/******************************************************/
GlobalData* GlobalData::getInstance() {
- if( _uniqueInstance == 0 ) {
+ if( _uniqueInstance == 0) {
_uniqueInstance = new GlobalData();
}
return _uniqueInstance;
reset();
//clears out data from previous read
- if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
+ if((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
clear();
gGroupmap = NULL;
gListVector = NULL;
}
//saves help request
- if (commandName =="help") {
+ if(commandName =="help") {
helpRequest = optionText;
}
- if (commandName == "libshuff") {
+ if(commandName == "libshuff") {
iters = "10000";
cutoff = "1.0";
}
//set default value for cutoff
- if (commandName == "dist.seqs") { cutoff = "1.0"; }
+ if(commandName == "dist.seqs") { cutoff = "1.0"; }
string key, value;
//reads in parameters and values
splitAtComma(value, optionText);
splitAtEquals(key, value);
- if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
- if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
- if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
- if (key == "name" ) { namefile = value; }
- if (key == "order" ) { orderfile = value; }
- if (key == "group" ) { groupfile = value; }
- if (key == "cutoff" ) { cutoff = value; }
- if (key == "precision" ) { precision = value; }
- if (key == "iters" ) { iters = value; }
- if (key == "jumble" ) { jumble = value; }
- if (key == "freq" ) { freq = value; }
- if (key == "method" ) { method = value; }
- if (key == "fileroot" ) { fileroot = value; }
- if (key == "abund" ) { abund = value; }
- if (key == "random" ) { randomtree = value; }
- if (key == "calc") { calc = value; }
- if (key == "step") { step = value; }
- if (key == "form") { form = value; }
- if (key == "sorted") { sorted = value; }
- if (key == "vertical") { vertical = value; }
- if (key == "trump") { trump = value; }
- if (key == "hard") { hard = value; }
- if (key == "soft") { soft = value; }
- if (key == "scale") { scale = value; }
- if (key == "countends" ) { countends = value; }
- if (key == "processors" ) { processors = value; }
- if (key == "size" ) { size = value; }
- if (key == "candidate") { candidatefile = value; }
- if (key == "search") { search = value; }
- if (key == "ksize") { ksize = value; }
- if (key == "align") { align = value; }
- if (key == "match") { match = value; }
- if (key == "mismatch") { mismatch = value; }
- if (key == "gapopen") { gapopen = value; }
- if (key == "gapextend" ) { gapextend = value; }
- if (key == "start" ) { startPos = value; }
- if (key == "end" ) { endPos = value; }
- if (key == "maxambig" ) { maxAmbig = value; }
- if (key == "maxhomop" ) { maxHomoPolymer = value; }
- if (key == "minlength" ) { minLength = value; }
- if (key == "maxlength" ) { maxLength = value; }
-
- if (key == "line") {//stores lines to be used in a vector
+ if(key == "phylip") { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
+ if(key == "column") { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
+ if(key == "list") { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
+ if(key == "rabund") { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
+ if(key == "sabund") { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
+ if(key == "fasta") { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
+ if(key == "tree") { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if(key == "shared") { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
+ if(key == "name") { namefile = value; }
+ if(key == "order") { orderfile = value; }
+ if(key == "group") { groupfile = value; }
+ if(key == "cutoff") { cutoff = value; }
+ if(key == "precision") { precision = value; }
+ if(key == "iters") { iters = value; }
+ if(key == "jumble") { jumble = value; }
+ if(key == "freq") { freq = value; }
+ if(key == "method") { method = value; }
+ if(key == "fileroot") { fileroot = value; }
+ if(key == "abund") { abund = value; }
+ if(key == "random") { randomtree = value; }
+ if(key == "calc") { calc = value; }
+ if(key == "step") { step = value; }
+ if(key == "form") { form = value; }
+ if(key == "sorted") { sorted = value; }
+ if(key == "vertical") { vertical = value; }
+ if(key == "trump") { trump = value; }
+ if(key == "hard") { hard = value; }
+ if(key == "soft") { soft = value; }
+ if(key == "scale") { scale = value; }
+ if(key == "countends") { countends = value; }
+ if(key == "processors") { processors = value; }
