1.21.0

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 550a6b74ebd99d81c47a169c99462f2a53b6b2b4..3f6e0c975750d7e6bd69845a32e11e7e20b2b68a 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -42,7 +42,7 @@ string PreClusterCommand::getHelpString(){
                helpString += "The pre.cluster command should be in the following format: \n";
                helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
                helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -73,6 +73,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -123,6 +124,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        //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"){  
@@ -135,7 +137,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
                        else if (namefile == "not open") { abort = true; }      
-                       else {  readNameFile();  }
+                       else {  readNameFile();  m->setNameFile(namefile); }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
                        convert(temp, diffs); 
@@ -224,7 +226,7 @@ int PreClusterCommand::execute(){
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); 
                
-               if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+               if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();