X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=353a1397e45c6aa15fb247a34ce1759440b96ae6;hb=d919b93d3c0a57e36c2a90a34a6788bca86bfe81;hp=d984f3ce0fc4d0a286758cd0fc0eb521630dab1a;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index d984f3c..353a139
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,29 +1,34 @@
/*
- * 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 2.8.0b1)
+ * 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
+ * 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.
- *
- * 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
+ *
+ * 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 .
+ * 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.analysis.ScoreModelI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
@@ -75,12 +80,13 @@ 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;
@@ -112,6 +118,7 @@ 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 +139,7 @@ import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ IProgressIndicator, AlignViewControllerGuiI
{
/** DOCUMENT ME!! */
@@ -144,6 +151,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public AlignmentPanel alignPanel;
AlignViewport viewport;
+
+ public AlignViewControllerI avc;
+
Vector alignPanels = new Vector();
@@ -287,6 +297,7 @@ 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 +329,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
+ buildTreeMenu();
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
@@ -329,7 +341,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
addKeyListener();
-
+
}
/**
@@ -475,8 +487,7 @@ 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;
@@ -557,6 +568,7 @@ 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);
@@ -734,7 +746,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
rnahelicesColour
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
-
updateEditMenuBar();
}
@@ -808,7 +819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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()
{
@@ -841,6 +852,10 @@ 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
*/
@@ -978,7 +993,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -988,8 +1003,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (currentFileFormat == null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
value = chooser.showSaveDialog(this);
return;
}
@@ -1025,8 +1040,8 @@ 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
@@ -1047,9 +1062,8 @@ 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);
@@ -1079,8 +1093,7 @@ 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;
@@ -1091,8 +1104,8 @@ 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;
@@ -1129,9 +1142,8 @@ 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);
@@ -1150,7 +1162,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600, 500);
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1246,8 +1258,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -1347,12 +1359,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText("Undo " + command.getDescription());
+ 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)
@@ -1360,12 +1372,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText("Redo " + command.getDescription());
+ redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
}
else
{
redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
}
}
@@ -1693,7 +1705,7 @@ 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()}));
}
/**
@@ -2051,7 +2063,59 @@ 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!
*
@@ -2135,12 +2199,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@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);
+ }
}
/**
@@ -2294,7 +2357,7 @@ 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);
@@ -2342,8 +2405,7 @@ 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
@@ -2537,7 +2599,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.viewName = newViewName;
addAlignmentPanel(newap, true);
-
+ newap.alignmentChanged();
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
@@ -2951,12 +3014,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
}
/**
@@ -2976,7 +3038,7 @@ 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(),
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -3362,7 +3424,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@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);
}
@@ -3411,8 +3473,8 @@ 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)
{
@@ -3564,14 +3626,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| (viewport.getSelectionGroup().getSize() < 2))
{
JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.", "Invalid Selection",
+ 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);
}
}
@@ -3590,9 +3652,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| (viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
- "Principal component analysis must take\n"
- + "at least 4 input sequences.",
- "Sequence selection insufficient",
+ MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager.getString("label.sequence_selection_insufficient"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3694,8 +3755,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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;
}
@@ -3709,10 +3770,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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;
@@ -3730,10 +3789,8 @@ 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;
@@ -3886,6 +3943,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ NewTreePanel(type, (String) pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
+ }
sortByTreeMenu.removeAll();
Vector comps = (Vector) PaintRefresher.components.get(viewport
@@ -4030,8 +4116,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -4047,13 +4133,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
+ 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",
+ fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@@ -4158,6 +4244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
+ final List legacyItems=new ArrayList();
try
{
System.err.println("Building ws menu again "
@@ -4189,28 +4276,10 @@ 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
@@ -4220,35 +4289,23 @@ 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 submens=new ArrayList();
- // submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
// No search services yet
// wsmenu.add(seqsrchmenu);
@@ -4273,6 +4330,7 @@ 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();
@@ -4281,6 +4339,16 @@ 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())
{
@@ -4291,7 +4359,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
-
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
@@ -4357,12 +4424,6 @@ 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);
- }
}
/*
@@ -4573,13 +4634,13 @@ 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(),
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
@@ -4603,20 +4664,26 @@ 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(),
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
DEFAULT_WIDTH, DEFAULT_HEIGHT);
}
}
@@ -4810,10 +4877,9 @@ 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)
{
@@ -4846,10 +4912,8 @@ 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;
@@ -4908,8 +4972,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
tcoffeeColour.setSelected(true);
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar
- .setText("Successfully pasted T-Coffee scores to alignment.");
+ statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
@@ -4918,9 +4981,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+ tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
: tcf.getWarningMessage(),
- "Problem reading T-COFFEE score file",
+ MessageManager.getString("label.problem_reading_tcoffee_score_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@@ -5027,6 +5090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
viewport = alignPanel.av;
+ avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
}
}
@@ -5037,7 +5101,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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)
@@ -5132,12 +5196,23 @@ 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()
+ {
+ 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()
{
@@ -5241,8 +5316,7 @@ 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
@@ -5317,7 +5391,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
++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;
@@ -5329,7 +5403,7 @@ 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;
@@ -5467,34 +5541,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
- if (viewport.getSelectionGroup() != null)
- {
- 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 (SequenceI s : gps[g].getSequences())
- viewport.setSequenceColour(s, col);
- }
+ if (avc.makeGroupsFromSelection()) {
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
*