X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=4a338419af8900f8b7ebd693225a7e9f4d193481;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=2e37e7caedc35b67609e7c27e263261abd6f88f9;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 2e37e7c..4a33841 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -66,6 +66,28 @@ string ClusterFragmentsCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ClusterFragmentsCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fragclust.fasta"; }
+            else if (type == "name") {  outputFileName =  "fragclust.names"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterFragmentsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(){	
 	try {
@@ -138,6 +160,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (fastafile == "not open") { fastafile = ""; abort = true; }	
+			else { m->setFastaFile(fastafile); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(fastafile); 	}
@@ -146,15 +169,20 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
 			// ...at some point should added some additional type checking...
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not found") { namefile =  "";  }
-			else if (namefile == "not open") { abort = true; }	
-			else {  readNameFile();  }
+			else if (namefile == "not open") { namefile = ""; abort = true; }	
+			else {  readNameFile(); m->setNameFile(namefile); }
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "diffs", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, diffs); 
+			m->mothurConvert(temp, diffs); 
 			
 			temp = validParameter.validFile(parameters, "percent", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, percent);
+			m->mothurConvert(temp, percent);
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 			
 		}
 				
@@ -224,8 +252,8 @@ int ClusterFragmentsCommand::execute(){
 		
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 		
-		string newFastaFile = fileroot + "fragclust.fasta";
-		string newNamesFile = fileroot + "names";
+		string newFastaFile = fileroot + getOutputFileNameTag("fasta");
+		string newNamesFile = fileroot + getOutputFileNameTag("name");
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -237,7 +265,7 @@ int ClusterFragmentsCommand::execute(){
 		
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); 
 		
-		if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+		if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();