X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3736791d243a98fdfef2308aca1aab6af9e00604;hb=492b8dc7cde0b6f527d78d2b67a4d4ddc693e006;hp=0d8149c6b809313b291400f56cec5d40b9f278a6;hpb=77ecb160b47e44406ebdb597c89470612544fee4;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index 0d8149c..3736791
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,43 +1,155 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * 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 jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.CrossRef;
+import jalview.analysis.Dna;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+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.AlignmentExportData;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenSequences;
+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.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.io.gff.SequenceOntologyI;
+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.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.SequenceFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+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.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.FocusAdapter;
+import java.awt.event.FocusEvent;
+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.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
@@ -46,20 +158,23 @@ import jalview.ws.jws2.Jws2Discoverer;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ 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
@@ -166,21 +281,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
alignPanel = new AlignmentPanel(this, viewport);
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection hiddenColumns, int width, int height)
+ {
+ setSize(width, height);
+
if (al.getDataset() == null)
{
al.setDataset(null);
}
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
init();
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
@@ -201,7 +338,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- if (viewport.conservation == null)
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
+
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
+ if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
@@ -227,12 +371,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
+ setGUINucleotide(viewport.getAlignment().isNucleotide());
}
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
- if (viewport.wrapAlignment)
+ buildTreeMenu();
+
+ if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
@@ -244,6 +393,90 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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();
+
+ }
+ }
+ });
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ .indexOf("devel") > -1
+ || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ .indexOf("test") > -1)
+ {
+ formatMenu.add(vsel);
+ }
+ addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ Jalview.setCurrentAlignFrame(AlignFrame.this);
+ }
+ });
+
}
/**
@@ -258,14 +491,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void setFileName(String file, String format)
{
fileName = file;
- currentFileFormat = format;
+ setFileFormat(format);
reload.setEnabled(true);
}
+ /**
+ * Add a KeyListener with handlers for various KeyPressed and KeyReleased
+ * events
+ */
void addKeyListener()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -273,7 +511,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ {
+ alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
@@ -285,42 +525,70 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(false);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, 1);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(-1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ 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)
@@ -329,8 +597,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().deleteGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
@@ -338,19 +607,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRow();
+ alignPanel.getSeqPanel().setCursorRow();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
- alignPanel.seqPanel.setCursorColumn();
+ alignPanel.getSeqPanel().setCursorColumn();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorPosition();
+ alignPanel.getSeqPanel().setCursorPosition();
}
break;
@@ -358,46 +627,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRowAndColumn();
+ alignPanel.getSeqPanel().setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
}
- alignPanel.seqPanel.seqCanvas.repaint();
+ alignPanel.getSeqPanel().seqCanvas.repaint();
break;
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);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
@@ -411,7 +674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
break;
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(true);
}
@@ -422,7 +685,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ if (viewport.getWrapAlignment())
{
alignPanel.scrollUp(false);
}
@@ -435,20 +698,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
{
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;
}
}
@@ -458,8 +726,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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());
@@ -487,12 +757,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
}
}
@@ -501,7 +772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
- AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ AlignmentPanel first = alignPanels.get(0);
tabbedPane.addTab(first.av.viewName, first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
@@ -514,16 +785,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener, thatListener;
- // Do this once to get current state
- BuildWebServiceMenu();
- Desktop.discoverer
- .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+ final java.beans.PropertyChangeListener thisListener;
+ 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"))
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
{
@@ -531,56 +801,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
- System.err.println("Change support JWS1: build services again.");
+ System.err
+ .println("Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
-
+
});
}
}
});
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .addPropertyChangeListener(
- thatListener = new java.beans.PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- System.err.println("Change support JWS2: build services again.");
- BuildWebServiceMenu();
- }
- });
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
- Desktop.discoverer.removePropertyChangeListener(thisListener);
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .removePropertyChangeListener(thatListener);
+ 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);
+ showReverse.setVisible(nucleotide);
+ showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
- // Remember AlignFrame always starts as protein
- if (!nucleotide)
- {
- calculateMenu.remove(calculateMenu.getItemCount() - 2);
- }
+ 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 currently viewport. This may be called after any
+ * 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.
