X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=216db0e2ba9d5e42084ea191ed0ff15cdc1d8a41;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=fe9641964e0ab131ad9b3c222dfd08591ed2edf3;hpb=64f5a7fa2c8da37ce4a30f2b38147d143f165a66;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index fe96419..216db0e
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,32 +1,41 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.analysis.CrossRef;
import jalview.analysis.NJTree;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
@@ -75,12 +84,13 @@ import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
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.Color;
import java.awt.Component;
import java.awt.GridLayout;
import java.awt.Rectangle;
@@ -106,12 +116,14 @@ import java.beans.PropertyChangeEvent;
import java.io.File;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
@@ -132,7 +144,7 @@ import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ IProgressIndicator, AlignViewControllerGuiI
{
/** DOCUMENT ME!! */
@@ -145,8 +157,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignViewport viewport;
+ public AlignViewControllerI avc;
+
Vector alignPanels = new Vector();
-
+
/**
* Last format used to load or save alignments in this window
*/
@@ -252,21 +266,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
-
- alignPanel = new AlignmentPanel(this, viewport);
if (al.getDataset() == null)
{
al.setDataset(null);
}
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+
addAlignmentPanel(alignPanel, true);
init();
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
@@ -287,6 +303,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
@@ -318,6 +336,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
+ buildTreeMenu();
+
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
@@ -352,6 +372,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -359,7 +380,9 @@ 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());
+ }
switch (evt.getKeyCode())
{
@@ -371,32 +394,48 @@ 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);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
@@ -474,8 +513,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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;
@@ -487,14 +527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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();
@@ -532,20 +565,25 @@ 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;
}
}
@@ -555,6 +593,8 @@ 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);
@@ -616,6 +656,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
// // System.out.println("Discoverer property change.");
@@ -624,6 +665,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
System.err
@@ -637,6 +679,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -649,6 +692,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
+ @Override
public void run()
{
BuildWebServiceMenu();
@@ -704,6 +748,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
scaleLeft.setVisible(av.wrapAlignment);
scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
+ /*
+ * 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.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -718,7 +769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
@@ -728,10 +779,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
rnahelicesColour
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
-
updateEditMenuBar();
}
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
Hashtable progressBars, progressBarHandlers;
/*
@@ -739,6 +791,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
@@ -786,30 +839,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
validate();
}
+ @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.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -820,6 +872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
if (progressBars != null && progressBars.size() > 0)
@@ -829,6 +882,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return false;
}
+ @Override
+ public void setStatus(String text)
+ {
+ statusBar.setText(text);
+ };
+
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
@@ -842,16 +901,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
@@ -866,6 +928,7 @@ 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
@@ -903,6 +966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
@@ -916,16 +980,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
}
+ @Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
@@ -947,6 +1014,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
@@ -956,8 +1024,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -966,9 +1034,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat = chooser.getSelectedFormat();
if (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);
value = chooser.showSaveDialog(this);
return;
}
@@ -1004,8 +1077,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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 String[]
+ { fileName, format }));
}
else
@@ -1026,9 +1100,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to save only the visible alignment?",
- "Save / Omit Hidden Columns",
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
@@ -1038,9 +1113,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(
- format,
- (Alignment) viewport.getAlignment(), // class cast exceptions will
+ String output = f.formatSequences(format,
+ viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
@@ -1059,8 +1133,10 @@ 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 String[]
+ { fileName, format }));
} catch (Exception ex)
{
success = false;
@@ -1071,8 +1147,11 @@ 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 String[]
+ { fileName }), MessageManager
+ .getString("label.error_saving_file"),
+ JOptionPane.WARNING_MESSAGE);
}
return success;
@@ -1099,6 +1178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
String[] omitHidden = null;
@@ -1108,9 +1188,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
@@ -1128,8 +1209,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1144,6 +1226,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
new HTMLOutput(alignPanel,
@@ -1162,6 +1245,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1173,11 +1257,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1190,6 +1280,7 @@ 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
@@ -1197,11 +1288,13 @@ 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,
@@ -1211,14 +1304,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getAlignment()).alignmentProperties);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
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);
@@ -1237,6 +1333,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
@@ -1316,26 +1413,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText("Undo " + command.getDescription());
+ CommandI command = viewport.historyList.peek();
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
}
