+
+/*
#include "globaldata.hpp"
-#include "sparsematrix.hpp"
-#include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
/*******************************************************/
-/******************************************************/
+/******************************************************
GlobalData* GlobalData::getInstance() {
- if( _uniqueInstance == 0 ) {
+ if( _uniqueInstance == 0) {
_uniqueInstance = new GlobalData();
}
return _uniqueInstance;
}
/*******************************************************/
-/******************************************************/
-//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;
- gTree.clear();
- labels.clear(); lines.clear(); groups.clear();
- allLines = 1;
- }
-
- //saves help request
- if (commandName =="help") {
- helpRequest = optionText;
- }
-
- 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 == "line") {//stores lines to be used in a set
- lines.clear();
- line = value;
- label = "";
- splitAtDash(value, lines);
- allLines = 0;
- }
- if (key == "label") {//stores labels to be used in a set
- labels.clear();
- label = value;
- line = "";
- splitAtDash(value, labels);
- allLines = 0;
- }
-
- if (key == "groups") {//stores groups to be used in a vector
- Groups.clear();
- groups = value;
- splitAtDash(value, Groups);
- }
-
- }
-
- //saves the last parameter
- 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 == "line") {//stores lines to be used in a vector
- lines.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();
- 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"; }
-
- //input defaults for calculators
- if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-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-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if (commandName == "summary.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if (commandName == "rarefaction.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
-
- //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"; }
- }
- }
- 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);
- }
-}
-/*******************************************************/
-
-/******************************************************/
+/******************************************************
// 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; }
-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;}
+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::getOrderGroupFile() { return ordergroup; }
+string GlobalData::getTreeFile() { return treefile; }
+string GlobalData::getSharedFile() { return sharedfile; }
+string GlobalData::getRelAbundFile() { return relAbundfile; }
+string GlobalData::getFormat() { return format; }
+
+void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
+void GlobalData::setTreeFile(string file) { treefile = 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; }
+void GlobalData::setRelAbundFile(string file) { relAbundfile = file; inputFileName = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
+void GlobalData::setOrderFile(string file) { orderfile = file; }
+void GlobalData::setOrderGroupFile(string file) { ordergroup = 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; }
+
/*******************************************************/
-/******************************************************/
+/******************************************************
GlobalData::GlobalData() {
+ m = MothurOut::getInstance();
//option definitions should go here...
- helpRequest = "";
clear();
+ gListVector = NULL;
+ gSparseMatrix = NULL;
+ ginput = NULL;
+ gorder = NULL;
+ glist = NULL;
+ gSharedList = NULL;
+ sabund = NULL;
+ rabund = NULL;
+ gGroupmap = NULL;
+ gMatrix = NULL;
+ gTreemap = NULL;
+ gSequenceDB = NULL;
+ nameMap = NULL;
+ saveNextLabel = "";
}
/*******************************************************/
-/******************************************************/
+/******************************************************
void GlobalData::clear() {
//option definitions should go here...
- phylipfile = "";
- columnfile = "";
+ phylipfile = ""; //do we need this?
+ columnfile = ""; //do we need this?
listfile = "";
rabundfile = "";
sabundfile = "";
- namefile = "";
- groupfile = "";
+ namefile = ""; //do we need this?
+ groupfile = ""; //do we need this?
orderfile = "";
- fastafile = "";
+ ordergroup = "";
+// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
- cutoff = "10.00";
- format = "";
- precision = "100";
- iters = "1000";
- line = "";
- label = "";
- 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 = "";
- abund = "10";
+ relAbundfile = "";
+ format = "";
+ saveNextLabel = "";
}
-//*******************************************************/
-/******************************************************/
-void GlobalData::reset() {
- cutoff = "10.00";
- precision = "100";
- iters = "1000";
- 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";
- calc = "";
- abund = "10";
-}
/*******************************************************/
-/******************************************************/
+/******************************************************
+void GlobalData::newRead() {
+ try{
+ //remove old file names
+ clear();
+
+ //free memory
+ if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+
+ if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+
+ if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+
+ if (ginput != NULL) { delete ginput; ginput = NULL;}
+
+ if (gorder != NULL) { delete gorder; gorder = NULL; }
+
+ if (glist != NULL) { delete glist; glist = NULL;}
+
+ if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+
+ if (sabund != NULL) { delete sabund; sabund = NULL;}
+
+ if (rabund != NULL) { delete rabund; rabund = NULL; }
+
+ if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+
+ if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+
+ if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+
+ if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
+
+
+ gTree.clear();
+ Treenames.clear();
+ labels.clear(); Groups.clear();
+ allLines = 1;
+ runParse = true;
+ names.clear();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GlobalData", "newRead");
+ exit(1);
+ }
+}
+
+//******************************************************/
+
+/*****************************************************
GlobalData::~GlobalData() {
_uniqueInstance = 0;
- if(gListVector != NULL) { delete gListVector; }
- if(gSparseMatrix != NULL) { delete gSparseMatrix; }
- if(gorder != NULL) { delete gorder; }
+ try {
+ if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+ if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+ if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+ if (ginput != NULL) { delete ginput; ginput = NULL;}
+ if (gorder != NULL) { delete gorder; gorder = NULL; }
+ if (glist != NULL) { delete glist; glist = NULL;}
+ if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+ if (sabund != NULL) { delete sabund; sabund = NULL;}
+ if (rabund != NULL) { delete rabund; rabund = NULL; }
+ if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+ if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+ if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+ if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GlobalData", "~GlobalData");
+ exit(1);
+ }
}
/*******************************************************/
+
+/*******************************************************/
+
+
projects / mothur.git / blobdiff