*/
+ @Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
@@ -595,133 +876,100 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
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);
- showUnconservedMenuItem.setSelected(av.showUnconserved);
- showGroupConsensus.setSelected(av.showGroupConsensus);
- showGroupConservation.setSelected(av.showGroupConservation);
- showConsensusHistogram.setSelected(av.showConsensusHistogram);
- showSequenceLogo.setSelected(av.showSequenceLogo);
+ 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.showSequenceFeatures);
- hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
- showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
- showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
- setShowProductsEnabled();
+ 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);
+
+ showProducts.setEnabled(canShowProducts());
+ setGroovyEnabled(Desktop.getGroovyConsole() != null);
updateEditMenuBar();
}
- Hashtable progressBars, progressBarHandlers;
+ /**
+ * Set the enabled state of the 'Run Groovy' option in the Calculate menu
+ *
+ * @param b
+ */
+ public void setGroovyEnabled(boolean b)
+ {
+ runGroovy.setEnabled(b);
+ }
+
+ private IProgressIndicator progressBar;
/*
* (non-Javadoc)
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
- if (progressBars == null)
- {
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
- }
-
- JPanel progressPanel;
- Long lId = new Long(id);
- GridLayout layout = (GridLayout) statusPanel.getLayout();
- 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);
- }
- if (progressBarHandlers.contains(lId))
- {
- progressBarHandlers.remove(lId);
- }
- layout.setRows(layout.getRows() - 1);
- }
- else
- {
- progressPanel = new JPanel(new BorderLayout(10, 5));
-
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
-
- progressPanel.add(new JLabel(message), BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
-
- layout.setRows(layout.getRows() + 1);
- statusPanel.add(progressPanel);
-
- progressBars.put(lId, progressPanel);
- }
- // update GUI
- setMenusForViewport();
- validate();
+ progressBar.setProgressBar(message, id);
}
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
- if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
- {
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
- }
- progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
- if (handler.canCancel())
- {
- JButton cancel = new JButton("Cancel");
- final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- handler.cancelActivity(id);
- us.setProgressBar("Cancelled "
- + ((JLabel) progressPanel.getComponent(0)).getText(), id);
- }
- });
- progressPanel.add(cancel, BorderLayout.EAST);
- }
+ progressBar.registerHandler(id, handler);
}
/**
*
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
- if (progressBars != null && progressBars.size() > 0)
- {
- return true;
- }
- return false;
+ return progressBar.operationInProgress();
+ }
+
+ @Override
+ public void setStatus(String text)
+ {
+ statusBar.setText(text);
}
/*
@@ -734,23 +982,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureRenderer getFeatureRenderer()
{
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
}
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
- new SequenceFetcher(this);
+ new jalview.gui.SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
{
+ // 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"))
@@ -759,6 +1012,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
&& ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
@@ -796,6 +1050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
@@ -809,16 +1064,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+ .getAlignPanel());
}
+ @Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
@@ -840,30 +1099,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"),
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_alignment_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
+ while (currentFileFormat == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified", JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager
+ .getString("label.file_format_not_specified"),
+ JOptionPane.WARNING_MESSAGE);
+ currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
- return;
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
}
fileName = chooser.getSelectedFile().getPath();
@@ -895,10 +1165,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().SaveAlignment(this, file, shortName);
+ 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
@@ -907,34 +1178,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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
+ if (!Jalview.isHeadlessMode())
+ {
+ saveAs_actionPerformed(null);
+ }
return false;
}
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns)
+ AlignmentExportData exportData = getAlignmentForExport(format,
+ viewport, null);
+ if (exportData.getSettings().isCancelled())
{
- 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);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
+ return false;
}
- FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(format,
- (Alignment) viewport.alignment, // class cast exceptions will
+ FormatAdapter f = new FormatAdapter(alignPanel,
+ exportData.getSettings());
+ String output = f.formatSequences(
+ format,
+ exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
if (output == null)
{
@@ -950,8 +1215,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
out.print(output);
out.close();
this.setTitle(file);
- 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 }));
} catch (Exception ex)
{
success = false;
@@ -962,8 +1228,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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;
@@ -990,34 +1259,79 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
- String[] omitHidden = null;
- if (viewport.hasHiddenColumns)
+ AlignmentExportData exportData = getAlignmentForExport(
+ e.getActionCommand(), viewport, null);
+ if (exportData.getSettings().isCancelled())
{
- 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);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
+ return;
}
-
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + e.getActionCommand(), 600, 500);
+ try
+ {
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(e.getActionCommand(),
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ 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();
+ }
+
+ }
+
+ public static AlignmentExportData getAlignmentForExport(
+ String exportFormat, AlignViewportI viewport,
+ AlignExportSettingI exportSettings)
+ {
+ AlignmentI alignmentToExport = null;
+ AlignExportSettingI settings = exportSettings;
+ String[] omitHidden = null;
+
+ HiddenSequences hiddenSeqs = viewport.getAlignment()
+ .getHiddenSequences();
+
+ alignmentToExport = viewport.getAlignment();
+
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ if (settings == null)
+ {
+ settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFormat);
+ }
+ // settings.isExportAnnotations();
+
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
+ }
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.alignment, omitHidden, viewport.colSel));
+ int[] alignmentStartEnd = new int[2];
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = viewport.getAlignment();
+ }
+ alignmentStartEnd = alignmentToExport
+ .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+ .getHiddenColumns());
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+ omitHidden, alignmentStartEnd, settings);
+ return ed;
}
/**
@@ -1026,11 +1340,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
- .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer());
+ new HtmlSvgOutput(null, alignPanel);
+ }
+
+ @Override
+ public void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
public void createImageMap(File file, String image)
@@ -1044,6 +1364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1055,11 +1376,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ @Override
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
+
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1072,6 +1401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
@@ -1079,28 +1409,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -1108,7 +1439,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice);
+ loadJalviewDataFile(choice, null, null, null);
}
}
@@ -1119,6 +1450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
@@ -1138,7 +1470,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// setClosed(true) is called
for (int i = 0; i < alignPanels.size(); i++)
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ AlignmentPanel ap = alignPanels.get(i);
ap.closePanel();
}
}
@@ -1151,6 +1483,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (closeAllTabs)
{
+ /*
+ * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+ * be called recursively, with the frame now in 'closed' state
+ */
this.setClosed(true);
}
} catch (Exception ex)
@@ -1160,22 +1496,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * close alignPanel2 and shuffle tabs appropriately.
