X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=8396e6a80d109b87b368ab3296b1a04e3c9aa8d5;hb=2503f4dfa319a2854d2cc8f7e07e7b979df6bff6;hp=f53638234f3579da27b8edd81759cba378f60a59;hpb=fd29e047719a470cf304c5a41abfff5c1eac3ee8;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index f536382..80838e2
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,113 +1,305 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Softwarechang
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.MenuEvent;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.Dna;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.FeaturesFile;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.seqfetcher.DbSourceProxy;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AlignFrame
- extends GAlignFrame implements DropTargetListener
+public class AlignFrame extends GAlignFrame implements DropTargetListener,
+ IProgressIndicator, AlignViewControllerGuiI
{
- /** DOCUMENT ME!! */
+
public static final int DEFAULT_WIDTH = 700;
- /** DOCUMENT ME!! */
public static final int DEFAULT_HEIGHT = 500;
+
+ /*
+ * The currently displayed panel (selected tabbed view if more than one)
+ */
public AlignmentPanel alignPanel;
AlignViewport viewport;
- Vector alignPanels = new Vector();
+ public AlignViewControllerI avc;
+ List alignPanels = new ArrayList();
- /**
- * Last format used to load or save alignments in this window
+ /**
+ * Last format used to load or save alignments in this window
*/
String currentFileFormat = null;
+
/**
* Current filename for this alignment
*/
String fileName = null;
-
-
-
/**
- * Creates a new AlignFrame object.
- *
- * @param al DOCUMENT ME!
+ * Creates a new AlignFrame object with specific width and height.
+ *
+ * @param al
+ * @param width
+ * @param height
*/
public AlignFrame(AlignmentI al, int width, int height)
{
this(al, null, width, height);
}
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
+ {
+ this(al, null, width, height, sequenceSetId);
+ }
+
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * @param viewId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
+ {
+ this(al, null, width, height, sequenceSetId, viewId);
+ }
/**
* new alignment window with hidden columns
- * @param al AlignmentI
- * @param hiddenColumns ColumnSelection or null
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
- int width, int height)
+ int width, int height)
{
- this.setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns);
+ this(al, hiddenColumns, width, height, null);
+ }
- alignPanel = new AlignmentPanel(this, viewport);
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId)
+ {
+ this(al, hiddenColumns, width, height, sequenceSetId, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId, String viewId)
+ {
+ setSize(width, height);
- if(al.getDataset()==null)
+ if (al.getDataset() == null)
{
al.setDataset(null);
}
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+
addAlignmentPanel(alignPanel, true);
init();
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
- * @param ap AlignmentPanel
- * @param av AlignViewport
+ * Make a new AlignFrame from existing alignmentPanels
+ *
+ * @param ap
+ * AlignmentPanel
+ * @param av
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
@@ -117,19 +309,26 @@ public class AlignFrame
init();
}
+ /**
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
+ */
void init()
{
- if (viewport.conservation == null)
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
+ if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
- // PIDColour.setEnabled(false);
- // abovePIDThreshold.setEnabled(false);
- // modifyPID.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ "No sort");
if (sortby.equals("Id"))
{
@@ -141,291 +340,357 @@ public class AlignFrame
}
if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
- }
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide(viewport.getAlignment().isNucleotide());
+ }
- setMenusFromViewport(viewport);
- buildSortByAnnotationScoresMenu();
- if (viewport.wrapAlignment)
- {
- wrapMenuItem_actionPerformed(null);
- }
+ setMenusFromViewport(viewport);
+ buildSortByAnnotationScoresMenu();
+ buildTreeMenu();
+
+ if (viewport.getWrapAlignment())
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
- addKeyListener();
+ addKeyListener();
+
+ final List selviews = new ArrayList();
+ final List origview = new ArrayList();
+ final String menuLabel = MessageManager
+ .getString("label.copy_format_from");
+ ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
+ new ViewSetProvider()
+ {
+
+ @Override
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ origview.clear();
+ origview.add(alignPanel);
+ // make an array of all alignment panels except for this one
+ List aps = new ArrayList(
+ Arrays.asList(Desktop.getAlignmentPanels(null)));
+ aps.remove(AlignFrame.this.alignPanel);
+ return aps.toArray(new AlignmentPanel[aps.size()]);
+ }
+ }, selviews, new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (origview.size() > 0)
+ {
+ final AlignmentPanel ap = origview.get(0);
+
+ /*
+ * Copy the ViewStyle of the selected panel to 'this one'.
+ * Don't change value of 'scaleProteinAsCdna' unless copying
+ * from a SplitFrame.
+ */
+ ViewStyleI vs = selviews.get(0).getAlignViewport()
+ .getViewStyle();
+ boolean fromSplitFrame = selviews.get(0)
+ .getAlignViewport().getCodingComplement() != null;
+ if (!fromSplitFrame)
+ {
+ vs.setScaleProteinAsCdna(ap.getAlignViewport()
+ .getViewStyle().isScaleProteinAsCdna());
+ }
+ ap.getAlignViewport().setViewStyle(vs);
+
+ /*
+ * Also rescale ViewStyle of SplitFrame complement if there is
+ * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
+ * the whole ViewStyle (allow cDNA protein to have different
+ * fonts)
+ */
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ if (complement != null && vs.isScaleProteinAsCdna())
+ {
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ ((SplitFrame) af.getSplitViewContainer())
+ .adjustLayout();
+ af.setMenusForViewport();
+ }
+
+ ap.updateLayout();
+ ap.setSelected(true);
+ ap.alignFrame.setMenusForViewport();
+
+ }
+ }
+ });
+ formatMenu.add(vsel);
}
+
/**
- * Change the filename and format for the alignment, and
- * enable the 'reload' button functionality.
- * @param file valid filename
- * @param format format of file
+ * Change the filename and format for the alignment, and enable the 'reload'
+ * button functionality.
+ *
+ * @param file
+ * valid filename
+ * @param format
+ * format of file
*/
public void setFileName(String file, String format)
{
- fileName = file;
- currentFileFormat = format;
- reload.setEnabled(true);
+ fileName = file;
+ setFileFormat(format);
+ reload.setEnabled(true);
}
+ /**
+ * Add a KeyListener with handlers for various KeyPressed and KeyReleased
+ * events
+ */
void addKeyListener()
{
- addKeyListener(new KeyAdapter()
+ addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
{
- public void keyPressed(KeyEvent evt)
+ if (viewport.cursorMode
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && Character.isDigit(evt.getKeyChar()))
{
- if (viewport.cursorMode &&
- ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
- evt.getKeyCode() <= KeyEvent.VK_9)
- ||
- (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
- evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
- )
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
- switch (evt.getKeyCode())
- {
-
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
-
- break;
-
- case KeyEvent.VK_DOWN:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(false);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
- break;
-
- case KeyEvent.VK_UP:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(true);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
-
- break;
-
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( -1, 0);
+ alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+ }
+ switch (evt.getKeyCode())
+ {
- break;
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor(1, 0);
- break;
+ break;
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
- break;
+ case KeyEvent.VK_DOWN:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ moveSelectedSequences(false);
+ }
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().moveCursor(0, 1);
+ }
+ break;
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (!viewport.cursorMode)
- {
- cut_actionPerformed(null);
- }
- else
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
+ case KeyEvent.VK_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ moveSelectedSequences(true);
+ }
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().moveCursor(0, -1);
+ }
- break;
+ break;
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.getSeqPanel().moveCursor(-1, 0);
+ }
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ break;
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.getSeqPanel().moveCursor(1, 0);
+ }
+ break;
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is " +
- (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- alignPanel.seqPanel.seqCanvas.repaint();
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
+
+ // case KeyEvent.VK_A:
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ // //System.out.println("A");
+ // }
+ // break;
+ /*
+ * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
+ * System.out.println("closing bracket"); } break;
+ */
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ {
+ alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
- case KeyEvent.VK_F1:
- try
- {
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+ break;
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- break
- ;
- case KeyEvent.VK_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.getSeqPanel().setCursorColumn();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().setCursorPosition();
+ }
+ break;
- boolean hide = false;
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().setCursorRowAndColumn();
+ }
+ break;
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (! (toggleCols &&
- viewport.colSel.getSelected().size() > 0))
- {
- showAllSeqs_actionPerformed(null);
- }
- }
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
+ if (viewport.cursorMode)
+ {
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.getSeqPanel().seqCanvas.repaint();
+ break;
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- showAllColumns_actionPerformed(null);
- }
- }
- break;
- }
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
- break;
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
- break;
+ case KeyEvent.VK_F1:
+ try
+ {
+ Help.showHelpWindow();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(false);
}
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
}
+ }
+ @Override
public void keyReleased(KeyEvent evt)
{
- switch(evt.getKeyCode())
+ switch (evt.getKeyCode())
{
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- break;
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ break;
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- break;
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ break;
}
}
- });
+ });
}
-
- public void addAlignmentPanel(final AlignmentPanel ap,
- boolean newPanel)
+ public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
- alignPanels.addElement(ap);
+ alignPanels.add(ap);
PaintRefresher.Register(ap, ap.av.getSequenceSetId());
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
- if (aSize == 1 && ap.av.viewName==null)
+ if (aSize == 1 && ap.av.viewName == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
@@ -443,14 +708,15 @@ public class AlignFrame
ap.setVisible(false);
}
- if(newPanel)
+ if (newPanel)
{
- if (ap.av.padGaps)
+ if (ap.av.isPadGaps())
{
- ap.av.alignment.padGaps();
+ ap.av.getAlignment().padGaps();
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
}
}
@@ -459,12 +725,11 @@ public class AlignFrame
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
- tabbedPane.addTab(first.av.viewName,first);
+ AlignmentPanel first = alignPanels.get(0);
+ tabbedPane.addTab(first.av.viewName, first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
-
public AlignViewport getViewport()
{
return viewport;
@@ -474,109 +739,177 @@ public class AlignFrame
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
- // Do this once to get current state
- BuildWebServiceMenu();
- Desktop.discoverer.addPropertyChangeListener(
- thisListener = new java.beans.PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- // System.out.println("Discoverer property change.");
- if (evt.getPropertyName().equals("services"))
- {
- // System.out.println("Rebuilding web service menu");
- BuildWebServiceMenu();
- }
- }
- });
+ Desktop.instance.addJalviewPropertyChangeListener("services",
+ thisListener = new java.beans.PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
- addInternalFrameListener(new javax.swing.event.
