict.put(position.asSymbol, positionHolder);
-			this.updatePositionLookup(position, true);
-			new = 1;
-			positions = positions+1;
-		});
-		if(snp.hasResolver.not,{//if the SNP has no resolver, update the unknown lookup table
-			this.updateUnknownLookup(position, true);
-		});
-		^new;
-	}
+  orderLookup{//order the lookup tables (position and unknown) and store them to Arrays (for sequential access)
+    arg table;
+    switch(table,
+      0,{
+        snpArr = positionLookup.order;
+        ("Done sorting position lookup table. Positions: "++snpArr.size.asString).postln;
+        ^true;
+      },
+      1,{
+        unknownArr = unknownLookup.order;
+        ("Done sorting unknown lookup table. Unknowns: "++snpArr.size.asString).postln;
+        ^true;
+      },
+      2,{
+        snpArr = positionLookup.order;
+        ("Done sorting position lookup table. Positions: "++snpArr.size.asString).postln;
+        unknownArr = unknownLookup.order;
+        ("Done sorting unknown lookup table. Unknowns: "++snpArr.size.asString).postln;
+        unknownLookup = nil;
+        positionLookup = nil;
+        ^true;
+      },{
+        ("Unknown operation on sorting lookup tables: "++table.asString).postln;
+        ^false;
+      }
+    );
+  }
 
-	storeSNPFromFile{//store a combo to the snpDict and the lookup tables when reading from own file
-		arg snp, position;
-		var positionHolder, new = 0;//the SNP holder in snpDict
-		if(snpDict.includesKey(position.asSymbol), {//if there is an entry already, add this one after it
-			snpDict.at(position.asSymbol).add(snp.chromosome -> snp);
-		},{//else create the first one in this slot
-			positionHolder = Dictionary.new(25);
-			positionHolder.add(snp.chromosome -> snp);
-			snpDict.put(position.asSymbol, positionHolder);
-		});
-	}
-	
-	initLookupFromFile{//init lookup table from file with size given
-		arg posLookup, unLookup;
-		snpArr = Array.new(posLookup);
-		unknownArr = Array.new(unLookup);
-	}
+  storeSNP{//store a combo to the snpDict and the lookup tables when reading from opensnp.org -file
+    arg snp, position;
+    var positionHolder, new = 0;//the SNP holder in snpDict
+    if(snpDict.includesKey(position.asSymbol), {//if there is an entry already, add this one after it
+      snpDict.at(position.asSymbol).add(snp.chromosome -> snp);
+      new = -1;
+    },{//else create the first one in this slot
+      positionHolder = Dictionary.new(25);  
+      positionHolder.add(snp.chromosome -> snp);
+      snpDict.put(position.asSymbol, positionHolder);
+      this.updatePositionLookup(position, true);
+      new = 1;
+      positions = positions+1;
+    });
+    if(snp.hasResolver.not,{//if the SNP has no resolver, update the unknown lookup table
+      this.updateUnknownLookup(position, true);
+    });
+    ^new;
+  }
 
-	addPositionLookupFromFile{//put a position to the position lookup table when reading from own file
-		arg posArr, posSNP;
-		snpArr.add(posSNP);
-	}
+  storeSNPFromFile{//store a combo to the snpDict and the lookup tables when reading from own file
+    arg snp, position;
+    var positionHolder, new = 0;//the SNP holder in snpDict
+    if(snpDict.includesKey(position.asSymbol), {//if there is an entry already, add this one after it
+      snpDict.at(position.asSymbol).add(snp.chromosome -> snp);
+    },{//else create the first one in this slot
+      positionHolder = Dictionary.new(25);
+      positionHolder.add(snp.chromosome -> snp);
+      snpDict.put(position.asSymbol, positionHolder);
+    });
+  }
 
-	addUnknownLookupFromFile{//put a position to the position lookup table when reading from own file
-		arg posArr, posSNP;
-		unknownArr.add(posSNP);
-	}
-	
-	updateResolver{//update a SNP resolver at a given position
-		arg position, id, resolver;
-		var resolverLeft;
-		if(resolver!=SNPInfo.emptyBasePair && resolver!=SNPInfo.emptyBase,{//if the resolver is none, don't do anything
-			snpDict.at(position.asSymbol).do({
-				arg snpItem;
-				if(id==snpItem.id, {
-					snpItem.resolver_(resolver);
-					("Resolver updated.").postln;
-					^true;
-				});
-			});
-//			resolverLeft = this.noneResolverAtPosition(position);
-//			if(resolverLeft == false,{//if there are no unknowns left, delete position from lookup table
-//				unknownArr.removeAt(unknownArr.indexOf(position.asFloat));
-//			});
-//			resolverLeft = nil;
-		},{
-			("Not updating position "++position++". Resolver is none.").postln;
-			^false;
-		});
-	}
+  initLookupFromFile{//init lookup table from file with size given
+    arg posLookup, unLookup;
+    snpArr = Array.new(posLookup);
+    unknownArr = Array.new(unLookup);
+  }
 
-	deleteSNP{//delete a SNP at a given position
-		arg snp, position;
-		var snpCounter = 0, deleted = false;
-		snpDict.at(position.asSymbol).do({
-			arg snpItem, i;
-//			if(snpItem.notNil, {
-				snpCounter = snpCounter + 1;
-				if(snp.id == snpItem.id{
-					snpItem.removeAt(position.asSymbol);
-					snpCounter = snpCounter - 1;
-					deleted = true;
-				});
-//			});
-		});
-		if(snpCounter < 1,{//delete the complete position if there is no SNP left
-			snpDict.removeAt(position.asSymbol);
-			this.sortPositionLookup(-1, position);
-			this.sortUnknownLookup(-1, position);
-		});
-		^deleted;
-	}
+  addPositionLookupFromFile{//put a position to the position lookup table when reading from own file
+    arg posArr, posSNP;
+    snpArr.add(posSNP);
+  }
 
