X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=6a0eb259379df8480341a5542a7456fc674aea74;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=afb215932958e273093726a3b71a398faabc4dc2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index afb2159..6a0eb25 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -86,7 +86,27 @@ string ClearcutCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string ClearcutCommand::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 == "tree") {  outputFileName =  "tre"; }
+            else if (type == "matrixout") {  outputFileName =  ""; }
+            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, "ClearcutCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){	
 	try {
@@ -108,6 +128,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -154,21 +175,21 @@ ClearcutCommand::ClearcutCommand(string option)  {
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { fastafile = ""; abort = true; }
 			else if (fastafile == "not found") { fastafile = ""; }	
-			else { inputFile = fastafile;  }
+			else { inputFile = fastafile;  m->setFastaFile(fastafile); }
 			
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }
-			else { inputFile = phylipfile;  }
+			else { inputFile = phylipfile;  m->setPhylipFile(phylipfile); }
 				
 			if ((phylipfile == "") && (fastafile == "")) {  
 				//is there are current file available for either of these?
 				//give priority to phylip, then fasta
 				phylipfile = m->getPhylipFile(); 
-				if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+				if (phylipfile != "") {  inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 
 					fastafile = m->getFastaFile(); 
-					if (fastafile != "") {  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+					if (fastafile != "") { inputFile = fastafile;  m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 					else { 
 						m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine(); 
 						abort = true;
@@ -243,7 +264,7 @@ int ClearcutCommand::execute() {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//prepare filename
-		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
 		outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
 		
 		vector<char*> cPara;