- InternalFrameAdapter()
+ @Override
+ public void run()
+ {
+ System.err
+ .println("Rebuild WS Menu for service change");
+ BuildWebServiceMenu();
+ }
+
+ });
+ }
+ }
+ });
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
- Desktop.discoverer.removePropertyChangeListener(thisListener);
+ System.out.println("deregistering discoverer listener");
+ Desktop.instance.removeJalviewPropertyChangeListener("services",
+ thisListener);
closeMenuItem_actionPerformed(true);
- }
- ;
+ };
});
+ // Finally, build the menu once to get current service state
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BuildWebServiceMenu();
+ }
+ }).start();
}
+ /**
+ * Configure menu items that vary according to whether the alignment is
+ * nucleotide or protein
+ *
+ * @param nucleotide
+ */
public void setGUINucleotide(boolean nucleotide)
{
- showTranslation.setVisible( nucleotide );
- conservationMenuItem.setEnabled( !nucleotide );
- modifyConservation.setEnabled( !nucleotide );
-
- //Remember AlignFrame always starts as protein
- if(!nucleotide)
- {
- calculateMenu.remove(calculateMenu.getItemCount()-2);
- }
- setShowProductsEnabled();
+ showTranslation.setVisible(nucleotide);
+ conservationMenuItem.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide);
+ showGroupConservation.setEnabled(!nucleotide);
+ rnahelicesColour.setEnabled(nucleotide);
+ purinePyrimidineColour.setEnabled(nucleotide);
+ showComplementMenuItem.setText(MessageManager
+ .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+ setColourSelected(jalview.bin.Cache.getDefault(
+ nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
-
+ /**
+ * set up menus for the current viewport. This may be called after any
+ * operation that affects the data in the current view (selection changed,
+ * etc) to update the menus to reflect the new state.
+ */
+ public void setMenusForViewport()
+ {
+ setMenusFromViewport(viewport);
+ }
/**
- * Need to call this method when tabs are selected for multiple views,
- * or when loading from Jalview2XML.java
- * @param av AlignViewport
+ * Need to call this method when tabs are selected for multiple views, or when
+ * loading from Jalview2XML.java
+ *
+ * @param av
+ * AlignViewport
*/
void setMenusFromViewport(AlignViewport av)
{
- padGapsMenuitem.setSelected(av.padGaps);
- colourTextMenuItem.setSelected(av.showColourText);
+ padGapsMenuitem.setSelected(av.isPadGaps());
+ colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.rightAlignIds);
- centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
- renderGapsMenuItem.setSelected(av.renderGaps);
- wrapMenuItem.setSelected(av.wrapAlignment);
- scaleAbove.setVisible(av.wrapAlignment);
- scaleLeft.setVisible(av.wrapAlignment);
- scaleRight.setVisible(av.wrapAlignment);
- annotationPanelMenuItem.setState(av.showAnnotation);
- viewBoxesMenuItem.setSelected(av.showBoxes);
- viewTextMenuItem.setSelected(av.showText);
-
- setColourSelected(ColourSchemeProperty.
- getColourName(av.getGlobalColourScheme()));
-
- showSeqFeatures.setSelected(av.showSequenceFeatures);
- hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
-
+ idRightAlign.setSelected(av.isRightAlignIds());
+ centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
+ renderGapsMenuItem.setSelected(av.isRenderGaps());
+ wrapMenuItem.setSelected(av.getWrapAlignment());
+ scaleAbove.setVisible(av.getWrapAlignment());
+ scaleLeft.setVisible(av.getWrapAlignment());
+ scaleRight.setVisible(av.getWrapAlignment());
+ annotationPanelMenuItem.setState(av.isShowAnnotation());
+ /*
+ * Show/hide annotations only enabled if annotation panel is shown
+ */
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ viewBoxesMenuItem.setSelected(av.getShowBoxes());
+ viewTextMenuItem.setSelected(av.getShowText());
+ showNonconservedMenuItem.setSelected(av.getShowUnconserved());
+ showGroupConsensus.setSelected(av.isShowGroupConsensus());
+ showGroupConservation.setSelected(av.isShowGroupConservation());
+ showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
+ showSequenceLogo.setSelected(av.isShowSequenceLogo());
+ normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+
+ setColourSelected(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
+
+ showSeqFeatures.setSelected(av.isShowSequenceFeatures());
+ hiddenMarkers.setState(av.getShowHiddenMarkers());
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
+ showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
+ showDbRefsMenuitem.setSelected(av.isShowDBRefs());
+ autoCalculate.setSelected(av.autoCalculateConsensus);
+ sortByTree.setSelected(av.sortByTree);
+ listenToViewSelections.setSelected(av.followSelection);
+ rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
+ rnahelicesColour
+ .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ setShowProductsEnabled();
updateEditMenuBar();
}
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
+ Hashtable progressBars, progressBarHandlers;
- Hashtable progressBars;
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
public void setProgressBar(String message, long id)
{
- if(progressBars == null)
+ if (progressBars == null)
{
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
JPanel progressPanel;
+ Long lId = new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if(progressBars.get( new Long(id) )!=null)
- {
- progressPanel = (JPanel)progressBars.get( new Long(id) );
- statusPanel.remove(progressPanel);
- progressBars.remove( progressPanel );
- progressPanel = null;
- if(message!=null)
+ if (progressBars.get(lId) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(lId);
+ progressPanel = null;
+ if (message != null)
{
- statusBar.setText(message);
+ statusBar.setText(message);
}
-
- layout.setRows(layout.getRows() - 1);
- }
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
+ layout.setRows(layout.getRows() - 1);
+ }
else
{
progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -590,74 +923,119 @@ public class AlignFrame
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, progressPanel);
}
-
+ // update GUI
+ // setMenusForViewport();
validate();
}
- /**
- *
- * @return true if any progress bars are still active
- */
- public boolean operationInProgress()
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
{
- if (progressBars!=null && progressBars.size()>0)
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- return true;
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
- return false;
- }
- /*
- Added so Castor Mapping file can obtain Jalview Version
- */
- public String getVersion()
- {
- return jalview.bin.Cache.getProperty("VERSION");
- }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
- public FeatureRenderer getFeatureRenderer()
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public void setStatus(String text)
+ {
+ statusBar.setText(text);
+ };
+
+ /*
+ * Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
{
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ return jalview.bin.Cache.getProperty("VERSION");
}
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
+ }
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
- if(fileName!=null)
+ if (fileName != null)
{
- if(currentFileFormat.equals("Jalview"))
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (currentFileFormat.equals("Jalview"))
{
- JInternalFrame [] frames = Desktop.desktop.getAllFrames();
- for(int i=0; i-1)
+ if (currentFileFormat.indexOf(" ") > -1)
{
- currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+ currentFileFormat = currentFileFormat.substring(0,
+ currentFileFormat.indexOf(" "));
}
saveAlignment(fileName, currentFileFormat);
}
@@ -761,50 +1166,58 @@ public class AlignFrame
if (shortName.indexOf(java.io.File.separatorChar) > -1)
{
- shortName = shortName.substring(shortName.lastIndexOf(
- java.io.File.separatorChar) + 1);
+ shortName = shortName.substring(shortName
+ .lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().SaveAlignment(this, file, shortName);
+ /*
+ * First save any linked Chimera session.
+ */
+ Desktop.instance.saveChimeraSessions(file);
+
+ success = new Jalview2XML().saveAlignment(this, file, shortName);
- statusBar.setText("Successfully saved to file: "
- +fileName+" in "
- +format +" format.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format }));
}
else
- {
+ {
if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
{
- // JBPNote need to have a raise_gui flag here
- JOptionPane.showInternalMessageDialog(
- this, "Cannot save file " + fileName + " using format "+format,
- "Alignment output format not supported",
- JOptionPane.WARNING_MESSAGE);
+ warningMessage("Cannot save file " + fileName + " using format "
+ + format, "Alignment output format not supported");
saveAs_actionPerformed(null);
+ // JBPNote need to have a raise_gui flag here
return false;
}
-
+
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to save only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
if (reply == JOptionPane.YES_OPTION)
{
omitHidden = viewport.getViewAsString(false);
- }
+ }
}
FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(
- format,
- (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+ String output = f.formatSequences(format,
+ viewport.getAlignment(), // class cast exceptions will
+ // occur in the distant future
+ omitHidden, f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
if (output == null)
{
@@ -815,16 +1228,16 @@ public class AlignFrame
try
{
java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ new java.io.FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText("Successfully saved to file: "
- + fileName + " in "
- + format + " format.");
- }
- catch (Exception ex)
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format }));
+ } catch (Exception ex)
{
success = false;
ex.printStackTrace();
@@ -834,33 +1247,55 @@ public class AlignFrame
if (!success)
{
- JOptionPane.showInternalMessageDialog(
- this, "Couldn't save file: " + fileName,
- "Error Saving File",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { fileName }), MessageManager
+ .getString("label.error_saving_file"),
+ JOptionPane.WARNING_MESSAGE);
}
return success;
}
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
- String [] omitHidden = null;
+ String[] omitHidden = null;
- if(viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "The Alignment contains hidden columns."
- +"\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
- if(reply==JOptionPane.YES_OPTION)
+ if (reply == JOptionPane.YES_OPTION)
{
omitHidden = viewport.getViewAsString(false);
}
@@ -868,29 +1303,44 @@ public class AlignFrame
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600,
- 500);
+ try
+ {
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ viewport.getAlignment(), omitHidden,
+ viewport.getColumnSelection()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
- cap.setText(new FormatAdapter().formatSequences(
- e.getActionCommand(),
- viewport.alignment,
- omitHidden, viewport.colSel));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // new HTMLOutput(alignPanel,
+ // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+ // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ new HtmlSvgOutput(null, alignPanel);
}
+ @Override
+ public void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+ new BioJsHTMLOutput(alignPanel,
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
@@ -898,9 +1348,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -908,15 +1360,21 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
-
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -925,42 +1383,41 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
- //Putting in a thread avoids Swing painting problems
+ // Putting in a thread avoids Swing painting problems
PrintThread thread = new PrintThread(alignPanel);
thread.start();
}
+ @Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportFeatures(alignPanel);
}
-
+ @Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(
- alignPanel,
- viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups(),
- ((Alignment)viewport.alignment).alignmentProperties
- );
+ new AnnotationExporter().exportAnnotations(alignPanel);
}
-
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Jalview Annotations or Features File");
- chooser.setToolTipText("Load Jalview Annotations / Features file");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
@@ -968,76 +1425,82 @@ public class AlignFrame
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice);
+ loadJalviewDataFile(choice, null, null, null);
}
}
-
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
+ *
+ * @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
- if(alignPanels!=null && alignPanels.size()<2)
+ if (alignPanels != null && alignPanels.size() < 2)
{
closeAllTabs = true;
}
try
{
- if(alignPanels!=null)
+ if (alignPanels != null)
{
if (closeAllTabs)
{
- for (int i = 0; i < alignPanels.size(); i++)
+ if (this.isClosed())
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(ap.seqPanel, null);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
- ap.av.alignment = null;
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = alignPanels.get(i);
+ ap.closePanel();
+ }
}
}
else
{
- int index = tabbedPane.getSelectedIndex();
-
- alignPanels.removeElement(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel);
- viewport.alignment = null;
- alignPanel = null;
- viewport = null;
-
- tabbedPane.removeTabAt(index);
- tabbedPane.validate();
-
- if(index==tabbedPane.getTabCount())
- {
- index --;
- }
-
- this.tabSelectionChanged(index);
+ closeView(alignPanel);
}
}
if (closeAllTabs)
{
this.setClosed(true);
- }
- }
- catch (Exception ex)
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
+ /**
+ * Close the specified panel and close up tabs appropriately.
