sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 940672c1bef7f6ab2004a9b374011cd1f8420e85..8687194778d2da8360b3367c3c5ec2bb00108431 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -13,9 +13,9 @@
 //**********************************************************************************************************************
 vector<string> DegapSeqsCommand::setParameters(){      
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               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", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+               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);          }
@@ -46,6 +46,21 @@ string DegapSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string DegapSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],ng.fasta"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "DegapSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -156,7 +171,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
-                                               }
+                                               }else { m->setFastaFile(fastaFileNames[i]); }
                                        }
                                }
                                
@@ -193,11 +208,13 @@ int DegapSeqsCommand::execute(){
                        ofstream outFASTA;
                        string tempOutputDir = outputDir;
                        if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
-                       string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+            map<string, string> variables; 
+            variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+                       string degapFile = getOutputFileName("fasta", variables);
                        m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){
-                               if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } return 0; }
+                               if (m->control_pressed) {   outputTypes.clear(); inFASTA.close();  outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } return 0; }
                                 
                                Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
@@ -210,7 +227,7 @@ int DegapSeqsCommand::execute(){
                        
                        outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
                        
-                       if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        } return 0; }
                }
                
                //set fasta file as new current fastafile
@@ -221,7 +238,7 @@ int DegapSeqsCommand::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();    }       
                m->mothurOutEndLine();