fixes while testing 1.33.0

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 0a2e9380ebd71a5deae50725d3b36c2d10b52c4e..a9b297731a346999b155c61d7cab47ff7089063c 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -14,10 +14,10 @@
 //**********************************************************************************************************************
 vector<string> ReverseSeqsCommand::setParameters(){    
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); parameters.push_back(pqfile);
+               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);          }
@@ -43,7 +43,22 @@ string ReverseSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string ReverseSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],rc,[extension]"; } 
+        else if (type == "qfile") {  pattern = "[filename],rc,[extension]"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){      
        try {
@@ -66,6 +81,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(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();
@@ -112,11 +128,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                        fastaFileName = validParameter.validFile(parameters, "fasta", true);
                        if (fastaFileName == "not open") { abort = true; }
                        else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }    
+                       else { m->setFastaFile(fastaFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if (qualFileName == "not open") { abort = true; }
                        else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }      
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        if((fastaFileName == "") && (qualFileName == "")){
                                fastaFileName = m->getFastaFile(); 
                                if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -159,11 +177,14 @@ int ReverseSeqsCommand::execute(){
                        ofstream outFASTA;
                        string tempOutputDir = outputDir;
                        if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
-                       fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
+            variables["[extension]"] = m->getExtension(fastaFileName);
+                       fastaReverseFileName = getOutputFileName("fasta", variables);
                        m->openOutputFile(fastaReverseFileName, outFASTA);
                        
                        while(!inFASTA.eof()){
-                               if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
                                 
                                Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
@@ -187,11 +208,14 @@ int ReverseSeqsCommand::execute(){
                        ofstream outQual;
                        string tempOutputDir = outputDir;
                        if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
-                       string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
-                       m->openOutputFile(qualReverseFileName, outQual);
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
+            variables["[extension]"] = m->getExtension(qualFileName);
+                       string qualReverseFileName = getOutputFileName("qfile", variables);
+            m->openOutputFile(qualReverseFileName, outQual);
 
                        while(!inQual.eof()){
-                               if (m->control_pressed) {  inQual.close();  outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+                               if (m->control_pressed) {  inQual.close();  outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
                                currQual = QualityScores(inQual);  m->gobble(inQual);
                                currQual.flipQScores(); 
                                currQual.printQScores(outQual);
@@ -201,7 +225,7 @@ int ReverseSeqsCommand::execute(){
                        outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
                }
                
-               if (m->control_pressed) {  remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+               if (m->control_pressed) {  m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
                
                //set fasta file as new current fastafile
                string current = "";
@@ -217,7 +241,7 @@ int ReverseSeqsCommand::execute(){
                
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for(int i=0;i<outputNames.size();i++){
                        m->mothurOut(outputNames[i]);
                        m->mothurOutEndLine();