+ * Close the specified panel and close up tabs appropriately.
*
- * @param alignPanel2
+ * @param panelToClose
*/
- public void closeView(AlignmentPanel alignPanel2)
+ public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
- int closedindex = tabbedPane.indexOfComponent(alignPanel2);
- alignPanels.removeElement(alignPanel2);
- // Unnecessary
- // if (viewport == alignPanel2.av)
- // {
- // viewport = null;
- // }
- alignPanel2.closePanel();
- alignPanel2 = null;
+ int closedindex = tabbedPane.indexOfComponent(panelToClose);
+ alignPanels.remove(panelToClose);
+ panelToClose.closePanel();
+ panelToClose = null;
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
@@ -1195,42 +1526,49 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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"));
}
}
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
{
- viewport.historyList.push(command);
- viewport.redoList.clear();
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
updateEditMenuBar();
- viewport.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
+ viewport.updateHiddenColumns();
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
}
}
@@ -1242,18 +1580,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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)
{
- return new AlignmentI[]
- { viewport.alignment };
+ return new AlignmentI[] { viewport.getAlignment() };
}
return null;
}
@@ -1264,24 +1601,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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)
{
- originalSource.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
- 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());
}
}
@@ -1291,33 +1639,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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)
{
- originalSource.hasHiddenColumns = (viewport.colSel != null
- && viewport.colSel.getHiddenColumns() != null && viewport.colSel
- .getHiddenColumns().size() > 0);
- 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;
+ 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
@@ -1326,16 +1684,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
+ 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;
}
}
@@ -1348,7 +1706,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1371,69 +1729,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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();
+ List sg = new ArrayList();
if (viewport.cursorMode)
{
- sg.addElement(viewport.alignment
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
- .getHeight())
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
@@ -1441,44 +1755,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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());
+ }
else
+ {
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)
@@ -1489,17 +1817,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
+ /*
+ * just extend the last slide command if compatible; but not if in
+ * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
+ */
boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ Deque historyList = viewport.getHistoryList();
+ boolean inSplitFrame = getSplitViewContainer() != null;
+ if (!inSplitFrame && historyList != null && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .appendSlideCommand((SlideSequencesCommand) historyList
.peek());
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
@@ -1510,6 +1846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1522,13 +1859,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
@@ -1537,36 +1874,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.gui.Desktop.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(""), null);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
} catch (OutOfMemoryError er)
{
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.");
+ Desktop.jalviewClipboard = new Object[] { seqs,
+ viewport.getAlignment().getDataset(), hiddenColumns };
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new Object[] { Integer
+ .valueOf(seqs.length).toString() }));
}
/**
@@ -1575,6 +1914,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1586,6 +1926,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1619,7 +1960,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- format = new IdentifyFile().Identify(str, "Paste");
+ format = new IdentifyFile().identify(str, "Paste");
} catch (OutOfMemoryError er)
{
@@ -1654,6 +1995,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups = new ArrayList();
+ int fgroup = -1;
if (newAlignment)
{
@@ -1721,6 +2064,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
newDs.clear(); // tidy up
}
+ 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.
