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

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index a691a405ddb31fb022ebf37c98b40deb8e54c6a5..e51f7f22acda22ac6a852dfebad627275c58d073 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -10,6 +10,56 @@
 #include "sffinfocommand.h"
 #include "endiannessmacros.h"
 
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getValidParameters(){   
+       try {
+               string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SffInfoCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SffInfoCommand::SffInfoCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["flow"] = tempOutNames;
+               outputTypes["sfftxt"] = tempOutNames;
+               outputTypes["qual"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getRequiredParameters(){        
+       try {
+               string Array[] =  {"sff"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SffInfoCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getRequiredFiles(){     
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SffInfoCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 SffInfoCommand::SffInfoCommand(string option)  {
@@ -34,6 +84,13 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["flow"] = tempOutNames;
+                       outputTypes["sfftxt"] = tempOutNames;
+                       outputTypes["qual"] = tempOutNames;
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
@@ -65,6 +122,17 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                                        filenames[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(filenames[i]);
+                                                       m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       filenames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
@@ -105,6 +173,15 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                                        accnosFileNames[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(accnosFileNames[i]);
+                                                       m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       accnosFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
@@ -227,10 +304,10 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
                        outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
                }
                
-               if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }
-               if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); }
-               if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName);  }
-               if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  }
+               if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
+               if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
+               if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
+               if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outputTypes["flow"].push_back(outFlowFileName);  }
                
                ifstream in;
                in.open(input.c_str(), ios::binary);