-#include <iostream>
-#include <iomanip>
-#include <string>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-
-using namespace std;
-
#include "globaldata.hpp"
-#include "sparsematrix.hpp"
#include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
-#include <exception>
-#include <iostream>
+#include "sparsematrix.hpp"
/*******************************************************/
/******************************************************/
GlobalData* GlobalData::getInstance() {
- if( _uniqueInstance == 0 ) {
+ if( _uniqueInstance == 0) {
_uniqueInstance = new GlobalData();
}
return _uniqueInstance;
}
/*******************************************************/
-/******************************************************/
-
-ListVector* GlobalData::getListVector() { return gListVector; }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setListVector(ListVector* lv){
- try {
- if(gListVector != NULL){ delete gListVector; }
- gListVector = new ListVector(*lv);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/*******************************************************/
-
-/******************************************************/
-
-SparseMatrix* GlobalData::getSparseMatrix() { return gSparseMatrix; }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setSparseMatrix(SparseMatrix* sm){
- try{
- if(gSparseMatrix != NULL){ delete gSparseMatrix; }
- gSparseMatrix = new SparseMatrix(*sm);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/*******************************************************/
-
/******************************************************/
//This function parses through the option string of the command to remove its parameters
void GlobalData::parseGlobalData(string commandString, string optionText){
try {
- allLines = 1;
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")) {
+ 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") {
+ 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")){
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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- 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 == "single") {//stores estimators in a vector
- singleEstimators.clear(); //clears out old values
- if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
- splitAtDash(value, singleEstimators);
- }
- if (key == "rarefaction") {//stores estimators in a vector
- rareEstimators.clear(); //clears out old values
- if (value == "default") { value = "rarefraction"; }
- splitAtDash(value, rareEstimators);
- }
- if (key == "shared") {//stores estimators in a vector
- sharedEstimators.clear(); //clears out old values
- if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
- splitAtDash(value, sharedEstimators);
- }
- if (key == "summary") { //stores summaries to be used in a vector
- summaryEstimators.clear();
- if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
- splitAtDash(value, summaryEstimators);
- }
- if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
- sharedSummaryEstimators.clear();
- if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
- splitAtDash(value, sharedSummaryEstimators);
- }
- if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
- sharedRareEstimators.clear();
- if (value == "default") { value = "sharedobserved"; }
- splitAtDash(value, sharedRareEstimators);
- }
- 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 == "line") {//stores lines to be used in a vector
lines.clear();
+ labels.clear();
line = value;
- splitAtDash(value, lines);
- allLines = 0;
+ label = "";
+ 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;
- splitAtDash(value, labels);
- allLines = 0;
+ 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
+ //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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- 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 == "single") {//stores estimators in a vector
- singleEstimators.clear(); //clears out old values
- if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
- splitAtDash(value, singleEstimators);
- }
- if (key == "rarefaction") {//stores estimators in a vector
- rareEstimators.clear(); //clears out old values
- if (value == "default") { value = "rarefraction"; }
- splitAtDash(value, rareEstimators);
- }
- if (key == "shared") {//stores estimators in a vector
- sharedEstimators.clear(); //clears out old values
- if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
- splitAtDash(value, sharedEstimators);
- }
- if (key == "summary") { //stores summaries to be used in a vector
- summaryEstimators.clear();
- if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
- splitAtDash(value, summaryEstimators);
- }
- if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
- sharedSummaryEstimators.clear();
- if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
- splitAtDash(value, sharedSummaryEstimators);
- }
- if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
- sharedRareEstimators.clear();
- if (value == "default") { value = "sharedobserved"; }
- splitAtDash(value, sharedRareEstimators);
- }
+ 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
+
+ if(key == "line") {//stores lines to be used in a vector
lines.clear();
+ labels.clear();
line = value;
- splitAtDash(value, lines);
- allLines = 0;
+ label = "";
+ 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;
- splitAtDash(value, labels);
- allLines = 0;
+ 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"; }
-
- //input defaults
- if (commandName == "collect.single") {
- if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
+ 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 == "rarefaction.single") {
- if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); }
+ 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 == "collect.shared") {
- if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
+ if(commandName == "summary.single") {
+ if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
- if (commandName == "summary.single") {
- if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
+ 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 == "summary.shared") {
- if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
+ if(commandName == "rarefaction.shared") {
+ if((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
- if (commandName == "rarefaction.shared") {
- if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
+ 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 = '.';
+ }
+ }
- //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) {
cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
}
/*******************************************************/
/******************************************************/
// 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::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; }
-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::setNameFile(string file) { namefile = file; }
-void GlobalData::setFormat(string Format) { format = Format; }
+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; }
+
+
+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::setCountEnds(string e) { countends = e; }
+void GlobalData::setProcessors(string p) { processors = p; }
/*******************************************************/
/******************************************************/
-
GlobalData::GlobalData() {
//option definitions should go here...
helpRequest = "";
clear();
+ gListVector = NULL;
+ gSparseMatrix = NULL;
}
/*******************************************************/
/******************************************************/
-
void GlobalData::clear() {
//option definitions should go here...
phylipfile = "";
orderfile = "";
fastafile = "";
treefile = "";
+ sharedfile = "";
+ candidatefile = "";
cutoff = "10.00";
format = "";
precision = "100";
iters = "1000";
line = "";
label = "";
- jumble = "1";
+ groups = "";
+ jumble = "1"; //0 means don't jumble, 1 means jumble.
+ randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
freq = "100";
method = "furthest";
fileroot = "";
- single = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
- rarefaction = "rarefaction";
- shared = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
- sharedsummary = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
- summary = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
- sharedrarefaction = "sharedobserved";
+ abund = "10";
+ step = "0.01";
+ form = "integral";
+ sorted = "T"; //F means don't sort, T means sort.
+ vertical = "F";
+ trump = "";
+ hard = "";
+ soft = "";
+ scale = "log10";
+ countends = "T"; //yes
+ processors = "1";
+ size = "0";
+ search = "kmer";
+ ksize = "8";
+ align = "needleman";
+ match = "1.0";
+ mismatch = "-1.0";
+ gapopen = "-1.0";
+ gapextend = "-2.0";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+ flip = "0";
+ oligoFile = "";
}
-/*******************************************************/
+
+//*******************************************************/
/******************************************************/
+void GlobalData::reset() {
+ label = "";
+ line = "";
+ cutoff = "10.00";
+ precision = "100";
+ iters = "1000";
+ groups = "";
+ jumble = "1"; //0 means don't jumble, 1 means jumble.
+ sorted = "T"; //F means don't sort, T means sort.
+ randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
+ freq = "100";
+ method = "furthest";
+ calc = "";
+ abund = "10";
+ step = "0.01";
+ form = "integral";
+ countends = "T";
+ processors = "1";
+ size = "0";
+ search = "kmer";
+ ksize = "8";
+ align = "needleman";
+ match = "1.0";
+ mismatch = "-1.0";
+ gapopen = "-1.0";
+ gapextend = "-2.0";
+ vertical = "";
+ trump = "";
+ hard = "";
+ soft = "";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+ flip = "0";
+ oligoFile = "";
+
+}
+/*******************************************************/
+/******************************************************/
GlobalData::~GlobalData() {
_uniqueInstance = 0;
if(gListVector != NULL) { delete gListVector; }
}
/*******************************************************/
-/******************************************************/
-//This function parses the estimator options and puts them in a vector
-void GlobalData::splitAtDash(string& estim, vector<string>& container) {
- try {
- string individual;
-
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- container.push_back(individual);
- }
- }
- //get last one
- container.push_back(estim);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
/*******************************************************/
-
-/******************************************************/
-//This function parses the label options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<string>& container) {
+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 individual;
+ string filename = treefile;
+ ifstream filehandle;
+ openInputFile(filename, filehandle);
+ int c, comment;
+ comment = 0;
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- container.insert(individual);
+ //ifyou are not a nexus file
+ if((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != ';') {
+ while ((c = filehandle.peek()) != ';') {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ readTreeString(filehandle);
+ }
+ //ifyou are a nexus file
+ }else if((c = filehandle.peek()) == '#') {
+ string holder = "";
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+
+ //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)) {;}
+
+ 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")) {
+
+ string number, name, h;
+ h = ""; // so it enters the loop the first time
+ while((h != ";") && (number != ";")) {
+ filehandle >> number;
+ filehandle >> name;
+
+ //c = , until done with translation then c = ;
+ h = name.substr(name.length()-1, name.length());
+ 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
}
}
- //get last one
- container.insert(estim);
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
- }
-
+ }
}
/*******************************************************/
-/******************************************************/
-//This function parses the line options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<int>& container) {
+/*******************************************************/
+void GlobalData::readTreeString(ifstream& filehandle) {
try {
- string individual;
- int lineNum;
+ int c;
+ string name; //k
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- convert(individual, lineNum); //convert the string to int
- container.insert(lineNum);
+ while((c = filehandle.peek()) != ';') {
+ //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 << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ // k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
+ Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
+ }
+
+ 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;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
}
- }
- //get last one
- convert(estim, lineNum); //convert the string to int
- container.insert(lineNum);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
+ c = filehandle.get();
+ if(c == ';') { break; }
+ // k = c;
+//cout << k << endl;
-}
-/*******************************************************/
-
-/******************************************************/
-
-//This function splits up the various option parameters
-void GlobalData::splitAtComma(string& prefix, string& suffix){
- try {
- prefix = suffix.substr(0,suffix.find_first_of(','));
- if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
- suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
- }
+ }
+}
-}
/*******************************************************/
-/******************************************************/
-//This function separates the key value from the option value i.e. distfile = "96_..."
-void GlobalData::splitAtEquals(string& key, string& value){
- try {
- if(value.find_first_of('=') != -1){
- key = value.substr(0,value.find_first_of('='));
- if ((value.find_first_of('=')+1) <= value.length()) {
- value = value.substr(value.find_first_of('=')+1, value.length());
- }
- }else{
- key = value;
- value = 1;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
/*******************************************************/
-/******************************************************/
+
projects / mothur.git / blobdiff