*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
-import jalview.bin.Cache;
+import jalview.api.AlignViewportI;
+import jalview.bin.Console;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueColourScheme;
+import jalview.util.Comparison;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.util.UrlLink;
-
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
/*
+ * maximum length of feature description to include in popup menu item text
+ */
+ private static final int FEATURE_DESC_MAX = 40;
+
+ /*
* true for ID Panel menu, false for alignment panel menu
*/
private final boolean forIdPanel;
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ Console.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
}
/**
- * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
+ * Constructor for a PopupMenu for a click in the alignment panel (on a
+ * residue)
*
* @param ap
+ * the panel in which the mouse is clicked
* @param seq
- * @param features
- * sequence features overlapping the clicked residue
+ * the sequence under the mouse
+ * @throws NullPointerException
+ * if seq is null
*/
- public PopupMenu(final AlignmentPanel ap, SequenceI seq,
- List<SequenceFeature> features)
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
{
- this(false, ap, seq, features, null);
+ this(false, ap, seq, column, null);
}
/**
* Constructor for a PopupMenu for a click in the sequence id panel
*
* @param alignPanel
+ * the panel in which the mouse is clicked
* @param seq
- * @param features
- * non-positional features for the sequence
+ * the sequence under the mouse click
* @param groupLinks
+ * templates for sequence external links
+ * @throws NullPointerException
+ * if seq is null
*/
public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
- List<SequenceFeature> features, List<String> groupLinks)
+ List<String> groupLinks)
{
- this(true, alignPanel, seq, features, groupLinks);
+ this(true, alignPanel, seq, -1, groupLinks);
}
/**
* @param fromIdPanel
* @param alignPanel
* @param seq
- * @param features
+ * @param column
+ * aligned column position (0...)
* @param groupLinks
*/
- private PopupMenu(boolean fromIdPanel,
- final AlignmentPanel alignPanel,
- final SequenceI seq, List<SequenceFeature> features,
- List<String> groupLinks)
+ private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
+ final SequenceI seq, final int column, List<String> groupLinks)
{
+ Objects.requireNonNull(seq);
this.forIdPanel = fromIdPanel;
this.ap = alignPanel;
sequence = seq;
* 'reference annotations' that may be added to the alignment. First for the
* currently selected sequence (if there is one):
*/
- final List<SequenceI> selectedSequence = (forIdPanel
+ final List<SequenceI> selectedSequence = (forIdPanel && seq != null
? Arrays.asList(seq)
: Collections.<SequenceI> emptyList());
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
/*
* And repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
- ? Collections.<SequenceI> emptyList()
- : alignPanel.av.getSelectionGroup().getSequences());
+ final List<SequenceI> selectedGroup = (alignPanel.av
+ .getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+ reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
+ editGroupMenu
+ .setText(MessageManager.getString("action.edit_new_group"));
}
else
{
rnaStructureMenu.setVisible(false);
}
+ addLinksAndFeatures(seq, column);
+ }
+
+ /**
+ * Adds
+ * <ul>
+ * <li>configured sequence database links (ID panel popup menu)</li>
+ * <li>non-positional feature links (ID panel popup menu)</li>
+ * <li>positional feature links (alignment panel popup menu)</li>
+ * <li>feature details links (alignment panel popup menu)</li>
+ * </ul>
+ * If this panel is also showed complementary (CDS/protein) features, then
+ * links to their feature details are also added.
+ *
+ * @param seq
+ * @param column
+ */
+ void addLinksAndFeatures(final SequenceI seq, final int column)
+ {
+ List<SequenceFeature> features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
+ {
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
+ }
+
addLinks(seq, features);
if (!forIdPanel)
{
- addFeatureDetails(features);
+ addFeatureDetails(features, seq, column);
}
}
/**
- * Add a link to show feature details for each sequence feature
+ * Add a menu item to show feature details for each sequence feature. Any
+ * linked 'virtual' features (CDS/protein) are also optionally found and
+ * included.
*
* @param features
+ * @param seq
+ * @param column
*/
- protected void addFeatureDetails(List<SequenceFeature> features)
+ protected void addFeatureDetails(List<SequenceFeature> features,
+ final SequenceI seq, final int column)
{
- if (features == null || features.isEmpty())
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ MappedFeatures mf = null;
+ if (ap.av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
+ {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ int seqPos = sequence.findPosition(column);
+ mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
+ }
+ }
+
+ if (features.isEmpty() && mf == null)
{
+ /*
+ * no features to show at this position
+ */
return;
}
+
JMenu details = new JMenu(
MessageManager.getString("label.feature_details"));
add(details);
+ String name = seq.getName();
for (final SequenceFeature sf : features)
{
- int start = sf.getBegin();
- int end = sf.getEnd();
- String desc = null;
- if (start == end)
+ addFeatureDetailsMenuItem(details, name, sf, null);
+ }
+
+ if (mf != null)
+ {
+ for (final SequenceFeature sf : mf.features)
{
- desc = String.format("%s %d", sf.getType(), start);
+ addFeatureDetailsMenuItem(details, name, sf, mf);
}
- else
+ }
+ }
+
+ /**
+ * A helper method to add one menu item whose action is to show details for
+ * one feature. The menu text includes feature description, but this may be
+ * truncated.
+ *
+ * @param details
+ * @param seqName
+ * @param sf
+ * @param mf
+ */
+ void addFeatureDetailsMenuItem(JMenu details, final String seqName,
+ final SequenceFeature sf, MappedFeatures mf)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ if (mf != null)
+ {
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
{
- desc = String.format("%s %d-%d", sf.getType(), start, end);
+ // e.g. variant extending to stop codon so not mappable
+ return;
}
- String tooltip = desc;
- String description = sf.getDescription();
- if (description != null)
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
+ }
+ StringBuilder desc = new StringBuilder();
+ desc.append(sf.getType()).append(" ").append(String.valueOf(start));
+ if (start != end)
+ {
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ desc.append(" ");
+ description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * truncate overlong descriptions unless they contain an href
+ * (as truncation could leave corrupted html)
+ */
+ boolean hasLink = description.indexOf("a href") > -1;
+ if (description.length() > FEATURE_DESC_MAX && !hasLink)
{
- description = StringUtils.stripHtmlTags(description);
- if (description.length() > 12)
- {
- desc = desc + " " + description.substring(0, 12) + "..";
- }
- else
- {
- desc = desc + " " + description;
- }
- tooltip = tooltip + " " + description;
+ description = description.substring(0, FEATURE_DESC_MAX) + "...";
}
- if (sf.getFeatureGroup() != null)
+ desc.append(description);
+ }
+ String featureGroup = sf.getFeatureGroup();
+ if (featureGroup != null)
+ {
+ desc.append(" (").append(featureGroup).append(")");
+ }
+ String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
+ JMenuItem item = new JMenuItem(htmlText);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
+ showFeatureDetails(sf, seqName, mf);
}
- JMenuItem item = new JMenuItem(desc);
- item.setToolTipText(tooltip);
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- showFeatureDetails(sf);
- }
- });
- details.add(item);
- }
+ });
+ details.add(item);
}
/**
- * Opens a panel showing a text report of feature dteails
+ * Opens a panel showing a text report of feature details
*
* @param sf
+ * @param seqName
+ * @param mf
*/
- protected void showFeatureDetails(SequenceFeature sf)
+ protected void showFeatureDetails(SequenceFeature sf, String seqName,
+ MappedFeatures mf)
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- // it appears Java's CSS does not support border-collapse :-(
- cap.addStylesheetRule("table { border-collapse: collapse;}");
- cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
- cap.setText(sf.getDetailsReport(sequence));
-
- Desktop.addInternalFrame(cap,
+ JInternalFrame details;
+ if (Platform.isJS())
+ {
+ details = new JInternalFrame();
+ details.setFrameIcon(null);
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.setOpaque(true);
