added pipeline commands which involved change to command factory and command class...

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index e475727cb68dd0a28c27ffb64f699a9e633229f8..290d5dc0996a62783ab3365513f7441b1aafd717 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -10,8 +10,54 @@
 #include "degapseqscommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"fasta", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DegapSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+DegapSeqsCommand::DegapSeqsCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DegapSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
-
 DegapSeqsCommand::DegapSeqsCommand(string option)  {
        try {
                abort = false;
@@ -35,6 +81,11 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -65,6 +116,17 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
+                                       
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getOutputDir() != "") { //default path is set
+                                                       string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
@@ -137,7 +199,7 @@ int DegapSeqsCommand::execute(){
                        m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){
-                               if (m->control_pressed) {  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(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } return 0; }
                                 
                                Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
@@ -148,9 +210,9 @@ int DegapSeqsCommand::execute(){
                        inFASTA.close();
                        outFASTA.close();
                        
-                       outputNames.push_back(degapFile);
+                       outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
                        
-                       if (m->control_pressed) {  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(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); } return 0; }
                }
                
                m->mothurOutEndLine();