if (viewport.redoList.size() > 0)
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText("Redo " + command.getDescription());
+ CommandI command = viewport.redoList.peek();
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
@@ -1384,11 +1485,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
+ {
return;
- CommandI command = (CommandI) viewport.historyList.pop();
+ }
+ CommandI command = viewport.historyList.pop();
viewport.redoList.push(command);
command.undoCommand(getViewAlignments());
@@ -1419,6 +1523,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.redoList.size() < 1)
@@ -1426,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
+ CommandI command = viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand(getViewAlignments());
@@ -1508,61 +1613,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().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 Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.getAlignment().getSequenceAt(
+ sg.add(viewport.getAlignment().getSequenceAt(
alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
@@ -1583,39 +1644,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ }
}
- 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);
+ }
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);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
@@ -1636,7 +1711,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
@@ -1647,6 +1724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1706,7 +1784,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new String[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
@@ -1715,6 +1795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1726,6 +1807,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1794,6 +1876,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups = new ArrayList();
+ int fgroup = -1;
if (newAlignment)
{
@@ -1861,6 +1945,17 @@ 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.
@@ -1871,6 +1966,22 @@ 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);
}
@@ -1882,7 +1993,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
@@ -1890,11 +2003,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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);
+ 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
@@ -1917,7 +2050,9 @@ 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)
@@ -1934,6 +2069,9 @@ 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);
}
}
@@ -1943,6 +2081,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : ((Vector) alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
+ {
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
@@ -2000,12 +2149,67 @@ 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)
+ {
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ 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()
+ .transferSettings(
+ alignPanel.seqPanel.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);
@@ -2018,6 +2222,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -2027,17 +2232,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector seqs = new Vector();
+ List seqs = new ArrayList(sg.getSize());
SequenceI seq;
for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
+ seqs.add(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ // If the cut affects all sequences, warn, remove highlighted columns
if (sg.getSize() == viewport.getAlignment().getHeight())
{
+ 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 (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
@@ -2045,14 +2260,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceI[] cut = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
- cut[i] = (SequenceI) seqs.elementAt(i);
+ cut[i] = seqs.get(i);
}
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
@@ -2078,14 +2294,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- viewport.getAlignment().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);
+ }
}
/**
@@ -2094,6 +2311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -2116,6 +2334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
@@ -2139,6 +2358,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2160,6 +2380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
@@ -2173,6 +2394,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2184,6 +2406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2233,16 +2456,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getSelectionGroup());
}
- 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.getAlignment().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)))
{
@@ -2261,6 +2482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2284,8 +2506,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new String[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
@@ -2308,6 +2531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2346,6 +2570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
@@ -2369,11 +2594,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
newView(true);
@@ -2444,7 +2671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
- viewTitle = "View";
+ viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
@@ -2475,6 +2702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.viewName = newViewName;
addAlignmentPanel(newap, true);
+ newap.alignmentChanged();
if (alignPanels.size() == 2)
{
@@ -2484,11 +2712,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return newap;
}
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
@@ -2500,6 +2730,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
@@ -2511,6 +2742,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2520,12 +2752,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.rightAlignIds = idRightAlign.isSelected();
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
@@ -2537,6 +2771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2552,6 +2787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2564,6 +2800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2573,17 +2810,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
}
+ @Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+ @Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
repaint();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
@@ -2667,6 +2907,7 @@ 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);
@@ -2679,6 +2920,7 @@ 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();
@@ -2695,6 +2937,7 @@ 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();
@@ -2702,12 +2945,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
+ @Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2720,6 +2965,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2732,6 +2978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2744,6 +2991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2756,6 +3004,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2768,6 +3017,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2780,6 +3030,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2788,6 +3039,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2810,6 +3062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2826,6 +3079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2844,29 +3098,42 @@ 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);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