@@ -1731,6 +2085,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ 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();
+ }
+
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
@@ -1742,22 +2112,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- sequences, 0, alignment.getWidth(), alignment));
+ 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;
- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
+ 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);
@@ -1777,7 +2168,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
+ {
continue;
+ }
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
@@ -1794,6 +2187,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
}
}
@@ -1801,8 +2197,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null, alignment
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : alignPanels)
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
@@ -1814,19 +2221,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List hc = (List) Desktop.jalviewClipboard[2];
+ for (int[] region : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
@@ -1860,12 +2267,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
+ @Override
+ protected void expand_newalign(ActionEvent e)
+ {
+ try
+ {
+ 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());
+
+ // 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);
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Viewing flanking region of alignment", oom);
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
@@ -1878,6 +2340,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1887,37 +2350,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector seqs = new Vector();
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
+ /*
+ * If the cut affects all sequences, warn, remove highlighted columns
+ */
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
- seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
- }
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
+ {
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
- {
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- SequenceI[] cut = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- cut[i] = (SequenceI) seqs.elementAt(i);
- }
-
- /*
- * //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
viewport.sendSelection();
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
@@ -1938,14 +2404,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ if (avc.deleteGroups())
+ {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
}
/**
@@ -1954,6 +2421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -1963,7 +2431,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth() - 1);
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
viewport.sendSelection();
alignPanel.paintAlignment(true);
@@ -1976,20 +2444,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
{
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
+ alignPanel.getSeqPanel().keyboardNo1 = null;
+ alignPanel.getSeqPanel().keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ alignPanel.getIdPanel().getIdCanvas().searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
/**
@@ -1998,6 +2468,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2015,14 +2486,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
alignPanel.paintAlignment(true);
- viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/**
@@ -2031,6 +2504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2042,6 +2516,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2052,7 +2527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
@@ -2067,44 +2542,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getSelectionGroup() != null)
{
seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
+ 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)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
@@ -2119,34 +2589,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
+ 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);
+ "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);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
@@ -2165,30 +2639,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
+ 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);
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.alignment));
+ viewport.getAlignment()));
viewport.setStartRes(seq.findIndex(startRes) - 1);
@@ -2203,88 +2678,166 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
- viewport.padGaps = padGapsMenuitem.isSelected();
+ viewport.setPadGaps(padGapsMenuitem.isSelected());
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
- // else
- {
- // if (justifySeqs>0)
- {
- // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
- }
- }
-
- // }
-
/**
* 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)
{
+ 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
+ */
+ newap.av.setHistoryList(viewport.getHistoryList());
+ newap.av.setRedoList(viewport.getRedoList());
+
+ /*
+ * Views share the same mappings; need to deregister any new mappings
+ * created by copyAlignPanel, and register the new reference to the shared
+ * mappings
+ */
+ newap.av.replaceMappings(viewport.getAlignment());
+
+ 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.size(); i++)
+ if (alignPanels.size() == 2)
{
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
- if (!existingNames.contains(ap.av.viewName))
- {
- existingNames.addElement(ap.av.viewName);
- }
- }
+ viewport.setGatherViewsHere(true);
}
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
+ }
- while (existingNames.contains(newViewName))
+ /**
+ * Make a new name for the view, ensuring it is unique within the current
+ * sequenceSetId. (This used to be essential for Jalview Project archives, but
+ * these now use viewId. Unique view names are still desirable for usability.)
+ *
+ * @param viewTitle
+ * @return
+ */
+ protected String getNewViewName(String viewTitle)
+ {
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());
+ boolean addFirstIndex = false;
+ if (viewTitle == null || viewTitle.trim().length() == 0)
+ {
+ viewTitle = MessageManager.getString("action.view");
+ addFirstIndex = true;
+ }
+ else
{
- newViewName = "View " + (++index);
+ index = 1;// we count from 1 if given a specific name
}
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- newap.av.viewName = newViewName;
+ List comps = PaintRefresher.components.get(viewport
+ .getSequenceSetId());
- addAlignmentPanel(newap, true);
+ 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);
}
+ /**
+ * Gather views in separate windows back into a tabbed presentation.
+ */
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
@@ -2296,6 +2849,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
@@ -2307,24 +2861,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
}
@@ -2333,12 +2890,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
- if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ /*
+ * 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.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.getSeqPanel().seqCanvas.searchResults, false);
}
}
@@ -2348,6 +2912,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2360,30 +2925,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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();
+ viewport.sendSelection();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ // alignPanel.paintAlignment(true);
}
/**
@@ -2402,8 +2972,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// 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.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
- .getSelected().size() > 0)
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
@@ -2426,12 +2997,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (toggleSeqs)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
{
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
{
showAllSeqs_actionPerformed(null);
}
@@ -2439,12 +3011,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (toggleCols)
{
- if (viewport.colSel.getSelected().size() > 0)
+ if (viewport.getColumnSelection().getSelected().size() > 0)
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
{
- viewport.selectionGroup = sg;
+ viewport.setSelectionGroup(sg);
}
}
else if (!hide)
@@ -2461,9 +3033,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+ @Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
+ viewport.sendSelection();
}
/*
@@ -2473,6 +3047,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2480,6 +3055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/*
@@ -2489,19 +3065,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
+ @Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
+ @Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2514,6 +3095,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2526,6 +3108,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2538,6 +3121,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2550,6 +3134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2562,6 +3147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2574,6 +3160,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2582,6 +3169,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2604,6 +3198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2620,11 +3215,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
@@ -2638,78 +3234,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * DOCUMENT ME!
