added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 7e71a1a836b2e6306b40d67f5cdce0d7f35dbcdc..61092372b18ae196a652d0b0f66c6b04d22d0266 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
@@ -979,6 +979,7 @@ 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 +1000,7 @@ 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 +1043,7 @@ 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 + ",";
@@ -1100,7 +1101,6 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
                ifstream in;
                m->openInputFile(filename, in);
                
-               int i = 0;
         string tempGroup = "";
         in >> tempGroup; m->gobble(in);
         
@@ -1112,8 +1112,8 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
     
         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 +1178,7 @@ 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 +1186,9 @@ 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 +1206,7 @@ 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 +1247,6 @@ int GetOTURepCommand::processNames(string filename, string label) {
                ifstream in;
                m->openInputFile(filename, in);
                
-               int i = 0;
                string rep, binnames;
         
         string tempGroup = "";
@@ -1259,7 +1260,8 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
                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 {