}
+ @Override
public void alignmentProperties()
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText("" + contents.toString() + "");
+ editPane.setText(MessageManager.formatMessage("label.html_content",
+ new String[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
- + getTitle(), 500, 400);
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 500, 400);
}
/**
@@ -2875,6 +3142,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2885,12 +3153,14 @@ 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 String[]
+ { this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -2901,6 +3171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2912,6 +3183,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2923,10 +3195,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(viewport.getAlignment()
- .getSequences(), viewport.getAlignment().getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
}
/**
@@ -2935,6 +3208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2946,6 +3220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2957,6 +3232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2968,6 +3244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2979,6 +3256,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2990,6 +3268,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -3001,6 +3280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -3012,11 +3292,13 @@ 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());
@@ -3028,11 +3310,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
+ @Override
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
@@ -3044,6 +3328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -3066,10 +3351,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
}
else
{
@@ -3104,12 +3386,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getColourAppliesToAllGroups())
{
- Vector groups = viewport.getAlignment().getGroups();
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
if (cs == null)
{
sg.cs = null;
@@ -3118,8 +3397,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
- .getHiddenRepSequences()), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
@@ -3181,6 +3460,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
@@ -3198,6 +3478,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
@@ -3215,6 +3496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3233,6 +3515,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3251,9 +3534,11 @@ 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);
}
@@ -3292,6 +3577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
@@ -3301,8 +3587,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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)
{
@@ -3314,6 +3602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3325,6 +3614,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3343,6 +3633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -3354,6 +3645,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -3365,6 +3657,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3381,6 +3674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3396,6 +3690,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3411,6 +3706,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3427,6 +3723,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
@@ -3438,20 +3735,24 @@ 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);
}
}
@@ -3461,6 +3762,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
@@ -3468,11 +3770,14 @@ 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;
}
@@ -3480,6 +3785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3490,6 +3796,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
@@ -3507,6 +3814,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3518,6 +3826,7 @@ 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");
@@ -3529,6 +3838,7 @@ 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");
@@ -3540,6 +3850,7 @@ 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");
@@ -3559,34 +3870,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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;
@@ -3604,10 +3917,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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;
@@ -3644,10 +3957,11 @@ 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 String[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3680,6 +3994,7 @@ 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();
@@ -3704,6 +4019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* rebuilding in subsequence calls.
*
*/
+ @Override
public void buildSortByAnnotationScoresMenu()
{
if (viewport.getAlignment().getAlignmentAnnotation() == null)
@@ -3717,10 +4033,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.getAlignment().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)
@@ -3755,8 +4070,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param title
* SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
+ calculateTree.removeAll();
+ // build the calculate menu
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
+ {
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
+ {
+ JMenuItem tm = new JMenuItem();
+ ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+ if (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, (String) pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
+ }
sortByTreeMenu.removeAll();
Vector comps = (Vector) PaintRefresher.components.get(viewport
@@ -3788,6 +4136,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
tp.sortByTree_actionPerformed(null);
@@ -3837,16 +4186,20 @@ 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;
@@ -3893,14 +4246,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
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);
@@ -3915,14 +4270,20 @@ 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",
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@@ -4024,8 +4385,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
buildingMenu = true;
new Thread(new Runnable()
{
+ @Override
public void run()
{
+ final List legacyItems = new ArrayList();
try
{
System.err.println("Building ws menu again "
@@ -4047,7 +4410,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Disorder");
+ 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)
@@ -4057,28 +4430,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
- Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // No MSAWS used any more:
+ // Vector msaws = null; // (Vector)
+ // Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
- Vector seqsrch = null; // (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)
- {
- // Add any Multiple Sequence Alignment Services
