From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 5 Jul 2017 10:34:50 +0000 (+0100)
Subject: JAL-147 prevent overview box move up over hidden first sequence
X-Git-Tag: Release_2_10_3b1~132^2~48
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5c41e4193f3bebb1c8e11c124a4928d1419b052c

JAL-147 prevent overview box move up over hidden first sequence
---

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index a98b10e..a57dc9c 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -253,7 +253,8 @@ public class HiddenSequences
   }
 
   /**
-   * Convert absolute alignment index to visible alignment index
+   * Convert absolute alignment index to visible alignment index (or -1 if
+   * before the first visible sequence)
    * 
    * @param alignmentIndex
    * @return
diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index 4b396a6..2216f33 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -135,10 +135,12 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     // so convert back after getting visible region position
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
             .findIndexWithoutHiddenSeqs(yAsSeq));
+    yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
 
     // check in case we went off the edge of the alignment
     int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
     int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
     if (visYAsSeq + vpheight - 1 > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
@@ -156,7 +158,6 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     // update viewport
     ranges.setStartRes(visXAsRes);
     ranges.setStartSeq(visYAsSeq);
-
   }
 
   /**
diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index 7795988..5b2bbd4 100644
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -181,7 +181,8 @@ public class HiddenSequencesTest
   {
     AlignmentI al = new Alignment(seqs);
     HiddenSequences hs = al.getHiddenSequences();
-    for (int i = 0; i < SEQ_COUNT; i++)
+    int height = al.getHeight();
+    for (int i = 0; i < height; i++)
     {
       assertEquals(i, hs.findIndexWithoutHiddenSeqs(i));
     }
@@ -194,7 +195,7 @@ public class HiddenSequencesTest
     /*
      * alignment is now seq0/2/3/4/7/8/9
      */
-    assertEquals(SEQ_COUNT - 3, al.getHeight());
+    assertEquals(height - 3, al.getHeight());
     assertEquals(0, hs.findIndexWithoutHiddenSeqs(0));
     assertEquals(0, hs.findIndexWithoutHiddenSeqs(1));
     assertEquals(1, hs.findIndexWithoutHiddenSeqs(2));
@@ -205,6 +206,17 @@ public class HiddenSequencesTest
     assertEquals(4, hs.findIndexWithoutHiddenSeqs(7));
     assertEquals(5, hs.findIndexWithoutHiddenSeqs(8));
     assertEquals(6, hs.findIndexWithoutHiddenSeqs(9));
+
+    /*
+     * hide first sequence only
+     */
+    hs.showAll(null);
+    hs.hideSequence(seqs[0]);
+    for (int i = 1; i < height; i++)
+    {
+      assertEquals(i - 1, hs.findIndexWithoutHiddenSeqs(i));
+    }
+    assertEquals(-1, hs.findIndexWithoutHiddenSeqs(0));
   }
 
   /**