JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 036bbe3..535dc62 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -20,33 +20,36 @@
  */
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Button;
-import java.awt.Dialog;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Label;
-import java.awt.Panel;
-import java.awt.TextArea;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
 import jalview.analysis.AlignmentUtils;
+import jalview.api.ComplexAlignFile;
 import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Dialog;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
 {
@@ -60,6 +63,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
+  FileParse source = null;
+
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
     try
@@ -163,7 +168,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     }
     else if (alignFrame != null)
     {
-      loadAlignment(text, newWindow);
+      loadAlignment(text, newWindow, alignFrame.getAlignViewport());
     }
 
     // TODO: dialog should indicate if data was parsed correctly or not - see
@@ -212,16 +217,18 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param text
    * @param newWindow
    */
-  protected void loadAlignment(String text, boolean newWindow)
+  protected void loadAlignment(String text, boolean newWindow,
+          AlignViewport viewport)
   {
-    Alignment al = null;
+    AlignmentI al = null;
 
     String format = new IdentifyFile().Identify(text,
             AppletFormatAdapter.PASTE);
+    AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
     try
     {
-      al = new AppletFormatAdapter().readFile(text,
-              AppletFormatAdapter.PASTE, format);
+      al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+      source = afa.getAlignFile();
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -230,14 +237,41 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (al != null)
     {
       al.setDataset(null); // set dataset on alignment/sequences
-      if (openSplitFrame(al, format))
+
+      /*
+       * SplitFrame option dependent on applet parameter for now.
+       */
+      boolean allowSplitFrame = alignFrame.viewport.applet
+              .getDefaultParameter("enableSplitFrame", false);
+      if (allowSplitFrame && openSplitFrame(al, format))
       {
         return;
       }
       if (newWindow)
       {
-        AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
-                "Cut & Paste input - " + format, false);
+        AlignFrame af;
+
+        if (source instanceof ComplexAlignFile)
+        {
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          boolean showSeqFeatures = ((ComplexAlignFile) source)
+                  .isShowSeqFeatures();
+          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          af = new AlignFrame(al, hiddenSeqs, colSel,
+                  alignFrame.viewport.applet, "Cut & Paste input - "
+                          + format, false);
+          af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.changeColour(cs);
+        }
+        else
+        {
+          af = new AlignFrame(al, alignFrame.viewport.applet,
+                  "Cut & Paste input - " + format, false);
+        }
+
         af.statusBar
                 .setText(MessageManager
                         .getString("label.successfully_pasted_annotation_to_alignment"));
@@ -259,7 +293,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param al
    * @return
    */
-  protected boolean openSplitFrame(Alignment al, String format)
+  protected boolean openSplitFrame(AlignmentI al, String format)
   {
     final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
     if (thisAlignment.isNucleotide() == al.isNucleotide())