From: westcott <westcott>
Date: Wed, 8 Jul 2009 17:06:42 +0000 (+0000)
Subject: added stricter compilation requirements and fixed resulting errors
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=28d65de5f06f5b033109a3b8bbb6d3c4060914d3

added stricter compilation requirements and fixed resulting errors
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 136b75f..7959c79 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1194,11 +1194,20 @@
 				);
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+				GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
-				GCC_WARN_PEDANTIC = NO;
+				GCC_WARN_MISSING_PARENTHESES = YES;
+				GCC_WARN_PEDANTIC = YES;
+				GCC_WARN_UNUSED_FUNCTION = YES;
+				GCC_WARN_UNUSED_PARAMETER = NO;
+				GCC_WARN_UNUSED_VALUE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
-				OTHER_CPLUSPLUSFLAGS = "";
+				OTHER_CPLUSPLUSFLAGS = (
+					"-ansi",
+					"-pedantic",
+					"-wall",
+				);
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 				WARNING_CFLAGS = "";
diff --git a/blastalign.cpp b/blastalign.cpp
index 0645fb0..624210f 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -82,13 +82,13 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 	
 	string candidateName, templateName;
 	
-	while(d=blastFile.get() != '='){}
+	while((d=blastFile.get()) != '='){}
 	blastFile >> candidateName;					//	Get the candidate sequence name from flatfile
 	
-	while(d=blastFile.get() != '('){}
+	while((d=blastFile.get()) != '('){}
 	blastFile >> candidateLength;				//	Get the candidate sequence length from flatfile
 	
-	while(d=blastFile.get()){
+	while((d=blastFile.get())){
 		if(d == '>'){
 			blastFile >> templateName;			//	Get the template sequence name from flatfile
 			break;
@@ -114,10 +114,10 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 		}
 	}
 	
-	while(d=blastFile.get() != '='){}
+	while((d=blastFile.get()) != '='){}
 	blastFile >> templateLength;				//	Get the template sequence length from flatfile
 		
-	while(d=blastFile.get() != 'Q'){}			//	Suck up everything else until we get to the start of the alignment
+	while((d=blastFile.get()) != 'Q'){}			//	Suck up everything else until we get to the start of the alignment
 	int queryStart, sbjctStart, queryEnd, sbjctEnd;
 	string queryLabel, sbjctLabel, query, sbjct;
 
@@ -127,7 +127,7 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 	while(queryLabel == "Query:"){
 		blastFile >> queryStart >> query >> queryEnd;
 		
-		while(d=blastFile.get() != 'S'){};
+		while((d=blastFile.get()) != 'S'){};
 		
 		blastFile >> sbjctLabel >> sbjctStart >> sbjct >> sbjctEnd;
 		
diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index f19fe11..b451721 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -352,8 +352,7 @@ void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap>
 			pref[i].leftParent[1] = "";
 			pref[i].rightParent[1] = "";
 		}
-
-//cout << "in generate left.size() = " << left.size() << endl;		
+	
 		for (int i = 0; i < left.size(); i++) {
 			
 			SeqMap currentLeft = left[i];    //example i = 3;   currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
diff --git a/jackknife.cpp b/jackknife.cpp
index 1082465..35f0910 100644
--- a/jackknife.cpp
+++ b/jackknife.cpp
@@ -122,7 +122,7 @@ EstOutput Jackknife::getValues(SAbundVector* rank){
 			}
 			ci = 1.96 * sqrt(ci - jack);
 		}
-		else if(k=1){
+		else if(k==1){
 			jack = N[1];
 			ci = 1.96*sqrt(variance[1]);
 		}else{
diff --git a/mothur.h b/mothur.h
index 5d9dc96..2efdda8 100644
--- a/mothur.h
+++ b/mothur.h
@@ -60,7 +60,7 @@ using namespace std;
 #endif
 
 
-typedef unsigned long long ull;
+typedef unsigned long ull;
 
 struct IntNode {
 	int lvalue;
diff --git a/nameassignment.cpp b/nameassignment.cpp
index 3bcf6f9..c31468c 100644
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -52,8 +52,8 @@ ListVector NameAssignment::getListVector(void){
 
 void NameAssignment::print(void){
 	try {
-		map<string,int>::iterator it = (*this).begin();
-		for(it;it!=(*this).end();it++){
+		map<string,int>::iterator it;
+		for(it = (*this).begin(); it!=(*this).end(); it++){
 			mothurOut(it->first + "\t" + toString(it->second)); mothurOutEndLine();  //prints out keys and values of the map this.
 		}
 	}
diff --git a/shen.cpp b/shen.cpp
index 2be566c..0d515eb 100644
--- a/shen.cpp
+++ b/shen.cpp
@@ -36,7 +36,7 @@ EstOutput Shen::getValues(SAbundVector* rank){
 		errorOut(e, "Shen", "getValues");
 		exit(1);
 	}
-};
+}
 
 
 /***********************************************************************/