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 a041b38aadac3c3cc28bf7313eeb4e8bde6e4535..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
@@ -261,11 +261,15 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                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")) {
@@ -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 + ",";
@@ -1100,20 +1101,19 @@ 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);
+            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 +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 = "";
@@ -1253,13 +1254,14 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile);
+            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 {