From e4ca037c5e637e3d34e64cb5e8ab11b03220188d Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Wed, 14 Apr 2010 12:44:12 +0000
Subject: [PATCH] pat's minor edits to distance calculations

---
 Mothur.xcodeproj/project.pbxproj | 32 +++-----------------------------
 distancecommand.cpp              |  2 --
 eachgapdist.h                    |  1 +
 eachgapignore.h                  | 15 ++++++++++++---
 onegapignore.h                   |  9 ++++++---
 5 files changed, 22 insertions(+), 37 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8fc67bd..79c1e5b 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -908,6 +908,9 @@
 /* Begin PBXProject section */
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			isa = PBXProject;
+			attributes = {
+				BuildIndependentTargetsInParallel = YES;
+			};
 			buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.0";
 			hasScannedForEncodings = 1;
@@ -921,23 +924,6 @@
 /* End PBXProject section */
 
 /* Begin XCBuildConfiguration section */
-		1DEB919008733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				COPY_PHASE_STRIP = NO;
-				DEBUGGING_SYMBOLS = YES;
-				GCC_DYNAMIC_NO_PIC = NO;
-				GCC_ENABLE_FIX_AND_CONTINUE = YES;
-				GCC_GENERATE_DEBUGGING_SYMBOLS = YES;
-				GCC_OPTIMIZATION_LEVEL = 0;
-				OPTIMIZATION_CFLAGS = "-O0";
-				OTHER_CFLAGS = "";
-				OTHER_LDFLAGS = "";
-				PRODUCT_NAME = mothur;
-				ZERO_LINK = YES;
-			};
-			name = Debug;
-		};
 		1DEB919108733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -950,16 +936,6 @@
 			};
 			name = Release;
 		};
-		1DEB919408733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				GCC_WARN_ABOUT_RETURN_TYPE = YES;
-				GCC_WARN_UNUSED_VARIABLE = YES;
-				PREBINDING = NO;
-				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
-			};
-			name = Debug;
-		};
 		1DEB919508733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -981,7 +957,6 @@
 		1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919008733D9F0010E9CD /* Debug */,
 				1DEB919108733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;
@@ -990,7 +965,6 @@
 		1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919408733D9F0010E9CD /* Debug */,
 				1DEB919508733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;
diff --git a/distancecommand.cpp b/distancecommand.cpp
index 47e22ad..2cc92a7 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -205,8 +205,6 @@ int DistanceCommand::execute(){
 			
 			MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 			
-			if (m->control_pressed) {   MPI_File_close(&outMPI);  delete distCalculator;  return 0;  }
-
 			if (pid == 0) { //you are the root process 
 			
 				//do your part
diff --git a/eachgapdist.h b/eachgapdist.h
index ac9b453..9034dbe 100644
--- a/eachgapdist.h
+++ b/eachgapdist.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
diff --git a/eachgapignore.h b/eachgapignore.h
index 9763a6d..8e027b7 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -22,19 +22,28 @@ public:
 		int diff = 0;
 		int length = 0;
 		int start = 0;
+		int end = 0;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
 		int alignLength = seqA.length();
 		
-		for(int i=0; i<alignLength; i++){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+		for(int i=0;i<alignLength;i++){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
+				cout << "start: " << start << endl;
+				break;
+			}
+		}
+		for(int i=alignLength-1;i>=0;i--){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
+				end = i;
+				cout << "end: " << end << endl;
 				break;
 			}
 		}
 		
-		for(int i=start;i<alignLength;i++){
+		for(int i=start;i<=end;i++){
 			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;	
 			}
diff --git a/onegapignore.h b/onegapignore.h
index 6421741..af284fc 100644
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -28,17 +29,19 @@ public:
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
 		int alignLength = seqA.length();
-		
+
 		// this assumes that sequences start and end with '.'s instead of'-'s.
 		for(int i=0;i<alignLength;i++){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
+				cout << "start: " << start << endl;
 				break;
 			}
 		}
 		for(int i=alignLength-1;i>=0;i--){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
+				cout << "end: " << end << endl;
 				break;
 			}
 		}
-- 
2.39.2