From 7f2a5060015acbd1f5c1d45f8483329492876f87 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 5 Sep 2006 13:36:07 +0000
Subject: [PATCH] getVisibleContigs() returns start and end positions of
 visible regions of an alignmentView.

---
 src/jalview/datamodel/AlignmentView.java |   47 +++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 6d94ff1..a76e90e 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -385,5 +385,50 @@ public class AlignmentView
         return getAlignmentAndColumnSelection(gapCharacter);
     }
   }
-
+  /**
+   * returns simple array of start end positions of visible range on alignment.
+   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment. 
+   * @return int[] { start_i, end_i } for 1<i<n visible regions.
+   */
+  public int[] getVisibleContigs() {
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      int nvis = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          nvis++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        nvis++;
+      }
+      int viscontigs[] = new int[nvis*2];
+      nvis=0;
+      start=0;
+      for (int contig=0; contig<contigs.length; contig+=3) {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          viscontigs[nvis] = start;
+          viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
+          nvis+=2;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];              
+      }
+      if (start<fwidth) {
+        viscontigs[nvis] = start;
+        viscontigs[nvis+1]=fwidth; // end is inclusive
+        nvis+=2;
+      }
+      return viscontigs;
+    } else {
+      return new int[] { 0, width};
+    }
+  }
 }
-- 
1.7.10.2