X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=4e02d21250aeab598121cd7e89a097515b9737e9;hb=refs%2Fheads%2Ffeature%2FJAL-3181linkOrdering;hp=3e2eba92d90392cb94821926a0398d3bab00cfd1;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3e2eba9..4e02d21 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -34,7 +34,6 @@ import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@ -50,6 +49,7 @@ import jalview.schemes.PIDColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.util.UrlLink;
import java.awt.Color;
@@ -75,10 +75,8 @@ import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision: 1.118 $
+ * The popup menu that is displayed on right-click on a sequence id, or in the
+ * sequence alignment.
*/
public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
@@ -173,28 +171,215 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
JMenuItem hideInsertions = new JMenuItem();
/**
+ * Constructs a menu with sub-menu items for any hyperlinks for the sequence
+ * and/or features provided. Hyperlinks may include a lookup by sequence id,
+ * or database cross-references, depending on which links are enabled in user
+ * preferences.
+ *
+ * @param seq
+ * @param features
+ * @return
+ */
+ static JMenu buildLinkMenu(final SequenceI seq,
+ List features)
+ {
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+
+ List nlinks = null;
+ if (seq != null)
+ {
+ nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ UrlLink.sort(nlinks);
+ }
+ else
+ {
+ nlinks = new ArrayList<>();
+ }
+
+ if (features != null)
+ {
+ for (SequenceFeature sf : features)
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ nlinks.add(link);
+ }
+ }
+ }
+ }
+
+ /*
+ * instantiate the hyperlinklink templates from sequence data;
+ * note the order of the templates is preserved in the map
+ */
+ Map> linkset = new LinkedHashMap<>();
+ for (String link : nlinks)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ /*
+ * construct menu items for the hyperlinks (still preserving
+ * the order of the sorted templates)
+ */
+ addUrlLinks(linkMenu, linkset.values());
+
+ return linkMenu;
+ }
+
+ /**
+ * A helper method that builds menu items from the given links, with action
+ * handlers to open the link URL, and adds them to the linkMenu. Each provided
+ * link should be a list whose second item is the menu text, and whose fourth
+ * item is the URL to open when the menu item is selected.
+ *
+ * @param linkMenu
+ * @param linkset
+ */
+ static private void addUrlLinks(JMenu linkMenu,
+ Collection> linkset)
+ {
+ for (List linkstrset : linkset)
+ {
+ final String url = linkstrset.get(3);
+ JMenuItem item = new JMenuItem(linkstrset.get(1));
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_param", new Object[]
+ { url }));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ showLink(url);
+ }
+ }).start();
+ }
+ });
+ linkMenu.add(item);
+ }
+ }
+
+ /**
+ * Opens the provided url in the default web browser, or shows an error
+ * message if this fails
+ *
+ * @param url
+ */
+ static void showLink(String url)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * add a late bound groupURL item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
+ */
+ static void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_seqs_param", new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e2)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
* Creates a new PopupMenu object.
*
* @param ap
- * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * @param features
+ * non-positional features (for seq not null), or positional features
+ * at residue (for seq equal to null)
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq,
- List links)
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq,
+ List features)
{
- this(ap, seq, links, null);
+ this(ap, seq, features, null);
}
/**
+ * Constructor
*
- * @param ap
+ * @param alignPanel
* @param seq
- * @param links
+ * the sequence under the cursor if in the Id panel, null if in the
+ * sequence panel
+ * @param features
+ * non-positional features if in the Id panel, features at the
+ * clicked residue if in the sequence panel
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
- List links, List groupLinks)
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List features, List groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
@@ -202,7 +387,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
//
// If from the IDPanel, we must display the sequence menu
// ////////////////////////////////////////////////////////
- this.ap = ap;
+ this.ap = alignPanel;
sequence = seq;
for (String ff : FileFormats.getInstance().getWritableFormats(true))
@@ -237,9 +422,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
/*
* And repeat for the current selection group (if there is one):
*/
- final List selectedGroup = (ap.av.getSelectionGroup() == null
+ final List selectedGroup = (alignPanel.av.getSelectionGroup() == null
? Collections. emptyList()
- : ap.av.getSelectionGroup().getSequences());
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -257,7 +442,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- if (seq == ap.av.getAlignment().getSeqrep())
+ if (seq == alignPanel.av.getAlignment().getSeqrep())
{
makeReferenceSeq.setText(
MessageManager.getString("action.unmark_as_reference"));
@@ -268,7 +453,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
MessageManager.getString("action.set_as_reference"));
}
- if (!ap.av.getAlignment().isNucleotide())
+ if (!alignPanel.av.getAlignment().isNucleotide())
{
remove(rnaStructureMenu);
}
@@ -279,7 +464,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* add menu items to 2D-render any alignment or sequence secondary
* structure annotation
*/
- AlignmentAnnotation[] aas = ap.av.getAlignment()
+ AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
.getAlignmentAnnotation();
if (aas != null)
