JAL-2446 merged to spike branch

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 70a7319..1e806a5 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -22,14 +22,17 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesSourceI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
@@ -50,6 +53,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
+import java.io.IOException;
 
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
@@ -64,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
-  FileParse source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
@@ -116,6 +120,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     addSequences.setVisible(false);
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == accept)
@@ -192,7 +197,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   {
     try
     {
-      NewickFile fin = new NewickFile(textarea.getText(), "Paste");
+      NewickFile fin = new NewickFile(textarea.getText(),
+              DataSourceType.PASTE);
 
       fin.parse();
       if (fin.getTree() != null)
@@ -223,17 +229,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   {
     AlignmentI al = null;
 
-    String format = new IdentifyFile().Identify(text,
-            AppletFormatAdapter.PASTE);
-    AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
     try
     {
-      al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+      FileFormatI format = new IdentifyFile().identify(text,
+              DataSourceType.PASTE);
+      AppletFormatAdapter afa = new AppletFormatAdapter(
+              alignFrame.alignPanel);
+      al = afa.readFile(text, DataSourceType.PASTE, format);
       source = afa.getAlignFile();
-    } catch (java.io.IOException ex)
-    {
-      ex.printStackTrace();
-    }
 
     if (al != null)
     {
@@ -254,8 +257,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+            HiddenColumns colSel = ((ComplexAlignFile) source)
+                    .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
@@ -277,6 +280,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         {
           af = new AlignFrame(al, alignFrame.viewport.applet,
                   "Cut & Paste input - " + format, false);
+          if (source instanceof FeaturesSourceI)
+          {
+            af.getAlignViewport().setShowSequenceFeatures(true);
+          }
         }
 
         af.statusBar
@@ -290,6 +297,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
                 .getString("label.successfully_pasted_alignment_file"));
       }
     }
+    } catch (IOException ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   /**
@@ -300,7 +311,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param al
    * @return
    */
-  protected boolean openSplitFrame(AlignmentI al, String format)
+  protected boolean openSplitFrame(AlignmentI al, FileFormatI format)
   {
     final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
             .getAlignment();
@@ -370,7 +381,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     try
     {
       tcf = new TCoffeeScoreFile(textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE);
+              jalview.io.DataSourceType.PASTE);
       if (tcf.isValid())
       {
         if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
@@ -403,7 +414,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (tcf == null)
     {
       if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
-              textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
+              textarea.getText(), jalview.io.DataSourceType.PASTE))
       {
         alignFrame.alignPanel.fontChanged();
         alignFrame.alignPanel.setScrollValues(0, 0);
@@ -415,7 +426,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       else
       {
         if (!alignFrame.parseFeaturesFile(textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE))
+                jalview.io.DataSourceType.PASTE))
         {
           alignFrame.statusBar
                   .setText(MessageManager
@@ -439,12 +450,12 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
       new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
-              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+              alignFrame.alignPanel, DataSourceType.PASTE);
     }
     else
     {
       new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
-              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+              alignFrame.alignPanel, DataSourceType.PASTE);
     }
   }
 
@@ -490,6 +501,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     this.add(textarea, java.awt.BorderLayout.CENTER);
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     if (textarea.getText().startsWith(
@@ -499,18 +511,22 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }