X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=ea98dfb4f35d91c0968898a9ab6ef931cc137d5c;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=82cfa3683cbd0801da4a9805a567c84f67d3c427;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 82cfa36..ea98dfb 100644
--- 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; }
@@ -758,6 +759,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
 		}
 		
 		//for each bin
+		vector<string> newBinLabels;
 		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 +774,19 @@ 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" + toString(i+1);
+				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 +871,14 @@ 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 +887,7 @@ 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 +895,6 @@ int CorrAxesCommand::getMetadata(){
 			for (int i = 0; i < count; i++) {
 				float temp = 0.0;
 				in >> temp; 
-				
 				tempLookup->push_back(temp, group);
 			}