From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 26 Sep 2017 13:04:36 +0000 (+0100)
Subject: JAL-2674 more List<int[]> -> HiddenColumns copy changes
X-Git-Tag: Release_2_10_4~55^2~1^2~105
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=15f319be6f7781efdca23314ec9a13595e938eb9;p=jalview.git

JAL-2674 more List<int[]> -> HiddenColumns copy changes
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d843c7f..4e23f2b 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2259,11 +2259,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-        for (int region[] : hc)
-        {
-          af.viewport.hideColumns(region[0], region[1]);
-        }
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
       }
 
       // >>>This is a fix for the moment, until a better solution is
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index d07cae2..76c711f 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -49,7 +50,6 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.regex.Pattern;
@@ -962,12 +962,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset