fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 4e244905ff6b755fd064617368506b9160770048..b6dc24fe5751867c6b79f71fb50e3b7b74ad75a6 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -465,8 +465,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                     }
                 }
             }
-                       
-               }
+        }
        }
        catch(exception& e) {
                m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
@@ -503,11 +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()); }
-                       if (RippedTaxName != "") { 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";