X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c3d80d15bbf73df2203c8a914e9a7fbbf67f17c8;hb=bdba25716eaa9492681532cb443c18ed34237488;hp=fd6fe245bff3992ddce8fa8632ba18ec385ce6f9;hpb=d5ad9ef13d6f9d542e89d97b82cbd86b11ed7bae;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fd6fe24..c3d80d1 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,25 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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;
@@ -73,7 +76,6 @@ import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
@@ -87,7 +89,6 @@ 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;
@@ -119,6 +120,7 @@ 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;
@@ -151,9 +153,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public AlignmentPanel alignPanel;
AlignViewport viewport;
-
+
public AlignViewControllerI avc;
-
Vector alignPanels = new Vector();
@@ -262,15 +263,17 @@ 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();
}
@@ -297,7 +300,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
@@ -341,7 +345,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
addKeyListener();
-
+
}
/**
@@ -487,7 +491,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(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;
@@ -568,7 +574,8 @@ 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);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
alignPanels.addElement(ap);
@@ -812,14 +819,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
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(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
@@ -828,10 +835,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -853,9 +857,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
@Override
- public void setStatus(String text) {
+ public void setStatus(String text)
+ {
statusBar.setText(text);
};
+
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
@@ -992,8 +998,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText(MessageManager.getString("action.save"));
+ chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -1002,9 +1008,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat = chooser.getSelectedFormat();
if (currentFileFormat == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.select_file_format_before_saving"),
- MessageManager.getString("label.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;
}
@@ -1040,8 +1051,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
success = new Jalview2XML().SaveAlignment(this, file, shortName);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
-
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new String[]
+ { fileName, format }));
}
else
@@ -1062,8 +1074,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.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);
@@ -1093,7 +1107,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new String[]
+ { fileName, format }));
} catch (Exception ex)
{
success = false;
@@ -1104,8 +1121,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
- MessageManager.getString("label.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;
@@ -1142,8 +1162,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.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);
@@ -1161,8 +1183,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{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);
@@ -1258,8 +1281,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));
- chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
@@ -1359,7 +1384,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
@@ -1372,7 +1399,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
@@ -1705,7 +1734,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new String[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
@@ -1912,7 +1943,7 @@ 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"), EditCommand.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
@@ -2064,6 +2095,60 @@ 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!
*
@@ -2117,7 +2202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
@@ -2147,7 +2232,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- if (avc.deleteGroups()) {
+ if (avc.deleteGroups())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
@@ -2305,7 +2391,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getSelectionGroup());
}
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
@@ -2353,7 +2441,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+ 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
@@ -2516,7 +2606,7 @@ 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
@@ -2548,7 +2638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addAlignmentPanel(newap, true);
newap.alignmentChanged();
-
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
@@ -2962,11 +3052,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{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, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 500, 400);
}
/**
@@ -2986,8 +3080,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{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()
@@ -3183,10 +3278,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
}
else
{
@@ -3372,7 +3464,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
new UserDefinedColours(alignPanel, null);
}
@@ -3421,8 +3514,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.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)
{
@@ -3573,15 +3668,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.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, MessageManager.getString("action.pairwise_alignment"), 600, 500);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
@@ -3599,10 +3697,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager.getString("label.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;
}
@@ -3703,8 +3805,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager.getString("label.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;
}
@@ -3718,8 +3823,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
- MessageManager.getString("label.sequences_selection_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;
@@ -3737,8 +3844,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager.getString("label.sequences_not_aligned"),
+ MessageManager
+ .getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager
+ .getString("label.sequences_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3775,7 +3884,7 @@ 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()
{
@@ -3893,23 +4002,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
calculateTree.removeAll();
// build the calculate menu
- for (final String type:new String[] {"NJ", "AV"})
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
{
- for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
+ 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);
- final String title="Calculate "+type+" using "+sm.getName();
- tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
- tm
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- NewTreePanel(type, (String) pwtype, title);
- }
- });
- calculateTree.add(tm);
+ 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);
+ }
}
}
@@ -4057,8 +4175,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));
- chooser.setToolTipText(MessageManager.getString("label.load_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);
@@ -4073,14 +4192,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.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(), MessageManager.getString("label.possible_problem_with_tree_file"),
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@@ -4185,7 +4310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
- final List legacyItems=new ArrayList();
+ final List legacyItems = new ArrayList();
try
{
System.err.println("Building ws menu again "
@@ -4202,12 +4327,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// object broker mechanism.
final Vector wsmenu = new Vector();
final IProgressIndicator af = me;
- final JMenu msawsmenu = new JMenu("Alignment");
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Protein Disorder");
+ final JMenu msawsmenu = new JMenu(MessageManager.getString("label.alignment"));
+ final JMenu secstrmenu = new JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ final JMenu seqsrchmenu = new JMenu(MessageManager.getString("label.sequence_database_search"));
+ final JMenu analymenu = new JMenu(MessageManager.getString("label.analysis"));
+ final JMenu dismenu = new JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4218,7 +4342,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// be
// stored or retrieved from elsewhere
// No MSAWS used any more:
- // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // Vector msaws = null; // (Vector)
+ // Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
@@ -4230,17 +4355,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
- int p=secstrmenu.getItemCount();
+ int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- int q=secstrmenu.getItemCount();
- for (int litm=p;litm"
- + 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++;
}
@@ -5252,7 +5421,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));
+ fetchr = new JMenuItem(MessageManager.formatMessage(
+ "label.fetch_all_param", new String[]
+ { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
@@ -5273,15 +5444,11 @@ 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;
@@ -5294,7 +5461,7 @@ 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 =
@@ -5321,13 +5488,13 @@ 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(MessageManager.formatMessage("label.source_to_target",imname,sname));
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
@@ -5339,7 +5506,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
@@ -5477,7 +5645,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
- if (avc.makeGroupsFromSelection()) {
+ if (avc.makeGroupsFromSelection())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
@@ -5512,8 +5681,7 @@ 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