added modify names parameter to set.dir

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 6a4732cf72cd4222e539beb93c6b0b45226d2a08..31a36f73c6d0339d775dd6a1a4efa8e523c0f14f 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -13,16 +13,16 @@
 //**********************************************************************************************************************
 vector<string> ChimeraCheckCommand::setParameters(){   
        try {
-               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-               CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
-               CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
-               CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+               CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
+               CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
+               CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+               CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
 
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -65,24 +65,19 @@ string ChimeraCheckCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ChimeraCheckCommand::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 == "chimera") {  outputFileName =  "chimeracheck.chimeras"; }
-            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, "ChimeraCcodeCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "chimera") {  pattern = "[filename],chimeracheck.chimeras"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){    
@@ -362,7 +357,9 @@ int ChimeraCheckCommand::execute(){
                        if (m->control_pressed) { delete chimera;       return 0;       }
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
-                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+                       string outputFileName = getOutputFileName("chimera", variables);
                        outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        
                #ifdef USE_MPI
@@ -550,11 +547,10 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
-            count++;
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");     }
                
                out.close();
                inFASTA.close();
@@ -602,10 +598,10 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                return 0;
        }