From 80eb270cc07e78155b82264e16cbb6bc8ade55ce Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Wed, 27 Jan 2010 21:08:49 +0000
Subject: [PATCH] fixed some bugs found while testing 1.8

---
 ccode.cpp               |  4 ++--
 ccode.h                 |  2 +-
 chimeraseqscommand.cpp  |  2 +-
 classifyseqscommand.cpp |  1 -
 commandfactory.cpp      | 11 ++++++++---
 5 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/ccode.cpp b/ccode.cpp
index a86e0fd..c474d7a 100644
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -13,7 +13,7 @@
 
 
 //***************************************************************************************************************
-Ccode::Ccode(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
+Ccode::Ccode(string filename, string temp, string o) {  fastafile = filename;  templateFile = temp;  outputDir = o; }
 //***************************************************************************************************************
 
 Ccode::~Ccode() {
@@ -32,7 +32,7 @@ void Ccode::print(ostream& out) {
 		
 		mothurOutEndLine();
 		
-		string mapInfo = getRootName(fastafile) + "mapinfo";
+		string mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
 		ofstream out2;
 		openOutputFile(mapInfo, out2);
 		
diff --git a/ccode.h b/ccode.h
index 0ea2753..52592f9 100644
--- a/ccode.h
+++ b/ccode.h
@@ -24,7 +24,7 @@
 class Ccode : public Chimera {
 	
 	public:
-		Ccode(string, string);	
+		Ccode(string, string, string);	
 		~Ccode();
 		
 		int getChimeras();
diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 63d02f5..4941488 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -254,7 +254,7 @@ int ChimeraSeqsCommand::execute(){
 		
 		if (method == "bellerophon")			{		chimera = new Bellerophon(fastafile, outputDir);			}
 		else if (method == "pintail")			{		chimera = new Pintail(fastafile, templatefile, outputDir);	}
-		else if (method == "ccode")				{		chimera = new Ccode(fastafile, templatefile);				}
+		else if (method == "ccode")				{		chimera = new Ccode(fastafile, templatefile, outputDir);			}
 		else if (method == "chimeracheck")		{		chimera = new ChimeraCheckRDP(fastafile, templatefile, outputDir);	}
 		else if (method == "chimeraslayer")		{		chimera = new ChimeraSlayer(fastafile, templatefile);		}
 		else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;		}
diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e6eb560..51578e3 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -528,7 +528,6 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 						outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
 					}else{
 						outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
-						cout << classify->getSimpleTax() << endl;
 					}
 					
 					outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
diff --git a/commandfactory.cpp b/commandfactory.cpp
index ddb7029..5eb4ff5 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -155,11 +155,16 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		delete command;   //delete the old command
 		
 		//user has opted to redirect output from dir where input files are located to some other place
-		if (outputDir != "") { optionString += ", outputdir=" + outputDir; }
+		if (outputDir != "") { 
+			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+			else { optionString += "outputdir=" + outputDir; }
+		}
 		
 		//user has opted to redirect input from dir where mothur.exe is located to some other place
-		if (inputDir != "") { optionString += ", inputdir=" + inputDir; }
-
+		if (inputDir != "") { 
+			if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+			else { optionString += "inputdir=" + inputDir; }
+		}
 		
 		if(commandName == "read.dist")					{	command = new ReadDistCommand(optionString);			}
 		else if(commandName == "read.otu")				{	command = new ReadOtuCommand(optionString);				}
-- 
2.39.2