From 5d03d249ea5f0fff6b23e1f7d30494434bd4903b Mon Sep 17 00:00:00 2001
From: Mathieu Fourment <m.fourment@gmail.com>
Date: Fri, 27 Nov 2015 15:40:06 +1100
Subject: [PATCH] Fixed a major leak in MFDistanceMatrix and its subclass.
 MFDistanceMatrixOperation is now allowed to be cancelled.

---
 Seqotron/MFDistanceMatrix.m           | 10 +++++-----
 Seqotron/MFDistanceMatrixOperation.m  | 14 ++++++++++++--
 Seqotron/MFJukeCantorDistanceMatrix.m | 10 +++++-----
 Seqotron/MFK83DistanceMatrix.m        | 10 +++++-----
 4 files changed, 27 insertions(+), 17 deletions(-)

diff --git a/Seqotron/MFDistanceMatrix.m b/Seqotron/MFDistanceMatrix.m
index e0a16ad..8f7c30a 100755
--- a/Seqotron/MFDistanceMatrix.m
+++ b/Seqotron/MFDistanceMatrix.m
@@ -54,14 +54,14 @@ -(void)dealloc{
 - (float)calculatePairwiseDistanceBetween:(MFSequence*)sequence1 and:(MFSequence*)sequence2{
     NSUInteger d = 0;
     NSUInteger n = 0;
-    const char *c1 = [[sequence1 sequence]UTF8String];
-    const char *c2 = [[sequence2 sequence]UTF8String];
     MFDataType *dataType = sequence1.dataType;
     NSUInteger dimension = [sequence1 length];
-    
+    char c1,c2;
     for ( NSUInteger k = 0; k < dimension; k++ ) {
-        if( [dataType isKnownChar:c1[k]] && [dataType isKnownChar:c2[k]] ){
-            if(c1[k] != c2[k] ){
+        c1 = [[sequence1 sequence ]characterAtIndex:k];
+        c2 = [[sequence2 sequence ]characterAtIndex:k];
+        if( [dataType isKnownChar:c1] && [dataType isKnownChar:c2] ){
+            if(c1 != c2 ){
                 d++;
             }
             n++;
diff --git a/Seqotron/MFDistanceMatrixOperation.m b/Seqotron/MFDistanceMatrixOperation.m
index 4089aff..df05e2f 100644
--- a/Seqotron/MFDistanceMatrixOperation.m
+++ b/Seqotron/MFDistanceMatrixOperation.m
@@ -83,8 +83,18 @@ -(void)main{
 //            [self.delegate operation:self setDescription:self.description];
 //        });
 //    }
-    
-    [_matrix calculateDistances];
+    float **matrix = [_matrix floatMatrix];
+    NSUInteger dimension = [_sequences count];
+    for ( NSUInteger i = 0; i < dimension; i++ ) {
+        MFSequence *seq1 = [_sequences objectAtIndex:i];
+        
+        for ( NSUInteger j = i+1; j < dimension; j++ ) {
+            MFSequence *seq2 = [_sequences objectAtIndex:j];
+            matrix[i][j] = matrix[j][i] = [_matrix calculatePairwiseDistanceBetween:seq1 and:seq2];
+        }
+        if( [self isCancelled] )break;
+    }
+    //[_matrix calculateDistances];
     
 //    [(NSObject *)self.delegate performSelectorOnMainThread: @selector(distanceMatrixDidFinish:)
 //                                       withObject: self
diff --git a/Seqotron/MFJukeCantorDistanceMatrix.m b/Seqotron/MFJukeCantorDistanceMatrix.m
index 5b01f9b..563cb84 100755
--- a/Seqotron/MFJukeCantorDistanceMatrix.m
+++ b/Seqotron/MFJukeCantorDistanceMatrix.m
@@ -28,14 +28,14 @@ @implementation MFJukeCantorDistanceMatrix
 - (float)calculatePairwiseDistanceBetween:(MFSequence*)sequence1 and:(MFSequence*)sequence2{
     NSUInteger d = 0;
     NSUInteger n = 0;
-    const char *c1 = [[sequence1 sequence]UTF8String];
-    const char *c2 = [[sequence2 sequence]UTF8String];
     MFDataType *dataType = sequence1.dataType;
     NSUInteger dimension = [sequence1 length];
-    
+    char c1,c2;
     for ( NSUInteger k = 0; k < dimension; k++ ) {
-        if( [dataType isKnownChar:c1[k]] && [dataType isKnownChar:c2[k]] ){
-            if( c1[k] != c2[k] ){
+        c1 = [[sequence1 sequence ]characterAtIndex:k];
+        c2 = [[sequence2 sequence ]characterAtIndex:k];
+        if( [dataType isKnownChar:c1] && [dataType isKnownChar:c2] ){
+            if( c1 != c2 ){
                 d++;
             }
             n++;
diff --git a/Seqotron/MFK83DistanceMatrix.m b/Seqotron/MFK83DistanceMatrix.m
index dea9089..806a0f1 100644
--- a/Seqotron/MFK83DistanceMatrix.m
+++ b/Seqotron/MFK83DistanceMatrix.m
@@ -28,14 +28,14 @@ @implementation MFK83DistanceMatrix
 - (float)calculatePairwiseDistanceBetween:(MFSequence*)sequence1 and:(MFSequence*)sequence2{
     float d = 0;
     NSUInteger n = 0;
-    const char *c1 = [[sequence1 sequence]UTF8String];
-    const char *c2 = [[sequence2 sequence]UTF8String];
     MFDataType *dataType = sequence1.dataType;
     NSUInteger dimension = [sequence1 length];
-    
+    char c1,c2;
     for ( NSUInteger k = 0; k < dimension; k++ ) {
-        if( [dataType isKnownChar:c1[k]] && [dataType isKnownChar:c2[k]] ){
-            if( c1[k] != c2[k] ){
+        c1 = [[sequence1 sequence ]characterAtIndex:k];
+        c2 = [[sequence2 sequence ]characterAtIndex:k];
+        if( [dataType isKnownChar:c1] && [dataType isKnownChar:c2] ){
+            if( c1 != c2 ){
                 d++;
             }
             n++;