working on pam

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index fe79fbbae883a409187730e1899fde8b05493193..3e954759b078ff9371f5c28b64b3de86ef3c89cc 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -76,7 +76,7 @@ string SubSampleCommand::getOutputPattern(string type) {
         else if (type == "name")        {   pattern = "[filename],subsample,[extension]";    }
         else if (type == "group")       {   pattern = "[filename],subsample,[extension]";    }
         else if (type == "count")       {   pattern = "[filename],subsample,[extension]";    }
-        else if (type == "list")        {   pattern = "[filename],subsample,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[distance],subsample,[extension]";    }
         else if (type == "taxonomy")    {   pattern = "[filename],subsample,[extension]";    }
         else if (type == "shared")      {   pattern = "[filename],[distance],subsample,[extension]";    }
         else if (type == "rabund")      {   pattern = "[filename],subsample,[extension]";    }
@@ -273,7 +273,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
             }
             
             if ((namefile != "") && (countfile != "")) {
@@ -552,7 +552,7 @@ int SubSampleCommand::getSubSampleFasta() {
                     else{
                         itGroupCounts = groupCounts.find(group);
                         if (itGroupCounts != groupCounts.end()) {
-                            if (groupCounts[group] < size) {   subset.insert(names[j]);        groupCounts[group]++; }
+                            if (itGroupCounts->second < size) {        subset.insert(names[j]);        (itGroupCounts->second)++; }
                         }
                     }                          
                 }
@@ -947,7 +947,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
        try {
                
                //save mothurOut's binLabels to restore for next label
-               vector<string> saveBinLabels = m->currentBinLabels;
+               vector<string> saveBinLabels = m->currentSharedBinLabels;
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
@@ -965,7 +965,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
                m->openOutputFile(outputFileName, out);
                outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
                
-        m->currentBinLabels = subsampledLabels;
+        m->currentSharedBinLabels = subsampledLabels;
         
                thislookup[0]->printHeaders(out);
                
@@ -977,7 +977,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
         
         
         //save mothurOut's binLabels to restore for next label
-               m->currentBinLabels = saveBinLabels;
+               m->currentSharedBinLabels = saveBinLabels;
                
                return 0;
                
@@ -993,16 +993,6 @@ int SubSampleCommand::getSubSampleList() {
         
                if (namefile != "") { m->readNames(namefile, nameMap); }
         
-               string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               map<string, string> variables; 
-        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
-        variables["[extension]"] = m->getExtension(listfile);
-               string outputFileName = getOutputFileName("list", variables);   
-               ofstream out;
-               m->openOutputFile(outputFileName, out);
-               outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
-               
                InputData* input = new InputData(listfile, "list");
                ListVector* list = input->getListVector();
                string lastLabel = list->getLabel();
@@ -1029,7 +1019,7 @@ int SubSampleCommand::getSubSampleList() {
                        //file mismatch quit
                        if (list->getNumSeqs() != groupMap.getNumSeqs()) { 
                                m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct."); 
-                               m->mothurOutEndLine(); delete list; delete input; out.close(); outGroup.close(); return 0;
+                               m->mothurOutEndLine(); delete list; delete input;  outGroup.close(); return 0;
                        }                       
                }else if (countfile != "") {
             if (ct.hasGroupInfo()) {
@@ -1193,13 +1183,13 @@ int SubSampleCommand::getSubSampleList() {
                //as long as you are not at the end of the file or done wih the lines you want
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  delete list; delete input;  out.close();  return 0;  }
+                       if (m->control_pressed) {  delete list; delete input;  return 0;  }
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                
                                m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                
-                               processList(list, out, subset);
+                               processList(list,  subset);
                                
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -1213,7 +1203,7 @@ int SubSampleCommand::getSubSampleList() {
                                list = input->getListVector(lastLabel);
                                m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                
-                               processList(list, out, subset);
+                               processList(list,  subset);
                                
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -1231,7 +1221,7 @@ int SubSampleCommand::getSubSampleList() {
                }
                
                
-               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
+               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input;  return 0;  }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -1254,12 +1244,11 @@ int SubSampleCommand::getSubSampleList() {
                        
                        m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                        
-                       processList(list, out, subset);
+                       processList(list, subset);
                        
                        delete list; list = NULL;
                }
                
-               out.close();  
                if (list != NULL) { delete list; }
                delete input;
         
@@ -1336,14 +1325,26 @@ int SubSampleCommand::getSubSampleList() {
        }
 }
 //**********************************************************************************************************************
-int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
+int SubSampleCommand::processList(ListVector*& list, set<string>& subset) {
        try {
-                               
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
+               map<string, string> variables;
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[extension]"] = m->getExtension(listfile);
+        variables["[distance]"] = list->getLabel();
+               string outputFileName = getOutputFileName("list", variables);
+               ofstream out;
+               m->openOutputFile(outputFileName, out);
+               outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+               
                int numBins = list->getNumBins();
 
                ListVector* temp = new ListVector();
                temp->setLabel(list->getLabel());
                
+        vector<string> binLabels = list->getLabels();
+        vector<string> newLabels;
                for (int i = 0; i < numBins; i++) {
                        
                        if (m->control_pressed) { break; }
@@ -1359,15 +1360,19 @@ int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>&
                        if (newNames != "") { 
                                newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
                                temp->push_back(newNames);
+                newLabels.push_back(binLabels[i]);
                        }
                }
                
+        temp->setLabels(newLabels);
                delete list;
                list = temp;
                
-               if (m->control_pressed) { return 0; }
+               if (m->control_pressed) { out.close(); return 0; }
                
+        list->printHeaders(out);
                list->print(out);
+        out.close();
                
                return 0;