added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 20bdcbd11cb63408c5ab3fc55af1e07122b0f9ba..4e9c3c6270b9142ba69963ab0ee2283668473a8b 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -158,7 +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);  }
                        
@@ -187,7 +187,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        }
                        string temp;
                        temp = validParameter.validFile(parameters, "numaxes", false);          if (temp == "not found"){       temp = "3";                             }
-                       convert(temp, numaxes); 
+                       m->mothurConvert(temp, numaxes); 
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        
@@ -759,6 +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; }
                        
@@ -773,12 +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;
                
@@ -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--;