created mothurOut class to handle logfiles

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 70b1b4ae8a0c931ff3f84a56d4dd68fa1edd537a..1b5c7cf1416f9a8d4fe68ac3a1c6d7e751eb7d18 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -11,7 +11,7 @@
 
 //***************************************************************************************************************
 
-TrimSeqsCommand::TrimSeqsCommand(string option){
+TrimSeqsCommand::TrimSeqsCommand(string option)  {
        try {
                
                abort = false;
@@ -70,7 +70,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                        
                        //check for required parameters
                        fastaFile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
+                       if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.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 
@@ -121,22 +121,22 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                        allFiles = isTrue(temp);
                        
                        if(allFiles && oligoFile == ""){
-                               mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); mothurOutEndLine();
+                               m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
                        }
                        if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
-                               mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
+                               m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
                                qAverage=0;
                                qThreshold=0;
                        }
                        if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){               
-                               mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
+                               m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
                                abort = true;
                        }
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+               m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
                exit(1);
        }
 }
@@ -144,30 +144,30 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 
 void TrimSeqsCommand::help(){
        try {
-               mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
-               mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, qtrim and allfiles.\n");
-               mothurOut("The fasta parameter is required.\n");
-               mothurOut("The flip parameter .... The default is 0.\n");
-               mothurOut("The oligos parameter .... The default is "".\n");
-               mothurOut("The maxambig parameter .... The default is -1.\n");
-               mothurOut("The maxhomop parameter .... The default is 0.\n");
-               mothurOut("The minlength parameter .... The default is 0.\n");
-               mothurOut("The maxlength parameter .... The default is 0.\n");
-               mothurOut("The qfile parameter .....\n");
-               mothurOut("The qthreshold parameter .... The default is 0.\n");
-               mothurOut("The qaverage parameter .... The default is 0.\n");
-               mothurOut("The allfiles parameter .... The default is F.\n");
-               mothurOut("The qtrim parameter .... The default is F.\n");
-               mothurOut("The trim.seqs command should be in the following format: \n");
-               mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
-               mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");       
-               mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
-               mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
+               m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
+               m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, qtrim and allfiles.\n");
+               m->mothurOut("The fasta parameter is required.\n");
+               m->mothurOut("The flip parameter .... The default is 0.\n");
+               m->mothurOut("The oligos parameter .... The default is "".\n");
+               m->mothurOut("The maxambig parameter .... The default is -1.\n");
+               m->mothurOut("The maxhomop parameter .... The default is 0.\n");
+               m->mothurOut("The minlength parameter .... The default is 0.\n");
+               m->mothurOut("The maxlength parameter .... The default is 0.\n");
+               m->mothurOut("The qfile parameter .....\n");
+               m->mothurOut("The qthreshold parameter .... The default is 0.\n");
+               m->mothurOut("The qaverage parameter .... The default is 0.\n");
+               m->mothurOut("The allfiles parameter .... The default is F.\n");
+               m->mothurOut("The qtrim parameter .... The default is F.\n");
+               m->mothurOut("The trim.seqs command should be in the following format: \n");
+               m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
+               m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");    
+               m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
+               m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "help");
+               m->errorOut(e, "TrimSeqsCommand", "help");
                exit(1);
        }
 }
@@ -184,6 +184,8 @@ int TrimSeqsCommand::execute(){
        
                if (abort == true) { return 0; }
                
+               vector<string> outputNames;
+               
                numFPrimers = 0;  //this needs to be initialized
                numRPrimers = 0;
                
@@ -193,18 +195,21 @@ int TrimSeqsCommand::execute(){
                ofstream outFASTA;
                string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
                openOutputFile(trimSeqFile, outFASTA);
+               outputNames.push_back(trimSeqFile);
                
                ofstream outGroups;
                vector<ofstream*> fastaFileNames;
                if(oligoFile != ""){
                        string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups"; 
                        openOutputFile(groupFile, outGroups);
+                       outputNames.push_back(groupFile);
                        getOligos(fastaFileNames);
                }
                
                ofstream scrapFASTA;
                string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
                openOutputFile(scrapSeqFile, scrapFASTA);
+               outputNames.push_back(scrapSeqFile);
                
                ifstream qFile;
                if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
@@ -293,6 +298,7 @@ int TrimSeqsCommand::execute(){
                        openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
                        ofstream outGroups;
                        openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
+                       outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
                        
                        while(!inFASTA.eof()){
                                if(inFASTA.get() == '>'){
@@ -304,11 +310,16 @@ int TrimSeqsCommand::execute(){
                        outGroups.close();
                        inFASTA.close();
                }
+               
+               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();
                        
                return 0;               
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "execute");
+               m->errorOut(e, "TrimSeqsCommand", "execute");
                exit(1);
        }
 }
@@ -366,7 +377,7 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
                
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "getOligos");
+               m->errorOut(e, "TrimSeqsCommand", "getOligos");
                exit(1);
        }
 
@@ -397,7 +408,7 @@ bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
                
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "stripBarcode");
+               m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
                exit(1);
        }
 
@@ -429,7 +440,7 @@ bool TrimSeqsCommand::stripForward(Sequence& seq){
                
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "stripForward");
+               m->errorOut(e, "TrimSeqsCommand", "stripForward");
                exit(1);
        }
 }
@@ -459,7 +470,7 @@ bool TrimSeqsCommand::stripReverse(Sequence& seq){
                
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "stripReverse");
+               m->errorOut(e, "TrimSeqsCommand", "stripReverse");
                exit(1);
        }
 }
@@ -480,7 +491,7 @@ bool TrimSeqsCommand::cullLength(Sequence& seq){
        
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "cullLength");
+               m->errorOut(e, "TrimSeqsCommand", "cullLength");
                exit(1);
        }
        
@@ -499,7 +510,7 @@ bool TrimSeqsCommand::cullHomoP(Sequence& seq){
                return success;
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "cullHomoP");
+               m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
                exit(1);
        }
        
@@ -518,7 +529,7 @@ bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
                return success;
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "cullAmbigs");
+               m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
                exit(1);
        }
        
@@ -557,7 +568,7 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
                return success;
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+               m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
                exit(1);
        }
 
@@ -572,7 +583,7 @@ bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
                string name;
                
                qFile >> name;
-               if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine();       }  } 
+               if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  } 
                while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
                
                int score;
@@ -595,7 +606,7 @@ bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+               m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
                exit(1);
        }
 }
@@ -610,7 +621,7 @@ bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
                string name;
                
                qFile >> name;
-               if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine();       } }
+               if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
                
                while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
                
@@ -629,7 +640,7 @@ bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
                return success;
        }
        catch(exception& e) {
-               errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+               m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
                exit(1);
        }
 }