X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.cpp;h=74d63688333be27374c36fecc8147bc4419ee8bc;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=fd818acb44c4c5280c6a54971d3d39413307861d;hpb=ac663461b19ad1436a06aa63f97221d1ff105482;p=mothur.git

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index fd818ac..74d6368 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -490,17 +490,17 @@ int IndicatorCommand::GetIndicatorSpecies(){
 				
 			if (m->control_pressed) { out.close(); return 0; }
 			
-			out << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t'; 
+			out << m->currentSharedBinLabels[j] << '\t' << indicatorGroups[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 << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j]  << '\t';
+				cout << m->currentSharedBinLabels[j] << '\t' << indicatorGroups[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(m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+				m->mothurOutJustToLog(m->currentSharedBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
 				m->mothurOutEndLine(); 
 			}
 		}
@@ -538,7 +538,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 		
 		//print headings
 		out << "TreeNode\t";
-		for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndGroups" << '\t' << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
+		for (int i = 0; i < numBins; i++) { out << m->currentSharedBinLabels[i] << "_IndGroups" << '\t' << m->currentSharedBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
 		out << endl;
 		
 		m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n");
@@ -697,11 +697,11 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 				}
 				
 				if (pValues[j] <= 0.05) {
-					cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j]  << '\t';
+					cout << i+1 << '\t' << m->currentSharedBinLabels[j] << '\t' << indicatorGroups[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) + "\t" + m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+					m->mothurOutJustToLog(toString(i) + "\t" + m->currentSharedBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
 					m->mothurOutEndLine(); 
 				}
 			}
@@ -1191,7 +1191,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundFloatVecto
 						
 			//loop through and create all the processes you want
 			while (process != processors) {
-				int pid = fork();
+				pid_t pid = fork();
 				
 				if (pid > 0) {
 					processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -1201,7 +1201,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundFloatVecto
 					
 					//pass pvalues to parent
 					ofstream out;
-					string tempFile = toString(getpid()) + ".pvalues.temp";
+					string tempFile = m->mothurGetpid(process) + ".pvalues.temp";
 					m->openOutputFile(tempFile, out);
 					
 					//pass values
@@ -1369,7 +1369,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundVector*> >
             
 			//loop through and create all the processes you want
 			while (process != processors) {
-				int pid = fork();
+				pid_t pid = fork();
 				
 				if (pid > 0) {
 					processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -1379,7 +1379,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundVector*> >
 					
 					//pass pvalues to parent
 					ofstream out;
-					string tempFile = toString(getpid()) + ".pvalues.temp";
+					string tempFile = m->mothurGetpid(process) + ".pvalues.temp";
 					m->openOutputFile(tempFile, out);
 					
 					//pass values