-	noneResolverAtPosition{//return a Dictionary of Chromosome -> SNP pairs that don't have a resolver or false if none found
-		arg position;
-		var noneResolver = Dictionary.new(25), noneResolverCount = 0;
-		if(snpDict.includesKey(position.asSymbol),{//if the position exists, check it
-			snpDict.at(position.asSymbol).keysValuesDo({
-				arg chromosome, snp;
-				if(snp.hasResolver.not,{
-					noneResolver.add(chromosome -> snp);
-					noneResolverCount = noneResolverCount + 1;
-				});
-			});
-			if(noneResolverCount>0,{
-				^noneResolver;
-			},{
-				^false;
-			});
-		},{
-			^false;
-		});
-	}
+  addUnknownLookupFromFile{//put a position to the position lookup table when reading from own file
+    arg posArr, posSNP;
+    unknownArr.add(posSNP);
+  }
+  
+  updateResolver{//update a SNP resolver at a given position
+    arg position, id, resolver;
+    var resolverLeft;
+    if(resolver!=SNPInfo.emptyBasePair && resolver!=SNPInfo.emptyBase,{//if the resolver is none, don't do anything
+      snpDict.at(position.asSymbol).do({
+        arg snpItem;
+        if(id==snpItem.id, {
+          snpItem.resolver_(resolver);
+          ("Resolver updated.").postln;
+          ^true;
+        });
+      });
+//      resolverLeft = this.noneResolverAtPosition(position);
+//      if(resolverLeft == false,{//if there are no unknowns left, delete position from lookup table
+//        unknownArr.removeAt(unknownArr.indexOf(position.asFloat));
+//      });
+//      resolverLeft = nil;
+    },{
+      ("Not updating position "++position++". Resolver is none.").postln;
+      ^false;
+    });
+  }
 
-	snpAtPosition{//return a Dictionary of chromosome -> SNP pairs at a given position, or false if none available
-		arg position;
-		if(snpDict.includesKey(position.asSymbol),{//check if the key is there
-			^snpDict.at(position.asSymbol);//return the Dictionary at position
-		},{
-			^false;
-		});
-	}
-	
-	distanceToNextPosition{//calculate the distance from current position, to the one following
-		arg position;
-		var now; 
-		if(position==0.0,{//if it's the beginning, return first position later on
-			now = -1;
-		},{
-			now = snpArr.indexOf(position.asFloat);
-		});
-		switch(now,
-			nil,{^position},
-			snpArr.size-1,{^0},
-			-1,{^snpArr[0]},
-			{^snpArr[(snpArr.indexOf(position.asFloat)+1)]-position;}
-		);
-	}
+  deleteSNP{//delete a SNP at a given position
+    arg snp, position;
+    var snpCounter = 0, deleted = false;
+    snpDict.at(position.asSymbol).do({
+      arg snpItem, i;
+//      if(snpItem.notNil, {
+        snpCounter = snpCounter + 1;
+        if(snp.id == snpItem.id{
+          snpItem.removeAt(position.asSymbol);
+          snpCounter = snpCounter - 1;
+          deleted = true;
+        });
+//      });
+    });
+    if(snpCounter < 1,{//delete the complete position if there is no SNP left
+      snpDict.removeAt(position.asSymbol);
+      this.sortPositionLookup(-1, position);
+      this.sortUnknownLookup(-1, position);
+    });
+    ^deleted;
+  }
 
-	queryStatistics{//query statistics about this SNPDict
-		//TODO: shortest/longest/mean distance between SNPs
-		//TODO: unknown/total SNPs
-		//TODO: number of SNPs per chromosome
-		//TODO: unknown/total SNPs per chromosome
-		//TODO: total positions
-	}
+  noneResolverAtPosition{//return a Dictionary of Chromosome -> SNP pairs that don't have a resolver or false if none found
+    arg position;
+    var noneResolver = Dictionary.new(25), noneResolverCount = 0;
+    if(snpDict.includesKey(position.asSymbol),{//if the position exists, check it
+      snpDict.at(position.asSymbol).keysValuesDo({
+        arg chromosome, snp;
+        if(snp.hasResolver.not,{
+          noneResolver.add(chromosome -> snp);
+          noneResolverCount = noneResolverCount + 1;
+        });
+      });
+      if(noneResolverCount>0,{
+        ^noneResolver;
+      },{
+        ^false;
+      });
+    },{
+      ^false;
+    });
+  }
+
+  snpAtPosition{//return a Dictionary of chromosome -> SNP pairs at a given position, or false if none available
+    arg position;
+    if(snpDict.includesKey(position.asSymbol),{//check if the key is there
+      ^snpDict.at(position.asSymbol);//return the Dictionary at position
+    },{
+      ^false;
+    });
+  }
+
+  distanceToNextPosition{//calculate the distance from current position, to the one following
+    arg position;
+    var now; 
+    if(position==0.0,{//if it's the beginning, return first position later on
+      now = -1;
+    },{
+      now = snpArr.indexOf(position.asFloat);
+    });
+    switch(now,
+      nil,{^position},
+      snpArr.size-1,{^0},
+      -1,{^snpArr[0]},
+      {^snpArr[(snpArr.indexOf(position.asFloat)+1)]-position;}
+    );
+  }
+
+  queryStatistics{//query statistics about this SNPDict
+    //TODO: shortest/longest/mean distance between SNPs
+    //TODO: unknown/total SNPs
+    //TODO: number of SNPs per chromosome
+    //TODO: unknown/total SNPs per chromosome
+    //TODO: total positions
+  }
 }