-#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>
/*******************************************************/
exit(1);
}
}
-
/*******************************************************/
/******************************************************/
cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
}
/*******************************************************/
allLines = 1;
commandName = commandString; //save command name to be used by other classes
- //clears out data from previous read and sets format
- setReadFormat(commandName);
+ //set all non filename paramters to default values
+ reset();
+
+ //clears out data from previous read
+ if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) {
+ clear();
+ gGroupmap = NULL;
+ }
//saves help request
if (commandName =="help") {
splitAtComma(value, optionText);
splitAtEquals(key, value);
- if (key == "distfile" ) { distfile = value; inputFileName = value; fileroot = value;}
- if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value;}
- if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value;}
- if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value;}
- if (key == "namefile" ) { namefile = value; }
- if (key == "orderfile" ) { orderfile = value; }
- if (key == "groupfile" ) { 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 == "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 == "randomtree" ) { randomtree = value; }
+ if (key == "groups" ) { groups = value; }
+ if (key == "calc") { calc = 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 == "line") {//stores lines to be used in a set
lines.clear();
line = value;
+ label = "";
splitAtDash(value, lines);
allLines = 0;
}
- if (key == "label") {//stores lines to be used in a vector
+ 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 == "distfile" ) { distfile = value; inputFileName = value; fileroot = value; }
- if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; }
- if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; }
- if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; }
- if (key == "namefile" ) { namefile = value; }
- if (key == "orderfile" ) { orderfile = value; }
- if (key == "groupfile" ) { 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 == "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 == "randomtree" ) { randomtree = value; }
+ if (key == "groups" ) { groups = value; }
+ if (key == "calc") { calc = 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
lines.clear();
line = value;
+ label = "";
splitAtDash(value, lines);
allLines = 0;
}
if (key == "label") {//stores lines to be used in a vector
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);
+ }
}
+ //set format for shared
+ if ((listfile != "") && (groupfile != "")) { format = "shared"; }
- //input defaults
- if (commandString == "collect.single") {
- if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
+ //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 (commandString == "rarefaction.single") {
- if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); }
+ if (commandName == "rarefaction.single") {
+ if ((calc == "default") || (calc == "")) { calc = "sobs"; }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
- if (commandString == "collect.shared") {
- if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
+ 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 (commandString == "summary.single") {
- if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
+ if (commandName == "summary.single") {
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
- if (commandString == "summary.shared") {
- if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
+ 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 (commandString == "rarefaction.shared") {
- if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
+ 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";
cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
-}
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setReadFormat(string command){
- try {
- if (command == "read.phylip") {
- clear();
- format = "phylip";
- }else if (command == "read.column") {
- clear();
- format = "column";
- }else if (command == "read.list") {
- clear();
- format = "list";
- }else if (command == "read.rabund") {
- clear();
- format = "rabund";
- }else if (command == "read.sabund") {
- clear();
- format = "sabund";
- }else if (command == "read.shared") {
- clear();
- format = "shared";
- }else if (command == "parselist") { format = "list"; }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
/*******************************************************/
/******************************************************/
// These functions give you the option parameters of the commands
-string GlobalData::getDistFile() { return distfile; }
+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::getIters() { return iters; }
string GlobalData::getJumble() { return jumble; }
string GlobalData::getFreq() { return freq; }
+string GlobalData::getRandomTree() { return randomtree; }
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::setDistFile(string file) { distfile = file; inputFileName = file;}
-void GlobalData::setNameFile(string file) { namefile = file; }
-void GlobalData::setFormat(string Format) { format = Format; }
-
+void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file;}
+void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file;}
+void GlobalData::setNameFile(string file) { namefile = file; }
+void GlobalData::setFormat(string Format) { format = Format; }
+void GlobalData::setRandomTree(string Random) { randomtree = Random; }
+void GlobalData::setCalc(string Calc) { calc = Calc; }
/*******************************************************/
/******************************************************/
-
GlobalData::GlobalData() {
//option definitions should go here...
helpRequest = "";
/*******************************************************/
/******************************************************/
-
void GlobalData::clear() {
//option definitions should go here...
- distfile = "";
- listfile = "";///users/westcott/desktop/s.list
+ phylipfile = "";
+ columnfile = "";
+ listfile = "";
rabundfile = "";
sabundfile = "";
namefile = "";
- groupfile = ""; ///users/westcott/desktop/s.names
+ groupfile = "";
orderfile = "";
+ fastafile = "";
+ treefile = "";
+ sharedfile = "";
cutoff = "10.00";
format = "";
precision = "100";
iters = "1000";
line = "";
label = "";
- jumble = "0";
+ groups = "";
+ jumble = "1"; //0 means don't jumble, 1 means jumble.
+ randomtree = "0"; //0 means user will enter some user trees, 1 means they just want the random tree distribution.
freq = "100";
method = "furthest";
fileroot = "";
- single = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
- rarefaction = "rarefaction";
- shared = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
- sharedsummary = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
- summary = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
- sharedrarefaction = "sharedobserved";
+ calc = "";
}
/*******************************************************/
/******************************************************/
+void GlobalData::reset() {
+ cutoff = "10.00";
+ precision = "100";
+ iters = "1000";
+ line = "";
+ label = "";
+ groups = "";
+ jumble = "1"; //0 means don't jumble, 1 means jumble.
+ randomtree = "0"; //0 means user will enter some user trees, 1 means they just want the random tree distribution.
+ freq = "100";
+ method = "furthest";
+ calc = "";
+}
+/*******************************************************/
+/******************************************************/
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) {
- 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.insert(individual);
- }
- }
- //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";
- 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 line options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<int>& container) {
- try {
- string individual;
- int lineNum;
-
- 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);
- }
- }
- //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);
- }
-
-}
-/*******************************************************/
-
-/******************************************************/
-
-//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";
- 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";
- 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);
- }
-
-}
-/*******************************************************/
-
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projects / mothur.git / blobdiff