X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyotucommand.cpp;h=f4a551cf59ffc95c587f47ea111081e0cfb6a727;hp=d0ddc691236e59cdd0fcb6a2578249375fd8ad0e;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=7aa301dfa67cfcb5b00c6b4e38a7ad56eb8337db

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d0ddc69..f4a551c 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::execute(){
 		if (namefile != "")     {	m->readNames(namefile, nameMap, true);	}
         if (groupfile != "")    {   groupMap = new GroupMap(groupfile);  groupMap->readMap();  groups = groupMap->getNamesOfGroups(); }
         else { groupMap = NULL;  }
-        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true, false);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
         else {  ct = NULL;    }
         
 		//read taxonomy file and save in map for easy access in building bin trees
@@ -544,11 +544,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 		
 		PhyloSummary* taxaSum;
         if (countfile != "") {
-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct);  }
-            else {  taxaSum = new PhyloSummary(ct); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct,false);  }
+            else {  taxaSum = new PhyloSummary(ct,false); }
 		}else {
-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap);  }
-            else {  taxaSum = new PhyloSummary(groupMap); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap,false);  }
+            else {  taxaSum = new PhyloSummary(groupMap,false); }
         }
         
         vector<ofstream*> outSums;
@@ -574,11 +574,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                 
                 PhyloSummary* taxaSumt;
                 if (countfile != "") {
-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct);  }
-                    else {  taxaSumt = new PhyloSummary(ct); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct, false);  }
+                    else {  taxaSumt = new PhyloSummary(ct, false); }
                 }else {
-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap);  }
-                    else {  taxaSumt = new PhyloSummary(groupMap); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap,false);  }
+                    else {  taxaSumt = new PhyloSummary(groupMap,false); }
                 }
                 taxaSums.push_back(taxaSumt);
             }
@@ -586,6 +586,7 @@ int ClassifyOtuCommand::process(ListVector* processList) {
         
 		//for each bin in the list vector
         string snumBins = toString(processList->getNumBins());
+        vector<string> binLabels = processList->getLabels();
 		for (int i = 0; i < processList->getNumBins(); i++) {
 			
 			if (m->control_pressed) { break; }
@@ -598,17 +599,8 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 			names = findConsensusTaxonomy(thisNames, size, conTax);
 		
 			if (m->control_pressed) { break; }
-			
-			//output to new names file
-            string binLabel = "Otu";
-            string sbinNumber = toString(i+1);
-            if (sbinNumber.length() < snumBins.length()) { 
-                int diff = snumBins.length() - sbinNumber.length();
-                for (int h = 0; h < diff; h++) { binLabel += "0"; }
-            }
-            binLabel += sbinNumber;
 
-			out << binLabel << '\t' << size << '\t' << conTax << endl;
+			out << binLabels[i] << '\t' << size << '\t' << conTax << endl;
 			
 			string noConfidenceConTax = conTax;
 			m->removeConfidences(noConfidenceConTax);
@@ -616,9 +608,10 @@ int ClassifyOtuCommand::process(ListVector* processList) {
 			//add this bins taxonomy to summary
 			if (basis == "sequence") {
 				for(int j = 0; j < names.size(); j++) {  
-                    int numReps = 1;
-                    if (countfile != "") {  numReps = ct->getNumSeqs(names[j]); }
-                    for(int k = 0; k < numReps; k++) {  taxaSum->addSeqToTree(names[j], noConfidenceConTax);  }
+                    //int numReps = 1;
+                    //if (countfile != "") {  numReps = ct->getNumSeqs(names[j]); }
+                    //for(int k = 0; k < numReps; k++) {  taxaSum->addSeqToTree(names[j], noConfidenceConTax);  }
+                    taxaSum->addSeqToTree(names[j], noConfidenceConTax);
                 }
 			}else { //otu
                 map<string, bool> containsGroup; 
@@ -682,16 +675,8 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                     
                     if (m->control_pressed) { break; }
                     
-                    //output to new names file
-                    string binLabel = "Otu";
-                    string sbinNumber = toString(i+1);
-                    if (sbinNumber.length() < snumBins.length()) { 
-                        int diff = snumBins.length() - sbinNumber.length();
-                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
-                    }
-                    binLabel += sbinNumber;
                     
-                    (*outs[groupIndex[itParsed->first]]) << binLabel << '\t' << size << '\t' << conTax << endl;
+                    (*outs[groupIndex[itParsed->first]]) << binLabels[i] << '\t' << size << '\t' << conTax << endl;
                     
                     string noConfidenceConTax = conTax;
                     m->removeConfidences(noConfidenceConTax);