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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 1d70fb17d7fd7391de4a147ea73367c67f96f786..1f8dc579a986350d51d88f3be2e84cd9617f90d7 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -10,6 +10,56 @@
 #include "trimseqscommand.h"
 #include "needlemanoverlap.hpp"
 
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", 
+                                                                       "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+TrimSeqsCommand::TrimSeqsCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["qual"] = tempOutNames;
+               outputTypes["group"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
 
 TrimSeqsCommand::TrimSeqsCommand(string option)  {
@@ -39,6 +89,12 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["qual"] = tempOutNames;
+                       outputTypes["group"] = 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 = "";          }
@@ -72,7 +128,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        
                        //check for required parameters
                        fastaFile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
+                       if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
                        else if (fastaFile == "not open") { abort = true; }     
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -220,18 +276,18 @@ int TrimSeqsCommand::execute(){
                numRPrimers = 0;
                
                string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
-               outputNames.push_back(trimSeqFile);
+               outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
                string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
-               outputNames.push_back(scrapSeqFile);
+               outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
                string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
                string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
-               if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  }
+               if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
                string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
                
                vector<string> fastaFileNames;
                vector<string> qualFileNames;
                if(oligoFile != ""){
-                       outputNames.push_back(groupFile);
+                       outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
                        getOligos(fastaFileNames, qualFileNames);
                }
 
@@ -339,7 +395,7 @@ int TrimSeqsCommand::execute(){
                                ofstream outGroups;
                                string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
                                m->openOutputFile(outGroupFilename, outGroups);
-                               outputNames.push_back(outGroupFilename);
+                               outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);  
                                
                                string thisGroup = "";
                                if (i > comboStarts) {
@@ -791,8 +847,10 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                                        }
                                                }else {
                                                        outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                        if(qFileName != ""){
                                                                outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
                                                        }                                                       
                                                }
                                        }
@@ -814,11 +872,13 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        groupVector.push_back(group);
                                        
                                        if(allFiles){
+                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                if(qFileName != ""){
                                                        outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
                                                        outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
                                                }                                                       
                                        }
                                }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
@@ -835,12 +895,14 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
                                        if (groupVector[itPrime->second] != "") { //there is a group for this primer
                                                outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+                                               outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
                                                outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
                                                combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
                                                
                                                if(qFileName != ""){
                                                        outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
                                                        outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
                                                }
                                        }
                                }