diff options
| -rw-r--r-- | SNPDict.sc | 418 |
1 files changed, 209 insertions, 209 deletions
@@ -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 + } } |