import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.datamodel.SequenceI;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BioJsHTMLOutput;
import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
+import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.io.File;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
- buildShowHideAnnotationMenus();
if (viewport.wrapAlignment)
{
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ {
+ alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(false);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, 1);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(-1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
break;
}
else
{
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRow();
+ alignPanel.getSeqPanel().setCursorRow();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
- alignPanel.seqPanel.setCursorColumn();
+ alignPanel.getSeqPanel().setCursorColumn();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorPosition();
+ alignPanel.getSeqPanel().setCursorPosition();
}
break;
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRowAndColumn();
+ alignPanel.getSeqPanel().setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
}
break;
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
}
- alignPanel.seqPanel.seqCanvas.repaint();
+ alignPanel.getSeqPanel().seqCanvas.repaint();
break;
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();
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
}
}
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.rightAlignIds);
+ idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
renderGapsMenuItem.setSelected(av.renderGaps);
wrapMenuItem.setSelected(av.wrapAlignment);
scaleAbove.setVisible(av.wrapAlignment);
scaleLeft.setVisible(av.wrapAlignment);
scaleRight.setVisible(av.wrapAlignment);
- annotationPanelMenuItem.setState(av.showAnnotation);
+ annotationPanelMenuItem.setState(av.isShowAnnotation());
+ /*
+ * Show/hide annotations only enabled if annotation panel is shown
+ */
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
- showSeqFeatures.setSelected(av.showSequenceFeatures);
+ showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
{
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);
public FeatureRenderer getFeatureRenderer()
{
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
}
@Override
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);
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // new HTMLOutput(alignPanel,
+ // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+ // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ new HtmlSvgOutput(null, alignPanel);
}
+ @Override
+ public void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+ new BioJsHTMLOutput(alignPanel,
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportAnnotations(alignPanel,
- viewport.showAnnotation ? viewport.getAlignment()
+ viewport.isShowAnnotation() ? viewport.getAlignment()
.getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), ((Alignment) viewport
.getAlignment()).alignmentProperties);
if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
+ CommandI command = viewport.historyList.peek();
undoMenuItem.setText(MessageManager.formatMessage(
"label.undo_command", new String[]
{ command.getDescription() }));
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
+ CommandI command = viewport.redoList.peek();
redoMenuItem.setText(MessageManager.formatMessage(
"label.redo_command", new String[]
{ command.getDescription() }));
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
+ {
return;
- CommandI command = (CommandI) viewport.historyList.pop();
+ }
+ CommandI command = viewport.historyList.pop();
viewport.redoList.push(command);
command.undoCommand(getViewAlignments());
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
+ CommandI command = viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand(getViewAlignments());
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ alignPanel.getSeqPanel().seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() != viewport
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(-size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
+ {
continue;
+ }
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
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,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
{
if (viewport.cursorMode)
{
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
+ alignPanel.getSeqPanel().keyboardNo1 = null;
+ alignPanel.getSeqPanel().keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ alignPanel.getIdPanel().getIdCanvas().searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
- viewTitle = "View";
+ viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+ alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
.calculateIdWidth());
alignPanel.paintAlignment(true);
}
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
- viewport.rightAlignIds = idRightAlign.isSelected();
+ viewport.setRightAlignIds(idRightAlign.isSelected());
alignPanel.paintAlignment(true);
}
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
alignPanel.scrollToPosition(
- alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.getSeqPanel().seqCanvas.searchResults, false);
}
}
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
}
/**
- * DOCUMENT ME!
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
}
@Override
public void 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()
{
*/
msa = viewport.getAlignmentView(true);
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ int option = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.oneseq_msainput_selection"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+ }
else
{
- /*
- * Vector seqs = viewport.getAlignment().getSequences();
- *
- * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
- * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
- * seqs.elementAt(i); } }
- */
msa = viewport.getAlignmentView(false);
}
return msa;
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
if (ds.getSequences() == null
|| !ds.getSequences().contains(
sprods[s].getDatasetSequence()))
+ {
ds.addSequence(sprods[s].getDatasetSequence());
+ }
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
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);
}
try
{
featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, false,
+ .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getFeatureColours(), false,
jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
if (featuresFile)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.seqPanel.seqCanvas.fr != null)
+ if (alignPanel.getSeqPanel().seqCanvas.fr != null)
{
// update the min/max ranges where necessary
- alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
}
if (featureSettings != null)
{
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- MessageManager
+ "<html>"+MessageManager
.formatMessage(
"label.ignore_unmatched_dropped_files_info",
new String[]
{ Integer.valueOf(
filesnotmatched
.size())
- .toString() }),
+ .toString() })+"</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
}
});
- 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
}
/**
- * On menu option, open a panel to allow choice of annotation types to
- * show/hide.
+ * Action on selection of menu options to Show or Hide annotations.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
@Override
- protected void chooseAnnotations_actionPerformed()
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
- new AnnotationChooser(this.alignPanel);
- }
-
- /**
- * Get a list of unique annotation types for the alignment, optionally
- * restricted to sequence-specific annotations.
- */
- protected List<String> getAnnotationTypes(boolean sequenceSpecificOnly)
- {
- // TODO move this to an AlignmentUtils class or similar
- List<String> types = new ArrayList<String>();
for (AlignmentAnnotation aa : alignPanel.getAlignment()
.getAlignmentAnnotation())
{
- if (sequenceSpecificOnly && aa.sequenceRef == null)
- {
- continue;
- }
- String type = aa.label;
- if (!types.contains(type))
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
{
- types.add(type);
+ aa.visible = visible;
}
}
- return types;
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
}
/**
- * Action on selection of an annotation type to Show or Hide.
- *
- * @param type
- * @param doShow
+ * Store selected annotation sort order for the view and repaint.
*/
@Override
- protected void showHideAnnotation_actionPerformed(String type, boolean doShow)
+ protected void sortAnnotations_actionPerformed()
{
- for (AlignmentAnnotation aa : alignPanel.getAlignment()
- .getAlignmentAnnotation())
- {
- if (type.equals(aa.label))
- {
- aa.visible = doShow;
- }
- }
- this.alignPanel.paintAlignment(true);
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
}
/**
- * Dynamically build the list of annotation types to show or hide.
+ *
+ * @return alignment panels in this alignemnt frame
*/
- @Override
- protected void buildShowHideAnnotationMenus()
+ public List<AlignmentViewPanel> getAlignPanels()
{
- showAnnotations.removeAll();
- hideAnnotations.removeAll();
-
- List<String> 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);
- }
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
}
}