added output filenames and m->control_pressed stuff to seq.error command

diff --git a/mothur b/mothur
index c6482bc86f8fd40ea34c22a19fc57f0f6cb96959..8cfb18cb92ad4398f654ae4650360722d0dc3d41 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 615206b5b84c4c717ad9e17c5dcb1710091c308f..58140ab3554a0e406c041cf483e15953b453a7be 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -29,8 +29,15 @@ SeqErrorCommand::SeqErrorCommand(){
                abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
-               outputTypes["error"] = tempOutNames;
-               outputTypes["count"] = tempOutNames;
+               outputTypes["error.summary"] = tempOutNames;
+               outputTypes["error.seq"] = tempOutNames;
+               outputTypes["error.quality"] = tempOutNames;
+               outputTypes["error.qual.forward"] = tempOutNames;
+               outputTypes["error.qual.reverse"] = tempOutNames;
+               outputTypes["error.forward"] = tempOutNames;
+               outputTypes["error.reverse"] = tempOutNames;
+               outputTypes["error.count"] = tempOutNames;
+               outputTypes["error.matrix"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
@@ -91,8 +98,16 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        
                        //initialize outputTypes
                        vector<string> tempOutNames;
-                       outputTypes["error"] = tempOutNames;
-                       outputTypes["count"] = tempOutNames;
+                       outputTypes["error.summary"] = tempOutNames;
+                       outputTypes["error.seq"] = tempOutNames;
+                       outputTypes["error.quality"] = tempOutNames;
+                       outputTypes["error.qual.forward"] = tempOutNames;
+                       outputTypes["error.qual.reverse"] = tempOutNames;
+                       outputTypes["error.forward"] = tempOutNames;
+                       outputTypes["error.reverse"] = tempOutNames;
+                       outputTypes["error.count"] = tempOutNames;
+                       outputTypes["error.matrix"] = 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);              
@@ -176,15 +191,6 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
                        convert(temp, threshold);  
-                                               
-                       errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
-                       m->openOutputFile(errorSummaryFileName, errorSummaryFile);
-                       outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
-                       printErrorHeader();
-
-                       errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
-                       m->openOutputFile(errorSeqFileName, errorSeqFile);
-                       outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
                        
                        substitutionMatrix.resize(6);
                        for(int i=0;i<6;i++){   substitutionMatrix[i].assign(6,0);      }
@@ -201,9 +207,6 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 void SeqErrorCommand::help(){
        try {
                m->mothurOut("The seq.error command reads a query alignment file and a reference alignment file and creates .....\n");
-               
-               
-               
                m->mothurOut("Example seq.error(...).\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/seq.error .\n\n");
@@ -217,8 +220,7 @@ void SeqErrorCommand::help(){
 //***************************************************************************************************************
 
 SeqErrorCommand::~SeqErrorCommand(){
-       errorSummaryFile.close();       
-       errorSeqFile.close();
+
 }
 
 //***************************************************************************************************************
@@ -226,6 +228,16 @@ SeqErrorCommand::~SeqErrorCommand(){
 int SeqErrorCommand::execute(){
        try{
                if (abort == true) { return 0; }
+               
+               errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
+               m->openOutputFile(errorSummaryFileName, errorSummaryFile);
+               outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
+               printErrorHeader();
+               
+               errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
+               m->openOutputFile(errorSeqFileName, errorSeqFile);
+               outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
+               printErrorHeader();
 
                getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 
@@ -288,6 +300,9 @@ int SeqErrorCommand::execute(){
                
                
                while(queryFile){
+                       
+                       if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       
                        Compare minCompare;
                        Sequence query(queryFile);
                        
@@ -378,6 +393,9 @@ int SeqErrorCommand::execute(){
                        
                        for(int i=0;i<lastColumn;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
                        for(int i=0;i<lastRow;i++){
+                               
+                               if (m->control_pressed) { qualityForwardFile.close(); errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                               
                                qualityForwardFile << i+1;
                                for(int j=0;j<lastColumn;j++){
                                        qualityForwardFile << '\t' << qualForwardMap[i][j];
@@ -394,13 +412,16 @@ int SeqErrorCommand::execute(){
 
                        for(int i=0;i<lastColumn;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
                        for(int i=0;i<lastRow;i++){
+                               
+                               if (m->control_pressed) { qualityReverseFile.close(); errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                               
                                qualityReverseFile << i+1;
                                for(int j=0;j<lastColumn;j++){
                                        qualityReverseFile << '\t' << qualReverseMap[i][j];
                                }
                                qualityReverseFile << endl;
                        }
-                       
+                       qualityReverseFile.close();
                }
                
                
@@ -421,7 +442,8 @@ int SeqErrorCommand::execute(){
                        errorForwardFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
                }
                errorForwardFile.close();
-
+               
+               if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
                
                string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
                ofstream errorReverseFile;
@@ -440,9 +462,9 @@ int SeqErrorCommand::execute(){
                        errorReverseFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
                }
                errorReverseFile.close();
-
-
                
+               if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
                string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
                ofstream errorCountFile;
                m->openOutputFile(errorCountFileName, errorCountFile);
@@ -455,11 +477,9 @@ int SeqErrorCommand::execute(){
                        errorCountFile << i << '\t' << misMatchCounts[i] << endl;
                }
                errorCountFile.close();
-
-
-               
-               
                
+               if (m->control_pressed) { errorSummaryFile.close();     errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
                string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
                ofstream subMatrixFile;
                m->openOutputFile(subMatrixFileName, subMatrixFile);
@@ -497,7 +517,15 @@ int SeqErrorCommand::execute(){
                subMatrixFile << endl;
                subMatrixFile.close();
                
+               errorSummaryFile.close();       
+               errorSeqFile.close();
+               
+               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
                
+               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;       
        }