+ * 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
- * DOCUMENT ME!
*/
+ @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", "");
editPane.setEditable(false);
- StringBuffer contents = new StringBuffer("");
-
- float avg = 0;
- int min = Integer.MAX_VALUE, max = 0;
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
- {
- int size = viewport.alignment.getSequenceAt(i).getEnd()
- - viewport.alignment.getSequenceAt(i).getStart();
- avg += size;
- if (size > max)
- max = size;
- if (size < min)
- min = size;
- }
- avg = avg / (float) viewport.alignment.getHeight();
-
- contents.append("
Sequences: " + 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);
}
/**
@@ -2718,6 +3277,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2728,23 +3288,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2756,6 +3318,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2767,11 +3330,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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()));
}
/**
@@ -2780,6 +3343,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2791,6 +3355,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2802,6 +3367,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2813,6 +3379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2824,6 +3391,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2835,6 +3403,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -2846,6 +3415,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -2857,22 +3427,49 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -2884,122 +3481,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param cs
* DOCUMENT ME!
*/
+ @Override
public void changeColour(ColourSchemeI cs)
{
- int threshold = 0;
+ // TODO: pull up to controller method
if (cs != null)
{
+ // Make sure viewport is up to date w.r.t. any sliders
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ viewport.setThreshold(threshold);
}
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- cs.setConservation(c);
-
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
- else
+ if (cs instanceof TCoffeeColourScheme)
{
- cs.setConservation(null);
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
}
-
- cs.setConsensus(viewport.hconsensus);
}
viewport.setGlobalColourScheme(cs);
- if (viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
-
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(viewport.hiddenRepSequences), sg.getWidth());
- }
- else if (cs instanceof UserColourScheme)
- {
- sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
- }
- else
- {
- try
- {
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- } catch (Exception ex)
- {
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- }
- }
- }
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
alignPanel.paintAlignment(true);
}
@@ -3009,13 +3519,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
@@ -3026,13 +3537,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
@@ -3043,6 +3555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3061,6 +3574,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3079,9 +3593,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
}
@@ -3098,8 +3614,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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"))
@@ -3120,18 +3636,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -3143,6 +3660,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3154,6 +3672,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3172,6 +3691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -3183,6 +3703,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -3194,13 +3715,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3210,11 +3732,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
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);
}
@@ -3224,12 +3748,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3239,12 +3764,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3255,6 +3781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
@@ -3266,20 +3793,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.", "Invalid Selection",
+ 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);
}
}
@@ -3289,6 +3820,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
@@ -3296,11 +3828,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.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;
}
@@ -3308,6 +3843,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3318,15 +3854,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @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!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel("AV", "PID", "Average distance tree using PID");
}
/**
@@ -3335,9 +3884,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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");
}
/**
@@ -3346,9 +3896,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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");
}
/**
@@ -3357,9 +3908,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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");
}
/**
@@ -3372,38 +3924,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
+ 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",
+ MessageManager
+ .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager
+ .getString("label.sequences_selection_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3416,21 +3970,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
else
{
// are the visible sequences aligned?
- if (!viewport.alignment.isAligned(false))
+ 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",
+ 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;
}
@@ -3461,10 +4015,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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();
@@ -3473,8 +4029,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// 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);
}
@@ -3497,13 +4053,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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());
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,
+ viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
});
@@ -3521,23 +4078,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* 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();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.alignment.getSequences().elements();
- while (sq.hasMoreElements())
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
- aann = ((SequenceI) sq.nextElement()).getAnnotation();
+ aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
{
if (aann[i].hasScore() && aann[i].sequenceRef != null)
@@ -3549,13 +4106,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Enumeration labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
- .nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore,
+ (String) labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
- _annotationScoreVectorHash = viewport.alignment
+ _annotationScoreVectorHash = viewport.getAlignment()
.getAlignmentAnnotation().hashCode();
}
}
@@ -3572,25 +4129,56 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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 < iSize; i++)
+ for (final String type : new String[] { "NJ", "AV" })
{
- if (comps.elementAt(i) instanceof TreePanel)
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
{
- treePanels.add(comps.elementAt(i));
- }
+ JMenuItem tm = new JMenuItem();
+ ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+ if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+ || sm.isProtein() == !viewport.getAlignment()
+ .isNucleotide())
+ {
+ String smn = MessageManager.getStringOrReturn(
+ "label.score_model_", sm.getName());
+ final String title = MessageManager.formatMessage(
+ "label.treecalc_title", treecalcnm, smn);
+ tm.setText(title);//
+ tm.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newTreePanel(type, pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
}
+ sortByTreeMenu.removeAll();
- iSize = treePanels.size();
+ List 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;
@@ -3598,23 +4186,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sortByTreeMenu.setVisible(true);
- for (i = 0; i < treePanels.size(); i++)
+ for (final TreePanel tp : treePanels)
{
- TreePanel tp = (TreePanel) treePanels.elementAt(i);
final JMenuItem item = new JMenuItem(tp.getTitle());
- final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+ tp.sortByTree_actionPerformed();
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
- addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
- viewport.alignment));
-
- alignPanel.paintAlignment(true);
}
});
@@ -3622,6 +4204,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
@@ -3646,16 +4241,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
msa = viewport.getAlignmentView(true);
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ 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 = 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;
@@ -3683,12 +4282,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
// limit sequences - JBPNote in future - could spawn multiple prediction
// jobs
- // TODO: viewport.alignment.isAligned is a global state - the local
+ // 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.alignment.isAligned(false))
+ if (!viewport.getAlignment().isAligned(false))
{
- seqs.setSequences(new SeqCigar[]
- { seqs.getSequences()[0] });
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
// TODO: if seqs.getSequences().length>1 then should really have warned
// user!
