X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=f69faff477aee954801f0d04bb3bce67f785d1e5;hb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;hp=a4ccbf8f33b34b5dd8eccebf91242249cc465f28;hpb=9d241ddf4c0e2467298a523e21a3b0de46902448;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index a4ccbf8..f69faff 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -19,7 +19,7 @@ vector<string> PairwiseSeqsCommand::setParameters(){
 		CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
 		CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
 		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+		CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
 		CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
 		CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
@@ -64,7 +64,27 @@ string PairwiseSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string PairwiseSeqsCommand::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 == "phylip") {  outputFileName =  "dist"; }
+            else if (type == "column") {  outputFileName =  "dist"; }
+            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, "PairwiseSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){	
 	try {
@@ -229,6 +249,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			align = validParameter.validFile(parameters, "align", false);		if (align == "not found"){	align = "needleman";	}
 			
 			output = validParameter.validFile(parameters, "output", false);		if(output == "not found"){	output = "column"; }
+            if (output=="phylip") { output = "lt"; }
 			if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
 			
 			calc = validParameter.validFile(parameters, "calc", false);			
@@ -272,14 +293,14 @@ int PairwiseSeqsCommand::execute(){
 			string outputFile = "";
 				
 			if (output == "lt") { //does the user want lower triangle phylip formatted file 
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip." + getOutputFileNameTag("phylip");
 				m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 			}else if (output == "column") { //user wants column format
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("column");
 				outputTypes["column"].push_back(outputFile);
 				m->mothurRemove(outputFile);
 			}else { //assume square
-				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square." + getOutputFileNameTag("phylip");
 				m->mothurRemove(outputFile);
 				outputTypes["phylip"].push_back(outputFile);
 			}