/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.api.FeaturesSourceI;
+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
boolean annotationImport = false;
- Sequence seq;
+ SequenceI seq;
AlignFrame alignFrame;
+ FileParse source = null;
+
public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
{
try
textarea.setText(text);
}
- public void setPDBImport(Sequence seq)
+ public void setPDBImport(SequenceI seq)
{
this.seq = seq;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
pdbImport = true;
}
public void setTreeImport()
{
treeImport = true;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
}
public void setAnnotationImport()
{
annotationImport = true;
- accept.setLabel("Accept");
+ accept.setLabel(MessageManager.getString("action.accept"));
addSequences.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == accept)
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);
+ }
+ }
+
+ /**
+ * 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");
- } catch (Exception ex)
+ fin.parse();
+ if (fin.getTree() != null)
{
- textarea.setText("Could not parse Newick file!\n" + ex);
- 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)
{
- if (new AnnotationFile().readAnnotationFile(
- alignFrame.viewport.alignment, textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE))
+ 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))
{
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
+ return;
+ }
+ if (newWindow)
+ {
+ AlignFrame af;
+ if (source instanceof ComplexAlignFile)
+ {
+ 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)
+ {
+ af.changeColour(cs);
+ }
+ }
+ else
+ {
+ af = new AlignFrame(al, alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ if (source instanceof FeaturesSourceI)
+ {
+ af.getAlignViewport().setShowSequenceFeatures(true);
+ }
+ }
+
+ af.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
}
else
{
- alignFrame.parseFeaturesFile(textarea.getText(),
- jalview.io.AppletFormatAdapter.PASTE);
+ alignFrame.addSequences(al.getSequencesArray());
+ alignFrame.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
}
}
- else if (alignFrame != 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)
{
- Alignment al = null;
+ return false;
+ }
- String format = new IdentifyFile().Identify(text,
- AppletFormatAdapter.PASTE);
- try
- {
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
+ /*
+ * 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;
+ }
- if (al != null)
+ /**
+ * 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 (newWindow)
+ if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
{
- AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
- "Cut & Paste input - " + format, false);
- af.statusBar.setText("Successfully pasted alignment file");
+ 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
{
- alignFrame.addSequences(al.getSequencesArray());
+ // 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;
}
+ if (tcf == null)
+ {
+ if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
+ textarea.getText(), jalview.io.AppletFormatAdapter.PASTE))
+ {
+ alignFrame.alignPanel.fontChanged();
+ alignFrame.alignPanel.setScrollValues(0, 0);
+ alignFrame.statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_annotation_to_alignment"));
- if (this.getParent() instanceof Frame)
+ }
+ 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"));
+ }
+ }
+ }
+ }
+
+ /**
+ * 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);
}
}
private void jbInit() throws Exception
{
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
- textarea.setText("Paste your alignment file here");
+ textarea.setText(MessageManager
+ .getString("label.paste_your_alignment_file"));
textarea.addMouseListener(this);
this.setLayout(borderLayout1);
accept.addActionListener(this);
this.add(textarea, java.awt.BorderLayout.CENTER);
}
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (textarea.getText().startsWith("Paste your"))
+ if (textarea.getText().startsWith(
+ MessageManager.getString("label.paste_your")))
{
textarea.setText("");
}
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
git://source.jalview.org / jalview.git / blobdiff