X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=b6dc24fe5751867c6b79f71fb50e3b7b74ad75a6;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=0504e6635802c3f6e3e186e4568675906774b3ff;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0504e66..b6dc24f 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -465,9 +465,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                     }
                 }
             }
-			
-		}
-		
+        }
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
@@ -486,7 +484,7 @@ ClassifySeqsCommand::~ClassifySeqsCommand(){
 int ClassifySeqsCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		
+        
 		if(method == "bayesian"){	classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);		}
 		else if(method == "knn"){	classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());				}
 		else {
@@ -504,11 +502,17 @@ int ClassifySeqsCommand::execute(){
 			string baseTName = taxonomyFileName;
 			if (taxonomyFileName == "saved") {baseTName = rdb->getSavedTaxonomy();	}
 			
-			string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
-			RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
-			if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
-			RippedTaxName +=  "."; 
-		
+            //set rippedTaxName to 
+			string RippedTaxName = "";
+            bool foundDot = false;
+            for (int i = baseTName.length()-1; i >= 0; i--) {
+                cout << baseTName[i] << endl;
+                if (foundDot && (baseTName[i] != '.')) {  RippedTaxName = baseTName[i] + RippedTaxName; }
+                else if (foundDot && (baseTName[i] == '.')) {  break; }
+                else if (!foundDot && (baseTName[i] == '.')) {  foundDot = true; }
+            }
+            if (RippedTaxName != "") { RippedTaxName +=  "."; }   
+          
 			if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
 			string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 			string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";