From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 19 Jan 2018 07:51:31 +0000 (+0000)
Subject: JAL-2759 Update to getVisibleStartAndEndIndex after review
X-Git-Tag: Release_2_10_4~55^2~1^2~28
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=14b0554d88b9c2f51c15b7398430efa4b70529d6;p=jalview.git

JAL-2759 Update to getVisibleStartAndEndIndex after review
---

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index ea8da8d..77d1c65 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1234,42 +1234,27 @@ public class HiddenColumns
     try
     {
       LOCK.readLock().lock();
-      int[] alignmentStartEnd = new int[] { 0, width - 1 };
-      int startPos = alignmentStartEnd[0];
-      int endPos = alignmentStartEnd[1];
 
-      int[] lowestRange = new int[] { -1, -1 };
-      int[] higestRange = new int[] { -1, -1 };
+      int firstVisible = 0;
+      int lastVisible = width - 1;
 
-      if (hiddenColumns.isEmpty())
-      {
-        return new int[] { startPos, endPos };
-      }
-
-      for (int[] range : hiddenColumns)
+      if (!hiddenColumns.isEmpty())
       {
-        lowestRange = (range[0] <= startPos) ? range : lowestRange;
-        higestRange = (range[1] >= endPos) ? range : higestRange;
-      }
+        // first visible col with index 0, convert to absolute index
+        firstVisible = visibleToAbsoluteColumn(0);
 
-      if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
-      {
-        startPos = alignmentStartEnd[0];
-      }
-      else
-      {
-        startPos = lowestRange[1] + 1;
+        // last visible column is either immediately to left of
+        // last hidden region, or is just the last column in the alignment
+        int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1);
+        if (lastregion[1] == width - 1)
+        {
+          // last region is at very end of alignment
+          // last visible column immediately precedes it
+          lastVisible = lastregion[0] - 1;
+        }
       }
+      return new int[] { firstVisible, lastVisible };
 
-      if (higestRange[0] == -1) // includes (higestRange[1] == -1)
-      {
-        endPos = alignmentStartEnd[1];
-      }
-      else
-      {
-        endPos = higestRange[0] - 1;
-      }
-      return new int[] { startPos, endPos };
     } finally
     {
       LOCK.readLock().unlock();
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 9bbba5f..151e31d 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -679,7 +679,7 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testHideBitset()
+  public void testHideColumns_BitSet()
   {
     HiddenColumns cs;
 
@@ -1200,7 +1200,7 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = "Functional")
-  public void testSubtractVisibleColumns()
+  public void testOffsetByVisibleColumns()
   {
     HiddenColumns h = new HiddenColumns();
     int result = h.offsetByVisibleColumns(-1, 10);