@@ -3702,14 +4300,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @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);
@@ -3724,19 +4324,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} 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())
{
JOptionPane.showMessageDialog(Desktop.desktop, fin
- .getWarningMessage(), "Possible problem with tree file",
+ .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);
@@ -3821,130 +4433,169 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception e)
{
}
- ;
}
+ final AlignFrame me = this;
buildingMenu = true;
- try
+ new Thread(new Runnable()
{
- 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.
- Vector wsmenu = new Vector();
- final IProgressIndicator af = this;
- if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
+ @Override
+ public void run()
{
- // 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)
- if (msaws != null)
+ final List legacyItems = new ArrayList();
+ try
{
- // Add any Multiple Sequence Alignment Services
+ // 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");
- for (int i = 0, j = msaws.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, this);
-
- }
- wsmenu.add(msawsmenu);
- }
- if (secstrpr != null)
- {
- // 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 ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, this);
- }
- wsmenu.add(secstrmenu);
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+ 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))
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, this);
+ // 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)
+ {
+ // Add any secondary structure prediction services
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ 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++)
+ {
+ legacyItems.add(secstrmenu.getItem(litm));
+ }
+ }
+ }
}
- wsmenu.add(seqsrchmenu);
- }
- }
- // TODO: move into separate menu builder class.
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- JMenu jws2men = new JMenu("Jalview 2 Services");
- jws2servs.attachWSMenuEntry(jws2men, this);
- wsmenu.add(jws2men);
- }
- else
+ // 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()
{
- if (!jws2servs.isRunning())
+ @Override
+ public void run()
{
- new Thread(jws2servs).start();
+ try
+ {
+ webService.removeAll();
+ // first, add discovered services onto the webservices menu
+ if (wsmenu.size() > 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)
+ {
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
+ }
}
- }
- }
- }
- resetWebServiceMenu();
- // finally, add the whole shebang onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
+ });
+ } catch (Exception e)
{
- webService.add((JMenu) wsmenu.get(i));
}
+ buildingMenu = false;
}
- else
- {
- this.webService.add(this.webServiceNoServices);
- }
- } catch (Exception e)
- {
- }
- ;
- buildingMenu = false;
- }
+ }).start();
- /**
- * empty the web service menu and add any ad-hoc functions not dynamically
- * discovered.
- *
- */
- private void resetWebServiceMenu()
- {
- webService.removeAll();
- build_fetchdbmenu(webService);
- build_urlServiceMenu(webService);
}
/**
@@ -3954,84 +4605,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
private void build_urlServiceMenu(JMenu webService)
{
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, 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()))
- {
- showProducts.setEnabled(true);
+ // 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
- }
- else
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+ .getRestClients())
{
- showProducts.setEnabled(false);
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
}
}
/**
- * search selection for sequence xRef products and build the show products
- * menu.
+ * Searches the alignment sequences for xRefs and builds the Show
+ * Cross-References menu (formerly called Show Products), with database
+ * sources for which cross-references are found (protein sources for a
+ * nucleotide alignment and vice versa)
*
- * @param selection
- * @param dataset
- * @return true if showProducts menu should be enabled.
