From f94ef0ca699bbb8f0d6dba8357c55f699a1ae29f Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 6 Mar 2009 15:00:15 +0000
Subject: [PATCH] fixed bug in random option of parsimony()

---
 Mothur.xcodeproj/project.pbxproj | 10 ++++++++--
 parsimonycommand.cpp             |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 483badd..e79c94c 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -14,6 +14,7 @@
 		3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
 		374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
 		3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
+		3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3782163C0F616079008E1F6D /* fullmatrix.cpp */; };
 		379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
 		379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
 		3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
@@ -126,6 +127,8 @@
 		374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
 		3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
 		3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
+		3782163B0F616079008E1F6D /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
+		3782163C0F616079008E1F6D /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
 		379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
 		379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
 		3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
@@ -380,8 +383,6 @@
 				37D928210F21331F001D4494 /* shared.h */,
 				37D928200F21331F001D4494 /* shared.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
-				37D928450F21331F001D4494 /* sparsematrix.hpp */,
-				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37D928480F21331F001D4494 /* summarydata.h */,
 				37D928490F21331F001D4494 /* summarydisplay.h */,
 				37D9284C0F21331F001D4494 /* utilities.hpp */,
@@ -516,6 +517,8 @@
 				37D927D50F21331F001D4494 /* datavector.hpp */,
 				37D927DC0F21331F001D4494 /* fastamap.h */,
 				37D927DB0F21331F001D4494 /* fastamap.cpp */,
+				3782163B0F616079008E1F6D /* fullmatrix.h */,
+				3782163C0F616079008E1F6D /* fullmatrix.cpp */,
 				37D927E20F21331F001D4494 /* groupmap.h */,
 				37D927E10F21331F001D4494 /* groupmap.cpp */,
 				37D927EE0F21331F001D4494 /* listvector.hpp */,
@@ -534,6 +537,8 @@
 				37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 				37D928330F21331F001D4494 /* sharedsabundvector.h */,
 				37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
+				37D928450F21331F001D4494 /* sparsematrix.hpp */,
+				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 				37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 				379293C10F2DE73400B9034A /* treemap.h */,
@@ -699,6 +704,7 @@
 				A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
 				A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
 				A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
+				3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 474f732..ee2125e 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -29,7 +29,7 @@ ParsimonyCommand::ParsimonyCommand() {
 			savetmap = globaldata->gTreemap;
 			getUserInput();
 			parsFile = randomtree + ".rd_parsimony";
-			openOutputFile(parsFile, out);
+			parsFileout = globaldata->getTreeFile() + "temp" + ".rd_parsimony";
 		}
 		
 		//set users groups to analyze
-- 
2.39.5