From: westcott <westcott>
Date: Wed, 16 Mar 2011 18:47:41 +0000 (+0000)
Subject: fixed catchall "clunky" names
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=264c8a3c759d9a999c485236e98dac98d4f0db5f

fixed catchall "clunky" names
---

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 66fbf9a..ace1b00 100644
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -182,6 +182,7 @@ int CatchAllCommand::execute() {
 		path = path.substr(0, (path.find_last_of("othur")-5));
 		path = m->getFullPathName(path);
 		
+		savedOutputDir = outputDir;
 		string catchAllCommandExe = ""; 
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
@@ -246,6 +247,7 @@ int CatchAllCommand::execute() {
 						remove(filename.c_str());
 					
 						filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+						if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 					
 						outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 						outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -289,6 +291,7 @@ int CatchAllCommand::execute() {
 						remove(filename.c_str());
 					
 						filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+						if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 					
 						outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 						outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -353,6 +356,7 @@ int CatchAllCommand::execute() {
 				remove(filename.c_str());
 				
 				filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+				if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 				
 				outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 				outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -372,7 +376,7 @@ int CatchAllCommand::execute() {
 		}
 		
 		if (sharedfile == "") {  
-			string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+			string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 			summaryfilename = m->getFullPathName(summaryfilename);
 			outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 		}else { //combine summaries
@@ -430,7 +434,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 	try {
 		
 		ofstream out;
-		string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+		string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 		
 		//open combined file
 		m->openOutputFile(combineFileName, out);
diff --git a/catchallcommand.h b/catchallcommand.h
index 49e0d54..44bde02 100644
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -39,7 +39,7 @@ private:
 
 	GlobalData* globaldata;
 	
-	string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
+	string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path, savedOutputDir;
 	bool abort, allLines;
 	set<string> labels;
 	vector<string> outputNames;