+ if(key == "size") { size = value; }
+ if(key == "candidate") { candidatefile = value; }
+ if(key == "search") { search = value; }
+ if(key == "ksize") { ksize = value; }
+ if(key == "align") { align = value; }
+ if(key == "match") { match = value; }
+ if(key == "mismatch") { mismatch = value; }
+ if(key == "gapopen") { gapopen = value; }
+ if(key == "gapextend") { gapextend = value; }
+ if(key == "start") { startPos = value; }
+ if(key == "end") { endPos = value; }
+ if(key == "maxambig") { maxAmbig = value; }
+ if(key == "maxhomop") { maxHomoPolymer = value; }
+ if(key == "minlength") { minLength = value; }
+ if(key == "maxlength") { maxLength = value; }
+ if(key == "flip" ) { flip = value; }
+ if(key == "oligos" ) { oligoFile = value; }
+ if(key == "forward" ) { forMismatch = value; }
+ if(key == "reverse" ) { revMismatch = value; }
+ if(key == "barcode" ) { barMismatch = value; }
+
+ if(key == "line") {//stores lines to be used in a vector
lines.clear();
labels.clear();
line = value;
label = "";
- if (line != "all") { splitAtDash(value, lines); allLines = 0; }
+ if(line != "all") { splitAtDash(value, lines); allLines = 0; }
else { allLines = 1; }
}
- if (key == "label") {//stores lines to be used in a vector
+ if(key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
label = value;
line = "";
- if (label != "all") { splitAtDash(value, labels); allLines = 0; }
+ if(label != "all") { splitAtDash(value, labels); allLines = 0; }
else { allLines = 1; }
}
- if (key == "groups") {//stores groups to be used in a vector
+ if(key == "groups") {//stores groups to be used in a vector
Groups.clear();
groups = value;
splitAtDash(value, Groups);
}
- //saves the last parameter
+ //saves the last parameter ==> this seems silly...
value = optionText;
splitAtEquals(key, value);
- if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
- if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
- if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
- if (key == "name" ) { namefile = value; }
- if (key == "order" ) { orderfile = value; }
- if (key == "group" ) { groupfile = value; }
- if (key == "cutoff" ) { cutoff = value; }
- if (key == "precision" ) { precision = value; }
- if (key == "iters" ) { iters = value; }
- if (key == "jumble" ) { jumble = value; }
- if (key == "freq" ) { freq = value; }
- if (key == "method" ) { method = value; }
- if (key == "fileroot" ) { fileroot = value; }
- if (key == "abund" ) { abund = value; }
- if (key == "random" ) { randomtree = value; }
- if (key == "calc") { calc = value; }
- if (key == "step") { step = value; }
- if (key == "form") { form = value; }
- if (key == "sorted") { sorted = value; }
- if (key == "vertical") { vertical = value; }
- if (key == "trump") { trump = value; }
- if (key == "hard") { hard = value; }
- if (key == "soft") { soft = value; }
- if (key == "scale") { scale = value; }
- if (key == "countends" ) { countends = value; }
- if (key == "processors" ) { processors = value; }
- if (key == "size" ) { size = value; }
- if (key == "candidate") { candidatefile = value; }
- if (key == "search") { search = value; }
- if (key == "ksize") { ksize = value; }
- if (key == "align") { align = value; }
- if (key == "match") { match = value; }
- if (key == "mismatch") { mismatch = value; }
- if (key == "gapopen") { gapopen = value; }
- if (key == "gapextend" ) { gapextend = value; }
- if (key == "start" ) { startPos = value; }
- if (key == "end" ) { endPos = value; }
- if (key == "maxambig" ) { maxAmbig = value; }
- if (key == "maxhomop" ) { maxHomoPolymer = value; }
- if (key == "minlength" ) { minLength = value; }
- if (key == "maxlength" ) { maxLength = value; }
-
+ if(key == "phylip") { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
+ if(key == "column") { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
+ if(key == "list") { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
+ if(key == "rabund") { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
+ if(key == "sabund") { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
+ if(key == "fasta") { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
+ if(key == "tree") { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if(key == "shared") { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
+ if(key == "name") { namefile = value; }
+ if(key == "order") { orderfile = value; }
+ if(key == "group") { groupfile = value; }
+ if(key == "cutoff") { cutoff = value; }