{
@@ -299,7 +484,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
@Override
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
@@ -328,7 +513,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
@@ -353,8 +538,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
});
add(menuItem);
- if (ap.av.getSelectionGroup() != null
- && ap.av.getSelectionGroup().getSize() > 1)
+ if (alignPanel.av.getSelectionGroup() != null
+ && alignPanel.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager
.formatMessage("label.represent_group_with", new Object[]
@@ -370,12 +555,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
sequenceMenu.add(menuItem);
}
- if (ap.av.hasHiddenRows())
+ if (alignPanel.av.hasHiddenRows())
{
- final int index = ap.av.getAlignment().findIndex(seq);
+ final int index = alignPanel.av.getAlignment().findIndex(seq);
- if (ap.av.adjustForHiddenSeqs(index)
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ if (alignPanel.av.adjustForHiddenSeqs(index)
+ - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
{
menuItem = new JMenuItem(
MessageManager.getString("action.reveal_sequences"));
@@ -384,10 +569,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
@Override
public void actionPerformed(ActionEvent e)
{
- ap.av.showSequence(index);
- if (ap.overviewPanel != null)
+ alignPanel.av.showSequence(index);
+ if (alignPanel.overviewPanel != null)
{
- ap.overviewPanel.updateOverviewImage();
+ alignPanel.overviewPanel.updateOverviewImage();
}
}
});
@@ -396,7 +581,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
// for the case when no sequences are even visible
- if (ap.av.hasHiddenRows())
+ if (alignPanel.av.hasHiddenRows())
{
{
menuItem = new JMenuItem(
@@ -406,10 +591,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
@Override
public void actionPerformed(ActionEvent e)
{
- ap.av.showAllHiddenSeqs();
- if (ap.overviewPanel != null)
+ alignPanel.av.showAllHiddenSeqs();
+ if (alignPanel.overviewPanel != null)
{
- ap.overviewPanel.updateOverviewImage();
+ alignPanel.overviewPanel.updateOverviewImage();
}
}
});
@@ -418,9 +603,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
- SequenceGroup sg = ap.av.getSelectionGroup();
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
boolean isDefinedGroup = (sg != null)
- ? ap.av.getAlignment().getGroups().contains(sg)
+ ? alignPanel.av.getAlignment().getGroups().contains(sg)
: false;
if (sg != null && sg.getSize() > 0)
@@ -455,10 +640,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable pdbe = new Hashtable(),
- reppdb = new Hashtable();
+ Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+
SequenceI sqass = null;
- for (SequenceI sq : ap.av.getSequenceSelection())
+ for (SequenceI sq : alignPanel.av.getSequenceSelection())
{
Vector pes = sq.getDatasetSequence().getAllPDBEntries();
if (pes != null && pes.size() > 0)
@@ -508,65 +693,118 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
rnaStructureMenu.setVisible(false);
}
- if (links != null && links.size() > 0)
+ addLinks(seq, features);
+
+ if (seq == null)
{
- addFeatureLinks(seq, links);
+ addFeatureDetails(features);
}
}
/**
- * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * Add a link to show feature details for each sequence feature
*
- * @param seq
- * @param links
+ * @param features
*/
- void addFeatureLinks(final SequenceI seq, List links)
+ protected void addFeatureDetails(List features)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Map> linkset = new LinkedHashMap>();
+ if (features == null || features.isEmpty())
+ {
+ return;
+ }
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
- for (String link : links)
+ for (final SequenceFeature sf : features)
{
- UrlLink urlLink = null;
- try
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ String desc = null;
+ if (start == end)
{
- urlLink = new UrlLink(link);
- } catch (Exception foo)
+ desc = String.format("%s %d", sf.getType(), start);
+ }
+ else
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
- continue;
+ desc = String.format("%s %d-%d", sf.getType(), start, end);
}
-
- if (!urlLink.isValid())
+ String tooltip = desc;
+ String description = sf.getDescription();
+ if (description != null)
{
- Cache.log.error(urlLink.getInvalidMessage());
- continue;
+ description = StringUtils.stripHtmlTags(description);
+ if (description.length() > 12)
+ {
+ desc = desc + " " + description.substring(0, 12) + "..";
+ }
+ else
+ {
+ desc = desc + " " + description;
+ }
+ tooltip = tooltip + " " + description;
}
-
- urlLink.createLinksFromSeq(seq, linkset);
+ if (sf.getFeatureGroup() != null)
+ {
+ tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
+ }
+ JMenuItem item = new JMenuItem(desc);
+ item.setToolTipText(tooltip);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showFeatureDetails(sf);
+ }
+ });
+ details.add(item);
}
+ }
- addshowLinks(linkMenu, linkset.values());
+ /**
+ * Opens a panel showing a text report of feature dteails
+ *
+ * @param sf
+ */
+ protected void showFeatureDetails(SequenceFeature sf)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collaps :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+ cap.setText(sf.getDetailsReport());
- // disable link menu if there are no valid entries
- if (linkMenu.getItemCount() > 0)
- {
- linkMenu.setEnabled(true);
- }
- else
- {
- linkMenu.setEnabled(false);
- }
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.feature_details"), 500, 500);
+ }
- if (sequence != null)
- {
- sequenceMenu.add(linkMenu);
- }
- else
+ /**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * When seq is not null, these are links for the sequence id, which may be to
+ * external web sites for the sequence accession, and/or links embedded in
+ * non-positional features. When seq is null, only links embedded in the
+ * provided features are added. If no links are found, the menu is not added.
