changes while testing

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 7311173265d55bbac59af028922de1f7f7e5d447..9d492afe950713cefd4d1fad7fcd72a6da74640c 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -14,18 +14,18 @@
 //**********************************************************************************************************************
 vector<string> ChimeraPintailCommand::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 pconservation("conservation", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pconservation);
-               CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pquantile);
-               CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
-               CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
-               CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
-               CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask);
-               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-accnos",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation);
+               CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile);
+               CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+               CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow);
+               CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
+               CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
+               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);          }
@@ -69,6 +69,22 @@ string ChimeraPintailCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraPintailCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "chimera") {  pattern = "[filename],[tag],pintail.chimeras-[filename],pintail.chimeras"; } 
+        else if (type == "accnos") {  pattern = "[filename],[tag],pintail.accnos-[filename],pintail.accnos"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ChimeraPintailCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(){        
        try {
                abort = true; calledHelp = true;
@@ -76,6 +92,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(){
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
+        
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
@@ -109,6 +126,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["chimera"] = tempOutNames;
                        outputTypes["accnos"] = tempOutNames;
+        
                
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        inputDir = validParameter.validFile(parameters, "inputdir", false);             
@@ -396,13 +414,12 @@ int ChimeraPintailCommand::execute(){
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
                        string outputFileName, accnosFileName;
-                       if (maskfile != "") {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
-                       }else {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";
-                       }
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+                       if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); }
+            outputFileName = getOutputFileName("chimera", variables);
+            accnosFileName = getOutputFileName("accnos", variables);
+                       
                        
                        if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
                        
@@ -619,10 +636,10 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
                        #endif
                        
                        //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");             }
                }
                //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();
                out2.close();
@@ -678,10 +695,10 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
                        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;