sped up the remove.seqs and remove.lineage and get.seqs and get.lineage. fixed bug...

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index a191515cb601408b2c7d884b895f7e14d668d798..ce820fea0da0bfecc47db0126c9c5c70425c74e6 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> GetSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["taxonomy"] = tempOutNames;
@@ -69,10 +68,10 @@ vector<string> GetSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -188,8 +187,6 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        if (accnosfile == "not open") { abort = true; }
                        else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }       
                        
-                       accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
-                       if (accnosfile2 == "not open") { abort = true; }
                        if (accnosfile2 == "not found") { accnosfile2 = ""; }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
@@ -221,7 +218,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        else if (qualfile == "not found") {  qualfile = "";  }
                        
                        string usedDups = "true";
-                       string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
+                       string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
                        dups = m->isTrue(temp);
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
@@ -259,7 +256,7 @@ void GetSeqsCommand::help(){
 int GetSeqsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //get names you want to keep
                readAccnos();
@@ -285,6 +282,39 @@ int GetSeqsCommand::execute(){
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
+                       
+                       //set fasta file as new current fastafile
+                       string current = "";
+                       itTypes = outputTypes.find("fasta");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("name");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("group");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("list");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("taxonomy");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("qfile");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+                       }
+                       
                }
                
                return 0;               
@@ -509,15 +539,7 @@ int GetSeqsCommand::readName(){
                        if (dups) { hold = secondCol; }
                        
                        vector<string> parsedNames;
-                       //parse second column saving each name
-                       while (secondCol.find_first_of(',') != -1) { 
-                               name = secondCol.substr(0,secondCol.find_first_of(','));
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                               parsedNames.push_back(name);
-                       }
-                       
-                       //get name after last ,
-                       parsedNames.push_back(secondCol);
+                       m->splitAtComma(secondCol, parsedNames);
                        
                        vector<string> validSecond;
                        for (int i = 0; i < parsedNames.size(); i++) {