+ panel.setBackground(Color.white);
+ // TODO JAL-3026 set style of table correctly for feature details
+ JLabel reprt = new JLabel(MessageManager
+ .formatMessage("label.html_content", new Object[]
+ { sf.getDetailsReport(seqName, mf) }));
+ reprt.setBackground(Color.WHITE);
+ reprt.setOpaque(true);
+ panel.add(reprt, BorderLayout.CENTER);
+ details.setContentPane(panel);
+ details.pack();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collapse :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+ cap.setText(sf.getDetailsReport(seqName, mf));
+ details = cap;
+ }
+ Desktop.addInternalFrame(details,
MessageManager.getString("label.feature_details"), 500, 500);
}
{
sqi = sqi.getDatasetSequence();
}
- DBRefEntry[] dbr = sqi.getDBRefs();
- if (dbr != null && dbr.length > 0)
+ List<DBRefEntry> dbr = sqi.getDBRefs();
+ int nd;
+ if (dbr != null && (nd = dbr.size()) > 0)
{
- for (int d = 0; d < dbr.length; d++)
+ for (int d = 0; d < nd; d++)
{
- String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ DBRefEntry e = dbr.get(d);
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
if (((String[]) sarray[1])[sq] == null)
{
- if (!dbr[d].hasMap() || (dbr[d].getMap()
- .locateMappedRange(start, end) != null))
+ if (!e.hasMap()
+ || (e.getMap().locateMappedRange(start, end) != null))
{
- ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((String[]) sarray[1])[sq] = e.getAccessionId();
((int[]) sarray[0])[0]++;
}
}
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
- ;
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- editSequence_actionPerformed(actionEvent);
+ editSequence_actionPerformed();
}
});
makeReferenceSeq.setText(
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ null);
refresh();
}
}
inserts.and(sq.getInsertionsAsBits());
}
- hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ hidden.clearAndHideColumns(inserts,
+ ap.av.getSelectionGroup().getStartRes(),
ap.av.getSelectionGroup().getEndRes());
}
public void createSequenceDetailsReport(SequenceI[] sequences)
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
StringBuilder contents = new StringBuilder(128);
+ contents.append("<html><body>");
for (SequenceI seq : sequences)
{
contents.append("<p><h2>" + MessageManager.formatMessage(
"label.create_sequence_details_report_annotation_for",
new Object[]
- { seq.getDisplayId(true) }) + "</h2></p><p>");
- new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("</p>");
}
- cap.setText("<html>" + contents.toString() + "</html>");
+ contents.append("</body></html>");
+ String report = contents.toString();
+
+ JInternalFrame frame;
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(report);
+ textLabel.setBackground(Color.WHITE);
+ JPanel pane = new JPanel(new BorderLayout());
+ pane.setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ pane.add(textLabel, BorderLayout.NORTH);
+ frame = new JInternalFrame();
+ frame.setFrameIcon(null);
+ frame.getContentPane().add(new JScrollPane(pane));
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ cap.setText(report);
+ frame = cap;
+ }
- Desktop.addInternalFrame(cap,
+ Desktop.addInternalFrame(frame,
MessageManager.formatMessage("label.sequence_details_for",
(sequences.length == 1 ? new Object[]
{ sequences[0].getDisplayId(true) }
{ MessageManager
.getString("label.selection") })),
500, 400);
-
}
protected void showNonconserved_actionPerformed()
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a dialog where group name and description may be edited
*/
protected void groupName_actionPerformed()
{
-
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
sg.getDescription(),
- " " + MessageManager.getString("label.group_name") + " ",
- MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.group_name"),
+ MessageManager.getString("label.group_description"));
+ dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_group_name_description"),
- ap.alignFrame);
-
- if (!dialog.accept)
- {
- return;
- }
-
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
- refresh();
+ () -> {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ });
}
/**
/**
* Shows a dialog where the sequence name and description may be edited. If a
- * name containing spaces is entered, these are converted to underscores, with a
- * warning message.
