X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=41685169e7ce5a0e028ea3dc0cf4720e74d15324;hb=27c019af21a3eddef893d67fcf27c70f33720a06;hp=57ff660e9f41a71548537f2b25ac4390e2e52064;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 57ff660..4168516 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,31 +1,36 @@
/*
- * 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;
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;
@@ -84,7 +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;
@@ -116,6 +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;
@@ -136,7 +141,7 @@ import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator
+ IProgressIndicator, AlignViewControllerGuiI
{
/** DOCUMENT ME!! */
@@ -148,9 +153,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public AlignmentPanel alignPanel;
AlignViewport viewport;
-
+
public AlignViewControllerI avc;
-
Vector alignPanels = new Vector();
@@ -259,15 +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();
}
@@ -294,7 +300,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
@@ -326,6 +333,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
+ buildTreeMenu();
+ buildShowHideAnnotationMenus();
+
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
@@ -337,7 +347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
addKeyListener();
-
+
}
/**
@@ -483,7 +493,9 @@ 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;
@@ -564,7 +576,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
alignPanels.addElement(ap);
@@ -815,7 +828,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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()
{
@@ -848,6 +862,12 @@ 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
*/
@@ -985,7 +1005,7 @@ 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);
@@ -994,9 +1014,14 @@ 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;
}
@@ -1032,8 +1057,9 @@ 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
@@ -1054,8 +1080,10 @@ 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);
@@ -1085,7 +1113,10 @@ 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;
@@ -1096,8 +1127,11 @@ 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;
@@ -1134,8 +1168,10 @@ 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);
@@ -1153,8 +1189,9 @@ 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);
@@ -1250,8 +1287,10 @@ 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);
@@ -1351,7 +1390,9 @@ 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
{
@@ -1364,7 +1405,9 @@ 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
{
@@ -1697,7 +1740,9 @@ 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() }));
}
/**
@@ -2056,6 +2101,60 @@ 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!
*
@@ -2139,7 +2238,8 @@ 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);
@@ -2297,7 +2397,9 @@ 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);
@@ -2345,7 +2447,9 @@ 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
@@ -2540,7 +2644,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addAlignmentPanel(newap, true);
newap.alignmentChanged();
-
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
@@ -2954,12 +3058,15 @@ 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, "Alignment Properties: "
- + getTitle(), 500, 400);
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 500, 400);
}
/**
@@ -2979,8 +3086,9 @@ 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()
@@ -3176,10 +3284,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
-
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
}
else
{
@@ -3365,7 +3470,8 @@ 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);
}
@@ -3414,8 +3520,10 @@ 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)
{
@@ -3566,15 +3674,18 @@ 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, "Pairwise Alignment", 600, 500);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
@@ -3592,10 +3703,14 @@ 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;
}
@@ -3696,8 +3811,11 @@ 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;
}
@@ -3711,8 +3829,10 @@ 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;
@@ -3730,8 +3850,10 @@ 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;
@@ -3884,6 +4006,38 @@ 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ NewTreePanel(type, (String) pwtype, title);
+ }
+ });
+ calculateTree.add(tm);
+ }
+
+ }
+ }
sortByTreeMenu.removeAll();
Vector comps = (Vector) PaintRefresher.components.get(viewport
@@ -4028,8 +4182,9 @@ 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);
@@ -4044,14 +4199,20 @@ 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);
}
}
@@ -4156,7 +4317,7 @@ 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 "
@@ -4189,7 +4350,8 @@ 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)
@@ -4201,17 +4363,17 @@ 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= mcomp || i == (otherdb.size()))
{
- ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
+ ifetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", imname, sname));
dfetch.add(ifetch);
ifetch = new JMenu();
imname = null;
@@ -5311,7 +5522,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
++dbi;
if (comp >= mcomp || dbi >= (dbclasses.length))
{
- dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
+ dfetch.setText(MessageManager.formatMessage(
+ "label.source_to_target", mname, dbclass));
rfetch.add(dfetch);
dfetch = new JMenu();
mname = null;
@@ -5449,7 +5661,8 @@ 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);
@@ -5494,6 +5707,95 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
}
+
+ /**
+ * On menu option, open a panel to allow choice of annotation types to
+ * show/hide.
+ */
+ @Override
+ protected void chooseAnnotations_actionPerformed()
+ {
+ new AnnotationChooser(this.alignPanel);
+ }
+
+ /**
+ * Get a list of unique annotation types for the alignment, optionally
+ * restricted to sequence-specific annotations.
+ */
+ protected List getAnnotationTypes(boolean sequenceSpecificOnly)
+ {
+ // TODO move this to an AlignmentUtils class or similar
+ List types = new ArrayList();
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (sequenceSpecificOnly && aa.sequenceRef == null)
+ {
+ continue;
+ }
+ String type = aa.label;
+ if (!types.contains(type))
+ {
+ types.add(type);
+ }
+ }
+ return types;
+ }
+
+ /**
+ * Action on selection of an annotation type to Show or Hide.
+ *
+ * @param type
+ * @param doShow
+ */
+ @Override
+ protected void showHideAnnotation_actionPerformed(String type, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (type.equals(aa.label))
+ {
+ aa.visible = doShow;
+ }
+ }
+ this.alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Dynamically build the list of annotation types to show or hide.
+ */
+ @Override
+ protected void buildShowHideAnnotationMenus()
+ {
+ showAnnotations.removeAll();
+ hideAnnotations.removeAll();
+
+ List types = getAnnotationTypes(false);
+ for (final String type : types)
+ {
+ final JMenuItem showitem = new JMenuItem(type);
+ showitem.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(type, true);
+ }
+ });
+ showAnnotations.add(showitem);
+ final JMenuItem hideitem = new JMenuItem(type);
+ hideitem.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(type, false);
+ }
+ });
+ hideAnnotations.add(hideitem);
+ }
+ }
}
class PrintThread extends Thread