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();
}
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
case KeyEvent.VK_F1:
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
- "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
scaleLeft.setVisible(av.wrapAlignment);
scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
+ /*
+ * Show/hide all annotations only enabled if annotation panel is shown
+ */
+ showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
{
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));
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);
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
+ chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
// /////
// 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
return;
}
- Vector seqs = new Vector();
+ List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
SequenceI seq;
for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
+ seqs.add(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ // If the cut affects all sequences, warn, remove highlighted columns
if (sg.getSize() == viewport.getAlignment().getHeight())
{
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
- cut[i] = (SequenceI) seqs.elementAt(i);
+ cut[i] = seqs.get(i);
}
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
- viewTitle = "View";
+ viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
}
/**
- * DOCUMENT ME!
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllAnnotations.setEnabled(setVisible);
+ this.hideAllAnnotations.setEnabled(setVisible);
}
@Override
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()
{
tm.setText(title);//
tm.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
NewTreePanel(type, (String) pwtype, title);
// object broker mechanism.
final Vector<JMenu> wsmenu = new Vector<JMenu>();
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)
public void run()
{
final long sttime = System.currentTimeMillis();
- ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
try
{
Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
jalview.bin.Cache.log.error("Error when finding crossreferences",
e);
}
- ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
sttime);
}
trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
trimrs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
}
});
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + src.getDbName()) + "<html>");
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
dfetch.add(fetchr);
comp++;
}
}
});
- fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from all "
- + otherdb.size() + " sources in "
- + src.getDbSource() + "<br>First is :"
- + src.getDbName()) + "<html>");
+ 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;
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 =
});
fetchr.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Retrieve from "
- + dbname) + "</html>");
+ + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
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
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
}
+
+ /**
+ * Action on selection of menu option to Show or Hide all annotations.
+ *
+ * @param visibile
+ */
+ @Override
+ protected void setAllAnnotationsVisibility(boolean visible)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ aa.visible = visible;
+ }
+ this.alignPanel.paintAlignment(true);
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff