X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=cbd3b34ac76e3d4c34e2f8af88b0fb9b7f98c169;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=ff0554740c7d750a7bb42755f7cdb033561a5510;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index ff05547..cbd3b34 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,31 +1,56 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.api.ComplexAlignFile;
+import jalview.bin.JalviewLite;
+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.json.binding.biojson.v1.ColourSchemeMapper;
+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
 {
@@ -35,10 +60,12 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   boolean annotationImport = false;
 
-  Sequence seq;
+  SequenceI seq;
 
   AlignFrame alignFrame;
 
+  FileParse source = null;
+
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
     try
@@ -67,7 +94,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     textarea.setText(text);
   }
 
-  public void setPDBImport(Sequence seq)
+  public void setPDBImport(SequenceI seq)
   {
     this.seq = seq;
     accept.setLabel(MessageManager.getString("action.accept"));
@@ -126,135 +153,298 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (pdbImport)
     {
-      PDBEntry pdb = new PDBEntry();
-      pdb.setFile(text);
-
-      if (alignFrame.alignPanel.av.applet.jmolAvailable)
-        new jalview.appletgui.AppletJmol(pdb, new Sequence[]
-        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
-      else
-
-        new MCview.AppletPDBViewer(pdb, new Sequence[]
-        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      openPdbViewer(text);
 
     }
     else if (treeImport)
     {
-      try
+      if (!loadTree())
       {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(
-                textarea.getText(), "Paste");
+        return;
+      }
+    }
+    else if (annotationImport)
+    {
+      loadAnnotations();
+    }
+    else if (alignFrame != null)
+    {
+      loadAlignment(text, newWindow, alignFrame.getAlignViewport());
+    }
 
-        fin.parse();
-        if (fin.getTree() != null)
-        {
-          alignFrame.loadTree(fin, "Pasted tree file");
-        }
+    // TODO: dialog should indicate if data was parsed correctly or not - see
+    // JAL-1102
+    if (this.getParent() instanceof Frame)
+    {
+      ((Frame) this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ((Dialog) this.getParent()).setVisible(false);
+    }
+  }
 
-      } catch (Exception ex)
+  /**
+   * Parses text as Newick Tree format, and loads on to the alignment. Returns
+   * true if successful, else false.
+   */
+  protected boolean loadTree()
+  {
+    try
+    {
+      NewickFile fin = new NewickFile(textarea.getText(), "Paste");
+
+      fin.parse();
+      if (fin.getTree() != null)
       {
-        // TODO: JAL-1102 - should have a warning message in dialog, not simply
-        // overwrite the broken input data with the exception
-        textarea.setText(MessageManager.formatMessage("label.could_not_parse_newick_file", new String[]{ex.getMessage()}));
-        return;
+        alignFrame.loadTree(fin, "Pasted tree file");
+        return true;
       }
+    } catch (Exception ex)
+    {
+      // TODO: JAL-1102 - should have a warning message in dialog, not simply
+      // overwrite the broken input data with the exception
+      textarea.setText(MessageManager.formatMessage(
+              "label.could_not_parse_newick_file",
+              new Object[] { ex.getMessage() }));
+      return false;
     }
-    else if (annotationImport)
+    return false;
+  }
+
+  /**
+   * Parse text as an alignment file and add to the current or a new window.
+   * 
+   * @param text
+   * @param newWindow
+   */
+  protected void loadAlignment(String text, boolean newWindow,
+          AlignViewport viewport)
+  {
+    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);
+      source = afa.getAlignFile();
+    } catch (java.io.IOException ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (al != null)
     {
-      TCoffeeScoreFile tcf = null;
-      try
+      al.setDataset(null); // set dataset on alignment/sequences
+
+      /*
+       * SplitFrame option dependent on applet parameter for now.
+       */
+      boolean allowSplitFrame = alignFrame.viewport.applet
+              .getDefaultParameter("enableSplitFrame", false);
+      if (allowSplitFrame && openSplitFrame(al, format))
+      {
+        return;
+      }
+      if (newWindow)
       {
-        tcf = new TCoffeeScoreFile(textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE);
-        if (tcf.isValid())
+        AlignFrame af;
+
+        if (source instanceof ComplexAlignFile)
         {
-          if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
-                  true))
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          boolean showSeqFeatures = ((ComplexAlignFile) source)
+                  .isShowSeqFeatures();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
+          af = new AlignFrame(al, hiddenSeqs, colSel,
+                  alignFrame.viewport.applet, "Cut & Paste input - "
+                          + format, false);
+          af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
+          if (cs != null)
           {
-            alignFrame.tcoffeeColour.setEnabled(true);
-            alignFrame.alignPanel.fontChanged();
-            alignFrame.changeColour(new TCoffeeColourScheme(
-                    alignFrame.viewport.getAlignment()));
-            alignFrame.statusBar
-                    .setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
-          }
-          else
-          {
-            // file valid but didn't get added to alignment for some reason
-            alignFrame.statusBar.setText(MessageManager.formatMessage("label.failed_add_tcoffee_scores", new String[]{(tcf.getWarningMessage() != null ? tcf.getWarningMessage() : "")}));
+            af.changeColour(cs);
           }
         }
         else
         {
-          tcf = null;
+          af = new AlignFrame(al, alignFrame.viewport.applet,
+                  "Cut & Paste input - " + format, false);
         }
-      } catch (Exception x)
+
+        af.statusBar
+                .setText(MessageManager
+                        .getString("label.successfully_pasted_annotation_to_alignment"));
+      }
+      else
       {
-        tcf = null;
+        alignFrame.addSequences(al.getSequencesArray());
+        alignFrame.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
       }
-      if (tcf == null)
+    }
+  }
+
+  /**
+   * Check whether the new alignment could be mapped to the current one as
+   * cDNA/protein, if so offer the option to open as split frame view. Returns
+   * true if a split frame view is opened, false if not.
+   * 
+   * @param al
+   * @return
+   */
+  protected boolean openSplitFrame(AlignmentI al, String format)
+  {
+    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+            .getAlignment();
+    if (thisAlignment.isNucleotide() == al.isNucleotide())
+    {
+      // both nucleotide or both protein
+      return false;
+    }
+    AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
+    AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
+    boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
+    if (!mapped)
+    {
+      return false;
+    }
+
+    /*
+     * A mapping is possible; ask user if they want a split frame.
+     */
+    String title = MessageManager.getString("label.open_split_window");
+    final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
+            true, 100, 400);
+    dialog.ok.setLabel(MessageManager.getString("action.yes"));
+    dialog.cancel.setLabel(MessageManager.getString("action.no"));
+    Panel question = new Panel(new BorderLayout());
+    final String text = MessageManager
+            .getString("label.open_split_window?");
+    question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
+    dialog.setMainPanel(question);
+    dialog.setVisible(true);
+    dialog.toFront();
+
+    if (!dialog.accept)
+    {
+      return false;
+    }
+
+    /*
+     * 'align' the added alignment to match the current one
+     */
+    al.alignAs(thisAlignment);
+
+    /*
+     * Open SplitFrame with DNA above and protein below, including the alignment
+     * from textbox and a copy of the original.
+     */
+    final JalviewLite applet = this.alignFrame.viewport.applet;
+    AlignFrame copyFrame = new AlignFrame(
+            this.alignFrame.viewport.getAlignment(), applet,
+            alignFrame.getTitle(), false, false);
+    AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
+            "Cut & Paste input - " + format, false, false);
+    AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
+    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
+    SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
+    sf.addToDisplay(false, applet);
+    return true;
+  }
+
+  /**
+   * Parse the text as a TCoffee score file, if successful add scores as
+   * alignment annotations.
+   */
+  protected void loadAnnotations()
+  {
+    TCoffeeScoreFile tcf = null;
+    try
+    {
+      tcf = new TCoffeeScoreFile(textarea.getText(),
+              jalview.io.AppletFormatAdapter.PASTE);
+      if (tcf.isValid())
       {
-        if (new AnnotationFile().readAnnotationFile(
-                alignFrame.viewport.getAlignment(), textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE))
+        if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
         {
+          alignFrame.tcoffeeColour.setEnabled(true);
           alignFrame.alignPanel.fontChanged();
-          alignFrame.alignPanel.setScrollValues(0, 0);
+          alignFrame.changeColour(new TCoffeeColourScheme(
+                  alignFrame.viewport.getAlignment()));
           alignFrame.statusBar
-                  .setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
-
+                  .setText(MessageManager
+                          .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
         }
         else
         {
-          if (!alignFrame.parseFeaturesFile(textarea.getText(),
-                  jalview.io.AppletFormatAdapter.PASTE))
-          {
-            alignFrame.statusBar
-                    .setText(MessageManager.getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
-          }
+          // file valid but didn't get added to alignment for some reason
+          alignFrame.statusBar.setText(MessageManager.formatMessage(
+                  "label.failed_add_tcoffee_scores",
+                  new Object[] { (tcf.getWarningMessage() != null ? tcf
+                          .getWarningMessage() : "") }));
         }
       }
+      else
+      {
+        tcf = null;
+      }
+    } catch (Exception x)
+    {
+      tcf = null;
     }
-    else if (alignFrame != null)
+    if (tcf == null)
     {
-      Alignment al = null;
-
-      String format = new IdentifyFile().Identify(text,
-              AppletFormatAdapter.PASTE);
-      try
+      if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+              textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
       {
-        al = new AppletFormatAdapter().readFile(text,
-                AppletFormatAdapter.PASTE, format);
-      } catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
+        alignFrame.alignPanel.fontChanged();
+        alignFrame.alignPanel.setScrollValues(0, 0);
+        alignFrame.statusBar
+                .setText(MessageManager
+                        .getString("label.successfully_pasted_annotation_to_alignment"));
 