+ * @return true if Show Cross-references menu should be enabled
*/
- public boolean canShowProducts(SequenceI[] selection,
- boolean isRegionSelection, Alignment dataset)
+ public boolean canShowProducts()
{
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ AlignmentI dataset = viewport.getAlignment().getDataset();
boolean showp = false;
try
{
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
- final Alignment ds = dataset;
- 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 < ptypes.length; t++)
+ List ptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
+
+ for (final String source : ptypes)
{
showp = true;
- final boolean isRegSel = isRegionSelection;
final AlignFrame af = this;
- final String source = ptypes[t];
- JMenuItem xtype = new JMenuItem(ptypes[t]);
+ JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
-
+ @Override
public void actionPerformed(ActionEvent e)
{
- // TODO: new thread for this call with vis-delay
- af.showProductsFor(af.viewport.getSequenceSelection(), ds,
- isRegSel, dna, source);
+ showProductsFor(af.viewport.getSequenceSelection(), dna, source);
}
-
});
showProducts.add(xtype);
}
@@ -4039,85 +4672,248 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showProducts.setEnabled(showp);
} catch (Exception e)
{
- jalview.bin.Cache.log
- .warn(
- "canTranslate threw an exception - please report to help@jalview.org",
+ Cache.log
+ .warn("canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
}
return showp;
}
- protected void showProductsFor(SequenceI[] sel, Alignment ds,
- boolean isRegSel, boolean dna, String source)
+ /**
+ * Finds and displays cross-references for the selected sequences (protein
+ * products for nucleotide sequences, dna coding sequences for peptides).
+ *
+ * @param sel
+ * the sequences to show cross-references for
+ * @param dna
+ * true if from a nucleotide alignment (so showing proteins)
+ * @param source
+ * the database to show cross-references for
+ */
+ protected void showProductsFor(final SequenceI[] sel,
+ final boolean _odna, final String source)
{
- final boolean fisRegSel = isRegSel;
- final boolean fdna = dna;
- final String fsrc = source;
- final AlignFrame ths = this;
- final SequenceI[] fsel = sel;
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from",
+ new Object[] { source }), sttime);
try
{
- Alignment ds = ths.getViewport().alignment.getDataset(); // update
- // our local
- // dataset
- // reference
- Alignment prods = CrossRef
- .findXrefSequences(fsel, fdna, fsrc, ds);
- if (prods != null)
+ AlignmentI alignment = AlignFrame.this.getViewport()
+ .getAlignment();
+ AlignmentI dataset = alignment.getDataset() == null ? alignment
+ : alignment.getDataset();
+ boolean dna = alignment.isNucleotide();
+ if (_odna != dna)
+ {
+ System.err
+ .println("Conflict: showProducts for alignment originally "
+ + "thought to be "
+ + (_odna ? "DNA" : "Protein")
+ + " now searching for "
+ + (dna ? "DNA" : "Protein") + " Context.");
+ }
+ AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
+ source, dna);
+ if (xrefs == null)
{
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
- for (int s = 0; s < sprods.length; s++)
+ return;
+ }
+ /*
+ * get display scheme (if any) to apply to features
+ */
+ FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(source);
+
+ AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
+ xrefs);
+ if (!dna)
+ {
+ xrefsAlignment = AlignmentUtils.makeCdsAlignment(
+ xrefsAlignment.getSequencesArray(), dataset, sel);
+ xrefsAlignment.alignAs(alignment);
+ }
+
+ /*
+ * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
+ * sequences). If we are DNA, drop introns and update mappings
+ */
+ AlignmentI copyAlignment = null;
+
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+ {
+ boolean copyAlignmentIsAligned = false;
+ if (dna)
+ {
+ copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
+ xrefsAlignment.getSequencesArray());
+ if (copyAlignment.getHeight() == 0)
+ {
+ System.err.println("Failed to make CDS alignment");
+ }
+
+ /*
+ * pending getting Embl transcripts to 'align',
+ * we are only doing this for Ensembl
+ */
+ // TODO proper criteria for 'can align as cdna'
+ if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+ || AlignmentUtils.looksLikeEnsembl(alignment))
+ {
+ copyAlignment.alignAs(alignment);
+ copyAlignmentIsAligned = true;
+ }
+ }
+ else
+ {
+ copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
+ xrefs.getSequencesArray(), dataset);
+ }
+ copyAlignment.setGapCharacter(AlignFrame.this.viewport
+ .getGapCharacter());
+
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+
+ /*
+ * register any new mappings for sequence mouseover etc
+ * (will not duplicate any previously registered mappings)
+ */
+ ssm.registerMappings(dataset.getCodonFrames());
+
+ if (copyAlignment.getHeight() <= 0)
{
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (ds.getSequences() == null
- || !ds.getSequences().contains(
- sprods[s].getDatasetSequence()))
- ds.addSequence(sprods[s].getDatasetSequence());
- sprods[s].updatePDBIds();
+ System.err.println("No Sequences generated for xRef type "
+ + source);
+ return;
}
- Alignment al = new Alignment(sprods);
- AlignedCodonFrame[] cf = prods.getCodonFrames();
- al.setDataset(ds);
- for (int s = 0; cf != null && s < cf.length; s++)
+ /*
+ * align protein to dna
+ */
+ if (dna && copyAlignmentIsAligned)
{
- al.addCodonFrame(cf[s]);
- cf[s] = null;
+ xrefsAlignment.alignAs(copyAlignment);
+ }
+ else
+ {
+ /*
+ * align cdna to protein - currently only if
+ * fetching and aligning Ensembl transcripts!