+ * name containing spaces is entered, these are converted to underscores, with
+ * a warning message.
*/
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
sequence.getDescription(),
- " " + MessageManager.getString("label.sequence_name")
- + " ",
- MessageManager.getString("label.sequence_description") + " ",
- MessageManager.getString(
- "label.edit_sequence_name_description"),
- ap.alignFrame);
-
- if (!dialog.accept)
- {
- return;
- }
-
- String name = dialog.getName();
- if (name != null)
- {
- if (name.indexOf(" ") > -1)
- {
- JvOptionPane.showMessageDialog(ap,
- MessageManager
- .getString("label.spaces_converted_to_backslashes"),
- MessageManager
- .getString("label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
- name = name.replace(' ', '_');
- }
-
- sequence.setName(name);
- ap.paintAlignment(false, false);
- }
-
- sequence.setDescription(dialog.getDescription());
-
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
-
+ MessageManager.getString("label.sequence_name"),
+ MessageManager.getString("label.sequence_description"));
+ dialog.showDialog(ap.alignFrame, MessageManager
+ .getString("label.edit_sequence_name_description"), () -> {
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ String ok = MessageManager.getString("action.ok");
+ String cancel = MessageManager.getString("action.cancel");
+ String message = MessageManager.getString(
+ "label.spaces_converted_to_underscores");
+ String title = MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name");
+ Object[] options = new Object[] { ok, cancel };
+
+ JvOptionPane.frameDialog(message, title,
+ JvOptionPane.WARNING_MESSAGE, null, null, null,
+ false);
+ }
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
+ }
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ });
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Offers a colour chooser and sets the selected colour as the group outline
*/
protected void outline_actionPerformed()
{
- SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_outline_colour"),
- Color.BLUE);
-
- if (col != null)
+ String title = MessageManager.getString("label.select_outline_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- sg.setOutlineColour(col);
- }
-
- refresh();
+ @Override
+ public void colourSelected(Color c)
+ {
+ getGroup().setOutlineColour(c);
+ refresh();
+ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
+ Color.BLUE, listener);
}
/**
public void copy_actionPerformed()
{
- ap.alignFrame.copy_actionPerformed(null);
+ ap.alignFrame.copy_actionPerformed();
}
public void cut_actionPerformed()
{
- ap.alignFrame.cut_actionPerformed(null);
+ ap.alignFrame.cut_actionPerformed();
}
void changeCase(ActionEvent e)
String[] omitHidden = null;
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
*/
if (!seqs.isEmpty())
{
- if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
- {
- ap.alignFrame.setShowSeqFeatures(true);
- ap.av.setSearchResults(null); // clear highlighting
- ap.repaint(); // draw new/amended features
- }
+ new FeatureEditor(ap, seqs, features, true).showDialog();
}
}
}
}
- public void editSequence_actionPerformed(ActionEvent actionEvent)
+ /**
+ * Shows a dialog where sequence characters may be edited. Any changes are
+ * applied, and added as an available 'Undo' item in the edit commands
+ * history.
+ */
+ public void editSequence_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
}
EditNameDialog dialog = new EditNameDialog(
- seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1),
- null, MessageManager.getString("label.edit_sequence"), null,
- MessageManager.getString("label.edit_sequence"),
- ap.alignFrame);
-
- if (dialog.accept)
- {
- EditCommand editCommand = new EditCommand(
- MessageManager.getString("label.edit_sequences"),
- Action.REPLACE,
- dialog.getName().replace(' ', ap.av.getGapCharacter()),
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
-
- ap.alignFrame.addHistoryItem(editCommand);
-
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null);
+ dialog.showDialog(ap.alignFrame,
+ MessageManager.getString("label.edit_sequence"), () -> {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ });
}
}