+ if(key == "precision") { precision = value; }
+ if(key == "iters") { iters = value; }
+ if(key == "jumble") { jumble = value; }
+ if(key == "freq") { freq = value; }
+ if(key == "method") { method = value; }
+ if(key == "fileroot") { fileroot = value; }
+ if(key == "abund") { abund = value; }
+ if(key == "random") { randomtree = value; }
+ if(key == "calc") { calc = value; }
+ if(key == "step") { step = value; }
+ if(key == "form") { form = value; }
+ if(key == "sorted") { sorted = value; }
+ if(key == "vertical") { vertical = value; }
+ if(key == "trump") { trump = value; }
+ if(key == "hard") { hard = value; }
+ if(key == "soft") { soft = value; }
+ if(key == "scale") { scale = value; }
+ if(key == "countends") { countends = value; }
+ if(key == "processors") { processors = value; }
+ if(key == "size") { size = value; }
+ if(key == "candidate") { candidatefile = value; }
+ if(key == "search") { search = value; }
+ if(key == "ksize") { ksize = value; }
+ if(key == "align") { align = value; }
+ if(key == "match") { match = value; }
+ if(key == "mismatch") { mismatch = value; }
+ if(key == "gapopen") { gapopen = value; }
+ if(key == "gapextend") { gapextend = value; }
+ if(key == "start") { startPos = value; }
+ if(key == "end") { endPos = value; }
+ if(key == "maxambig") { maxAmbig = value; }
+ if(key == "maxhomop") { maxHomoPolymer = value; }
+ if(key == "minlength") { minLength = value; }
+ if(key == "maxlength") { maxLength = value; }
+ if(key == "flip" ) { flip = value; }
+ if(key == "oligos" ) { oligoFile = value; }
+ if(key == "forward" ) { forMismatch = value; }
+ if(key == "reverse" ) { revMismatch = value; }
+ if(key == "barcode" ) { barMismatch = value; }
+
- if (key == "line") {//stores lines to be used in a vector
+ if(key == "line") {//stores lines to be used in a vector
lines.clear();
labels.clear();
line = value;
label = "";
- if (line != "all") { splitAtDash(value, lines); allLines = 0; }
+ if(line != "all") { splitAtDash(value, lines); allLines = 0; }
else { allLines = 1; }
}
- if (key == "label") {//stores lines to be used in a vector
+ if(key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
label = value;
line = "";
- if (label != "all") { splitAtDash(value, labels); allLines = 0; }
+ if(label != "all") { splitAtDash(value, labels); allLines = 0; }
else { allLines = 1; }
}
- if (key == "groups") {//stores groups to be used in a vector
+ if(key == "groups") {//stores groups to be used in a vector
Groups.clear();
groups = value;
splitAtDash(value, Groups);
}
//set format for shared
- if ((listfile != "") && (groupfile != "")) { format = "shared"; }
- if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
+ if((listfile != "") && (groupfile != "")) { format = "shared"; }
+ if((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
//input defaults for calculators
- if (commandName == "collect.single") {
+ if(commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "rarefaction.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs"; }
+ if(commandName == "rarefaction.single") {
+ if((calc == "default") || (calc == "")) { calc = "sobs"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "collect.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+ if(commandName == "collect.shared") {
+ if((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ if(commandName == "summary.single") {
+ if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "summary.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+ if(commandName == "summary.shared") {
+ if((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "rarefaction.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
+ if(commandName == "rarefaction.shared") {
+ if((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "dist.seqs") {
- if ((calc == "default") || (calc == "")) { calc = "onegap"; }
- if (countends == "") { countends = "T"; }
+ if(commandName == "dist.seqs") {
+ if((calc == "default") || (calc == "")) { calc = "onegap"; }
+ if(countends == "") { countends = "T"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "venn") {
- if ((calc == "default") || (calc == "")) {
- if (format == "list") { calc = "sobs"; }
+ if(commandName == "venn") {
+ if((calc == "default") || (calc == "")) {
+ if(format == "list") { calc = "sobs"; }
else { calc = "sharedsobs"; }
}
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
- if ((calc == "default") || (calc == "")) {
