From 290417727ff37c2d08bbe8962c6a6cd6a187cfe0 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 20 Sep 2017 16:25:06 +0100
Subject: [PATCH] JAL-2674 fix up interface of locateVisibleBoundsOfSequence

---
 src/jalview/datamodel/HiddenColumns.java      |    7 +--
 src/jalview/renderer/ScaleRenderer.java       |    6 +-
 test/jalview/datamodel/HiddenColumnsTest.java |   79 -------------------------
 3 files changed, 6 insertions(+), 86 deletions(-)

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index c0a43ee..305a6f1 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -923,7 +923,7 @@ public class HiddenColumns
       {
         int ifpos = seq.findIndex(fpos) - 1;
         int ilpos = seq.findIndex(lpos) - 1;
-        return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+        return new int[] { ifpos, ifpos, ilpos };
       }
 
       // Simply walk along the sequence whilst watching for hidden column
@@ -982,11 +982,10 @@ public class HiddenColumns
       }
       if (foundStart)
       {
-        return new int[] { findColumnPosition(start),
-            findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+        return new int[] { findColumnPosition(start), firstP, lastP };
       }
       // otherwise, sequence was completely hidden
-      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+      return new int[] { visPrev, firstP, lastP };
     } finally
     {
       LOCK.readLock().unlock();
diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index 9fec256..d310705 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -77,8 +77,8 @@ public class ScaleRenderer
               .locateVisibleBoundsOfSequence(refSeq);
 
       refSp = refbounds[0];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
+      refStartI = refbounds[1];
+      refEndI = refbounds[2];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -86,7 +86,7 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<ScaleMark> marks = new ArrayList<ScaleMark>();
+    List<ScaleMark> marks = new ArrayList<>();
     String string;
     int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 1aec1d3..6b4e05d 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -1055,85 +1055,6 @@ public class HiddenColumnsTest
     assertEquals(4, h.adjustForHiddenColumns(2));
   }
 
-  /*@Test(groups = "Functional")
-  public void testCompensateForEdit()
-  {
-    HiddenColumns2 h = new HiddenColumns2();
-  
-    ColumnSelection sel = new ColumnSelection();
-    assertNull(h.compensateForEdit(10, 3, sel));
-  
-    h.hideColumns(3, 4);
-    List<int[]> result = h.compensateForEdit(10, 3, sel);
-    assertEquals(0, result.size());
-  
-    // edit partially overlapping hidden
-  
-    h = new HiddenColumns2();
-    h.hideColumns(15, 17);
-    result = h.compensateForEdit(10, 6, sel);
-    assertEquals(0, result.size());
-  
-    HiddenColumns2 h2 = new HiddenColumns2();
-    h2.hideColumns(9, 11);
-    assertTrue(h.equals(h2));
-  
-    // edit fully overlapping hidden
-  
-    h = new HiddenColumns2();
-    h.hideColumns(15, 17);
-    result = h.compensateForEdit(10, 8, sel);
-    assertEquals(result.get(0)[0], 15);
-    assertEquals(result.get(0)[1], 17);
-    assertFalse(h.hasHiddenColumns());
-  
-    // edit at start
-  
-    h = new HiddenColumns2();
-    h.hideColumns(0, 3);
-    result = h.compensateForEdit(0, 4, sel);
-    assertEquals(0, result.size());
-    assertEquals(sel.getSelected().size(), 4);
-    assertFalse(h.hasHiddenColumns());
-  }*/
-
-  /*@Test(groups = "Functional")
-  public void testCompensateForDelEdits()
-  {
-    HiddenColumns2 h = new HiddenColumns2();
-    HiddenColumns2 h2 = new HiddenColumns2();
-  
-    h.compensateForDelEdits(10, 3);
-    assertFalse(h.hasHiddenColumns());
-  
-    h = new HiddenColumns2();
-    h.hideColumns(3, 4);
-    h.compensateForDelEdits(10, 3);
-    h2.hideColumns(3, 4);
-    assertTrue(h.equals(h2));
-  
-    h = new HiddenColumns2();
-    h.hideColumns(15, 17);
-    h.compensateForDelEdits(10, 6);
-    h2 = new HiddenColumns2();
-    h2.hideColumns(9, 11);
-    assertTrue(h.equals(h2));
-  
-    h = new HiddenColumns2();
-    h.hideColumns(15, 17);
-    h.compensateForDelEdits(10, 8);
-    h2 = new HiddenColumns2();
-    h2.hideColumns(7, 9);
-    assertTrue(h.equals(h2));
-  
-    h = new HiddenColumns2();
-    h.hideColumns(0, 3);
-    h.compensateForDelEdits(0, 4);
-    h2 = new HiddenColumns2();
-    h2.hideColumns(0, 0);
-    assertTrue(h.equals(h2));
-  }*/
-
   @Test(groups = "Functional")
   public void testGetHiddenBoundaryLeft()
   {
-- 
1.7.10.2