+ */
+ // TODO: generalise for other sources of locus/transcript/cds data
+ if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+ {
+ copyAlignment.alignAs(xrefsAlignment);
+ }
}
- 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
+ /*
+ * build AlignFrame(s) according to available alignment data
+ */
+ AlignFrame newFrame = new AlignFrame(xrefsAlignment,
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ if (Cache.getDefault("HIDE_INTRONS", true))
{
- System.err.println("No Sequences generated for xRef type "
- + fsrc);
+ newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
- } catch (Exception e)
- {
- jalview.bin.Cache.log.error(
- "Exception when finding crossreferences", e);
+ String newtitle = String.format("%s %s %s", MessageManager
+ .getString(dna ? "label.proteins" : "label.nucleotides"),
+ MessageManager.getString("label.for"), getTitle());
+ newFrame.setTitle(newtitle);
+
+ if (copyAlignment == null)
+ {
+ /*
+ * split frame display is turned off in preferences file
+ */
+ Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ return; // via finally clause
+ }
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(AlignFrame.this.getTitle());
+
+ boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
+ newFrame.setShowSeqFeatures(showSequenceFeatures);
+ copyThis.setShowSeqFeatures(showSequenceFeatures);
+ FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+
+ /*
+ * copy feature rendering settings to split frame
+ */
+ newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(myFeatureStyling);
+ copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(myFeatureStyling);
+
+ /*
+ * apply 'database source' feature configuration
+ * if any was found
+ */
+ // TODO is this the feature colouring for the original
+ // alignment or the fetched xrefs? either could be Ensembl
+ newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
+ copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+
+ SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
+ dna ? newFrame : copyThis);
+ newFrame.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ sf.adjustDivider();
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
- } catch (Error e)
+ } catch (Throwable e)
+ {
+ Cache.log.error("Error when finding crossreferences", e);
+ } finally
+ {
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[] { source }), sttime);
+ }
+ }
+
+ /**
+ * Makes an alignment containing the given sequences, and adds them to the
+ * given dataset, which is also set as the dataset for the new alignment
+ *
+ * TODO: refactor to DatasetI method
+ *
+ * @param dataset
+ * @param seqs
+ * @return
+ */
+ protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+ AlignmentI seqs)
+ {
+ SequenceI[] sprods = new SequenceI[seqs.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
{
- jalview.bin.Cache.log.error("Error when finding crossreferences",
- e);
+ sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
+ if (dataset.getSequences() == null
+ || !dataset.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
+ sprods[s].updatePDBIds();
}
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
- sttime);
+ Alignment al = new Alignment(sprods);
+ al.setDataset(dataset);
+ return al;
}
};
@@ -4125,91 +4921,70 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
frunner.start();
}
- public boolean canShowTranslationProducts(SequenceI[] selection,
- AlignmentI alignment)
- {
- // 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)
+ /**
+ * 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)
{
- // /////////////////////////////
- // 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());
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.translateCdna();
} catch (Exception ex)
{
- al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", 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 errorTitle = MessageManager
+ .getString("label.implementation_error")
+ + MessageManager.getString("label.translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JOptionPane.ERROR_MESSAGE);
+ return;
}
- if (al == null)
+ if (al == null || al.getHeight() == 0)
{
- 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);
+ final String msg = MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+ final String errorTitle = MessageManager
+ .getString("label.translation_failed");
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ 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, true))
+ {
+ final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+ viewport.openSplitFrame(af, new Alignment(seqs));
+ }
+ else
+ {
+ Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
}
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ /**
+ * Set the file format
+ *
+ * @param fileFormat
+ */
+ public void setFileFormat(String fileFormat)
{
- // /////////////////////////////
- // 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);
- }
+ this.currentFileFormat = fileFormat;
}
/**
@@ -4219,102 +4994,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
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)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- if (featuresFile)
+ }
+
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.seqPanel.seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
}
- return featuresFile;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
+ @Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
+ @Override
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
- java.util.List files = null;
+ java.util.List files = new ArrayList(), protocols = new ArrayList();
try
{
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- // Works on Windows and MacOSX
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t
- .getTransferData(DataFlavor.javaFileListFlavor);
- }
- else if (t.isDataFlavorSupported(uriListFlavor))
- {
- // This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- 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();)
- {
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
-
- java.net.URI uri = new java.net.URI(s);
- // 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());
- }
- }
- }
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
e.printStackTrace();
@@ -4323,68 +5054,252 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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