created mothurOut class to handle logfiles

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 8b07b857c73930bb24265c58da93b7702dccf42d..49edc36f8e7c3d94d32b7995f08c14e955cd232a 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -12,7 +12,7 @@
 
 //***************************************************************************************************************
 
-SeqSummaryCommand::SeqSummaryCommand(string option){
+SeqSummaryCommand::SeqSummaryCommand(string option)  {
        try {
                abort = false;
                
@@ -52,7 +52,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option){
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the summary.seqs command."); mothurOutEndLine(); abort = true;  }     
+                       else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true;  }       
                        
                        //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"){  
@@ -63,7 +63,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
+               m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
                exit(1);
        }
 }
@@ -71,14 +71,14 @@ SeqSummaryCommand::SeqSummaryCommand(string option){
 
 void SeqSummaryCommand::help(){
        try {
-               mothurOut("The summary.seqs command reads a fastafile and ....\n");
-               mothurOut("The summary.seqs command parameter is fasta and it is required.\n");
-               mothurOut("The summary.seqs command should be in the following format: \n");
-               mothurOut("summary.seqs(fasta=yourFastaFile) \n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");        
+               m->mothurOut("The summary.seqs command reads a fastafile and ....\n");
+               m->mothurOut("The summary.seqs command parameter is fasta and it is required.\n");
+               m->mothurOut("The summary.seqs command should be in the following format: \n");
+               m->mothurOut("summary.seqs(fasta=yourFastaFile) \n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");     
        }
        catch(exception& e) {
-               errorOut(e, "SeqSummaryCommand", "help");
+               m->errorOut(e, "SeqSummaryCommand", "help");
                exit(1);
        }
 }
@@ -147,22 +147,28 @@ int SeqSummaryCommand::execute(){
                if (startPosition[0] == -1) {  startPosition[0] = 0;    }
                if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
                
-               mothurOutEndLine();
-               mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); mothurOutEndLine();
-               mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); mothurOutEndLine();
-               mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); mothurOutEndLine();
-               mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); mothurOutEndLine();
-               mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); mothurOutEndLine();
-               mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); mothurOutEndLine();
-               mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); mothurOutEndLine();
-               mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); mothurOutEndLine();
-               mothurOut("# of Seqs:\t" + toString(numSeqs)); mothurOutEndLine();
+               m->mothurOutEndLine();
+               m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
+               m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
+               m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
+               m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
+               m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
+               m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
+               m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
+               m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
+               m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
                
                outSummary.close();
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(summaryFile); m->mothurOutEndLine();       
+               m->mothurOutEndLine();
+
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "SeqSummaryCommand", "execute");
+               m->errorOut(e, "SeqSummaryCommand", "execute");
                exit(1);
        }
 }