+ if((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
+ if((calc == "default") || (calc == "")) {
calc = "jclass-thetayc";
}
Estimators.clear();
}
- //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
- if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
- if (listfile != "") { format = "list"; }
- else if (sabundfile != "") { format = "sabund"; }
- else if (rabundfile != "") { format = "rabund"; }
+ //ifyou have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
+ if((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
+ if(listfile != "") { format = "list"; }
+ else if(sabundfile != "") { format = "sabund"; }
+ else if(rabundfile != "") { format = "rabund"; }
}
}
catch(exception& e) {
/******************************************************/
// These functions give you the option parameters of the commands
-string GlobalData::getPhylipFile() { return phylipfile; }
-string GlobalData::getColumnFile() { return columnfile; }
-string GlobalData::getListFile() { return listfile; }
-string GlobalData::getRabundFile() { return rabundfile; }
-string GlobalData::getSabundFile() { return sabundfile; }
-string GlobalData::getNameFile() { return namefile; }
-string GlobalData::getGroupFile() { return groupfile; }
-string GlobalData::getOrderFile() { return orderfile; }
-string GlobalData::getTreeFile() { return treefile; }
-string GlobalData::getSharedFile() { return sharedfile; }
-string GlobalData::getFastaFile() { return fastafile; }
-string GlobalData::getCutOff() { return cutoff; }
-string GlobalData::getFormat() { return format; }
-string GlobalData::getPrecision() { return precision; }
-string GlobalData::getMethod() { return method; }
-string GlobalData::getFileRoot() { return fileroot; }
-string GlobalData::getIters() { return iters; }
-string GlobalData::getJumble() { return jumble; }
-string GlobalData::getFreq() { return freq; }
-string GlobalData::getAbund() { return abund; }
-string GlobalData::getRandomTree() { return randomtree; }
-string GlobalData::getGroups() { return groups; }
-string GlobalData::getStep() { return step; }
-string GlobalData::getForm() { return form; }
-string GlobalData::getSorted() { return sorted; }
-string GlobalData::getVertical() { return vertical; }
-string GlobalData::getTrump() { return trump; }
-string GlobalData::getSoft() { return soft; }
-string GlobalData::getHard() { return hard; }
-string GlobalData::getScale() { return scale; }
-string GlobalData::getCountEnds() { return countends; }
-string GlobalData::getProcessors() { return processors; }
-string GlobalData::getSize() { return size; }
-string GlobalData::getCandidateFile() { return candidatefile;}
-string GlobalData::getSearch() { return search; }
-string GlobalData::getKSize() { return ksize; }
-string GlobalData::getAlign() { return align; }
-string GlobalData::getMatch() { return match; }
-string GlobalData::getMismatch() { return mismatch; }
-string GlobalData::getGapopen() { return gapopen; }
-string GlobalData::getGapextend() { return gapextend; }
-string GlobalData::getStartPos() { return startPos; }
-string GlobalData::getEndPos() { return endPos; }
-string GlobalData::getMaxAmbig() { return maxAmbig; }
+string GlobalData::getPhylipFile() { return phylipfile; }
+string GlobalData::getColumnFile() { return columnfile; }
+string GlobalData::getListFile() { return listfile; }
+string GlobalData::getRabundFile() { return rabundfile; }
+string GlobalData::getSabundFile() { return sabundfile; }
+string GlobalData::getNameFile() { return namefile; }
+string GlobalData::getGroupFile() { return groupfile; }
+string GlobalData::getOrderFile() { return orderfile; }
+string GlobalData::getTreeFile() { return treefile; }
+string GlobalData::getSharedFile() { return sharedfile; }
+string GlobalData::getFastaFile() { return fastafile; }
+string GlobalData::getCutOff() { return cutoff; }
+string GlobalData::getFormat() { return format; }
+string GlobalData::getPrecision() { return precision; }
+string GlobalData::getMethod() { return method; }
+string GlobalData::getFileRoot() { return fileroot; }
+string GlobalData::getIters() { return iters; }
+string GlobalData::getJumble() { return jumble; }
+string GlobalData::getFreq() { return freq; }
+string GlobalData::getAbund() { return abund; }
+string GlobalData::getRandomTree() { return randomtree; }
+string GlobalData::getGroups() { return groups; }