+ *
+ * @param panelToClose
+ */
+ public void closeView(AlignmentPanel panelToClose)
+ {
+ int index = tabbedPane.getSelectedIndex();
+ int closedindex = tabbedPane.indexOfComponent(panelToClose);
+ alignPanels.remove(panelToClose);
+ panelToClose.closePanel();
+ panelToClose = null;
+
+ tabbedPane.removeTabAt(closedindex);
+ tabbedPane.validate();
+
+ if (index > closedindex || index == tabbedPane.getTabCount())
+ {
+ // modify currently selected tab index if necessary.
+ index--;
+ }
+
+ this.tabSelectionChanged(index);
+ }
/**
* DOCUMENT ME!
@@ -1045,140 +1508,174 @@ public class AlignFrame
void updateEditMenuBar()
{
- if (viewport.historyList.size() > 0)
+ if (viewport.getHistoryList().size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText("Undo " + command.getDescription());
+ CommandI command = viewport.getHistoryList().peek();
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new Object[]
+ { command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
}
- if (viewport.redoList.size() > 0)
+ if (viewport.getRedoList().size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText("Redo " + command.getDescription());
+ CommandI command = viewport.getRedoList().peek();
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new Object[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
-
public void addHistoryItem(CommandI command)
{
- if(command.getSize()>0)
+ if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.clear();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
}
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
{
- if (alignPanels!=null)
+ if (alignPanels != null)
{
- Enumeration e = alignPanels.elements();
AlignmentI[] als = new AlignmentI[alignPanels.size()];
- for (int i=0; e.hasMoreElements(); i++)
+ int i = 0;
+ for (AlignmentPanel ap : alignPanels)
{
- als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+ als[i++] = ap.av.getAlignment();
}
return als;
}
- if (viewport!=null)
+ if (viewport != null)
{
- return new AlignmentI[] { viewport.alignment };
+ return new AlignmentI[]
+ { viewport.getAlignment() };
}
return null;
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.historyList.empty())
+ if (viewport.getHistoryList().isEmpty())
+ {
return;
- CommandI command = (CommandI)viewport.historyList.pop();
- viewport.redoList.push(command);
+ }
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
command.undoCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
- if(originalSource!=null)
+ if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- originalSource.firePropertyChange("alignment",
- null,
- originalSource.alignment.getSequences());
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for undo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
- if(viewport.redoList.size()<1)
+ if (viewport.getRedoList().size() < 1)
{
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
command.doCommand(getViewAlignments());
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
- if(originalSource!=null)
+ if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- originalSource.firePropertyChange("alignment",
- null,
- originalSource.alignment.getSequences());
+
+ if (originalSource != viewport)
+ {
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for redo");
+ }
+ originalSource.updateHiddenColumns();
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
- //For sequence removal and addition, we need to fire
- //the property change event FROM the viewport where the
- //original alignment was altered
- AlignmentI al=null;
+ AlignmentViewport originalSource = null;
+ // For sequence removal and addition, we need to fire
+ // the property change event FROM the viewport where the
+ // original alignment was altered
+ AlignmentI al = null;
if (command instanceof EditCommand)
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components
- .get(viewport.getSequenceSetId());
+ List comps = PaintRefresher.components.get(viewport
+ .getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
+ for (Component comp : comps)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
+ if (comp instanceof AlignmentPanel)
{
- if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+ if (al == ((AlignmentPanel) comp).av.getAlignment())
{
- originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ originalSource = ((AlignmentPanel) comp).av;
break;
}
}
@@ -1187,11 +1684,11 @@ public class AlignFrame
if (originalSource == null)
{
- //The original view is closed, we must validate
- //the current view against the closed view first
+ // The original view is closed, we must validate
+ // the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1202,8 +1699,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param up DOCUMENT ME!
+ *
+ * @param up
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
@@ -1213,153 +1711,120 @@ public class AlignFrame
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
-
-
-
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
- if(viewport.cursorMode)
+ List sg = new ArrayList();
+ if (viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
- sg.addElement(viewport.alignment.getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.getHiddenRepSequences());
}
- else if(viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
- if(sg.size()<1)
+ if (sg.size() < 1)
{
return;
}
- Vector invertGroup = new Vector();
+ List invertGroup = new ArrayList();
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ for (SequenceI seq : viewport.getAlignment().getSequences())
{
- if(!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.add(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(seq))
+ {
+ invertGroup.add(seq);
+ }
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ {
+ seqs2[i] = invertGroup.get(i);
+ }
SlideSequencesCommand ssc;
if (right)
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs2, seqs1, size,
- viewport.getGapCharacter()
- );
+ {
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
+ }
else
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs1, seqs2, size,
- viewport.getGapCharacter()
- );
+ {
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor( -size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
-
boolean appendHistoryItem = false;
- if(viewport.historyList!=null
- && viewport.historyList.size()>0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque historyList = viewport.getHistoryList();
+ if (historyList != null
+ && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc.appendSlideCommand(
- (SlideSequencesCommand)viewport.historyList.peek())
- ;
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) historyList
+ .peek());
}
- if(!appendHistoryItem)
+ if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1367,82 +1832,67 @@ public class AlignFrame
{
return;
}
- // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
- SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ // TODO: preserve the ordering of displayed alignment annotation in any
+ // internal paste (particularly sequence associated annotation)
+ SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns())
{
omitHidden = viewport.getViewAsString(true);
}
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,
+ omitHidden);
StringSelection ss = new StringSelection(output);
try
{
jalview.gui.Desktop.internalCopy = true;
- //Its really worth setting the clipboard contents
- //to empty before setting the large StringSelection!!
+ // Its really worth setting the clipboard contents
+ // to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(""), null);
+ .setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(ss, Desktop.instance);
- }
- catch (OutOfMemoryError er)
+ .setContents(ss, Desktop.instance);
+ } catch (OutOfMemoryError er)
{
- er.printStackTrace();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory copying region!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
+ new OOMWarning("copying region", er);
return;
}
- Vector hiddenColumns = null;
- if(viewport.hasHiddenColumns)
+ ArrayList hiddenColumns = null;
+ if (viewport.hasHiddenColumns())
{
- hiddenColumns =new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
- i++)
+ hiddenColumns = new ArrayList();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+ .getSelectionGroup().getEndRes();
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[])
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);
-
- hiddenColumns.addElement(new int[]
- {region[0] - hiddenOffset,
- region[1]-hiddenOffset});
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+ {
+ hiddenColumns.add(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
}
}
Desktop.jalviewClipboard = new Object[]
- {
- seqs,
- viewport.alignment.getDataset(),
- hiddenColumns};
- statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+ { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new Object[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1450,9 +1900,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1460,12 +1912,13 @@ public class AlignFrame
/**
* Paste contents of Jalview clipboard
- *
- * @param newAlignment true to paste to a new alignment, otherwise add to this.
+ *
+ * @param newAlignment
+ * true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
- boolean externalPaste=true;
+ boolean externalPaste = true;
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -1487,23 +1940,9 @@ public class AlignFrame
format = new IdentifyFile().Identify(str, "Paste");
- }
- catch (OutOfMemoryError er)
+ } catch (OutOfMemoryError er)
{
- er.printStackTrace();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory pasting sequences!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
+ new OOMWarning("Out of memory pasting sequences!!", er);
return;
}
@@ -1511,56 +1950,60 @@ public class AlignFrame
boolean annotationAdded = false;
AlignmentI alignment = null;
- if(Desktop.jalviewClipboard!=null)
- {
- // The clipboard was filled from within Jalview, we must use the sequences
- // And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
- // be doubly sure that we create *new* sequence objects.
- sequences = new SequenceI[newseq.length];
- for (int i=0;i newGraphGroups = new ArrayList();
+ int fgroup = -1;
+
+ if (newAlignment)
+ {
+
+ if (Desktop.jalviewClipboard != null)
+ {
+ // dataset is inherited
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ }
+ else
+ {
+ // new dataset is constructed
+ alignment.setDataset(null);
+ }
+ alwidth = alignment.getWidth() + 1;
+ }
+ else
+ {
+ AlignmentI pastedal = alignment; // preserve pasted alignment object
+ // Add pasted sequences and dataset into existing alignment.
+ alignment = viewport.getAlignment();
+ alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
boolean importDs = Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
Vector newDs = (importDs) ? new Vector() : null; // used to create
- // minimum dataset set
+ // minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
@@ -1569,7 +2012,7 @@ public class AlignFrame
newDs.addElement(null);
}
SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
- // paste
+ // paste
if (importDs && ds != null)
{
if (!newDs.contains(ds))
@@ -1588,7 +2031,8 @@ public class AlignFrame
{
// copy and derive new dataset sequence
sequences[i] = sequences[i].deriveSequence();
- alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
+ alignment.getDataset().addSequence(
+ sequences[i].getDatasetSequence());
// TODO: avoid creation of duplicate dataset sequences with a
// 'contains' method using SequenceI.equals()/SequenceI.contains()
}
@@ -1598,207 +2042,330 @@ public class AlignFrame
{
newDs.clear(); // tidy up
}
- if (pastedal.getAlignmentAnnotation()!=null) {
+ if (alignment.getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation alan : alignment
+ .getAlignmentAnnotation())
+ {
+ if (alan.graphGroup > fgroup)
+ {
+ fgroup = alan.graphGroup;
+ }
+ }
+ }
+ if (pastedal.getAlignmentAnnotation() != null)
+ {
// Add any annotation attached to alignment.
AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
- for (int i=0; i -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
}
}
- }
- if (!newAlignment) {
- ///////
- // ADD HISTORY ITEM
- //
- addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- sequences,
- 0,
- alignment.getWidth(),
- alignment)
- );
- }
- // Add any annotations attached to sequences
- for (int i = 0; i < sequences.length; i++)
- {
- if (sequences[i].getAnnotation() != null)
- {
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)
- {
- annotationAdded=true;
- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
- alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
- }
- }
- }
- if (!newAlignment) {
-
- // propagate alignment changed.
- viewport.setEndSeq(alignment.getHeight());
- if (annotationAdded)
- {
- // Duplicate sequence annotation in all views.
- AlignmentI[] alview = this.getViewAlignments();
- for (int i = 0; i < sequences.length; i++)
- {
- AlignmentAnnotation sann[] = sequences[i].getAnnotation();
- if (sann == null)
- continue;
- for (int avnum=0;avnum>>This is a fix for the moment, until a better solution is found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
- // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
- if (!externalPaste) {
- if (title.startsWith("Copied sequences"))
- {
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
- }
- } else {
- newtitle = new String("Pasted sequences");
- }
-
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
-
- }
-
-
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println("Exception whilst pasting: "+ex);
- // could be anything being pasted in here
- }
-
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void cut_actionPerformed(ActionEvent e)
- {
- copy_actionPerformed(null);
- delete_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void delete_actionPerformed(ActionEvent evt)
- {
+ }
+ if (!newAlignment)
+ {
+ // /////
+ // ADD HISTORY ITEM
+ //
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
+ sequences, 0, alignment.getWidth(), alignment));
+ }
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ AlignmentAnnotation newann;
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ annotationAdded = true;
+ newann = sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup > -1)
+ {
+ if (newann.graphGroup > -1)
+ {
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
+ {
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
+ }
+ }
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
+ // was
+ // duplicated
+ // earlier
+ alignment
+ .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
+ }
+ }
+ }
+ if (!newAlignment)
+ {
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
+ // propagate alignment changed.
