/******************************************************/
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;
+ gSparseMatrix = NULL;
gTree.clear();
Treenames.clear();
labels.clear(); lines.clear(); Groups.clear();
}
//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 == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; }
- if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
- 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 == "filter") { filter = value; }
- if (key == "soft") { soft = value; }
- if (key == "scale") { scale = value; }
- if (key == "ends" ) { ends = value; }
- if (key == "processors" ) { processors = value; }
- if (key == "size" ) { size = value; }
- if (key == "template") { templatefile = 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 == "line") {//stores lines to be used in a set
+ 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 = "";
- splitAtDash(value, lines);
- allLines = 0;
+ if(line != "all") { splitAtDash(value, lines); allLines = 0; }
+ else { allLines = 1; }
}
- if (key == "label") {//stores labels to be used in a set
+
+ if(key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
label = value;
line = "";
- 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 == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; }
- if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
- 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 == "filter") { filter = value; }
- if (key == "soft") { soft = value; }
- if (key == "scale") { scale = value; }
- if (key == "ends" ) { ends = value; }
- if (key == "processors" ) { processors = value; }
- if (key == "size" ) { size = value; }
- if (key == "template") { templatefile = 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 == "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(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 != "") {
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }else { cout << "You have not specified any calculators." << endl; }
+ if((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
+ if((calc == "default") || (calc == "")) {
+ calc = "jclass-thetayc";
+ }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
+
+ if(commandName == "filter.seqs"){
+ if(trump == "" && vertical == "" && hard == "" && soft == ""){
+ trump = '.';
+ }
+ }
- //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::getNexusFile() { return nexusfile; }
-string GlobalData::getClustalFile() { return clustalfile; }
-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::getTrump() { return trump; }
-string GlobalData::getSoft() { return soft; }
-string GlobalData::getFilter() { return filter; }
-string GlobalData::getScale() { return scale; }
-string GlobalData::getEnds() { return ends; }
-string GlobalData::getProcessors() { return processors; }
-string GlobalData::getSize() { return size; }
-string GlobalData::getTemplateFile() { return templatefile;}
-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::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::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;}
-void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;}
-void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file;}
-void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file;}
-void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file;}
-void GlobalData::setGroupFile(string file) { groupfile = file; }
-void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; fileroot = file;}
+void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
+void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file; }
+void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file; }
+void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file; }
+void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file; }
+void GlobalData::setGroupFile(string file) { groupfile = file; }
+void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; fileroot = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setFormat(string Format) { format = Format; }
void GlobalData::setRandomTree(string Random) { randomtree = Random; }
void GlobalData::setGroups(string g) { groups = g; }
void GlobalData::setCalc(string Calc) { calc = Calc; }
-void GlobalData::setEnds(string e) { ends = e; }
+void GlobalData::setCountEnds(string e) { countends = e; }
void GlobalData::setProcessors(string p) { processors = p; }
//option definitions should go here...
helpRequest = "";
clear();
- gListVector == NULL;
- gSparseMatrix == NULL;
+ gListVector = NULL;
+ gSparseMatrix = NULL;
}
/*******************************************************/
groupfile = "";
orderfile = "";
fastafile = "";
- nexusfile = "";
- clustalfile = "";
treefile = "";
sharedfile = "";
- templatefile = "";
+ candidatefile = "";
cutoff = "10.00";
format = "";
precision = "100";
step = "0.01";
form = "integral";
sorted = "T"; //F means don't sort, T means sort.
- vertical = "";
- trump = "";
- filter = "";
+ vertical = "F";
+ trump = "";
+ hard = "";
soft = "";
scale = "log10";
- ends = "T"; //yes
+ countends = "T"; //yes
processors = "1";
- size = "1000";
- search = "suffix";
- ksize = "7";
- align = "blast";
+ size = "0";
+ search = "kmer";
+ ksize = "8";
+ align = "needleman";
match = "1.0";
mismatch = "-1.0";
- gapopen = "-5.0";
+ gapopen = "-1.0";
gapextend = "-2.0";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+ flip = "0";
+ forMismatch = "0";
+ revMismatch = "0";
+ barMismatch = "0";
+ oligoFile = "";
}
//*******************************************************/
/******************************************************/
void GlobalData::reset() {
+ label = "";
+ line = "";
cutoff = "10.00";
precision = "100";
iters = "1000";
abund = "10";
step = "0.01";
form = "integral";
- ends = "T";
+ countends = "T";
processors = "1";
- size = "1000";
- search = "suffix";
- ksize = "7";
- align = "blast";
+ size = "0";
+ search = "kmer";
+ ksize = "8";
+ align = "needleman";
match = "1.0";
mismatch = "-1.0";
- gapopen = "-5.0";
+ gapopen = "-1.0";
gapextend = "-2.0";
+ vertical = "";
+ trump = "";
+ hard = "";
+ soft = "";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+ flip = "0";
+ forMismatch = "0";
+ revMismatch = "0";
+ barMismatch = "0";
+ oligoFile = "";
+
}
/*******************************************************/
/*******************************************************/
void GlobalData::parseTreeFile() {
+ //Why is THIS in GlobalData??? - PDS
+
//only takes names from the first tree and assumes that all trees use the same names.
try {
string filename = treefile;
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;
projects / mothur.git / blobdiff