added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index afb215932958e273093726a3b71a398faabc4dc2..6a0eb259379df8480341a5542a7456fc674aea74 100644 (file)
--- 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;