-      if (al != null)
+      }
+      else
       {
-        if (newWindow)
-        {
-          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
-                  "Cut & Paste input - " + format, false);
-          af.statusBar.setText(MessageManager.getString("label.successfully_pasted_annotation_to_alignment"));
-        }
-        else
+        if (!alignFrame.parseFeaturesFile(textarea.getText(),
+                jalview.io.AppletFormatAdapter.PASTE))
         {
-          alignFrame.addSequences(al.getSequencesArray());
           alignFrame.statusBar
-                  .setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+                  .setText(MessageManager
+                          .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
         }
       }
     }
-    // TODO: dialog should indicate if data was parsed correctly or not - see
-    // JAL-1102
-    if (this.getParent() instanceof Frame)
+  }
+
+  /**
+   * Open a Jmol viewer (if available), failing that the built-in PDB viewer,
+   * passing the input text as the PDB file data.
+   * 
+   * @param text
+   */
+  protected void openPdbViewer(String text)
+  {
+    PDBEntry pdb = new PDBEntry();
+    pdb.setFile(text);
+
+    if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
-      ((Frame) this.getParent()).setVisible(false);
+      new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
     else
     {
-      ((Dialog) this.getParent()).setVisible(false);
+      new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
   }
 
@@ -286,7 +476,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   private void jbInit() throws Exception
   {
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText(MessageManager.getString("label.paste_your_alignment_file"));
+    textarea.setText(MessageManager
+            .getString("label.paste_your_alignment_file"));
     textarea.addMouseListener(this);
     this.setLayout(borderLayout1);
     accept.addActionListener(this);
@@ -301,7 +492,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   public void mousePressed(MouseEvent evt)
   {
-    if (textarea.getText().startsWith(MessageManager.getString("label.paste_your")))
+    if (textarea.getText().startsWith(
+            MessageManager.getString("label.paste_your")))
     {
       textarea.setText("");
     }