working on pam

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 89668d9e7bd122577d9be167f590a96a6aedbf22..1b56433073d404e2c7f33513f7362f8306afcb42 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -258,7 +258,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 
                        namefile = validParameter.validFile(parameters, "name", false);
                        if (namefile == "not found") { namefile = "";  }
-
                        else { 
                                m->splitAtDash(namefile, namefileNames);
                                
@@ -610,7 +609,7 @@ int ClassifySeqsCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
         
-        string outputMethodTag = method + ".";
+        string outputMethodTag = method;
                if(method == "wang"){   classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);     }
                else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
         else if(method == "zap"){      
@@ -782,7 +781,7 @@ int ClassifySeqsCommand::execute(){
                        }
 #endif
                        
-                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
+                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification.  If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
                 outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
             }else { m->mothurRemove(newaccnosFile); }
 
@@ -813,7 +812,7 @@ int ClassifySeqsCommand::execute(){
                 PhyloSummary* taxaSum;
                 if (hasCount) { 
                     ct = new CountTable();
-                    ct->readTable(countfileNames[s]);
+                    ct->readTable(countfileNames[s], true, false);
                     taxaSum = new PhyloSummary(taxonomyFileName, ct);
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {
@@ -1044,6 +1043,9 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
@@ -1149,11 +1151,11 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n");              }
                        
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                        
                inFASTA.close();
                outTax.close();