- 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, me);
-
- }
- }
if (secstrpr != null)
{
// Add any secondary structure prediction services
@@ -4088,19 +4444,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
+ int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- }
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
- for (int i = 0, j = seqsrch.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, me);
+ int q = secstrmenu.getItemCount();
+ for (int litm = p; litm < q; litm++)
+ {
+ legacyItems.add(secstrmenu.getItem(litm));
+ }
}
}
}
@@ -4111,17 +4461,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
- // final ArrayList submens=new ArrayList();
- // submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
// No search services yet
// wsmenu.add(seqsrchmenu);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
try
@@ -4132,7 +4477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- webService.add((JMenu) wsmenu.get(i));
+ webService.add(wsmenu.get(i));
}
}
else
@@ -4140,6 +4485,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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();
@@ -4148,6 +4494,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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())
{
@@ -4158,7 +4515,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
-
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
@@ -4174,6 +4530,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception e)
{
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
}
;
}
@@ -4221,12 +4580,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
this);
}
-
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
- }
}
/*
@@ -4296,6 +4649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
xtype.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: new thread for this call with vis-delay
@@ -4329,10 +4683,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
try
{
Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
@@ -4350,7 +4705,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (ds.getSequences() == null
|| !ds.getSequences().contains(
sprods[s].getDatasetSequence()))
+ {
ds.addSequence(sprods[s].getDatasetSequence());
+ }
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
@@ -4386,7 +4743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.bin.Cache.log.error("Error when finding crossreferences",
e);
}
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
sttime);
}
@@ -4412,6 +4769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showProducts_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4434,17 +4792,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
+ MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.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);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
+ @Override
public void showTranslation_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4463,21 +4825,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} 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);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.error_when_translating_sequences_submit_bug_report"),
+ MessageManager
+ .getString("label.implementation_error")
+ + MessageManager
+ .getString("translation_failed"),
+ JOptionPane.ERROR_MESSAGE);
+ return;
}
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);
+ MessageManager
+ .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+ MessageManager.getString("label.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);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.translation_of_params", new String[]
+ { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
@@ -4523,22 +4900,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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();
@@ -4665,10 +5047,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| JOptionPane
.showConfirmDialog(
this,
- "Do you want to automatically associate the "
- + filesmatched.size()
- + " PDB files with sequences in the alignment that have the same name ?",
- "Automatically Associate PDB files by name",
+ MessageManager
+ .formatMessage(
+ "label.automatically_associate_pdb_files_with_sequences_same_name",
+ new String[]
+ { Integer.valueOf(
+ filesmatched
+ .size())
+ .toString() }),
+ MessageManager
+ .getString("label.automatically_associate_pdb_files_by_name"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
{
@@ -4681,7 +5069,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
@@ -4701,10 +5090,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- "Do you want to ignore the "
- + filesnotmatched.size()
- + " files whose names did not match any sequence IDs ?",
- "Ignore unmatched dropped files ?",
+ ""+MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new String[]
+ { Integer.valueOf(
+ filesnotmatched
+ .size())
+ .toString() })+"",
+ MessageManager
+ .getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
{
return;
@@ -4764,15 +5159,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
- .setText("Successfully pasted T-Coffee scores to alignment.");
+ .setText(MessageManager
+ .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
- // some problem - if no warning its probable that the ID matching process didn't work
- JOptionPane.showMessageDialog(Desktop.desktop,
- tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
- "Problem reading T-COFFEE score file",
- JOptionPane.WARNING_MESSAGE);
+ // some problem - if no warning its probable that the ID matching
+ // process didn't work
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ tcf.getWarningMessage() == null ? MessageManager
+ .getString("label.check_file_matches_sequence_ids_alignment")
+ : tcf.getWarningMessage(),
+ MessageManager
+ .getString("label.problem_reading_tcoffee_score_file"),
+ JOptionPane.WARNING_MESSAGE);
}
}
else
@@ -4781,7 +5183,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception x)
{
- Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
tcf = null;
}
if (tcf == null)
@@ -4850,25 +5254,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception ex)
{
ex.printStackTrace();
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "loading data "
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+ : "using " + protocol + " from " + file)
+ : ".")
+ + (format != null ? "(parsing as '" + format
+ + "' file)" : ""), oom, Desktop.desktop);
}
}
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
{
alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
}
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
{
String reply = JOptionPane.showInternalInputDialog(this,
- "Enter View Name", "Edit View Name",
+ MessageManager.getString("label.enter_view_name"),
+ MessageManager.getString("label.enter_view_name"),
JOptionPane.QUESTION_MESSAGE);
if (reply != null)
@@ -4887,6 +5311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Open the dialog for regex description parsing.
