From: westcott <westcott>
Date: Wed, 16 Jun 2010 13:59:57 +0000 (+0000)
Subject: fixes while testing
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=a6c4005cb8b45030d6621404d6082723b3b98003

fixes while testing
---

diff --git a/classify.cpp b/classify.cpp
index 22728eb..2eb3ec1 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -138,7 +138,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 		}else if ((method == "kmer") && (!needToGenerate)) {	
 			ifstream kmerFileTest(kmerDBName.c_str());
 			database->readKmerDB(kmerFileTest);	
-			
+		
 			ifstream fastaFile;
 			openInputFile(tempFile, fastaFile);
 			
@@ -150,7 +150,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 			}
 			fastaFile.close();
 		}
-#endif		
+#endif	
+	
 		database->setNumSeqs(names.size());
 		
 		//sanity check
diff --git a/phylotree.cpp b/phylotree.cpp
index 1c2deba..53492ca 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -598,7 +598,7 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 		for (int i = 0; i < templateFileNames.size(); i++) {
 			itFind = taxonomyFileNames.find(templateFileNames[i]);
 			
-			if (itFind != name2Taxonomy.end()) { //found it so erase it
+			if (itFind != taxonomyFileNames.end()) { //found it so erase it
 				taxonomyFileNames.erase(itFind);
 			}else {
 				m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index f86891b..df085b4 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -20,7 +20,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"name","group","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //"list",
+			string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);