From: westcott <westcott>
Date: Mon, 4 May 2009 20:19:18 +0000 (+0000)
Subject: fixed xp user bug with rarefact commands and cluster error checking
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=dc08123b7f14e2305e5bb2b3a8fcef96fc829b07

fixed xp user bug with rarefact commands and cluster error checking
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 2de1905..bfed0cb 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -424,16 +424,10 @@
 		08FB7795FE84155DC02AAC07 /* Source */ = {
 			isa = PBXGroup;
 			children = (
-				7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
-				7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
 				37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 				37D928A60F2133C0001D4494 /* calculators */,
 				37D927C20F21331F001D4494 /* cluster.hpp */,
 				37D927C10F21331F001D4494 /* cluster.cpp */,
-				7E412F470F8D21B600381DD0 /* slibshuff.h */,
-				7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
-				7E412F420F8D213C00381DD0 /* libshuff.h */,
-				7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
 				37D928A90F2133E5001D4494 /* commands */,
 				37D927C60F21331F001D4494 /* collect.h */,
 				37D927C50F21331F001D4494 /* collect.cpp */,
@@ -447,6 +441,8 @@
 				37D927D20F21331F001D4494 /* completelinkage.cpp */,
 				37D927D40F21331F001D4494 /* database.hpp */,
 				37D927D30F21331F001D4494 /* database.cpp */,
+				7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
+				7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
 				37D927D60F21331F001D4494 /* display.h */,
 				37D927D80F21331F001D4494 /* engine.hpp */,
 				37D927D70F21331F001D4494 /* engine.cpp */,
@@ -463,6 +459,8 @@
 				37D927E90F21331F001D4494 /* kmer.cpp */,
 				37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 				37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+				7E412F420F8D213C00381DD0 /* libshuff.h */,
+				7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
 				37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 				37D927EF0F21331F001D4494 /* mothur.cpp */,
 				37D927F10F21331F001D4494 /* nameassignment.hpp */,
@@ -491,6 +489,8 @@
 				211C38310F961DD400FEE541 /* sharedutilities.h */,
 				211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
+				7E412F470F8D21B600381DD0 /* slibshuff.h */,
+				7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
 				37D928480F21331F001D4494 /* summarydata.h */,
 				37D928490F21331F001D4494 /* summarydisplay.h */,
 				37519AB30F810FAE00FED5E8 /* venn.h */,
diff --git a/errorchecking.cpp b/errorchecking.cpp
index 1693354..728d4d2 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -177,7 +177,7 @@ bool ErrorCheck::checkInput(string input) {
 			validateReadFiles();
 		}
 		
-		//are you trying to cluster before you have read something			
+		//are you trying to cluster before you have read something	
 		if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
 			((commandName == "cluster") && (globaldata->gListVector == NULL))) {
 				cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
diff --git a/globaldata.cpp b/globaldata.cpp
index 312b314..ce10ee1 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -272,6 +272,8 @@ GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
+	gListVector == NULL;		
+	gSparseMatrix == NULL;	
 }
 /*******************************************************/
 
diff --git a/mothur.h b/mothur.h
index 8ad1645..c1d93ed 100644
--- a/mothur.h
+++ b/mothur.h
@@ -15,6 +15,7 @@ using namespace std;
 
 /* This file contains all the standard incudes we use in the project as well as some common utilities. */
 
+//#include <cstddef>
 
 //io libraries
 #include <iostream>
diff --git a/npshannon.cpp b/npshannon.cpp
index faabc98..73dd834 100644
--- a/npshannon.cpp
+++ b/npshannon.cpp
@@ -28,7 +28,7 @@ EstOutput NPShannon::getValues(SAbundVector* rank){
 				double ChatPi = Chat*pi;
 				if(ChatPi>0){
 					npShannon += rank->get(i) * ChatPi*log(ChatPi)/(1-pow(1-ChatPi,(double)sampled));
-					cout << ChatPi << '\t' << rank->get(i) * ChatPi*log(ChatPi)/(1-pow(1-ChatPi,(double)sampled)) << endl;
+					//cout << ChatPi << '\t' << rank->get(i) * ChatPi*log(ChatPi)/(1-pow(1-ChatPi,(double)sampled)) << endl;
 				}
 			}
 			npShannon = -npShannon;
diff --git a/raredisplay.cpp b/raredisplay.cpp
index 6843ebe..3d50b26 100644
--- a/raredisplay.cpp
+++ b/raredisplay.cpp
@@ -15,6 +15,7 @@ void RareDisplay::init(string label){
 	try {
 		this->label = label;
 		if(nIters != 1){
+			tempInFile.clear();
 			openOutputFile(tempOutName, tempOutFile);
 			openInputFile(tempInName, tempInFile);
 		}