added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index fd818acb44c4c5280c6a54971d3d39413307861d..74d63688333be27374c36fecc8147bc4419ee8bc 100644 (file)
--- 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