+ *
+ * @param seq
+ * @param features
+ */
+ void addLinks(final SequenceI seq, List features)
+ {
+ JMenu linkMenu = buildLinkMenu(seq, features);
+
+ // only add link menu if it has entries
+ if (linkMenu.getItemCount() > 0)
{
- add(linkMenu);
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
}
-
}
/**
@@ -609,8 +847,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map>> shownTypes = new LinkedHashMap>>();
- Map>> hiddenTypes = new LinkedHashMap>>();
+ Map>> shownTypes = new LinkedHashMap<>();
+ Map>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
@@ -716,7 +954,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable commonDbrefs = new Hashtable();
+ Hashtable commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
@@ -846,98 +1084,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
- private void addshowLinks(JMenu linkMenu,
- Collection> linkset)
- {
- for (List linkstrset : linkset)
- {
- // split linkstr into label and url
- addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
- }
- }
-
- /**
- * add a show URL menu item to the given linkMenu
- *
- * @param linkMenu
- * @param label
- * - menu label string
- * @param url
- * - url to open
- */
- private void addshowLink(JMenu linkMenu, String label, final String url)
- {
- JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
- new Object[]
- { url }));
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- showLink(url);
- }
-
- }).start();
- }
- });
-
- linkMenu.add(item);
- }
-
- /**
- * add a late bound groupURL item to the given linkMenu
- *
- * @param linkMenu
- * @param label
- * - menu label string
- * @param urlgenerator
- * GroupURLLink used to generate URL
- * @param urlstub
- * Object array returned from the makeUrlStubs function.
- */
- private void addshowLink(JMenu linkMenu, String label,
- final GroupUrlLink urlgenerator, final Object[] urlstub)
- {
- JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager
- .formatMessage("label.open_url_seqs_param", new Object[]
- { urlgenerator.getUrl_prefix(),
- urlgenerator.getNumberInvolved(urlstub) }));
- // TODO: put in info about what is being sent.
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- try
- {
- showLink(urlgenerator.constructFrom(urlstub));
- } catch (UrlStringTooLongException e2)
- {
- }
- }
-
- }).start();
- }
- });
-
- linkMenu.add(item);
- }
-
/**
* DOCUMENT ME!
*
@@ -1377,8 +1523,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap tipEntries = new TreeMap();
- final Map> candidates = new LinkedHashMap>();
+ SortedMap tipEntries = new TreeMap<>();
+ final Map> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
@@ -1453,15 +1599,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
-
- HiddenColumns hidden = new HiddenColumns();
- BitSet inserts = new BitSet(), mask = new BitSet();
-
- // set mask to preserve existing hidden columns outside selected group
- if (ap.av.hasHiddenColumns())
- {
- ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
- }
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
@@ -1469,10 +1608,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
- ap.av.getSelectionGroup().getEndRes() + 1);
-
- // and clear that part of the mask
- mask.andNot(inserts);
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
@@ -1483,29 +1619,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
inserts.and(sq.getInsertionsAsBits());
}
- }
- else
- {
- // initially, mark all columns to be hidden
- inserts.set(0, ap.av.getAlignment().getWidth());
-
- // and clear out old hidden regions completely
- mask.clear();
+ hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
- if (!markedPopup && sequence != null)
+ else if (!markedPopup && sequence != null)
{
- inserts.and(sequence.getInsertionsAsBits());
- }
-
- // finally, preserve hidden regions outside selection
- inserts.or(mask);
-
- // and set hidden columns accordingly
- hidden.hideMarkedBits(inserts);
+ inserts.or(sequence.getInsertionsAsBits());
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
@@ -1530,10 +1655,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
new Object[]
{ seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents, seq, true, true,
- (ap.getSeqPanel().seqCanvas.fr != null)
- ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
- : null);
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("
");
}
cap.setText("" + contents.toString() + "");
@@ -1561,7 +1683,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
void refresh()
{
ap.updateAnnotation();
- ap.paintAlignment(true);
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
@@ -1741,7 +1865,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
@@ -1829,22 +1953,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
refresh();
}
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"),
- JvOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
void hideSequences(boolean representGroup)
{
ap.av.hideSequences(sequence, representGroup);
@@ -1929,8 +2037,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
return;
}
- List seqs = new ArrayList();
- List features = new ArrayList();
+ List seqs = new ArrayList<>();
+ List features = new ArrayList<>();
/*
* assemble dataset sequences, and template new sequence features,
@@ -1944,8 +2052,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
- features.add(
- new SequenceFeature(null, null, null, start, end, null));
+ features.add(new SequenceFeature(null, null, start, end, null));
}
}
@@ -1958,7 +2065,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
.amendFeatures(seqs, features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
}
}
}