+ viewport.setEndSeq(alignment.getHeight());
+ if (annotationAdded)
+ {
+ // Duplicate sequence annotation in all views.
+ AlignmentI[] alview = this.getViewAlignments();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ AlignmentAnnotation sann[] = sequences[i].getAnnotation();
+ if (sann == null)
+ {
+ continue;
+ }
+ for (int avnum = 0; avnum < alview.length; avnum++)
+ {
+ if (alview[avnum] != alignment)
+ {
+ // duplicate in a view other than the one with input focus
+ int avwidth = alview[avnum].getWidth() + 1;
+ // this relies on sann being preserved after we
+ // modify the sequence's annotation array for each duplication
+ for (int a = 0; a < sann.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ sann[a]);
+ sequences[i].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ alview[avnum].addAnnotation(newann); // annotation was
+ // duplicated earlier
+ // TODO JAL-1145 graphGroups are not updated for sequence
+ // annotation added to several views. This may cause
+ // strangeness
+ alview[avnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ buildSortByAnnotationScoresMenu();
+ }
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : alignPanels)
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
+
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Copied sequences");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ List hc = (List) Desktop.jalviewClipboard[2];
+ for (int[] region : hc)
+ {
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ if (!externalPaste)
+ {
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+ else
+ {
+ newtitle = new String("Pasted sequences");
+ }
+
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+
+ }
+
+ } catch (Exception ex)
{
- return;
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
}
- Vector seqs = new Vector();
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
+ }
+
+ @Override
+ protected void expand_newalign(ActionEvent e)
+ {
+ try
{
- seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
- }
+ AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+ .getAlignment(), -1);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Flanking alignment");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ List hc = (List) Desktop.jalviewClipboard[2];
+ for (int region[] : hc)
+ {
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ {
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- SequenceI [] cut = new SequenceI[seqs.size()];
- for(int i=0; i 0)
{
- if(trimLeft)
+ if (trimLeft)
{
column = colSel.getMin();
}
@@ -1930,279 +2511,378 @@ public class AlignFrame
column = colSel.getMax();
}
- SequenceI [] seqs;
- if(viewport.getSelectionGroup()!=null)
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
-
TrimRegionCommand trimRegion;
- if(trimLeft)
+ if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
viewport.setStartRes(0);
}
- else
- {
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
- }
-
- statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
+ }
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.get(i);
-
- if ( (trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
- int start = 0, end = viewport.alignment.getWidth()-1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
-
- RemoveGapColCommand removeGapCols =
- new RemoveGapColCommand("Remove Gapped Columns",
- seqs,
- start, end,
- viewport.alignment);
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
- statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new Object[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
- //This is to maintain viewport position on first residue
- //of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- // ShiftList shifts;
- // viewport.getAlignment().removeGaps(shifts=new ShiftList());
- // edit.alColumnChanges=shifts.getInverse();
- // if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes)-1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
- int start = 0, end = viewport.alignment.getWidth()-1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
- //This is to maintain viewport position on first residue
- //of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",
- seqs,
- start, end,
- viewport.alignment));
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.getAlignment()));
- viewport.setStartRes(seq.findIndex(startRes)-1);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
- viewport.padGaps = padGapsMenuitem.isSelected();
-
- viewport.firePropertyChange("alignment",
- null,
- viewport.getAlignment().getSequences());
+ viewport.setPadGaps(padGapsMenuitem.isSelected());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ /**
+ * Create a new view of the current alignment.
+ */
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
- AlignmentPanel newap =
- new Jalview2XML().copyAlignPanel(alignPanel, true);
+ newView(null, true);
+ }
+
+ /**
+ * Creates and shows a new view of the current alignment.
+ *
+ * @param viewTitle
+ * title of newly created view; if null, one will be generated
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
+ /*
+ * Create a new AlignmentPanel (with its own, new Viewport)
+ */
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
+ true);
+ if (!copyAnnotation)
+ {
+ /*
+ * remove all groups and annotation except for the automatic stuff
+ */
+ newap.av.getAlignment().deleteAllGroups();
+ newap.av.getAlignment().deleteAllAnnotations(false);
+ }
- newap.av.gatherViewsHere = false;
+ newap.av.setGatherViewsHere(false);
if (viewport.viewName == null)
{
- viewport.viewName = "Original";
+ viewport.viewName = MessageManager
+ .getString("label.view_name_original");
}
- newap.av.historyList = viewport.historyList;
- newap.av.redoList = viewport.redoList;
+ /*
+ * Views share the same edits, undo and redo stacks, mappings.
+ */
+ newap.av.setHistoryList(viewport.getHistoryList());
+ newap.av.setRedoList(viewport.getRedoList());
+ newap.av.getAlignment().setCodonFrames(
+ viewport.getAlignment().getCodonFrames());
+
+ newap.av.viewName = getNewViewName(viewTitle);
- int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " +index;
+ addAlignmentPanel(newap, true);
+ newap.alignmentChanged();
- Vector comps = (Vector) PaintRefresher.components.get(viewport.
- getSequenceSetId());
- Vector existingNames = new Vector();
- for(int i=0; i comps = PaintRefresher.components.get(viewport
+ .getSequenceSetId());
- addAlignmentPanel(newap, false);
+ List existingNames = getExistingViewNames(comps);
- if(alignPanels.size()==2)
+ while (existingNames.contains(newViewName))
{
- viewport.gatherViewsHere = true;
+ newViewName = viewTitle + " " + (++index);
}
- tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newViewName;
+ }
+
+ /**
+ * Returns a list of distinct view names found in the given list of
+ * components. View names are held on the viewport of an AlignmentPanel.
+ *
+ * @param comps
+ * @return
+ */
+ protected List getExistingViewNames(List comps)
+ {
+ List existingNames = new ArrayList();
+ for (Component comp : comps)
+ {
+ if (comp instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel) comp;
+ if (!existingNames.contains(ap.av.viewName))
+ {
+ existingNames.add(ap.av.viewName);
+ }
+ }
+ }
+ return existingNames;
}
+ /**
+ * Explode tabbed views into separate windows.
+ */
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.explodeViews(this);
+ Desktop.instance.explodeViews(this);
}
+ /**
+ * Gather views in separate windows back into a tabbed presentation.
+ */
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
}
-
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+ alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
+ .calculateIdWidth());
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
- viewport.rightAlignIds = idRightAlign.isSelected();
+ viewport.setRightAlignIds(idRightAlign.isSelected());
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
- viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
alignPanel.paintAlignment(true);
}
-
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
+ */
+ @Override
+ protected void followHighlight_actionPerformed()
+ {
+ /*
+ * Set the 'follow' flag on the Viewport (and scroll to position if now
+ * true).
+ */
+ final boolean state = this.followHighlightMenuItem.getState();
+ viewport.setFollowHighlight(state);
+ if (state)
+ {
+ alignPanel.scrollToPosition(
+ alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+ }
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2211,63 +2891,189 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.updateLayout();
}
+ @Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+ @Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
repaint();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+// alignPanel.paintAlignment(true);
}
- public void hideSelColumns_actionPerformed(ActionEvent e)
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.getColumnSelection().getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.setSelectionGroup(sg);
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
}
- public void hiddenMarkers_actionPerformed(ActionEvent e)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
+ * event.ActionEvent)
+ */
+ @Override
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
{
- viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
- repaint();
+ toggleHiddenRegions(false, false);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
+ * .ActionEvent)
*/
- protected void scaleAbove_actionPerformed(ActionEvent e)
+ @Override
+ public void hideAllSelection_actionPerformed(ActionEvent e)
{
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ @Override
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ @Override
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2276,9 +3082,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2287,9 +3095,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2298,9 +3108,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2309,32 +3121,43 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
alignPanel.paintAlignment(true);
}
-
public FeatureSettings featureSettings;
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
- if(featureSettings !=null )
+ if (featureSettings != null)
{
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2346,80 +3169,75 @@ public class AlignFrame
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
+ if (viewport.isShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
+ *
+ * @param e
+ */
+ @Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
+ alignPanel.updateLayout();
}
+ @Override
public void alignmentProperties()
{
- JEditorPane editPane = new JEditorPane("text/html","");
+ JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
- StringBuffer contents = new StringBuffer("");
-
- float avg = 0;
- int min=Integer.MAX_VALUE, max=0;
- for(int i=0; imax)
- max = size;
- if(sizeSequences: "+ viewport.alignment.getHeight());
- contents.append("
Minimum Sequence Length: "+min);
- contents.append("
Maximum Sequence Length: "+max);
- contents.append("
Average Length: "+(int)avg);
-
- if (((Alignment)viewport.alignment).getProperties() != null)
- {
- Hashtable props = ((Alignment)viewport.alignment).getProperties();
- Enumeration en = props.keys();
- contents.append("
");
- while(en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- StringBuffer val = new StringBuffer();
- String vals = props.get(key).toString();
- int pos=0, npos;
- do {
- npos = vals.indexOf("\n",pos);
- if (npos==-1)
- {
- val.append(vals.substring(pos));
- } else {
- val.append(vals.substring(pos, npos));
- val.append("
");
- }
- pos = npos+1;
- } while (npos!=-1);
- contents.append("| "+key+" | "+val+" |
");
- }
- contents.append("
");
- }
- editPane.setText(contents.toString()+"");
+ StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+ .formatAsHtml();
+ editPane.setText(MessageManager.formatMessage("label.html_content",
+ new Object[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new Object[]
+ { getTitle() }), 500, 400);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2430,23 +3248,25 @@ public class AlignFrame
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
- frame.getWidth(), frame.getHeight());
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new Object[]
+ { this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ javax.swing.event.InternalFrameEvent evt)
{
alignPanel.setOverviewPanel(null);
- }
- ;
+ };
});
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2454,9 +3274,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2464,20 +3286,24 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2485,9 +3311,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2495,9 +3323,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2505,9 +3335,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2515,9 +3347,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2525,9 +3359,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -2535,9 +3371,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -2545,25 +3383,53 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void nucleotideColour_actionPerformed(ActionEvent e)
{
changeColour(new NucleotideColourScheme());
}
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+
+ /*
+ * public void covariationColour_actionPerformed(ActionEvent e) {
+ * changeColour(new
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+ * ()[0])); }
+ */
+ @Override
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ @Override
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
+
+ @Override
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -2571,65 +3437,59 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
+ // TODO: compare with applet and pull up to model method
int threshold = 0;
- if(cs!=null)
+ if (cs != null)
{
if (viewport.getAbovePIDThreshold())
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold,
- viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
+ "Background");
+ cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
}
else
{
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
if (viewport.getConservationSelected())
{
- Alignment al = (Alignment) viewport.alignment;
+ Alignment al = (Alignment) viewport.getAlignment();
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
cs.setConservation(c);
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
- "Background"));
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
}
else
{
cs.setConservation(null);
}
- cs.setConsensus(viewport.hconsensus);
+ cs.setConsensus(viewport.getSequenceConsensusHash());
}
viewport.setGlobalColourScheme(cs);
if (viewport.getColourAppliesToAllGroups())
{
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if (cs == null)
{
sg.cs = null;
@@ -2638,108 +3498,106 @@ public class AlignFrame
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
- sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+ sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
}
else
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }
- catch (Exception ex)
+ sg.cs = cs.getClass().newInstance();
+ } catch (Exception ex)
{
}
}
if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold,
- viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
- sg.getEndRes()+1));
- }
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
else
{
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
}
-
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.