*/
+ @Override
protected void extractScores_actionPerformed(ActionEvent e)
{
ParseProperties pp = new jalview.analysis.ParseProperties(
@@ -4909,6 +5334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4920,6 +5346,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4960,20 +5387,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
- final JMenu rfetch = new JMenu("Fetch DB References");
- rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ final JMenu rfetch = new JMenu(
+ MessageManager.getString("action.fetch_db_references"));
+ rfetch.setToolTipText(MessageManager
+ .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
webService.add(rfetch);
- JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
+ MessageManager.getString("option.trim_retrieved_seqs"));
+ trimrs.setToolTipText(MessageManager
+ .getString("label.trim_retrieved_sequences"));
+ trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ trimrs.setSelected(trimrs.isSelected());
+ Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Boolean.valueOf(trimrs.isSelected()).toString());
+ };
+ });
+ rfetch.add(trimrs);
+ JMenuItem fetchr = new JMenuItem(
+ MessageManager.getString("label.standard_databases"));
+ fetchr.setToolTipText(MessageManager
+ .getString("label.fetch_embl_uniprot"));
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4989,12 +5438,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final AlignFrame me = this;
new Thread(new Runnable()
{
+ @Override
public void run()
{
final jalview.ws.SequenceFetcher sf = SequenceFetcher
.getSequenceFetcherSingleton(me);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
String[] dbclasses = sf.getOrderedSupportedSources();
@@ -5035,11 +5486,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5051,9 +5504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
});
- fetchr.setToolTipText(""
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + src.getDbName()) + "");
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
dfetch.add(fetchr);
comp++;
}
@@ -5063,15 +5514,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
- + "'");
+ fetchr = new JMenuItem(MessageManager.formatMessage(
+ "label.fetch_all_param", new String[]
+ { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5083,15 +5537,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
});
- fetchr.setToolTipText(""
- + JvSwingUtils.wrapTooltip("Retrieve from all "
- + otherdb.size() + " sources in "
- + src.getDbSource() + "
First is :"
- + src.getDbName()) + "");
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
- ifetch = new JMenu("Sources from " + src.getDbSource());
+ ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
icomp = 0;
String imname = null;
int i = 0;
@@ -5104,7 +5554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
0, 10) + "..." : dbname;
if (imname == null)
{
- imname = "from '" + sname + "'";
+ imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
}
fetchr = new JMenuItem(msname);
final DbSourceProxy[] dassrc =
@@ -5112,11 +5562,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5129,13 +5581,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
fetchr.setToolTipText(""
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + dbname) + "");
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
{
- ifetch.setText(imname + " to '" + sname + "'");
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
@@ -5147,7 +5599,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(mname + " to '" + dbclass + "'");
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
@@ -5164,6 +5617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Left justify the whole alignment.
*/
+ @Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -5174,6 +5628,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Right justify the whole alignment.
*/
+ @Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -5194,6 +5649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+ @Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
@@ -5207,6 +5663,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -5221,6 +5678,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -5234,6 +5692,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -5247,18 +5706,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -5271,38 +5735,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
- if (viewport.getSelectionGroup() != null)
+ if (avc.makeGroupsFromSelection())
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- gps[g].setShowNonconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
- ;
- }
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
+ @Override
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.createGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ @Override
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
/**
* make the given alignmentPanel the currently selected tab
*
@@ -5313,8 +5774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (!viewport.getSequenceSetId().equals(
alignmentPanel.av.getSequenceSetId()))
{
- throw new Error(
- "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null
& alignPanels.indexOf(alignmentPanel) != tabbedPane
@@ -5323,6 +5783,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
}
+
+ /**
+ * Action on selection of menu options to Show or Hide annotations.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ @Override
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
+ {
+ aa.visible = visible;
+ }
+ }
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
+ }
+
+ /**
+ * Store selected annotation sort order for the view and repaint.
+ */
+ @Override
+ protected void sortAnnotations_actionPerformed()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ *
+ * @return alignment panels in this alignemnt frame
+ */
+ public List getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ }
}
class PrintThread extends Thread
@@ -5336,6 +5844,7 @@ class PrintThread extends Thread
static PageFormat pf;
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();