#include "globaldata.hpp"
#include "sparsematrix.hpp"
+#include "tree.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
allLines = 1;
commandName = commandString; //save command name to be used by other classes
- //clears out data from previous read and sets format
- setReadFormat(commandName);
+ //clears out data from previous read
+ if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
+ clear();
+ }
//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 == "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
//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 == "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
}
}
+ //set format for shared
+ if ((listfile != "") && (groupfile != "")) { format = "shared"; }
//input defaults
- if (commandString == "collect.single") {
- if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
+ if (commandName == "collect.single") {
+ if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
}
- if (commandString == "rarefaction.single") {
+ if (commandName == "rarefaction.single") {
if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); }
}
- if (commandString == "collect.shared") {
+ if (commandName == "collect.shared") {
if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
}
- if (commandString == "summary.single") {
+ if (commandName == "summary.single") {
if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
}
- if (commandString == "summary.shared") {
+ if (commandName == "summary.shared") {
if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
}
- if (commandString == "rarefaction.shared") {
+ if (commandName == "rarefaction.shared") {
if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
}
+
+ //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) {
}
/*******************************************************/
-/******************************************************/
-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::getFastaFile() { return fastafile; }
string GlobalData::getCutOff() { return cutoff; }
string GlobalData::getFormat() { return format; }
string GlobalData::getPrecision() { return precision; }
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::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; }
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 = "";
cutoff = "10.00";
format = "";
precision = "100";
iters = "1000";
line = "";
label = "";
- jumble = "0";
+ jumble = "1";
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";
+ 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";
}
projects / mothur.git / blobdiff