From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 7 Jun 2017 09:58:04 +0000 (+0100)
Subject: JAL-2591 updated HiddenColumns::findHiddenRegionPositions + test
X-Git-Tag: Release_2_10_3b1~183^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1c251a57c7b2fb70dabceb480d0170363357558f;p=jalview.git

JAL-2591 updated HiddenColumns::findHiddenRegionPositions + test
---

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 7ead681..5bb0f75 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -449,10 +449,11 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       if (av.getShowHiddenMarkers())
       {
         int widthx = 1 + endx - startx;
-        for (int i = 0; i < hidden.getHiddenRegions().size(); i++)
+        List<Integer> positions = hidden.findHiddenRegionPositions();
+        for (int pos : positions)
         {
 
-          res = hidden.findHiddenRegionPosition(i) - startx;
+          res = pos - startx;
 
           if (res < 0 || res > widthx)
           {
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index b96c491..94f1caa 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -37,6 +37,7 @@ import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
 import java.beans.PropertyChangeEvent;
+import java.util.List;
 
 public class SeqCanvas extends Panel implements ViewportListenerI
 {
@@ -487,11 +488,10 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        for (int i = 0; i < hidden.getHiddenRegions()
-                .size(); i++)
+        List<Integer> positions = hidden.findHiddenRegionPositions();
+        for (int pos : positions)
         {
-          res = hidden.findHiddenRegionPosition(i)
-                  - startRes;
+          res = pos - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 9722c0a..1e1a58b 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -273,39 +273,41 @@ public class HiddenColumns implements Iterable<int[]>
   }
 
   /**
-   * Use this method to determine where the next hiddenRegion starts
+   * Use this method to determine the set of hiddenRegion start positions
    * 
-   * @param hiddenRegion
-   *          index of hidden region (counts from 0)
-   * @return column number in visible view
+   * @return list of column number in visible view where hidden regions start
    */
-  public int findHiddenRegionPosition(int hiddenRegion)
+  public List<Integer> findHiddenRegionPositions()
   {
     try
     {
       lock.readLock().lock();
-      int result = 0;
-      if (hiddenColumns != null)
+      List<Integer> positions = new ArrayList<>(
+              hiddenColumns.size());
+
+      positions.add(hiddenColumns.elementAt(0)[0]);
+      for (int i = 1; i < hiddenColumns.size(); ++i)
       {
-        int index = 0;
-        int gaps = 0;
-        do
+
+        int result = 0;
+        if (hiddenColumns != null)
         {
-          int[] region = hiddenColumns.elementAt(index);
-          if (hiddenRegion == 0)
+          int index = 0;
+          int gaps = 0;
+          do
           {
-            return region[0];
-          }
-
-          gaps += region[1] + 1 - region[0];
-          result = region[1] + 1;
-          index++;
-        } while (index <= hiddenRegion);
+            int[] region = hiddenColumns.elementAt(index);
+            gaps += region[1] + 1 - region[0];
+            result = region[1] + 1;
+            index++;
+          } while (index <= i);
 
-        result -= gaps;
+          result -= gaps;
+        }
+        positions.add(result);
       }
 
-      return result;
+      return positions;
     }
     finally
     {
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 81befd8..dcaafcd 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -497,11 +497,10 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
       if (av.getShowHiddenMarkers())
       {
-        for (int i = 0; i < hidden.getHiddenRegions()
-                .size(); i++)
+        List<Integer> positions = hidden.findHiddenRegionPositions();
+        for (int pos : positions)
         {
-          res = hidden.findHiddenRegionPosition(i)
-                  - startx;
+          res = pos - startx;
 
           if (res < 0 || res > widthx)
           {
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 6f3ff58..4114385 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -40,6 +40,7 @@ import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
+import java.util.List;
 
 import javax.swing.JComponent;
 
@@ -562,9 +563,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         g.setColor(Color.blue);
         int res;
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        for (int i = 0; i < hidden.getHiddenRegions().size(); i++)
+        List<Integer> positions = hidden.findHiddenRegionPositions();
+        for (int pos : positions)
         {
-          res = hidden.findHiddenRegionPosition(i) - startRes;
+          res = pos - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 10808d6..b9becf3 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -585,4 +585,19 @@ public class HiddenColumnsTest
       assertEquals(toMark, fromMark);
     }
   }
+
+  @Test(groups = { "Functional" })
+  public void testFindHiddenRegionPositions()
+  {
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(3, 7);
+    hc.hideColumns(10, 10);
+    hc.hideColumns(14, 15);
+
+    List<Integer> positions = hc.findHiddenRegionPositions();
+    assertEquals(3, positions.size());
+    assertEquals(3, positions.get(0).intValue());
+    assertEquals(5, positions.get(1).intValue());
+    assertEquals(8, positions.get(2).intValue());
+  }
 }