X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=16d434bcb47dbd18e91914214cd8fda032e9f47b;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=714b5ad2e447a579872f9f5b8d8c7886303a8391;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index 714b5ad..16d434b 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -42,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ cutoff = "1.0"; } + //set default value for cutoff + if (commandName == "dist.seqs") { cutoff = "1.0"; } + string key, value; //reads in parameters and values if((optionText != "") && (commandName != "help")){ @@ -54,7 +57,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 == "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; } @@ -73,9 +78,22 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 lines.clear(); @@ -111,6 +129,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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; } @@ -129,8 +149,22 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 vector lines.clear(); @@ -163,7 +197,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ //input defaults for calculators 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-efron-boneh-solow-shen"; } Estimators.clear(); splitAtDash(calc, Estimators); } @@ -173,17 +208,18 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ splitAtDash(calc, Estimators); } if (commandName == "collect.shared") { - if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + + 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 ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; } Estimators.clear(); splitAtDash(calc, Estimators); } if (commandName == "summary.shared") { - if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } Estimators.clear(); splitAtDash(calc, Estimators); } @@ -192,6 +228,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ Estimators.clear(); splitAtDash(calc, Estimators); } + if (commandName == "dist.seqs") { + if ((calc == "default") || (calc == "")) { calc = "onegap"; } + Estimators.clear(); + splitAtDash(calc, Estimators); + } if (commandName == "venn") { if ((calc == "default") || (calc == "")) { if (format == "list") { calc = "sobs"; } @@ -200,7 +241,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ Estimators.clear(); splitAtDash(calc, Estimators); } - if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) { + if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) { if (calc != "") { Estimators.clear(); splitAtDash(calc, Estimators); @@ -239,6 +280,8 @@ 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; } @@ -253,17 +296,38 @@ 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; } + + 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::setProcessors(string p) { processors = p; } + /*******************************************************/ @@ -272,6 +336,8 @@ GlobalData::GlobalData() { //option definitions should go here... helpRequest = ""; clear(); + gListVector == NULL; + gSparseMatrix == NULL; } /*******************************************************/ @@ -287,8 +353,11 @@ void GlobalData::clear() { groupfile = ""; orderfile = ""; fastafile = ""; + nexusfile = ""; + clustalfile = ""; treefile = ""; sharedfile = ""; + templatefile = ""; cutoff = "10.00"; format = ""; precision = "100"; @@ -305,7 +374,21 @@ void GlobalData::clear() { step = "0.01"; form = "integral"; sorted = "T"; //F means don't sort, T means sort. + vertical = ""; + trump = ""; + filter = ""; + soft = ""; scale = "log10"; + ends = "T"; //yes + processors = "1"; + size = "1000"; + search = "suffix"; + ksize = "7"; + align = "blast"; + match = "1.0"; + mismatch = "-1.0"; + gapopen = "-5.0"; + gapextend = "-2.0"; } //*******************************************************/ @@ -325,6 +408,16 @@ void GlobalData::reset() { abund = "10"; step = "0.01"; form = "integral"; + ends = "T"; + processors = "1"; + size = "1000"; + search = "suffix"; + ksize = "7"; + align = "blast"; + match = "1.0"; + mismatch = "-1.0"; + gapopen = "-5.0"; + gapextend = "-2.0"; } /*******************************************************/