From 896a4f281982a3c2889f6ce6d73be997072aceae Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 9 Jan 2012 16:38:48 +0000
Subject: [PATCH] 1.23.0

---
 makefile     | 10 ++++-----
 seqnoise.cpp | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 66 insertions(+), 6 deletions(-)

diff --git a/makefile b/makefile
index c7dc1fd..e2e66c1 100644
--- a/makefile
+++ b/makefile
@@ -15,8 +15,8 @@ USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"12/7/2011\""
-VERSION = "\"1.22.0\""
+RELEASE_DATE = "\"1/9/2012\""
+VERSION = "\"1.23.0\""
 FORTAN_COMPILER = gfortran
 
 # Optimize to level 3:
@@ -24,10 +24,10 @@ CXXFLAGS += -O3
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
-	CXX = g++44
+	#CXX = g++44
 	
 	#if you are a mac user use the following line
-#	TARGET_ARCH += -arch x86_64
+	TARGET_ARCH += -arch x86_64
 	
 	#if you using cygwin to build Windows the following line
 	#CXX = x86_64-w64-mingw32-g++
@@ -35,7 +35,7 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
  	#TARGET_ARCH += -m64 -static
 
 	#if you are a linux user use the following line
-	CXXFLAGS += -mtune=native -march=native -m64
+	#CXXFLAGS += -mtune=native -march=native -m64
 	
 	 CXXFLAGS += -DBIT_VERSION
 endif
diff --git a/seqnoise.cpp b/seqnoise.cpp
index 578daaf..9ee8010 100644
--- a/seqnoise.cpp
+++ b/seqnoise.cpp
@@ -140,6 +140,8 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
 		m->openInputFile(listFileName, listFile);
 		double threshold;
 		int numOTUs;
+		string line = "";
+		bool adjustCutoff = true;
 		
 		if(listFile.peek() == 'u'){	m->getline(listFile);	}
 		
@@ -147,9 +149,10 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
 			listFile >> threshold;
 			
 			if(threshold < cutOff){
-				m->getline(listFile);	
+				line = m->getline(listFile); m->gobble(listFile);
 			}
 			else{
+				adjustCutoff = false;
 				listFile >> numOTUs;
 				otuFreq.resize(numOTUs, 0);
 				
@@ -201,6 +204,63 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
 				break;
 			}
 		}
+		
+		listFile.close();
+		
+		//the listfile does not contain a threshold greater than the cutoff so use highest value
+		if (adjustCutoff) {
+			istringstream iss (line,istringstream::in);
+			
+			iss >> numOTUs;
+			otuFreq.resize(numOTUs, 0);
+			
+			for(int i=0;i<numOTUs;i++){
+				
+				if (m->control_pressed) { return 0; }
+				
+				string otu;
+				iss >> otu;
+				
+				int count = 0;
+				
+				string number = "";
+				
+				for(int j=0;j<otu.size();j++){
+					if(otu[j] != ','){
+						number += otu[j];
+					}
+					else{
+						int index = atoi(number.c_str());
+						otuData[index] = i;
+						count++;
+						number = "";
+					}
+				}
+				
+				int index = atoi(number.c_str());
+				otuData[index] = i;
+				count++;
+				
+				otuFreq[i] = count;
+			}
+			
+			otuBySeqLookUp.resize(numOTUs);
+			
+			int numSeqs = otuData.size();
+			
+			for(int i=0;i<numSeqs;i++){
+				if (m->control_pressed) { return 0; }
+				otuBySeqLookUp[otuData[i]].push_back(i);
+			}
+			for(int i=0;i<numOTUs;i++){
+				if (m->control_pressed) { return 0; }
+				for(int j=otuBySeqLookUp[i].size();j<numSeqs;j++){
+					otuBySeqLookUp[i].push_back(0);
+				}
+			}
+			
+		}
+		
 		return 0;
 	}
 	catch(exception& e) {
-- 
2.39.2