JAL-2446 merged to spike branch

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index df0142c..3eced2f 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -28,9 +28,9 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -73,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewportI viewport;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer()
   {
@@ -233,7 +233,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
                 JvOptionPane.WARNING_MESSAGE);
       }
@@ -262,7 +262,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       String title = MessageManager.formatMessage(
               "label.input_cut_paste_params",
-              new String[] { format.toString() });
+              new String[] { format.getName() });
       FeatureSettingsModelI proxyColourScheme = source
               .getFeatureColourScheme();
 
@@ -284,8 +284,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         AlignFrame af;
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+          HiddenColumns hidden = ((ComplexAlignFile) source)
+                  .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
@@ -294,10 +294,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getGlobalColourScheme();
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
-          af = new AlignFrame(al, hiddenSeqs, colSel,
+          af = new AlignFrame(al, hiddenSeqs, hidden,
                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
+          af.setMenusForViewport();
           ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                   colourSchemeName, al);
           if (cs != null)
@@ -340,7 +341,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
                 JvOptionPane.WARNING_MESSAGE);
       }