X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=4e9c3c6270b9142ba69963ab0ee2283668473a8b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=07c5707e0c195cf26596e5ef328af83994ebd031;hpb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;p=mothur.git

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 07c5707..4e9c3c6 100644
--- 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";		}
 			
@@ -760,6 +760,7 @@ 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; }
 			
@@ -776,7 +777,13 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
 				}
 				
 				//if there is a bin label use it otherwise make one
-				string binLabel = "Otu" + (i+1);
+				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);
@@ -907,12 +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--;