fixed indentation in perl code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1103 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/AlignTwoSeq.pm b/code_perl/Maasha/AlignTwoSeq.pm
index 54234edea33a9ac9f2055628f3bee7e23de3232e..50d75c79206df9dbb23d9af81b8c383921e2beac 100644 (file)
--- a/code_perl/Maasha/AlignTwoSeq.pm
+++ b/code_perl/Maasha/AlignTwoSeq.pm
@@ -708,47 +708,47 @@ sub insert_indels
 
     if ( @{ $matches } > 0 )
     {
-    @{ $matches } = sort { $a->{ 'Q_BEG' } <=> $b->{ 'Q_BEG' } } @{ $matches };  # FIXME is this necessary?
+        @{ $matches } = sort { $a->{ 'Q_BEG' } <=> $b->{ 'Q_BEG' } } @{ $matches };  # FIXME is this necessary?
 
-    # >>>>>>>>>>>>>> FIRST MATCH <<<<<<<<<<<<<<
+        # >>>>>>>>>>>>>> FIRST MATCH <<<<<<<<<<<<<<
 
-    $diff = $matches->[ 0 ]->{ 'Q_BEG' } - $matches->[ 0 ]->{ 'S_BEG' };
-
-    if ( $diff > 0 )
-    {
-        substr ${ $s_seq }, 0, 0, '-' x $diff;
-
-        $s_indels += $diff;
-    }
-    elsif ( $diff < 0 )
-    {
-        substr ${ $q_seq }, 0, 0, '-' x abs $diff;
-
-        $q_indels += abs $diff;
-    }
-
-    # >>>>>>>>>>>>>> MIDDLE MATCHES <<<<<<<<<<<<<<
-
-    for ( $i = 0; $i < scalar @{ $matches } - 1; $i++ )
-    {
-        $q_dist = $matches->[ $i + 1 ]->{ 'Q_BEG' } - $matches->[ $i ]->{ 'Q_END' };
-        $s_dist = $matches->[ $i + 1 ]->{ 'S_BEG' } - $matches->[ $i ]->{ 'S_END' };
-
-        $diff   = $q_dist - $s_dist;
+        $diff = $matches->[ 0 ]->{ 'Q_BEG' } - $matches->[ 0 ]->{ 'S_BEG' };
 
         if ( $diff > 0 )
         {
-            substr ${ $s_seq }, $s_indels + $matches->[ $i ]->{ 'S_END' } + 1, 0, '-' x $diff;
+            substr ${ $s_seq }, 0, 0, '-' x $diff;
 
             $s_indels += $diff;
         }
         elsif ( $diff < 0 )
         {
-            substr ${ $q_seq }, $q_indels + $matches->[ $i ]->{ 'Q_END' } + 1, 0, '-' x abs $diff;
+            substr ${ $q_seq }, 0, 0, '-' x abs $diff;
 
             $q_indels += abs $diff;
         }
-    }
+
+        # >>>>>>>>>>>>>> MIDDLE MATCHES <<<<<<<<<<<<<<
+
+        for ( $i = 0; $i < scalar @{ $matches } - 1; $i++ )
+        {
+            $q_dist = $matches->[ $i + 1 ]->{ 'Q_BEG' } - $matches->[ $i ]->{ 'Q_END' };
+            $s_dist = $matches->[ $i + 1 ]->{ 'S_BEG' } - $matches->[ $i ]->{ 'S_END' };
+
+            $diff   = $q_dist - $s_dist;
+
+            if ( $diff > 0 )
+            {
+                substr ${ $s_seq }, $s_indels + $matches->[ $i ]->{ 'S_END' } + 1, 0, '-' x $diff;
+
+                $s_indels += $diff;
+            }
+            elsif ( $diff < 0 )
+            {
+                substr ${ $q_seq }, $q_indels + $matches->[ $i ]->{ 'Q_END' } + 1, 0, '-' x abs $diff;
+
+                $q_indels += abs $diff;
+            }
+        }
     }
 
     # >>>>>>>>>>>>>> LAST MATCH <<<<<<<<<<<<<<