From fe342304a0fdff3ab48226e1dcfdab95d3a94a64 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 21 Apr 2009 15:14:13 +0000
Subject: [PATCH] fixed bug with get.oturep and fixed problem with errorcheckor
 that did not allow the user to read a phylip and then a column.

---
 errorchecking.cpp    | 32 +++++++++++++++-----------------
 getoturepcommand.cpp | 15 ++++++++++++---
 2 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 4eef3b0..aa223a2 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -23,21 +23,21 @@ ErrorCheck::ErrorCheck() {
 /******************************************************/
 
 void ErrorCheck::refresh() {
-	columnfile = globaldata->getColumnFile();
-	phylipfile = globaldata->getPhylipFile();
-	listfile = globaldata->getListFile();
-	rabundfile = globaldata->getRabundFile();
-	sabundfile = globaldata->getSabundFile();
-	namefile = globaldata->getNameFile();
-	groupfile = globaldata->getGroupFile();
-	orderfile = globaldata->getOrderFile();
-	fastafile = globaldata->getFastaFile();
-	treefile = globaldata->getTreeFile();
-	cutoff = globaldata->getCutOff();
-	format = globaldata->getFormat();
-	method = globaldata->getMethod();
-	randomtree = globaldata->getRandomTree();
-	sharedfile = globaldata->getSharedFile();
+	//columnfile = globaldata->getColumnFile();
+	//phylipfile = globaldata->getPhylipFile();
+	//listfile = globaldata->getListFile();
+	//rabundfile = globaldata->getRabundFile();
+	//sabundfile = globaldata->getSabundFile();
+	//namefile = globaldata->getNameFile();
+	//groupfile = globaldata->getGroupFile();
+	//orderfile = globaldata->getOrderFile();
+	//fastafile = globaldata->getFastaFile();
+	//treefile = globaldata->getTreeFile();
+	//cutoff = globaldata->getCutOff();
+	//format = globaldata->getFormat();
+	//method = globaldata->getMethod();
+	//randomtree = globaldata->getRandomTree();
+	//sharedfile = globaldata->getSharedFile();
 }
 
 /*******************************************************/
@@ -85,8 +85,6 @@ bool ErrorCheck::checkInput(string input) {
 				
 				//is it a valid parameter
 				if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
-
-
 				
 				if (parameter == "phylip" )		{ phylipfile = value; }
 				if (parameter == "column" )		{ columnfile = value; }
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 064455f..6daad97 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -20,11 +20,19 @@ GetOTURepCommand::GetOTURepCommand(){
 		if(globaldata->gListVector != NULL)		{	
 			listOfNames = new ListVector(*globaldata->gListVector);	
 			
+			vector<string> names;
+			string binnames;
 			//map names to rows in sparsematrix
 			for (int i = 0; i < listOfNames->size(); i++) {
-				nameToIndex[listOfNames->get(i)] = i;
+				names.clear();
+				binnames = listOfNames->get(i);
+				splitAtComma(binnames, names);
+				
+				for (int j = 0; j < names.size(); j++) {
+					nameToIndex[names[j]] = i;
+				}
 			}
-		}else { cout << "error" << endl; }
+		}else { cout << "error, no listvector." << endl; }
 
 		
 		fastafile = globaldata->getFastaFile();
@@ -176,7 +184,7 @@ string GetOTURepCommand::FindRep(int bin) {
 		string minName;
 		
 		binnames = list->get(bin);
-		
+	
 		//parse names into vector
 		splitAtComma(binnames, names);
 		
@@ -186,6 +194,7 @@ string GetOTURepCommand::FindRep(int bin) {
 			//fill binMap
 			for (int i = 0; i < names.size(); i++) {
 				for (it3 = nameToIndex.begin(); it3 != nameToIndex.end(); it3++) {
+
 					if (it3->first == names[i]) {  
 						binMap[it3->second] = it3->first;
 
-- 
2.39.2