X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=b3bff0ddc2694e8aa299ebcfa8c8891d6b92239e;hb=fd5f6d3eed59b5f6d9a7cc09e4ddeb7e78eb2f17;hp=4184ecaadc9f5c673d303dc1717a7f4d0228032e;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 4184eca..b3bff0d 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -28,10 +28,13 @@ 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.AlignmentFileReaderI;
 import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
@@ -49,6 +52,9 @@ import java.awt.datatransfer.Transferable;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
 
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
@@ -67,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewportI viewport;
 
-  FileParse source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer()
   {
@@ -134,8 +140,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager
-            .getString("label.save_text_to_file"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -144,8 +150,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       try
       {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-                new java.io.FileWriter(chooser.getSelectedFile()));
+        PrintWriter out = new PrintWriter(
+                new FileWriter(chooser.getSelectedFile()));
 
         out.print(getText());
         out.close();
@@ -190,8 +196,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     try
     {
-      textarea.append((String) contents
-              .getTransferData(DataFlavor.stringFlavor));
+      textarea.append(
+              (String) contents.getTransferData(DataFlavor.stringFlavor));
     } catch (Exception ex)
     {
     }
@@ -212,15 +218,22 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       return;
     }
 
-    String format = new IdentifyFile().identify(text, "Paste");
-    if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+    FileFormatI format = null;
+    try
+    {
+      format = new IdentifyFile().identify(text, DataSourceType.PASTE);
+    } catch (FileFormatException e1)
+    {
+      // leave as null
+    }
+    if (format == null)
     {
-      System.err.println(MessageManager
-              .getString("label.couldnt_read_data"));
+      System.err
+              .println(MessageManager.getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
                 JvOptionPane.WARNING_MESSAGE);
       }
@@ -230,29 +243,26 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     // TODO: identify feature, annotation or tree file and parse appropriately.
     AlignmentI al = null;
 
-    if (FormatAdapter.isValidFormat(format))
+    try
     {
-      try
-      {
-        FormatAdapter fa = new FormatAdapter(alignpanel);
-        al = fa.readFile(getText(), "Paste", format);
-        source = fa.getAlignFile();
+      FormatAdapter fa = new FormatAdapter(alignpanel);
+      al = fa.readFile(getText(), DataSourceType.PASTE, format);
+      source = fa.getAlignFile();
 
-      } catch (java.io.IOException ex)
-      {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.formatMessage(
-                        "label.couldnt_read_pasted_text",
-                        new String[] { ex.toString() }), MessageManager
-                        .getString("label.error_parsing_text"),
-                JvOptionPane.WARNING_MESSAGE);
-      }
+    } catch (IOException ex)
+    {
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.couldnt_read_pasted_text", new String[]
+              { ex.toString() }),
+              MessageManager.getString("label.error_parsing_text"),
+              JvOptionPane.WARNING_MESSAGE);
     }
 
     if (al != null && al.hasValidSequence())
     {
-      String title = MessageManager.formatMessage(
-              "label.input_cut_paste_params", new String[] { format });
+      String title = MessageManager
+              .formatMessage("label.input_cut_paste_params", new String[]
+              { format.getName() });
       FeatureSettingsModelI proxyColourScheme = source
               .getFeatureColourScheme();
 
@@ -274,8 +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)
@@ -284,10 +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)
@@ -311,13 +322,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         af.currentFileFormat = format;
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager
+        af.setStatus(MessageManager
                 .getString("label.successfully_pasted_alignment_file"));
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
-                  false));
+          af.setMaximum(
+                  jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
         } catch (Exception ex)
         {
         }
@@ -325,12 +336,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
     else
     {
-      System.err.println(MessageManager
-              .getString("label.couldnt_read_data"));
+      System.err
+              .println(MessageManager.getString("label.couldnt_read_data"));
       if (!Jalview.isHeadlessMode())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                AppletFormatAdapter.SUPPORTED_FORMATS,
+                AppletFormatAdapter.getSupportedFormats(),
                 MessageManager.getString("label.couldnt_read_data"),
                 JvOptionPane.WARNING_MESSAGE);
       }