X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=corraxescommand.cpp;h=72fa03b75edc196aafcaaa4b6ade6f95d1106d48;hp=c4454a5181c719302011e6e98410408826183735;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a9dbc22713bfc056a797361dd757b1a5c98e1c01

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index c4454a5..72fa03b 100644
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -14,16 +14,16 @@
 //**********************************************************************************************************************
 vector<string> CorrAxesCommand::setParameters(){	
 	try {
-		CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes);
-		CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
-		CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
-		CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
-		CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","corraxes",false,true,true); parameters.push_back(paxes);
+		CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(pshared);
+		CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(prelabund);
+		CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false); parameters.push_back(pmetadata);
+		CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pnumaxes);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -56,25 +56,21 @@ string CorrAxesCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string CorrAxesCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string CorrAxesCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "corraxes") {  outputFileName =  "corr.axes"; }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CorrAxesCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "corraxes") {  pattern = "[filename],[tag],corr.axes"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CorrAxesCommand", "getOutputPattern");
+        exit(1);
+    }
 }
+
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(){	
 	try {
@@ -285,8 +281,10 @@ int CorrAxesCommand::execute(){
 		/*************************************************************************************/
 		// calc the r values																//
 		/************************************************************************************/
-		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + "." + getOutputFileNameTag("corraxes");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[tag]"] = method;
+		string outputFileName = getOutputFileName("corraxes", variables);
 		outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);	
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
@@ -341,7 +339,7 @@ int CorrAxesCommand::calcPearson(map<string, vector<float> >& axes, ofstream& ou
 	   //for each otu
 	   for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
 		   
-		   if (metadatafile == "") {  out << m->currentBinLabels[i];	}
+		   if (metadatafile == "") {  out << m->currentSharedBinLabels[i];	}
 		   else {  out << metadataLabels[i];		}
 		   		   
 		   //find the averages this otu - Y
@@ -476,7 +474,7 @@ int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& o
 		//for each otu
 		for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
 			
-			if (metadatafile == "") {  out << m->currentBinLabels[i];	}
+			if (metadatafile == "") {  out << m->currentSharedBinLabels[i];	}
 			else {  out << metadataLabels[i];		}
 			
 			//find the ranks of this otu - Y
@@ -629,7 +627,7 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
 		//for each otu
 		for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
 		
-			if (metadatafile == "") {  out << m->currentBinLabels[i];	}
+			if (metadatafile == "") {  out << m->currentSharedBinLabels[i];	}
 			else {  out << metadataLabels[i];		}
 			
 			//find the ranks of this otu - Y
@@ -836,7 +834,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber; 
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);
 			}
@@ -845,7 +843,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
 		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 		
 		thislookup = newLookup;
-		m->currentBinLabels = newBinLabels;
+		m->currentSharedBinLabels = newBinLabels;
 		
 		return 0;