X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.cpp;h=f98620b2ee0bd4cc70bc10d1db908d8de40de995;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=94d5c84344f86eb4676f0e71111e898c5c28596d;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109;p=mothur.git

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 94d5c84..f98620b 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -57,7 +57,27 @@ string IndicatorCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //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 == "tree")       {   outputFileName =  "indicator.tre";   }
+            else if (type == "summary")    {   outputFileName =  "indicator.summary";   }
+            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, "IndicatorCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 IndicatorCommand::IndicatorCommand(){	
 	try {
@@ -240,7 +260,6 @@ int IndicatorCommand::execute(){
 			util.setGroups(Groups, nameGroups);
 			designMap->setNamesOfGroups(nameGroups);
 			
-			//loop through the Groups and fill Globaldata's Groups with the design file info
 			vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
 			m->setGroups(namesSeqs);
 		}
@@ -386,7 +405,7 @@ int IndicatorCommand::GetIndicatorSpecies(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
 		outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 		
 		ofstream out;
@@ -468,17 +487,17 @@ int IndicatorCommand::GetIndicatorSpecies(){
 				
 			if (m->control_pressed) { out.close(); return 0; }
 			
-			out << (j+1) << '\t' << indicatorValues[j] << '\t'; 
+			out << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t'; 
 			
 			if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; } 
 			else { out << "<" << (1/(float)iters) << endl; }
 			
 			if (pValues[j] <= 0.05) {
-				cout << "OTU" << j+1 << '\t' << indicatorValues[j]  << '\t';
+				cout << m->currentBinLabels[j] << '\t' << indicatorValues[j]  << '\t';
 				string pValueString = "<" + toString((1/(float)iters)); 
 				if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} 
 				else { cout << "<" << (1/(float)iters); }
-				m->mothurOutJustToLog("OTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+				m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
 				m->mothurOutEndLine(); 
 			}
 		}
@@ -501,7 +520,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
 		outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 		
 		ofstream out;
@@ -514,14 +533,14 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 		
 		//print headings
 		out << "TreeNode\t";
-		for (int i = 0; i < numBins; i++) { out << "OTU" << (i+1) << "_IndValue" << '\t' << "pValue" << '\t'; }
+		for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
 		out << endl;
 		
 		m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n");
 		
 		string treeOutputDir = outputDir;
 		if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
-		string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+		string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
 		
 		
 		//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
@@ -671,11 +690,11 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 				}
 				
 				if (pValues[j] <= 0.05) {
-					cout << i+1 << "\tOTU" << j+1 << '\t' << indicatorValues[j]  << '\t';
+					cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorValues[j]  << '\t';
 					string pValueString = "<" + toString((1/(float)iters)); 
 					if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} 
 					else { cout << "<" << (1/(float)iters); }
-					m->mothurOutJustToLog(toString(i) + "\tOTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+					m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
 					m->mothurOutEndLine(); 
 				}
 			}