-/******************************************************/
-//This function parses through the option string of the command to remove its parameters
-void GlobalData::parseGlobalData(string commandString, string optionText){
- try {
- commandName = commandString; //save command name to be used by other classes
-
- //set all non filename paramters to default
- reset();
-
- //clears out data from previous read
- 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();
- allLines = 1;
- }
-
- //saves help request
- if(commandName =="help") {
- helpRequest = optionText;
- }
-
- if(commandName == "libshuff") {
- iters = "10000";
- cutoff = "1.0";
- }
-
- //set default value for cutoff and phylip
- if (commandName == "dist.seqs") { cutoff = "1.0"; phylipfile = "F"; }
-
- string key, value;
- //reads in parameters and values
- if((optionText != "") && (commandName != "help")){
- while((optionText.find_first_of(',') != -1)) { //while there are parameters
- 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 == "flip" ) { flip = value; }
- if(key == "oligos" ) { oligoFile = 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; }
- else { allLines = 1; }
- }
-
- 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; }
- else { allLines = 1; }
- }
-
- if(key == "groups") {//stores groups to be used in a vector
- Groups.clear();
- groups = value;
- splitAtDash(value, Groups);
- }
-
- }
-
- //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 == "flip" ) { flip = value; }
- if(key == "oligos" ) { oligoFile = 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; }
- else { allLines = 1; }
- }
-
- 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; }
- else { allLines = 1; }
- }
-
- 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"; }
-
- //set default value for cutoff
- if (commandName == "dist.seqs") { format = "fasta"; inputFileName = fastafile; fileroot = fastafile; }
-
- //input defaults for calculators
- if(commandName == "collect.single") {
-
- 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"; }
- 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"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- 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"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- 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"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- 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 == "")) {
- calc = "jclass-thetayc";
- }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
-
- if(commandName == "filter.seqs"){
- if(trump == "" && vertical == "" && hard == "" && soft == ""){
- trump = '.';
- }
-
- }
-
- //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) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-