X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getoturepcommand.cpp;h=c64549334ded9f4d32140ad64cbe898c5c41a023;hp=d476cc3499844c88014bcef9e1a005459fab3dda;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=875ab4b2eec77b920e9fa0042f9a2aae2faff2b0

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index d476cc3..c645493 100644
--- 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
@@ -261,7 +261,7 @@ 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; }
             }
             
@@ -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 {