From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Wed, 1 Nov 2023 15:15:21 +0000 (+0100)
Subject: JAL-4313 Clamp start and end ranges to array size
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=72e63582d51fbaa0cc5a3963abc96814f984039b;p=jalview.git

JAL-4313 Clamp start and end ranges to array size
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e832c2f..fdb62a1 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1625,6 +1625,8 @@ public class AlignmentAnnotation
   private void removeHiddenAnnotation(int start, int end,
           HiddenColumns hiddenColumns)
   {
+    start = Math.min(Math.max(0, start), annotations.length);
+    end = Math.min(Math.max(-1, end), annotations.length - 1);
     // mangle the alignmentAnnotation annotation array
     ArrayList<Annotation[]> annels = new ArrayList<>();
     Annotation[] els = null;
diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 2948f83..74c2b63 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -626,6 +626,50 @@ public class AlignmentAnnotationTests
     assertThat(ann.annotations, is(emptyArray()));
   }
 
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation_HiddenRegionBeyondSize()
+  {
+    Annotation[] annots = annotsRange(4);
+    AlignmentAnnotation ann = new AlignmentAnnotation("label", "desc", annots);
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(6, 7);
+    ann.makeVisibleAnnotation(hc);
+    assertThat(ann.annotations, matchesAnnotations(annots));
+  }
+
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation_HiddenRegionAndTrimEndBeyondSize()
+  {
+    Annotation[] annots = annotsRange(4);
+    AlignmentAnnotation ann = new AlignmentAnnotation("label", "desc", annots);
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(6, 7);
+    ann.makeVisibleAnnotation(0, 10, hc);
+    assertThat(ann.annotations, matchesAnnotations(annots));
+  }
+
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation_HiddenRegionBeforeStart()
+  {
+    Annotation[] annots = annotsRange(4);
+    AlignmentAnnotation ann = new AlignmentAnnotation("label", "desc", annots);
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(-3, -2);
+    ann.makeVisibleAnnotation(hc);
+    assertThat(ann.annotations, matchesAnnotations(annots));
+  }
+
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation_HiddenRegionAndTrimStartBeforeStart()
+  {
+    Annotation[] annots = annotsRange(4);
+    AlignmentAnnotation ann = new AlignmentAnnotation("label", "desc", annots);
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(-3, -2);
+    ann.makeVisibleAnnotation(-5, annots.length - 1, hc);
+    assertThat(ann.annotations, matchesAnnotations(annots));
+  }
+
   static Annotation[] annotsRange(int stop)
   {
     Annotation[] annotations = new Annotation[stop];