- hiddenRepSequences),
- sg.getStartRes(),
- sg.getEndRes()+1);
+ ResidueProperties.propHash, 3, sg.getSequences(viewport
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
sg.cs.setConservation(c);
}
else
{
sg.cs.setConservation(null);
+ }
}
}
- }
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
-
-
-
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ if (viewport.getAbovePIDThreshold()
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(),
- "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ if (viewport.getConservationSelected()
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme,
- "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -2754,9 +3612,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -2771,19 +3631,22 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
new UserDefinedColours(alignPanel, null);
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
changeColour(udc);
}
@@ -2793,11 +3656,11 @@ public class AlignFrame
{
Component[] menuItems = colourMenu.getMenuComponents();
- int i, iSize = menuItems.length;
- for (i = 0; i < iSize; i++)
+ int iSize = menuItems.length;
+ for (int i = 0; i < iSize; i++)
{
- if (menuItems[i].getName() != null &&
- menuItems[i].getName().equals("USER_DEFINED"))
+ if (menuItems[i].getName() != null
+ && menuItems[i].getName().equals("USER_DEFINED"))
{
colourMenu.remove(menuItems[i]);
iSize--;
@@ -2805,49 +3668,54 @@ public class AlignFrame
}
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.
- nextElement().toString());
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
{
- public void mousePressed(MouseEvent evt)
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
{
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ radioItem.addActionListener(new ActionListener()
{
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
- Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
- if(option == JOptionPane.YES_OPTION)
+ @Override
+ public void actionPerformed(ActionEvent evt)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(
- radioItem.getText());
- colourMenu.remove(radioItem);
+ userDefinedColour_actionPerformed(evt);
}
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ });
}
+ }
}
- });
+ });
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -2862,9 +3730,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -2872,9 +3742,11 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -2882,193 +3754,254 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0), null);
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
- if ( (viewport.getSelectionGroup() == null) ||
- (viewport.getSelectionGroup().getSize() < 2))
+ if ((viewport.getSelectionGroup() == null)
+ || (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.",
- "Invalid Selection",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .getString("label.you_must_select_least_two_sequences"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.WARNING_MESSAGE);
}
else
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
- if ( ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() < 4) &&
- (viewport.getSelectionGroup().getSize() > 0)) ||
- (viewport.getAlignment().getHeight() < 4))
+ if (((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() < 4) && (viewport
+ .getSelectionGroup().getSize() > 0))
+ || (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane.showInternalMessageDialog(this,
- "Principal component analysis must take\n" +
- "at least 4 input sequences.",
- "Sequence selection insufficient",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ this,
+ MessageManager
+ .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(alignPanel);
+ new PCAPanel(alignPanel);
}
-
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if(viewport.autoCalculateConsensus)
+ if (viewport.autoCalculateConsensus)
{
- viewport.firePropertyChange("alignment",
- null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
+ @Override
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+ viewport.sortByTree = sortByTree.isSelected();
+ }
+
+ @Override
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ viewport.followSelection = listenToViewSelections.isSelected();
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel("AV", "PID", "Average distance tree using PID");
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
/**
* DOCUMENT ME!
- *
- * @param type DOCUMENT ME!
- * @param pwType DOCUMENT ME!
- * @param title DOCUMENT ME!
+ *
+ * @param type
+ * DOCUMENT ME!
+ * @param pwType
+ * DOCUMENT ME!
+ * @param title
+ * DOCUMENT ME!
*/
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "You need to have more than two sequences selected to build a tree!",
- "Not enough sequences",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager
+ .getString("label.not_enough_sequences"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
- int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize())
+ for (SequenceI _s : sg.getSequences())
{
- if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
- sg.getEndRes())
+ if (_s.getLength() < sg.getEndRes())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The selected region to create a tree may\nonly contain residues or gaps.\n" +
- "Try using the Pad function in the edit menu,\n" +
- "or one of the multiple sequence alignment web services.",
- "Sequences in selection are not aligned",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager
+ .getString("label.sequences_selection_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -3079,20 +4012,22 @@ public class AlignFrame
}
else
{
- //are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the visible sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The sequences must be aligned before creating a tree.\n" +
- "Try using the Pad function in the edit menu,\n" +
- "or one of the multiple sequence alignment web services.",
- "Sequences not aligned",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager
+ .getString("label.sequences_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
- if(viewport.alignment.getHeight()<2)
+ if (viewport.getAlignment().getHeight() < 2)
{
return;
}
@@ -3102,9 +4037,9 @@ public class AlignFrame
title += " from ";
- if(viewport.viewName!=null)
+ if (viewport.viewName != null)
{
- title+= viewport.viewName+" of ";
+ title += viewport.viewName + " of ";
}
title += this.title;
@@ -3114,80 +4049,97 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param title DOCUMENT ME!
- * @param order DOCUMENT ME!
+ *
+ * @param title
+ * DOCUMENT ME!
+ * @param order
+ * DOCUMENT ME!
*/
- public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
+ public void addSortByOrderMenuItem(String title,
+ final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem("by " + title);
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ // TODO: JBPNote - have to map order entries to curent SequenceI
+ // pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
- addHistoryItem(new OrderCommand(order.getName(), oldOrder,
- viewport.alignment));
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
+ .getAlignment()));
alignPanel.paintAlignment(true);
}
});
}
+
/**
* Add a new sort by annotation score menu item
- * @param sort the menu to add the option to
- * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
+ *
+ * @param sort
+ * the menu to add the option to
+ * @param scoreLabel
+ * the label used to retrieve scores for each sequence on the
+ * alignment
*/
- public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
+ public void addSortByAnnotScoreMenuItem(JMenu sort,
+ final String scoreLabel)
{
final JMenuItem item = new JMenuItem(scoreLabel);
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
- addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,
+ viewport.getAlignment());// ,viewport.getSelectionGroup());
+ addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
});
}
+
/**
- * last hash for alignment's annotation array - used to minimise cost of rebuild.
+ * last hash for alignment's annotation array - used to minimise cost of
+ * rebuild.
*/
protected int _annotationScoreVectorHash;
+
/**
- * search the alignment and rebuild the sort by annotation score submenu
- * the last alignment annotation vector hash is stored to minimize
- * cost of rebuilding in subsequence calls.
- *
+ * search the alignment and rebuild the sort by annotation score submenu the
+ * last alignment annotation vector hash is stored to minimize cost of
+ * rebuilding in subsequence calls.
+ *
*/
+ @Override
public void buildSortByAnnotationScoresMenu()
{
- if(viewport.alignment.getAlignmentAnnotation()==null)
+ if (viewport.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
- if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
+ if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts=new Hashtable();
+ Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.alignment.getSequences().elements();
- while (sq.hasMoreElements())
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
- aann = ((SequenceI) sq.nextElement()).getAnnotation();
- for (int i=0;aann!=null && i0);
+ sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
- _annotationScoreVectorHash =
- viewport.alignment.getAlignmentAnnotation().hashCode();
+ _annotationScoreVectorHash = viewport.getAlignment()
+ .getAlignmentAnnotation().hashCode();
}
}
/**
- * Maintain the Order by->Displayed Tree menu.
- * Creates a new menu item for a TreePanel with an appropriate
- * jalview.analysis.AlignmentSorter call. Listeners are added
- * to remove the menu item when the treePanel is closed, and adjust
- * the tree leaf to sequence mapping when the alignment is modified.
- * @param treePanel Displayed tree window.
- * @param title SortBy menu item title.
+ * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
+ * TreePanel with an appropriate jalview.analysis.AlignmentSorter
+ * call. Listeners are added to remove the menu item when the treePanel is
+ * closed, and adjust the tree leaf to sequence mapping when the alignment is
+ * modified.
+ *
+ * @param treePanel
+ * Displayed tree window.
+ * @param title
+ * SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
- sortByTreeMenu.removeAll();
+ calculateTree.removeAll();
+ // build the calculate menu
- Vector comps = (Vector) PaintRefresher.components.get(viewport.
- getSequenceSetId());
- Vector treePanels = new Vector();
- int i, iSize = comps.size();
- for(i=0; i comps = PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ List treePanels = new ArrayList();
+ for (Component comp : comps)
+ {
+ if (comp instanceof TreePanel)
+ {
+ treePanels.add((TreePanel) comp);
+ }
+ }
- if(iSize<1)
+ if (treePanels.size() < 1)
{
sortByTreeMenu.setVisible(false);
return;
@@ -3241,23 +4227,17 @@ public class AlignFrame
sortByTreeMenu.setVisible(true);
- for(i=0; i 1))
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 1))
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
+ // some common interface!
+ /*
+ * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
+ * SequenceI[sz = seqs.getSize(false)];
+ *
+ * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
+ * seqs.getSequenceAt(i); }
+ */
+ msa = viewport.getAlignmentView(true);
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
{
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- /*SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz = seqs.getSize(false)];
-
- for (int i = 0; i < sz; i++)
+ int option = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.oneseq_msainput_selection"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
{
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- } */
- msa = viewport.getAlignmentView(true);
+ msa = viewport.getAlignmentView(false);
+ }
}
else
{
- /*Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1)
- {
- msa = new SequenceI[seqs.size()];
-
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
- }*/
msa = viewport.getAlignmentView(false);
}
return msa;
}
/**
- * Decides what is submitted to a secondary structure prediction service,
- * the currently selected sequence, or the currently selected alignment
- * (where the first sequence in the set is the one that the prediction
- * will be for).
+ * Decides what is submitted to a secondary structure prediction service: the
+ * first sequence in the alignment, or in the current selection, or, if the
+ * alignment is 'aligned' (ie padded with gaps), then the currently selected
+ * region or the whole alignment. (where the first sequence in the set is the
+ * one that the prediction will be for).
