added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 79b8fe7c10544dafd2675a963a2229eb2e3e7046..16407d59b9819183edb70748d0b3a0ca1ff9acda 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -15,7 +15,7 @@ vector<string> DistanceCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
                CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               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);
@@ -59,6 +59,27 @@ string DistanceCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string DistanceCommand::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, "DistanceCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -189,6 +210,7 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, compress);
 
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
+            if (output == "phylip") { output = "lt";  }
                        
                        if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
                        
@@ -229,12 +251,12 @@ int DistanceCommand::execute(){
                string outputFile;
                                
                if (output == "lt") { //does the user want lower triangle phylip formatted file 
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip." + getOutputFileNameTag("phylip");
                        m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
                        
                        //output numSeqs to phylip formatted dist file
                }else if (output == "column") { //user wants column format
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
                        outputTypes["column"].push_back(outputFile);
                        
                        //so we don't accidentally overwrite
@@ -245,7 +267,7 @@ int DistanceCommand::execute(){
                        
                        m->mothurRemove(outputFile);
                }else { //assume square
-                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square." + getOutputFileNameTag("phylip");
                        m->mothurRemove(outputFile);
                        outputTypes["phylip"].push_back(outputFile);
                }