From 5e8fcd2454ba4bd2e11983afd682b8aa6f7bb5c2 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Wed, 18 Feb 2009 15:56:06 +0000
Subject: [PATCH] fixed bug in read.tree

---
 Mothur.xcodeproj/project.pbxproj |  3 ++-
 readtree.cpp                     | 25 ++++++++++++++-----------
 readtree.h                       |  1 +
 unifracweightedcommand.cpp       |  4 ++--
 utilities.hpp                    |  2 +-
 5 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index c3c2a72..93e0e58 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -692,7 +692,7 @@
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_ENABLE_FIX_AND_CONTINUE = YES;
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"_GLIBCXX_DEBUG=1",
 					"_GLIBCXX_DEBUG_PEDANTIC=1",
@@ -708,6 +708,7 @@
 			buildSettings = {
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				GCC_MODEL_TUNING = G5;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				INSTALL_PATH = /usr/local/bin;
 				PRODUCT_NAME = mothur;
 			};
diff --git a/readtree.cpp b/readtree.cpp
index 77277e7..1910c4a 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -27,9 +27,10 @@ ReadTree::ReadTree() {
 /***********************************************************************/
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
-		char d;
 	
-		while(isspace(d=f.get()))		{;}
+		gobble(f);
+		char d = f.get();
+	
 		if(d == EOF){
 			cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
 			exit(1);
@@ -39,10 +40,8 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 			exit(1);
 		}
 		if(d == ')' && f.peek() == '\n'){
-			while(isspace(d=f.get()))		{;}
-			f.putback(d);
+			gobble(f);
 		}	
-	
 		return d;
 	}
 	catch(exception& e) {
@@ -58,8 +57,10 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 
 int ReadTree::readNodeChar(istream& f) {
 	try {
-		char d;
-		while(isspace(d=f.get()))		{;}
+//		while(isspace(d=f.get()))		{;}
+		gobble(f);
+		char d = f.get();
+
 		if(d == EOF){
 			cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
 			exit(1);
@@ -86,7 +87,7 @@ float ReadTree::readBranchLength(istream& f) {
 			cerr << "Error: Missing branch length in input tree.\n";
 			exit(1);
 		}
-    
+		gobble(f);
 		return b;
 	}
 	catch(exception& e) {
@@ -126,6 +127,7 @@ void ReadNewickTree::read() {
 				readTreeString();  
 				//save trees for later commands
 				globaldata->gTree.push_back(T); 
+				gobble(filehandle);
 			}
 		//if you are a nexus file
 		}else if ((c = filehandle.peek()) == '#') {
@@ -230,6 +232,7 @@ void ReadNewickTree::readTreeString() {
 		
 		if(ch == '('){
 			n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
+
 			lc = readNewickInt(filehandle, n, T);
 		
 			if(filehandle.peek()==','){							
@@ -253,8 +256,8 @@ void ReadNewickTree::readTreeString() {
 			filehandle.get(name, MAX_LINE,'\n');
 			SKIPLINE(filehandle, ch);
 		
-		
 			n = T->getIndex(name);
+
 			if(n!=0){
 				cerr << "Internal error: The only taxon is not taxon 0.\n";
 				exit(1);
@@ -263,7 +266,7 @@ void ReadNewickTree::readTreeString() {
 		} 
 		
 		while((ch=filehandle.get())!=';'){;}						
-			if(rooted != 1){									
+		if(rooted != 1){									
 			T->tree[n].setChildren(lc,rc);
 			T->tree[n].setBranchLength(0);
 			T->tree[n].setParent(-1);
@@ -291,7 +294,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 		if(c == '('){
 			int lc = readNewickInt(f, n, T);
 			readSpecialChar(f,',',"comma");
-		
+
 			int rc = readNewickInt(f, n, T);		
 			if(f.peek()==')'){	
 				readSpecialChar(f,')',"right parenthesis");					
diff --git a/readtree.h b/readtree.h
index 02b6129..653a853 100644
--- a/readtree.h
+++ b/readtree.h
@@ -14,6 +14,7 @@ using namespace std;
 #include <string>
 #include <iostream>
 #include "globaldata.hpp"
+#include "utilities.hpp"
 #include "tree.h"
 
 #define MAX_LINE		513
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 4a8325a..3b3abf8 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -122,7 +122,7 @@ int UnifracWeightedCommand::execute() {
 			//copy T[i]'s info.
 			randT->getCopy(T[i]); 
 			
-			//get pscores for random trees
+			//get scores for random trees
 			for (int j = 0; j < iters; j++) {
 				//create a random tree with same topology as T[i], but different labels
 				randT->assembleRandomUnifracTree();
@@ -178,7 +178,7 @@ int UnifracWeightedCommand::execute() {
 			float ucumul = 0.0000;
 			float rcumul = 0.0000;
 			//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-			for (it = validScores[b].begin(); it != validScores[b].end(); it++) { 
+			for (it = validScores[b].end(); it == validScores[b].begin(); it--) { 
 				it2 = uscoreFreq[b].find(it->first);
 				//user data has that score 
 				if (it2 != uscoreFreq[b].end()) { uscoreFreq[b][it->first] /= T.size(); ucumul+= it2->second;  }
diff --git a/utilities.hpp b/utilities.hpp
index 0c67561..bf7df2d 100644
--- a/utilities.hpp
+++ b/utilities.hpp
@@ -58,7 +58,7 @@ string toString(const T&x, int i){
 
 /***********************************************************************/
 
-inline void gobble(ifstream& f){
+inline void gobble(istream& f){
 	
 	char d;
     while(isspace(d=f.get()))		{;}
-- 
2.39.2