*/
- AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ public AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
- AlignmentView seqs = null;
+ AlignmentView seqs = null;
- if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 0))
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
@@ -3326,29 +4321,37 @@ public class AlignFrame
{
seqs = viewport.getAlignmentView(false);
}
- // limit sequences - JBPNote in future - could spawn multiple prediction jobs
- // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.alignment.isAligned())
+ // limit sequences - JBPNote in future - could spawn multiple prediction
+ // jobs
+ // TODO: viewport.getAlignment().isAligned is a global state - the local
+ // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.getAlignment().isAligned(false))
{
seqs.setSequences(new SeqCigar[]
- {seqs.getSequences()[0]});
+ { seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
+
}
return seqs;
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ @Override
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
@@ -3359,60 +4362,74 @@ public class AlignFrame
jalview.io.NewickFile fin = null;
try
{
- fin = new jalview.io.NewickFile(choice,
- "File");
+ fin = new jalview.io.NewickFile(choice, "File");
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- ex.getMessage(),
- "Problem reading tree file",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (fin!=null && fin.hasWarningMessage())
+ if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- "Possible problem with tree file",
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
}
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
- return ShowNewickTree(nf,title,600,500,4,5);
+ return ShowNewickTree(nf, title, 600, 500, 4, 5);
}
public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input)
+ AlignmentView input)
{
- return ShowNewickTree(nf,title, input, 600,500,4,5);
+ return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
}
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
- int x, int y)
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+ int h, int x, int y)
{
return ShowNewickTree(nf, title, null, w, h, x, y);
}
+
/**
- * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
- *
- * @param nf the tree
- * @param title tree viewer title
- * @param input Associated alignment input data (or null)
- * @param w width
- * @param h height
- * @param x position
- * @param y position
+ * Add a treeviewer for the tree extracted from a newick file object to the
+ * current alignment view
+ *
+ * @param nf
+ * the tree
+ * @param title
+ * tree viewer title
+ * @param input
+ * Associated alignment input data (or null)
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param x
+ * position
+ * @param y
+ * position
* @return TreePanel handle
*/
public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input, int w, int h, int x,
- int y)
+ AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
@@ -3422,310 +4439,316 @@ public class AlignFrame
if (nf.getTree() != null)
{
- tp = new TreePanel(alignPanel,
- "FromFile",
- title,
- nf, input);
+ tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
- tp.setSize(w,h);
+ tp.setSize(w, h);
- if(x>0 && y>0)
+ if (x > 0 && y > 0)
{
- tp.setLocation(x,y);
+ tp.setLocation(x, y);
}
-
Desktop.addInternalFrame(tp, title, w, h);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
-
+
return tp;
}
+ private boolean buildingMenu = false;
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
- // TODO: add support for context dependent disabling of services based on alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract handler class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or introduce object broker mechanism.
- if ( (Discoverer.services != null)
- && (Discoverer.services.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to be stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a client instance attaches itself to the GUI with method call like jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, alignframe)
- Vector wsmenu = new Vector();
- final AlignFrame af = this;
- if (msaws != null)
+ while (buildingMenu)
+ {
+ try
+ {
+ System.err.println("Waiting for building menu to finish.");
+ Thread.sleep(10);
+ } catch (Exception e)
{
- // Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
- for (int i = 0, j = msaws.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
- get(i);
- final JMenuItem method = new JMenuItem(sh.getName());
- method.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(sh, title, msa,
- false, true,
- viewport.getAlignment().getDataset(),
- af);
-
- }
-
- });
- msawsmenu.add(method);
- // Deal with services that we know accept partial alignments.
- // TODO: this should be a service property - ie sh.getProperty("submitGaps")==Boolean.true
- if (sh.getName().indexOf("lustal") > -1)
- {
- // We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
- methodR.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(sh, title, msa,
- true, true,
- viewport.getAlignment().getDataset(),
- af);
-
- }
-
- });
- msawsmenu.add(methodR);
-
- }
- }
- wsmenu.add(msawsmenu);
}
- if (secstrpr != null)
+ }
+ final AlignFrame me = this;
+ buildingMenu = true;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
{
- // Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
- for (int i = 0, j = secstrpr.size(); i < j; i++)
+ final List legacyItems = new ArrayList();
+ try
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
- secstrpr.get(i);
- final JMenuItem method = new JMenuItem(sh.getName());
- method.addActionListener(new ActionListener()
+ System.err.println("Building ws menu again "
+ + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based
+ // on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or
+ // introduce
+ // object broker mechanism.
+ final Vector wsmenu = new Vector();
+ final IProgressIndicator af = me;
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ final JMenu analymenu = new JMenu("Analysis");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // final JMenu msawsmenu = new
+ // JMenu(MessageManager.getString("label.alignment"));
+ // final JMenu secstrmenu = new
+ // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ // final JMenu seqsrchmenu = new
+ // JMenu(MessageManager.getString("label.sequence_database_search"));
+ // final JMenu analymenu = new
+ // JMenu(MessageManager.getString("label.analysis"));
+ // final JMenu dismenu = new
+ // JMenu(MessageManager.getString("label.protein_disorder"));
+ // JAL-940 - only show secondary structure prediction services from
+ // the legacy server
+ if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ // &&
+ Discoverer.services != null && (Discoverer.services.size() > 0))
{
- public void actionPerformed(ActionEvent e)
+ // TODO: refactor to allow list of AbstractName/Handler bindings to
+ // be
+ // stored or retrieved from elsewhere
+ // No MSAWS used any more:
+ // Vector msaws = null; // (Vector)
+ // Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services
+ .get("SecStrPred");
+ if (secstrpr != null)
{
- AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
- if (msa.getSequences().length == 1)
+ // Add any secondary structure prediction services
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- // Single Sequence prediction
- new jalview.ws.JPredClient(sh, title, false, msa, af, true);
- }
- else
- {
- if (msa.getSequences().length > 1)
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ int p = secstrmenu.getItemCount();
+ impl.attachWSMenuEntry(secstrmenu, me);
+ int q = secstrmenu.getItemCount();
+ for (int litm = p; litm < q; litm++)
{
- // Sequence profile based prediction
- new jalview.ws.JPredClient(sh,
- title, true, msa, af, true);
+ legacyItems.add(secstrmenu.getItem(litm));
}
}
}
- });
- secstrmenu.add(method);
- }
- wsmenu.add(secstrmenu);
-/* }
- if (seqsrch!=null)
- {
- // Add any secondary structure prediction services
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- Hashtable dbsrchs = new Hashtable();
- JMenu defmenu;
- dbsrchs.put("", defmenu = new JMenu("Default Database"));
- for (int i = 0, j = seqsrch.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
- seqsrch.elementAt(i);
-
- String dbs[] = null;
- try {
- dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
- } catch (Exception e)
- {
- jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);
- continue;
}
- JMenuItem method;
- // do default entry
- defmenu.add(method = new JMenuItem(sh.getName()));
- method.addActionListener(new ActionListener()
+
+ // Add all submenus in the order they should appear on the web
+ // services menu
+ wsmenu.add(msawsmenu);
+ wsmenu.add(secstrmenu);
+ wsmenu.add(dismenu);
+ wsmenu.add(analymenu);
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void run()
{
- // use same input gatherer as for secondary structure prediction
- // we could actually parameterise the gatherer method here...
- AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
- new jalview.ws.SeqSearchWSClient(sh, title, msa, null,
- viewport.getAlignment().getDataset(),
- af);
- }
- }
- );
- // add entry for each database the service supports
- for (int db=0; dbs!=null && db 0)
+ {
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add(wsmenu.get(i));
+ }
+ }
+ else
+ {
+ webService.add(me.webServiceNoServices);
+ }
+ // TODO: move into separate menu builder class.
+ boolean new_sspred = false;
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ for (Jws2Instance sv : jws2servs.getServices())
+ {
+ if (sv.description.toLowerCase().contains("jpred"))
+ {
+ for (JMenuItem jmi : legacyItems)
+ {
+ jmi.setVisible(false);
+ }
+ }
+ }
+
+ }
+ if (jws2servs.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+ "Still discovering JABA Services");
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
+ }
+ }
+ build_urlServiceMenu(me.webService);
+ build_fetchdbmenu(webService);
+ for (JMenu item : wsmenu)
+ {
+ if (item.getItemCount() == 0)
+ {
+ item.setEnabled(false);
+ }
+ else
+ {
+ item.setEnabled(true);
+ }
+ }
+ } catch (Exception e)
{
- AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
- new jalview.ws.SeqSearchWSClient(sh, title, msa, searchdb,
- viewport.getAlignment().getDataset(),
- af);
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
}
- });
- }
- }
- // add the databases onto the seqsearch menu
- Enumeration e = dbsrchs.elements();
- while (e.hasMoreElements())
+ }
+ });
+ } catch (Exception e)
{
- Object el = e.nextElement();
- if (el instanceof JMenu)
- {
- seqsrchmenu.add((JMenu) el);
- } else {
- seqsrchmenu.add((JMenuItem) el);
- }
}
- // finally, add the whole shebang onto the webservices menu
- wsmenu.add(seqsrchmenu); */
- }
- resetWebServiceMenu();
- for (int i = 0, j = wsmenu.size(); i < j; i++)
- {
- webService.add( (JMenu) wsmenu.get(i));
+ buildingMenu = false;
}
- }
- else
- {
- resetWebServiceMenu();
- this.webService.add(this.webServiceNoServices);
- }
- }
+ }).start();
+ }
/**
- * empty the web service menu and add any ad-hoc functions
- * not dynamically discovered.
- *
+ * construct any groupURL type service menu entries.
+ *
+ * @param webService
*/
- private void resetWebServiceMenu()
+ private void build_urlServiceMenu(JMenu webService)
{
- webService.removeAll();
- // Temporary hack - DBRef Fetcher always top level ws entry.
- JMenuItem rfetch = new JMenuItem("Fetch DB References");
- rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
- webService.add(rfetch);
- rfetch.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e)
- {
- new jalview.ws.DBRefFetcher(
- alignPanel.av.getSequenceSelection(),
- alignPanel.alignFrame).fetchDBRefs(false);
- }
-
- });
+ // TODO: remove this code when 2.7 is released
+ // DEBUG - alignmentView
+ /*
+ * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
+ * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent e) {
+ * jalview.datamodel.AlignmentView
+ * .testSelectionViews(af.viewport.getAlignment(),
+ * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
+ *
+ * }); webService.add(testAlView);
+ */
+ // TODO: refactor to RestClient discoverer and merge menu entries for
+ // rest-style services with other types of analysis/calculation service
+ // SHmmr test client - still being implemented.
+ // DEBUG - alignmentView
+
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+ .getRestClients())
+ {
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
+ }
}
- /* public void vamsasStore_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Export to Vamsas file");
- chooser.setToolTipText("Export");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- //vs.store(chooser.getSelectedFile().getAbsolutePath() );
- vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
- }
- }*/
+ /*
+ * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
+ * chooser = new JalviewFileChooser(jalview.bin.Cache.
+ * getProperty("LAST_DIRECTORY"));
+ *
+ * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
+ * to Vamsas file"); chooser.setToolTipText("Export");
+ *
+ * int value = chooser.showSaveDialog(this);
+ *
+ * if (value == JalviewFileChooser.APPROVE_OPTION) {
+ * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
+ * chooser.getSelectedFile().getAbsolutePath(), this); } }
+ */
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
- SequenceI [] selection = viewport.getSequenceSelection();
- if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset()))
+ SequenceI[] selection = viewport.getSequenceSelection();
+ if (canShowProducts(selection, viewport.getSelectionGroup() != null,
+ viewport.getAlignment().getDataset()))
{
showProducts.setEnabled(true);
-
- } else {
+
+ }
+ else
+ {
showProducts.setEnabled(false);
}
}
+
/**
- * search selection for sequence xRef products and build the
- * show products menu.
