Merge branch 'develop' into feature/JAL-2759

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 143e672..fa052f1 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -163,8 +163,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
-  ViewportRanges vpRanges;
-
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
@@ -336,7 +334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
-    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -654,9 +651,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+            ViewportRanges ranges = viewport.getRanges();
+            alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
                     .getStartRes();
-            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+            alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
                     .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
@@ -689,10 +687,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          vpRanges.pageUp();
+          viewport.getRanges().pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          vpRanges.pageDown();
+          viewport.getRanges().pageDown();
           break;
         }
       }
@@ -1864,23 +1862,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy();
-      for (int[] region : hiddenRegions)
-      {
-        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
-        {
-          hiddenColumns
-                  .add(new int[]
-                  { region[0] - hiddenOffset, region[1] - hiddenOffset });
-        }
-      }
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      hiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs,
@@ -2147,7 +2139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        vpRanges.setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2209,11 +2201,8 @@ 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
@@ -2268,11 +2257,8 @@ 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
@@ -2548,7 +2534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        vpRanges.setStartRes(0);
+        viewport.getRanges().setStartRes(0);
       }
       else
       {
@@ -2613,13 +2599,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    ViewportRanges ranges = viewport.getRanges();
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
 
@@ -2652,12 +2639,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    int startRes = seq.findPosition(viewport.getRanges().getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
@@ -2713,8 +2700,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
-            true);
+    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*