From 995238e9aa4455e3b59053e3dfe497b89caed79e Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 4 Feb 2011 12:54:38 +0000
Subject: [PATCH] fixed catchall hangup if it can't find the exe

---
 catchallcommand.cpp | 4 +++-
 corraxescommand.cpp | 8 ++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 69b9f04..b0e5eff 100644
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -500,8 +500,10 @@ int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out
 	try {
 		
 		ifstream in;
-		m->openInputFile(file1, in);
+		int able = m->openInputFile(file1, in, "noerror");
 		
+		if (able == 1) {  m->mothurOut("[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.");m->mothurOutEndLine();  m->control_pressed = true; return 0; }
+			
 		if (!in.eof()) {
 			
 			string header = m->getline(in); m->gobble(in);
diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index b6c1a70..3da6b82 100644
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -608,10 +608,10 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
 			vector<spearmanRank*> ties;
 			int rankTotal = 0;
 			for (int j = 0; j < scores[i].size(); j++) {
-				rankTotal += j;
+				rankTotal += (j+1);
 				ties.push_back(&(scores[i][j]));
 				
-				if (j != scores.size()-1) { // you are not the last so you can look ahead
+				if (j != scores[i].size()-1) { // you are not the last so you can look ahead
 					if (scores[i][j].score != scores[i][j+1].score) { // you are done with ties, rank them and continue
 						for (int k = 0; k < ties.size(); k++) {
 							float thisrank = rankTotal / (float) ties.size();
@@ -648,10 +648,10 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
 			vector<spearmanRank> ties;
 			int rankTotal = 0;
 			for (int j = 0; j < otuScores.size(); j++) {
-				rankTotal += j;
+				rankTotal += (j+1);
 				ties.push_back(otuScores[j]);
 				
-				if (j != scores.size()-1) { // you are not the last so you can look ahead
+				if (j != otuScores.size()-1) { // you are not the last so you can look ahead
 					if (otuScores[j].score != otuScores[j+1].score) { // you are done with ties, rank them and continue
 						for (int k = 0; k < ties.size(); k++) {
 							float thisrank = rankTotal / (float) ties.size();
-- 
2.39.2