+ * search selection for sequence xRef products and build the show products
+ * menu.
+ *
* @param selection
* @param dataset
* @return true if showProducts menu should be enabled.
*/
- public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
+ public boolean canShowProducts(SequenceI[] selection,
+ boolean isRegionSelection, Alignment dataset)
{
- boolean showp=false;
- try {
+ boolean showp = false;
+ try
+ {
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset);
- //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true);
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ // Object[] prods =
+ // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
+ // selection, dataset, true);
final SequenceI[] sel = selection;
- for (int t=0; ptypes!=null && t cf = prods.getCodonFrames();
+ for (AlignedCodonFrame acf : cf)
+ {
+ al.addCodonFrame(acf);
+ }
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
+ + " for " + ((isRegSel) ? "selected region of " : "")
+ + getTitle();
+ naf.setTitle(newtitle);
+
+ // temporary flag until SplitFrame is released
+ boolean asSplitFrame = Cache.getDefault(
+ Preferences.ENABLE_SPLIT_FRAME, false);
+ if (asSplitFrame)
+ {
+ /*
+ * Make a copy of this alignment (sharing the same dataset
+ * sequences). If we are DNA, drop introns and update mappings
+ */
+ AlignmentI copyAlignment = null;
+ final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+ .getSequenceSelection();
+ if (dna)
+ {
+ copyAlignment = AlignmentUtils.makeExonAlignment(
+ sequenceSelection, cf);
+ al.getCodonFrames().clear();
+ al.getCodonFrames().addAll(cf);
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addMappings(cf);
+ }
+ else
+ {
+ copyAlignment = new Alignment(new Alignment(
+ sequenceSelection));
+ }
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(AlignFrame.this.getTitle());
+ // SplitFrame with dna above, protein below
+ SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
+ dna ? naf : copyThis);
+ naf.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ }
+ else
+ {
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ }
+ else
+ {
+ System.err.println("No Sequences generated for xRef type "
+ + source);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "Exception when finding crossreferences", e);
+ } catch (OutOfMemoryError e)
{
- al.addCodonFrame(cf[s]);
- cf[s] = null;
+ new OOMWarning("whilst fetching crossreferences", e);
+ } catch (Error e)
+ {
+ jalview.bin.Cache.log.error("Error when finding crossreferences",
+ e);
}
- al.setDataset(ds);
- AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- String newtitle =""+((fdna) ? "Proteins " : "Nucleotides ") + " for "+((fisRegSel) ? "selected region of " : "")
- + getTitle();
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- } else {
- System.err.println("No Sequences generated for xRef type "+fsrc);
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[]
+ { source }),
+ sttime);
}
- }
- catch (Exception e)
- {
- jalview.bin.Cache.log.error("Exception when finding crossreferences",e);
- }
- catch (Error e)
- {
- jalview.bin.Cache.log.error("Error when finding crossreferences",e);
- }
- ths.setProgressBar("Finished searching for sequences from "+fsrc, sttime);
- }
-
- };
- Thread frunner = new Thread(foo);
- frunner.start();
- }
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
+ }
-public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment)
-{
- // old way
- try {
- return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true)));
- } catch (Exception e)
+ public boolean canShowTranslationProducts(SequenceI[] selection,
+ AlignmentI alignment)
{
- jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
- return false;
+ // old way
+ try
+ {
+ return (jalview.analysis.Dna.canTranslate(selection,
+ viewport.getViewAsVisibleContigs(true)));
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
+ e);
+ return false;
+ }
}
-}
-public void showProducts_actionPerformed(ActionEvent e)
-{
- ///////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI [] selection = viewport.getSequenceSelection();
- AlignmentI al = null;
- try {
- al = jalview.analysis.Dna.CdnaTranslate(selection, viewport.getViewAsVisibleContigs(true),
- viewport.getGapCharacter(), viewport.getAlignment().getDataset());
- } catch (Exception ex) {
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.",ex);
- }
- if (al==null)
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed",
- JOptionPane.WARNING_MESSAGE);
- } else {
+ /**
+ * Construct and display a new frame containing the translation of this
+ * frame's DNA sequences to their aligned protein (amino acid) equivalents.
+ */
+ @Override
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = null;
+ try
+ {
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.translateCdna();
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error(
+ "Exception during translation. Please report this !", ex);
+ final String msg = MessageManager
+ .getString("label.error_when_translating_sequences_submit_bug_report");
+ final String title = MessageManager
+ .getString("label.implementation_error")
+ + MessageManager.getString("translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ if (al == null || al.getHeight() == 0)
+ {
+ final String msg = MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+ final String title = MessageManager
+ .getString("label.translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
- DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ af.setFileFormat(this.currentFileFormat);
+ final String newTitle = MessageManager.formatMessage(
+ "label.translation_of_params", new Object[]
+ { this.getTitle() });
+ af.setTitle(newTitle);
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+ {
+ final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+ viewport.openSplitFrame(af, new Alignment(seqs),
+ al.getCodonFrames());
+ }
+ else
+ {
+ Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
}
-public void showTranslation_actionPerformed(ActionEvent e)
-{
- ///////////////////////////////
- // Collect Data to be translated/transferred
-
- SequenceI [] selection = viewport.getSequenceSelection();
- String [] seqstring = viewport.getViewAsString(true);
- AlignmentI al = null;
- try {
- al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
- viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
- viewport.alignment.getWidth(), viewport.getAlignment().getDataset());
- } catch (Exception ex) {
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.",ex);
- }
- if (al==null)
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
- "Translation Failed",
- JOptionPane.WARNING_MESSAGE);
- } else {
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
- DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ /**
+ * Set the file format
+ *
+ * @param fileFormat
+ */
+ public void setFileFormat(String fileFormat)
+ {
+ this.currentFileFormat = fileFormat;
}
-}
-/**
- * Try to load a features file onto the alignment.
- * @param file contents or path to retrieve file
- * @param type access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+ /**
+ * Try to load a features file onto the alignment.
+ *
+ * @param file
+ * contents or path to retrieve file
+ * @param type
+ * access mode of file (see jalview.io.AlignFile)
+ * @return true if features file was parsed corectly.
+ */
+ public boolean parseFeaturesFile(String file, String type)
+ {
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(file,
- type).parse(viewport.alignment.getDataset(),
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- false);
- }
- catch(Exception ex)
+ featuresFile = new FeaturesFile(file, type).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getFeatureColours(), false,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ } catch (Exception ex)
{
ex.printStackTrace();
}
- if(featuresFile)
+ if (featuresFile)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
+ if (alignPanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
+ }
+ if (featureSettings != null)
+ {
+ featureSettings.setTableData();
+ }
alignPanel.paintAlignment(true);
}
return featuresFile;
-}
+ }
-public void dragEnter(DropTargetDragEvent evt)
-{}
+ @Override
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
-public void dragExit(DropTargetEvent evt)
-{}
+ @Override
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
-public void dragOver(DropTargetDragEvent evt)
-{}
+ @Override
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
-public void dropActionChanged(DropTargetDragEvent evt)
-{}
+ @Override
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
-public void drop(DropTargetDropEvent evt)
-{
+ @Override
+ public void drop(DropTargetDropEvent evt)
+ {
Transferable t = evt.getTransferable();
java.util.List files = null;
try
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "text/uri-list;class=java.lang.String");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
- //Works on Windows and MacOSX
+ // Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t.getTransferData(DataFlavor.
- javaFileListFlavor);
+ files = (java.util.List) t
+ .getTransferData(DataFlavor.javaFileListFlavor);
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
@@ -3935,9 +5063,7 @@ public void drop(DropTargetDropEvent evt)
String data = (String) t.getTransferData(uriListFlavor);
files = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data,
- "\r\n");
- st.hasMoreTokens(); )
+ data, "\r\n"); st.hasMoreTokens();)
{
String s = st.nextToken();
if (s.startsWith("#"))
@@ -3947,12 +5073,20 @@ public void drop(DropTargetDropEvent evt)
}
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
@@ -3960,136 +5094,980 @@ public void drop(DropTargetDropEvent evt)
{
try
{
-
+ // check to see if any of these files have names matching sequences in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ .getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList filesmatched = new ArrayList();
+ ArrayList filesnotmatched = new ArrayList();
for (int i = 0; i < files.size(); i++)
{
- loadJalviewDataFile(files.get(i).toString());
+ String file = files.get(i).toString();
+ String pdbfn = "";
+ String protocol = FormatAdapter.checkProtocol(file);
+ if (protocol == jalview.io.FormatAdapter.FILE)
+ {
+ File fl = new File(file);
+ pdbfn = fl.getName();
+ }
+ else if (protocol == jalview.io.FormatAdapter.URL)
+ {
+ URL url = new URL(file);
+ pdbfn = url.getFile();
+ }
+ if (pdbfn.length() > 0)
+ {
+ // attempt to find a match in the alignment
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+ int l = 0, c = pdbfn.indexOf(".");
+ while (mtch == null && c != -1)
+ {
+ do
+ {
+ l = c;
+ } while ((c = pdbfn.indexOf(".", l)) > l);
+ if (l > -1)
+ {
+ pdbfn = pdbfn.substring(0, l);
+ }
+ mtch = idm.findAllIdMatches(pdbfn);
+ }
+ if (mtch != null)
+ {
+ String type = null;
+ try
+ {
+ type = new IdentifyFile().Identify(file, protocol);
+ } catch (Exception ex)
+ {
+ type = null;
+ }
+ if (type != null)
+ {
+ if (type.equalsIgnoreCase("PDB"))
+ {
+ filesmatched.add(new Object[]
+ { file, protocol, mtch });
+ continue;
+ }
+ }
+ }
+ // File wasn't named like one of the sequences or wasn't a PDB file.
+ filesnotmatched.add(file);
+ }
+ }
+ int assocfiles = 0;
+ if (filesmatched.size() > 0)
+ {
+ if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
+ || JOptionPane
+ .showConfirmDialog(
+ this,
+ MessageManager
+ .formatMessage(
+ "label.automatically_associate_pdb_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(
+ filesmatched
+ .size())
+ .toString() }),
+ MessageManager
+ .getString("label.automatically_associate_pdb_files_by_name"),
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+
+ {
+ for (Object[] fm : filesmatched)
+ {
+ // try and associate
+ // TODO: may want to set a standard ID naming formalism for
+ // associating PDB files which have no IDs.
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
+ {
+ PDBEntry pe = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq((String) fm[0],
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
+ if (pe != null)
+ {
+ System.err.println("Associated file : "
+ + ((String) fm[0]) + " with "
+ + toassoc.getDisplayId(true));
+ assocfiles++;
+ }
+ }
+ alignPanel.paintAlignment(true);
+ }
+ }
}
- }
- catch (Exception ex)
+ if (filesnotmatched.size() > 0)
+ {
+ if (assocfiles > 0
+ && (Cache.getDefault(
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ .showConfirmDialog(
+ this,
+ ""+MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[]
+ { Integer.valueOf(
+ filesnotmatched
+ .size())
+ .toString() })+"",
+ MessageManager
+ .getString("label.ignore_unmatched_dropped_files"),
+ JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ {
+ return;
+ }
+ for (String fn : filesnotmatched)
+ {
+ loadJalviewDataFile(fn, null, null, null);
+ }
+
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
-}
+ }
- /**
- * Attempt to load a "dropped" file: First by testing
- * whether it's and Annotation file, then a JNet file, and finally a features file. If all are
- * false then the user may have dropped an alignment file onto this
+ /**
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and Annotation file, then a JNet file, and finally a features file. If
+ * all are false then the user may have dropped an alignment file onto this
* AlignFrame.
