X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=158069e7ae596e3eebd6a9d2da5834ec3529dcdc;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=0504e6635802c3f6e3e186e4568675906774b3ff;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0504e66..158069e 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";
@@ -915,8 +919,8 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
         
 		for(int i=0;i<processIDS.size();i++){
-			appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
-			appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+			m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
+			m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
 				nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
 			}else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
@@ -930,7 +934,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 			rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
 			
 			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-				appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+				m->appendFiles(nonBlankAccnosFiles[h], accnos);
 				m->mothurRemove(nonBlankAccnosFiles[h]);
 			}
 		}else { //recreate the accnosfile if needed
@@ -947,30 +951,6 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		exit(1);
 	}
 }
-/**************************************************************************************************/
-
-void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
-	try{
-		
-		ofstream output;
-		ifstream input;
-		m->openOutputFileAppend(filename, output);
-		m->openInputFile(temp, input);
-		
-		while(char c = input.get()){
-			if(input.eof())		{	break;			}
-			else				{	output << c;	}
-		}
-		
-		input.close();
-		output.close();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
-		exit(1);
-	}
-}
-
 //**********************************************************************************************************************
 
 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){