created mothurOut class to handle logfiles

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index fa5329b1e4094b4c87d60b5b4dfbd211f1bc1aeb..66efd469fcf8631d8537b6c7e90ea066ef72c028 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -13,7 +13,7 @@
 inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
 //**********************************************************************************************************************
 
-PreClusterCommand::PreClusterCommand(string option){
+PreClusterCommand::PreClusterCommand(string option) {
        try {
                abort = false;
                
@@ -60,7 +60,7 @@ PreClusterCommand::PreClusterCommand(string option){
 
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
+                       if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the pre.cluster 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 
@@ -82,7 +82,7 @@ PreClusterCommand::PreClusterCommand(string option){
                                
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "PreClusterCommand");
+               m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
                exit(1);
        }
 }
@@ -93,18 +93,18 @@ PreClusterCommand::~PreClusterCommand(){}
 
 void PreClusterCommand::help(){
        try {
-               mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
-               mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
-               mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
-               mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
-               mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
-               mothurOut("The pre.cluster command should be in the following format: \n");
-               mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
-               mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               m->mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
+               m->mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
+               m->mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
+               m->mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
+               m->mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
+               m->mothurOut("The pre.cluster command should be in the following format: \n");
+               m->mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
+               m->mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "help");
+               m->errorOut(e, "PreClusterCommand", "help");
                exit(1);
        }
 }
@@ -118,8 +118,8 @@ int PreClusterCommand::execute(){
                //reads fasta file and return number of seqs
                int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
        
-               if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0;  }
-               if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0;  }
+               if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
+               if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
                
                //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
 //             sizes.clear();
@@ -167,15 +167,21 @@ int PreClusterCommand::execute(){
                string newNamesFile = fileroot + "precluster.names";
                
                
-               mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
-               mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine(); 
+               m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+               m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); 
                printData(newFastaFile, newNamesFile);
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               m->mothurOut(newFastaFile); m->mothurOutEndLine();      
+               m->mothurOut(newNamesFile); m->mothurOutEndLine();      
+               m->mothurOutEndLine();
 
                return 0;
                
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "execute");
+               m->errorOut(e, "PreClusterCommand", "execute");
                exit(1);
        }
 }
@@ -213,7 +219,7 @@ int PreClusterCommand::readFASTA(){
                                if (namefile != "") {
                                        itSize = sizes.find(seq.getName());
                                        
-                                       if (itSize == sizes.end()) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+                                       if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
                                        else{
                                                seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
                                                alignSeqs.push_back(tempNode);
@@ -232,7 +238,7 @@ int PreClusterCommand::readFASTA(){
        }
        
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "readFASTA");
+               m->errorOut(e, "PreClusterCommand", "readFASTA");
                exit(1);
        }
 }
@@ -252,7 +258,7 @@ int PreClusterCommand::calcMisMatches(string seq1, string seq2){
                return numBad;
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "calcMisMatches");
+               m->errorOut(e, "PreClusterCommand", "calcMisMatches");
                exit(1);
        }
 }
@@ -280,7 +286,7 @@ void PreClusterCommand::printData(string newfasta, string newname){
                
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "printData");
+               m->errorOut(e, "PreClusterCommand", "printData");
                exit(1);
        }
 }
@@ -306,7 +312,7 @@ void PreClusterCommand::readNameFile(){
                in.close();
        }
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "readNameFile");
+               m->errorOut(e, "PreClusterCommand", "readNameFile");
                exit(1);
        }
 }