fixes while testing 1.33.0

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index dbd19a8bfc7d5a266b131e74b18f3f2980c40aba..c64549334ded9f4d32140ad64cbe898c5c41a023 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -23,7 +23,7 @@ inline bool compareName(repStruct left, repStruct right){
 //********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareBin(repStruct left, repStruct right){
-       return (left.bin < right.bin);  
+       return (left.simpleBin < right.simpleBin);
 }
 //********************************************************************************************************************
 //sorts lowest to highest
@@ -261,11 +261,15 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { hasGroups = true; }
             }
             
-                               
+            groupfile = validParameter.validFile(parameters, "group", true);
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
+                       
             method = validParameter.validFile(parameters, "method", false);            if (method == "not found"){     method = "distance";    }
                        if ((method != "distance") && (method != "abundance")) {
                                m->mothurOut(method + " is not a valid option for the method parameter. The only options are: distance and abundance, aborting."); m->mothurOutEndLine(); abort = true;
@@ -337,11 +341,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
-                       groupfile = validParameter.validFile(parameters, "group", true);
-                       if (groupfile == "not open") { groupfile = ""; abort = true; }
-                       else if (groupfile == "not found") { groupfile = ""; }
-                       else { m->setGroupFile(groupfile); }
-                       
+                                               
                        sorted = validParameter.validFile(parameters, "sorted", false);         if (sorted == "not found"){     sorted = "";    }
                        if (sorted == "none") { sorted=""; }
                        if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
@@ -760,6 +760,8 @@ string GetOTURepCommand::findRepAbund(vector<string> names, string group) {
        try{
         vector<string> reps;
         string rep = "notFound";
+    
+        if (m->debug) { m->mothurOut("[DEBUG]: group=" + group + " names.size() = " + toString(names.size()) + " " + names[0] + "\n"); }
         
         if ((names.size() == 1)) {
             return names[0];
@@ -773,7 +775,7 @@ string GetOTURepCommand::findRepAbund(vector<string> names, string group) {
                 if (countfile != "") {  //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
                     int numRep = 0;
                     if (group != "") {  numRep = ct.getGroupCount(names[i], group);  }
-                    else { numRep = ct.getGroupCount(names[i]);  }
+                    else { numRep = ct.getNumSeqs(names[i]);  }
                     if (numRep > maxAbund) {
                         reps.clear();
                         reps.push_back(names[i]);
@@ -834,7 +836,7 @@ string GetOTURepCommand::findRep(vector<string> names, string group) {
                         if (countfile != "") {  //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
                             int numRep = 0;
                             if (group != "") {  numRep = ct.getGroupCount(names[i], group);  }
-                            else { numRep = ct.getGroupCount(names[i]);  }
+                            else { numRep = ct.getNumSeqs(names[i]);  }
                             for (int j = 1; j < numRep; j++) { //don't add yourself again
                                 seqIndex.push_back(nameToIndex[names[i]]);
                             }
@@ -979,6 +981,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                }
                
                //for each bin in the list vector
+        vector<string> binLabels = processList->getLabels();
                for (int i = 0; i < processList->size(); i++) {
                        if (m->control_pressed) { 
                                out.close();  
@@ -999,7 +1002,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                        
                        if (Groups.size() == 0) {
                                nameRep = findRep(namesInBin, "");
-                               newNamesOutput << i << '\t' << nameRep << '\t';
+                               newNamesOutput << binLabels[i] << '\t' << nameRep << '\t';
                 
                 //put rep at first position in names line
                 string outputString = nameRep + ",";
@@ -1042,7 +1045,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                                                nameRep = findRep(NamesInGroup[Groups[j]], Groups[j]);
                                                
                                                //output group rep and other members of this group
-                                               (*(filehandles[Groups[j]])) << i << '\t' << nameRep << '\t';
+                                               (*(filehandles[Groups[j]])) << binLabels[i] << '\t' << nameRep << '\t';
                                                
                         //put rep at first position in names line
                         string outputString = nameRep + ",";
@@ -1100,20 +1103,19 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
                ifstream in;
                m->openInputFile(filename, in);
                
-               int i = 0;
         string tempGroup = "";
         in >> tempGroup; m->gobble(in);
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile, true);
+            thisCt.readTable(countfile, true, false);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
     
         int thistotal = 0;
                while (!in.eof()) {
-                       string rep, binnames;
-                       in >> i >> rep >> binnames; m->gobble(in);
+                       string rep, binnames, binLabel;
+                       in >> binLabel >> rep >> binnames; m->gobble(in);
                        
                        vector<string> names;
                        m->splitAtComma(binnames, names);
@@ -1178,7 +1180,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
 
                        if (sequence != "not found") {
                                if (sorted == "") { //print them out
-                                       rep = rep + "\t" + toString(i+1);
+                                       rep = rep + "\t" + binLabel;
                                        rep = rep + "|" + toString(binsize);
                                        if (group != "") {
                                                rep = rep + "|" + group;
@@ -1186,7 +1188,9 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
                                        out << ">" << rep << endl;
                                        out << sequence << endl;
                                }else { //save them
-                                       repStruct newRep(rep, i+1, binsize, group);
+                    int simpleLabel;
+                    m->mothurConvert(m->getSimpleLabel(binLabel), simpleLabel);
+                                       repStruct newRep(rep, binLabel, simpleLabel, binsize, group);
                                        reps.push_back(newRep);
                                }
                        }else { 
@@ -1204,7 +1208,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
                        //print them
                        for (int i = 0; i < reps.size(); i++) {
                                string sequence = fasta->getSequence(reps[i].name);
-                               string outputName = reps[i].name + "\t" + toString(reps[i].bin);
+                               string outputName = reps[i].name + "\t" + reps[i].bin;
                                outputName = outputName + "|" + toString(reps[i].size);
                                if (reps[i].group != "") {
                                        outputName = outputName + "|" + reps[i].group;
@@ -1245,7 +1249,6 @@ int GetOTURepCommand::processNames(string filename, string label) {
                ifstream in;
                m->openInputFile(filename, in);
                
-               int i = 0;
                string rep, binnames;
         
         string tempGroup = "";
@@ -1253,13 +1256,14 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile, true);
+            thisCt.readTable(countfile, true, false);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
         
                while (!in.eof()) {
                        if (m->control_pressed) { break; }
-                       in >> i >> rep >> binnames; m->gobble(in);
+            string binLabel;
+                       in >> binLabel >> rep >> binnames; m->gobble(in);
             
                        if (countfile == "") { out2 << rep << '\t' << binnames << endl; }
             else {