fixes while testing 1.33.0

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 55fbe0a1dceb9a2d2c16e2f6936646d3e851ee19..1b0a532cace0792297ce3162a03c7a382b66b282 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -19,26 +19,26 @@ extern "C" {
 //**********************************************************************************************************************
 vector<string> ClearcutCommand::setParameters(){       
        try {
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip);
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose);
-               CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet);
-               CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion);
-               CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed);
-               CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom);
-               CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle);
-               CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor);
-               CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen);
-               CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist);
-               CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA);
-               CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein);
-               CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes);
-               CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura);
-               CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout);
-               CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees);
-               CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
+               CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
+               CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
+               CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
+               CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
+               CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
+               CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
+               CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
+               CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
+               CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
+               CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
+               CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
+               CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
+               CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
+               CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
+               CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
+               CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -87,25 +87,20 @@ string ClearcutCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ClearcutCommand::getOutputFileNameTag(string type, string inputName=""){        
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ClearcutCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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);
-       }
+        if (type == "matrixout") {  pattern = "[filename],"; } 
+        else if (type == "tree") {  pattern = "[filename],tre"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ClearcutCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){    
@@ -264,7 +259,9 @@ int ClearcutCommand::execute() {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //prepare filename
-               string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+               string outputName = getOutputFileName("tree", variables);
                outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
                
                vector<char*> cPara;