Merge branch 'features/JAL-2388OverviewWindow' into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 016ee85..4073e3e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -53,6 +53,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -233,7 +234,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param height
    *          height of frame.
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height)
   {
     this(al, hiddenColumns, width, height, null);
@@ -250,7 +251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param sequenceSetId
    *          (may be null)
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height, String sequenceSetId)
   {
     this(al, hiddenColumns, width, height, sequenceSetId, null);
@@ -269,7 +270,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param viewId
    *          (may be null)
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height, String sequenceSetId, String viewId)
   {
     setSize(width, height);
@@ -288,7 +289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection hiddenColumns, int width, int height)
+          HiddenColumns hiddenColumns, int width, int height)
   {
     setSize(width, height);
 
@@ -1192,8 +1193,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
               exportData.getOmitHidden(), exportData.getStartEndPostions(),
-              f.getCacheSuffixDefault(format),
-              viewport.getColumnSelection());
+              f.getCacheSuffixDefault(format), viewport.getAlignment()
+                      .getHiddenColumns());
 
       if (output == null)
       {
@@ -1271,8 +1272,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
               .formatSequences(format, exportData.getAlignment(),
                       exportData.getOmitHidden(),
-                      exportData.getStartEndPostions(),
-                      viewport.getColumnSelection()));
+ exportData
+                              .getStartEndPostions(), viewport
+                              .getAlignment().getHiddenColumns()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
               "label.alignment_output_command",
               new Object[] { e.getActionCommand() }), 600, 500);
@@ -1321,8 +1323,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignmentToExport = viewport.getAlignment();
     }
     alignmentStartEnd = alignmentToExport
-            .getVisibleStartAndEndIndex(viewport.getColumnSelection()
-                    .getHiddenColumns());
+            .getVisibleStartAndEndIndex(viewport.getAlignment()
+                    .getHiddenColumns()
+                    .getHiddenRegions());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1886,7 +1889,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       hiddenColumns = new ArrayList<int[]>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
-      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+      for (int[] region : viewport.getAlignment().getHiddenColumns()
+              .getHiddenRegions())
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
@@ -4655,9 +4659,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     viewport.getAlignment(), 0, false);
             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
             viewport.getAlignment().setSeqrep(repseq);
-            ColumnSelection cs = new ColumnSelection();
+            HiddenColumns cs = new HiddenColumns();
             cs.hideInsertionsFor(repseq);
-            viewport.setColumnSelection(cs);
+            viewport.getAlignment().setHiddenColumns(cs);
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))