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[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 82cfa3683cbd0801da4a9805a567c84f67d3c427..b943aa4bf9dd962a4364af7069d24eb64c380a78 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -46,7 +46,7 @@ string CorrAxesCommand::getHelpString(){
                helpString += "The corr.axes command should be in the following format: corr.axes(axes=yourPcoaFile, shared=yourSharedFile, method=yourMethod).\n";
                helpString += "Example corr.axes(axes=genus.pool.thetayc.genus.lt.pcoa, shared=genus.pool.shared, method=kendall).\n";
                helpString += "The corr.axes command outputs a .corr.axes file.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -74,6 +74,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -139,12 +140,12 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; }
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else { inputFileName = sharedfile; }
+                       else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { abort = true; }
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else { inputFileName = relabundfile; }
+                       else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        metadatafile = validParameter.validFile(parameters, "metadata", true);
                        if (metadatafile == "not open") { abort = true; }
@@ -157,7 +158,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups); 
                        }                       
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputFileName);  }
                        
@@ -758,6 +759,8 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                }
                
                //for each bin
+               vector<string> newBinLabels;
+               string snumBins = toString(thislookup[0]->getNumBins());
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -772,12 +775,25 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                                for (int j = 0; j < thislookup.size(); j++) {
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
+                               
+                               //if there is a bin label use it otherwise make one
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber; 
+                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               
+                               newBinLabels.push_back(binLabel);
                        }
                }
                
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                
                thislookup = newLookup;
+               m->currentBinLabels = newBinLabels;
                
                return 0;
                
@@ -862,14 +878,14 @@ int CorrAxesCommand::getMetadata(){
                //read the first label, because it refers to the groups
                string columnLabel;
                iss >> columnLabel; m->gobble(iss); 
-
+               
                //save names of columns you are reading
                while (!iss.eof()) {
                        iss >> columnLabel; m->gobble(iss);
                        metadataLabels.push_back(columnLabel);
                }
                int count = metadataLabels.size();
-               
+                       
                //read rest of file
                while (!in.eof()) {
                        
@@ -878,7 +894,7 @@ int CorrAxesCommand::getMetadata(){
                        string group = "";
                        in >> group; m->gobble(in);
                        groupNames.push_back(group);
-                       
+                               
                        SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
                        tempLookup->setGroup(group);
                        tempLookup->setLabel("1");
@@ -886,7 +902,6 @@ int CorrAxesCommand::getMetadata(){
                        for (int i = 0; i < count; i++) {
                                float temp = 0.0;
                                in >> temp; 
-                               
                                tempLookup->push_back(temp, group);
                        }
                        
@@ -899,12 +914,13 @@ int CorrAxesCommand::getMetadata(){
                //remove any groups the user does not want, and set globaldata->groups with only valid groups
                SharedUtil* util;
                util = new SharedUtil();
-               
-               util->setGroups(m->Groups, groupNames);
+               Groups = m->getGroups();
+               util->setGroups(Groups, groupNames);
+               m->setGroups(Groups);
                
                for (int i = 0; i < lookupFloat.size(); i++) {
                        //if this sharedrabund is not from a group the user wants then delete it.
-                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->Groups) == false) { 
+                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->getGroups()) == false) { 
                                delete lookupFloat[i]; lookupFloat[i] = NULL;
                                lookupFloat.erase(lookupFloat.begin()+i); 
                                i--;