From c4d991e1b3d77b8f18e705d671f0a26e289a5b5c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 2 Dec 2010 16:15:57 +0000
Subject: [PATCH] refactored visible contig/gap map array intersection code to
 alignmentView

---
 src/jalview/datamodel/AlignmentView.java |   38 ++++++++++++++++++++++++++++++
 src/jalview/ws/jws1/JPredClient.java     |   28 +---------------------
 2 files changed, 39 insertions(+), 27 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 4079c9c..76f7bd8 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -539,4 +539,42 @@ public class AlignmentView
     // TODO Auto-generated method stub
     return firstCol;
   }
+
+  /**
+   * compute a deletion map for the current view according to the given
+   * gap/match map
+   * 
+   * @param gapMap (as returned from SequenceI.gapMap())
+   * @return int[] {intersection of visible regions with gapMap)
+   */
+  public int[] getVisibleContigMapFor(int[] gapMap)
+  {
+    int[] delMap = null;
+    int[] viscontigs = getVisibleContigs();
+    int spos = 0;
+    int i = 0;
+    if (viscontigs != null)
+    {
+      // viscontigs maps from a subset of the gapMap to the gapMap, so it will
+      // always be equal to or shorter than gapMap
+      delMap = new int[gapMap.length];
+      for (int contig = 0; contig < viscontigs.length; contig += 2)
+      {
+
+        while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+        {
+          spos++;
+        }
+        while (spos < gapMap.length
+                && gapMap[spos] <= viscontigs[contig + 1])
+        {
+          delMap[i++] = spos++;
+        }
+      }
+      int tmap[] = new int[i];
+      System.arraycopy(delMap, 0, tmap, 0, i);
+      delMap = tmap;
+    }
+    return delMap;
+  }
 }
diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 8fff195..f479347 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -99,33 +99,7 @@ public class JPredClient extends WS1Client
 
     if (viewonly)
     {
-      int[] viscontigs = alview.getVisibleContigs();
-      int spos = 0;
-      int i = 0;
-      if (viscontigs != null)
-      {
-        // Construct the delMap - mapping from the positions within the input to
-        // Jnet to the contigs in the original sequence
-
-        delMap = new int[seq.getEnd() - seq.getStart() + 1];
-        int gapMap[] = seq.gapMap();
-        for (int contig = 0; contig < viscontigs.length; contig += 2)
-        {
-
-          while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
-          {
-            spos++;
-          }
-          while (spos < gapMap.length
-                  && gapMap[spos] <= viscontigs[contig + 1])
-          {
-            delMap[i++] = spos++;
-          }
-        }
-        int tmap[] = new int[i];
-        System.arraycopy(delMap, 0, tmap, 0, i);
-        delMap = tmap;
-      }
+      delMap = alview.getVisibleContigMapFor(seq.gapMap());
     }
     if (msa && msf.length > 1)
     {
-- 
1.7.10.2