+string GlobalData::getStep() { return step; }
+string GlobalData::getForm() { return form; }
+string GlobalData::getSorted() { return sorted; }
+string GlobalData::getVertical() { return vertical; }
+string GlobalData::getTrump() { return trump; }
+string GlobalData::getSoft() { return soft; }
+string GlobalData::getHard() { return hard; }
+string GlobalData::getScale() { return scale; }
+string GlobalData::getCountEnds() { return countends; }
+string GlobalData::getProcessors() { return processors; }
+string GlobalData::getSize() { return size; }
+string GlobalData::getCandidateFile() { return candidatefile; }
+string GlobalData::getSearch() { return search; }
+string GlobalData::getKSize() { return ksize; }
+string GlobalData::getAlign() { return align; }
+string GlobalData::getMatch() { return match; }
+string GlobalData::getMismatch() { return mismatch; }
+string GlobalData::getGapopen() { return gapopen; }
+string GlobalData::getGapextend() { return gapextend; }
+string GlobalData::getStartPos() { return startPos; }
+string GlobalData::getEndPos() { return endPos; }
+string GlobalData::getMaxAmbig() { return maxAmbig; }
string GlobalData::getMaxHomoPolymer() { return maxHomoPolymer; }
-string GlobalData::getMinLength() { return minLength; }
-string GlobalData::getMaxLength() { return maxLength; }
+string GlobalData::getMinLength() { return minLength; }
+string GlobalData::getMaxLength() { return maxLength; }
+string GlobalData::getFlip() { return flip; }
+string GlobalData::getOligosFile() { return oligoFile; }
+string GlobalData::getForwardMismatch() { return forMismatch; }
+string GlobalData::getReverseMismatch() { return revMismatch; }
+string GlobalData::getBarcodeMismatch() { return barMismatch; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
maxHomoPolymer = "-1";
minLength = "-1";
maxLength = "-1";
-
+ flip = "0";
+ forMismatch = "0";
+ revMismatch = "0";
+ barMismatch = "0";
+ oligoFile = "";
}
//*******************************************************/
maxHomoPolymer = "-1";
minLength = "-1";
maxLength = "-1";
+ flip = "0";
+ forMismatch = "0";
+ revMismatch = "0";
+ barMismatch = "0";
+ oligoFile = "";
}
/*******************************************************/
int c, comment;
comment = 0;
- //if you are not a nexus file
- if ((c = filehandle.peek()) != '#') {
+ //ifyou are not a nexus file
+ if((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != ';') {
while ((c = filehandle.peek()) != ';') {
// get past comments
readTreeString(filehandle);
}
- //if you are a nexus file
- }else if ((c = filehandle.peek()) == '#') {
+ //ifyou are a nexus file
+ }else if((c = filehandle.peek()) == '#') {
string holder = "";
// get past comments
}
filehandle >> holder;
- //if there is no translate then you must read tree string otherwise use translate to get names
+ //ifthere is no translate then you must read tree string otherwise use translate to get names
if(holder == "tree" && comment != 1){
//pass over the "tree rep.6878900 = "
- while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
- if (c == EOF ) { break; }
+ if(c == EOF) { break; }
filehandle.putback(c); //put back first ( of tree.
readTreeString(filehandle);
break;
}
//use nexus translation rather than parsing tree to save time
- if ((holder == "translate") || (holder == "Translate")) {
+ if((holder == "translate") || (holder == "Translate")) {
string number, name, h;
h = ""; // so it enters the loop the first time
name.erase(name.end()-1); //erase the comma
Treenames.push_back(number);
}
- if (number == ";") { Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ if(number == ";") { Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
}
}
string name; //k
while((c = filehandle.peek()) != ';') {
- //if you are a name
- if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+ //ifyou are a name
+ if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
name = "";
c = filehandle.get();
// k = c;
//cout << " after putback" << k << endl;
}
- if (c == ':') { //read until you reach the end of the branch length
+ if(c == ':') { //read until you reach the end of the branch length
while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
c = filehandle.get();
// k = c;
filehandle.putback(c);
}
c = filehandle.get();
- if (c == ';') { break; }
+ if(c == ';') { break; }
// k = c;
//cout << k << endl;
--- /dev/null
+/*
+ * trimseqscommand.cpp
+ * Mothur
+ *
+ * Created by Pat Schloss on 6/6/09.
+ * Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "sequence.hpp"
+#include "trimseqscommand.h"
+
+//***************************************************************************************************************
+
+TrimSeqsCommand::TrimSeqsCommand(){
+ try {
+
+ oligos = 0;
+ forwardPrimerMismatch = 0;
+ reversePrimerMismatch = 0;
+ barcodeMismatch = 0;
+
+ totalBarcodeCount = 0;
+ matchBarcodeCount = 0;
+
+ globaldata = GlobalData::getInstance();
+ if(globaldata->getFastaFile() == ""){
+ cout << "you need to at least enter a fasta file name" << endl;
+ }
+
+ if(isTrue(globaldata->getFlip())) { flip = 1; }
+
+ if(globaldata->getOligosFile() != ""){
+ oligos = 1;
+ forwardPrimerMismatch = atoi(globaldata->getForwardMismatch().c_str());
+ reversePrimerMismatch = atoi(globaldata->getReverseMismatch().c_str());
+ barcodeMismatch = atoi(globaldata->getBarcodeMismatch().c_str());
+ }
+
+ if(!flip && !oligos) { cout << "what was the point?" << endl; }
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TrimSeqsCommand class function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
+
+//***************************************************************************************************************
+
+int TrimSeqsCommand::execute(){
+ try{
+ getOligos();
+
+ ifstream inFASTA;
+ openInputFile(globaldata->getFastaFile(), inFASTA);
+
+ ofstream outFASTA;
+ string trimSeqFile = getRootName(globaldata->getFastaFile()) + "trim.fasta";
+ openOutputFile(trimSeqFile, outFASTA);
+
+ ofstream outGroups;
+ string groupFile = getRootName(globaldata->getFastaFile()) + "groups";
+ openOutputFile(groupFile, outGroups);
+
+ ofstream scrapFASTA;
+ string scrapSeqFile = getRootName(globaldata->getFastaFile()) + "scrap.fasta";
+ openOutputFile(scrapSeqFile, scrapFASTA);
+
+ bool success;
+
+ while(!inFASTA.eof()){
+ Sequence currSeq(inFASTA);
+ string group;
+ string trashCode = "";
+
+ if(barcodes.size() != 0){
+ success = stripBarcode(currSeq, group);
+ if(!success){ trashCode += 'b'; }
+ }
+ if(numFPrimers != 0){
+ success = stripForward(currSeq);
+ if(!success){ trashCode += 'f'; }
+ }
+ if(numRPrimers != 0){
+ success = stripReverse(currSeq);
+ if(!success){ trashCode += 'r'; }
+ }
+ if(flip){ currSeq.reverseComplement(); } // should go last
+
+ if(trashCode.length() == 0){
+ currSeq.printSequence(outFASTA);
+ outGroups << currSeq.getName() << '\t' << group << endl;
+ }
+ else{
+ currSeq.setName(currSeq.getName() + '|' + trashCode);
+ currSeq.printSequence(scrapFASTA);
+ }
+
+ gobble(inFASTA);
+ }
+ inFASTA.close();
+ outFASTA.close();
+ scrapFASTA.close();
+ outGroups.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TrimSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+void TrimSeqsCommand::getOligos(){
+
+ ifstream inOligos;
+ openInputFile(globaldata->getOligosFile(), inOligos);
+
+ string type, oligo, group;
+
+ while(!inOligos.eof()){
+ inOligos >> type;
+
+ if(type == "forward"){
+ inOligos >> oligo;
+ forPrimer.push_back(oligo);
+ }
+ else if(type == "reverse"){
+ inOligos >> oligo;
+ revPrimer.push_back(oligo);
+ }
+ else if(type == "barcode"){
+ inOligos >> oligo >> group;
+ barcodes[oligo]=group;
+ }
+ else if(type[0] == '#'){
+ char c;
+ while ((c = inOligos.get()) != EOF) { if (c == 10){ break; } } // get rest of line
+ }
+
+ gobble(inOligos);
+ }
+
+ numFPrimers = forPrimer.size();
+ numRPrimers = revPrimer.size();
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::stripBarcode(Sequence& seq, string& group){
+
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ for(map<string,string>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+
+ if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
+ success = 0;
+ break;
+ }
+
+ if (rawSequence.compare(0,oligo.length(),oligo) == 0){
+ group = it->second;
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ matchBarcodeCount++;
+ success = 1;
+ break;
+ }
+ }
+ totalBarcodeCount++;
+ return success;
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::stripForward(Sequence& seq){
+
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ for(int i=0;i<numFPrimers;i++){
+ string oligo = forPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if (rawSequence.compare(0,oligo.length(),oligo) == 0){
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ matchFPrimerCount++;
+ success = 1;
+ break;
+ }
+
+ }
+ totalFPrimerCount++;
+ return success;
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::stripReverse(Sequence& seq){
+
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ for(int i=0;i<numRPrimers;i++){
+ string oligo = revPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if(rawSequence.compare(rawSequence.length()-oligo.length(),oligo.length(),oligo) == 0){
+ seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
+ matchRPrimerCount++;
+ success = 1;
+ break;
+ }
+
+ }
+ totalRPrimerCount++;
+ return success;
+
+}
+
+//***************************************************************************************************************
projects / mothur.git / commitdiff