- * @param file either a filename or a URL string.
+ *
+ * @param file
+ * either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file)
- {
+ public void loadJalviewDataFile(String file, String protocol,
+ String format, SequenceI assocSeq)
+ {
try
{
- String protocol = "File";
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ if (protocol == null)
{
- protocol = "URL";
+ protocol = jalview.io.FormatAdapter.checkProtocol(file);
}
-
- boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
- alignment, file, protocol);
+ // if the file isn't identified, or not positively identified as some
+ // other filetype (PFAM is default unidentified alignment file type) then
+ // try to parse as annotation.
+ boolean isAnnotation = (format == null || format
+ .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
+ .annotateAlignmentView(viewport, file, protocol)
+ : false;
if (!isAnnotation)
{
- // try to see if its a JNet 'concise' style annotation file *before* we try to parse it as a features file
- String format = new IdentifyFile().Identify(file, protocol);
- if(format.equalsIgnoreCase("JnetFile"))
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- file, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(),
- 0, false);
- isAnnotation=true;
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar
+ .setText(MessageManager
+ .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching
+ // process didn't work
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ tcf.getWarningMessage() == null ? MessageManager
+ .getString("label.check_file_matches_sequence_ids_alignment")
+ : tcf.getWarningMessage(),
+ MessageManager
+ .getString("label.problem_reading_tcoffee_score_file"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
+ {
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
+ tcf = null;
}
- else
+ if (tcf == null)
{
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
// try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file,protocol);
- // if it wasn't a features file then we just treat it as a general alignment file to load into the current view.
- if (!isGroupsFile)
+ if (format == null)
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
- } else {
- alignPanel.paintAlignment(true);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker();
+ JnetAnnotationMaker.add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
+ viewport.getAlignment().setSeqrep(repseq);
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(repseq);
+ viewport.setColumnSelection(cs);
+ isAnnotation = true;
+ }
+ else
+ {
+ /*
+ * if (format.equalsIgnoreCase("PDB")) {
+ *
+ * String pdbfn = ""; // try to match up filename with sequence id
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
}
if (isAnnotation)
{
-
+
alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
alignPanel.paintAlignment(true);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "loading data "
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+ : "using " + protocol + " from " + file)
+ : ".")
+ + (format != null ? "(parsing as '" + format
+ + "' file)" : ""), oom, Desktop.desktop);
}
}
+ /**
+ * Method invoked by the ChangeListener on the tabbed pane, in other words
+ * when a different tabbed pane is selected by the user or programmatically.
+ */
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
{
- alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ alignPanel = alignPanels.get(index);
viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
+
+ /*
+ * If there is a frame linked to this one in a SplitPane, switch it to the
+ * same view tab index. No infinite recursion of calls should happen, since
+ * tabSelectionChanged() should not get invoked on setting the selected
+ * index to an unchanged value. Guard against setting an invalid index
+ * before the new view peer tab has been created.
+ */
+ final AlignViewportI peer = viewport.getCodingComplement();
+ if (peer != null)
+ {
+ AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
+ if (linkedAlignFrame.tabbedPane.getTabCount() > index)
+ {
+ linkedAlignFrame.tabbedPane.setSelectedIndex(index);
+ }
+ }
}
+ /**
+ * On right mouse click on view tab, prompt for and set new view name.
+ */
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
- if(SwingUtilities.isRightMouseButton(e))
+ if (SwingUtilities.isRightMouseButton(e))
{
- String reply = JOptionPane.showInternalInputDialog(this,
- "Enter View Name",
- "Edit View Name",
- JOptionPane.QUESTION_MESSAGE);
+ String msg = MessageManager.getString("label.enter_view_name");
+ String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
+ JOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
viewport.viewName = reply;
- tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ // TODO warn if reply is in getExistingViewNames()?
+ tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
}
}
-
public AlignViewport getCurrentView()
{
return viewport;
}
-
/**
* Open the dialog for regex description parsing.
*/
+ @Override
protected void extractScores_actionPerformed(ActionEvent e)
{
- ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
- if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0)
+ ParseProperties pp = new jalview.analysis.ParseProperties(
+ viewport.getAlignment());
+ // TODO: verify regex and introduce GUI dialog for version 2.5
+ // if (pp.getScoresFromDescription("col", "score column ",
+ // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
+ // true)>0)
+ if (pp.getScoresFromDescription("description column",
+ "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
{
buildSortByAnnotationScoresMenu();
}
}
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ @Override
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ @Override
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
+ }
+
+ /**
+ * find the viewport amongst the tabs in this alignment frame and close that
+ * tab
+ *
+ * @param av
+ */
+ public boolean closeView(AlignViewportI av)
+ {
+ if (viewport == av)
+ {
+ this.closeMenuItem_actionPerformed(false);
+ return true;
+ }
+ Component[] comp = tabbedPane.getComponents();
+ for (int i = 0; comp != null && i < comp.length; i++)
+ {
+ if (comp[i] instanceof AlignmentPanel)
+ {
+ if (((AlignmentPanel) comp[i]).av == av)
+ {
+ // close the view.
+ closeView((AlignmentPanel) comp[i]);
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ protected void build_fetchdbmenu(JMenu webService)
+ {
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ // TODO We probably want to store a sequence database checklist in
+ // preferences and have checkboxes.. rather than individual sources selected
+ // here
+ final JMenu rfetch = new JMenu(
+ MessageManager.getString("action.fetch_db_references"));
+ rfetch.setToolTipText(MessageManager
+ .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
+ webService.add(rfetch);
+
+ final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
+ MessageManager.getString("option.trim_retrieved_seqs"));
+ trimrs.setToolTipText(MessageManager
+ .getString("label.trim_retrieved_sequences"));
+ trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ trimrs.setSelected(trimrs.isSelected());
+ Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Boolean.valueOf(trimrs.isSelected()).toString());
+ };
+ });
+ rfetch.add(trimrs);
+ JMenuItem fetchr = new JMenuItem(
+ MessageManager.getString("label.standard_databases"));
+ fetchr.setToolTipText(MessageManager
+ .getString("label.fetch_embl_uniprot"));
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
+
+ }
+
+ });
+ rfetch.add(fetchr);
+ final AlignFrame me = this;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(me);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List otherdb;
+ JMenu dfetch = new JMenu();
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
+ String mname = null;
+ int dbi = 0;
+ for (String dbclass : dbclasses)
+ {
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
+ {
+ continue;
+ }
+ // List dbs=otherdb;
+ // otherdb=new ArrayList();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(MessageManager.formatMessage(
+ "label.fetch_all_param", new Object[]
+ { src.getDbSource() }));
+ fetchr.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+ dfetch.add(fetchr);
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
+ {
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText(""
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
+ }
+ }
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
+ }
+ }
+ });
+ }
+ }).start();
+
+ }
+
+ /**
+ * Left justify the whole alignment.
+ */
+ @Override
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ /**
+ * Right justify the whole alignment.
+ */
+ @Override
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ public void setShowSeqFeatures(boolean b)
+ {
+ showSeqFeatures.setSelected(true);
+ viewport.setShowSequenceFeatures(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
+ * awt.event.ActionEvent)
+ */
+ @Override
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ @Override
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (avc.makeGroupsFromSelection())
+ {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ public void clearAlignmentSeqRep()
+ {
+ // TODO refactor alignmentseqrep to controller
+ if (viewport.getAlignment().hasSeqrep()) {
+ viewport.getAlignment().setSeqrep(null);
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
+ @Override
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.createGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ @Override
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ /**
+ * make the given alignmentPanel the currently selected tab
+ *
+ * @param alignmentPanel
+ */
+ public void setDisplayedView(AlignmentPanel alignmentPanel)
+ {
+ if (!viewport.getSequenceSetId().equals(
+ alignmentPanel.av.getSequenceSetId()))
+ {
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+ }
+ if (tabbedPane != null
+ && tabbedPane.getTabCount() > 0
+ && alignPanels.indexOf(alignmentPanel) != tabbedPane
+ .getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
+
+ /**
+ * Action on selection of menu options to Show or Hide annotations.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ @Override
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
+ {
+ aa.visible = visible;
+ }
+ }
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
+ }
+
+ /**
+ * Store selected annotation sort order for the view and repaint.
+ */
+ @Override
+ protected void sortAnnotations_actionPerformed()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ *
+ * @return alignment panels in this alignment frame
+ */
+ public List getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel)
+ : alignPanels;
+ }
+
+ /**
+ * Open a new alignment window, with the cDNA associated with this (protein)
+ * alignment, aligned as is the protein.
+ */
+ protected void viewAsCdna_actionPerformed()
+ {
+ // TODO no longer a menu action - refactor as required
+ final AlignmentI alignment = getViewport().getAlignment();
+ Set mappings = alignment.getCodonFrames();
+ if (mappings == null)
+ {
+ return;
+ }
+ List cdnaSeqs = new ArrayList();
+ for (SequenceI aaSeq : alignment.getSequences()) {
+ for (AlignedCodonFrame acf : mappings) {
+ SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
+ if (dnaSeq != null)
+ {
+ /*
+ * There is a cDNA mapping for this protein sequence - add to new
+ * alignment. It will share the same dataset sequence as other mapped
+ * cDNA (no new mappings need to be created).
+ */
+ final Sequence newSeq = new Sequence(dnaSeq);
+ newSeq.setDatasetSequence(dnaSeq);
+ cdnaSeqs.add(newSeq);
+ }
+ }
+ }
+ if (cdnaSeqs.size() == 0)
+ {
+ // show a warning dialog no mapped cDNA
+ return;
+ }
+ AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
+ .size()]));
+ AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ cdna.alignAs(alignment);
+ String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ + this.title;
+ Desktop.addInternalFrame(alignFrame, newtitle,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Set visibility of dna/protein complement view (available when shown in a
+ * split frame).
+ *
+ * @param show
+ */
+ @Override
+ protected void showComplement_actionPerformed(boolean show)
+ {
+ SplitContainerI sf = getSplitViewContainer();
+ if (sf != null) {
+ sf.setComplementVisible(this, show);
+ }
+ }
}
-class PrintThread
- extends Thread
+class PrintThread extends Thread
{
AlignmentPanel ap;
+
public PrintThread(AlignmentPanel ap)
{
- this.ap = ap;
+ this.ap = ap;
}
+
static PageFormat pf;
+
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -4108,8 +6086,7 @@ class PrintThread
try
{
printJob.print();
- }
- catch (Exception PrintException)
+ } catch (Exception PrintException)
{
PrintException.printStackTrace();
}