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;
* 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<String> links)
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq,
+ List<SequenceFeature> 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<String> links, List<String> groupLinks)
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List<SequenceFeature> features, List<String> groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
//
// 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))
/*
* And repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null
+ final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
? Collections.<SequenceI> emptyList()
- : ap.av.getSelectionGroup().getSequences());
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
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"));
MessageManager.getString("action.set_as_reference"));
}
- if (!ap.av.getAlignment().isNucleotide())
+ if (!alignPanel.av.getAlignment().isNucleotide())
{
remove(rnaStructureMenu);
}
* 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)
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
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);
});
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[]
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"));
@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();
}
}
});
}
}
// for the case when no sequences are even visible
- if (ap.av.hasHiddenRows())
+ if (alignPanel.av.hasHiddenRows())
{
{
menuItem = new JMenuItem(
@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();
}
}
});
}
}
- 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)
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),
- reppdb = new Hashtable<String, PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+
SequenceI sqass = null;
- for (SequenceI sq : ap.av.getSequenceSelection())
+ for (SequenceI sq : alignPanel.av.getSequenceSelection())
{
Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
if (pes != null && pes.size() > 0)
rnaStructureMenu.setVisible(false);
}
- if (links != null && links.size() > 0)
+ addLinks(seq, features);
+
+ if (seq == null)
+ {
+ addFeatureDetails(features);
+ }
+ }
+
+ /**
+ * Add a link to show feature details for each sequence feature
+ *
+ * @param features
+ */
+ protected void addFeatureDetails(List<SequenceFeature> features)
+ {
+ if (features == null || features.isEmpty())
+ {
+ return;
+ }
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
+
+ for (final SequenceFeature sf : features)
{
- addFeatureLinks(seq, links);
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ String desc = null;
+ if (start == end)
+ {
+ desc = String.format("%s %d", sf.getType(), start);
+ }
+ else
+ {
+ desc = String.format("%s %d-%d", sf.getType(), start, end);
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ if (description.length() <= 6)
+ {
+ desc = desc + " " + description;
+ }
+ else
+ {
+ desc = desc + " " + description.substring(0, 6) + "..";
+ }
+ }
+ if (sf.getFeatureGroup() != null)
+ {
+ desc = desc + " (" + sf.getFeatureGroup() + ")";
+ }
+ JMenuItem item = new JMenuItem(desc);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showFeatureDetails(sf);
+ }
+ });
+ details.add(item);
}
}
/**
+ * Opens a panel showing a text report of feature dteails
+ *
+ * @param sf
+ */
+ protected void showFeatureDetails(SequenceFeature sf)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setText(sf.getDetailsReport());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.feature_details"), 500, 500);
+ }
+
+ /**
* 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.
*
* @param seq
- * @param links
+ * @param features
*/
- void addFeatureLinks(final SequenceI seq, List<String> links)
+ void addLinks(final SequenceI seq, List<SequenceFeature> features)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
- for (String link : links)
+ List<String> nlinks = null;
+ if (seq != null)
+ {
+ nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ }
+ else
+ {
+ nlinks = new ArrayList<>();
+ }
+
+ if (features != null)
+ {
+ for (SequenceFeature sf : features)
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ nlinks.add(link);
+ }
+ }
+ }
+ }
+
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
+
+ for (String link : nlinks)
{
UrlLink urlLink = null;
try
addshowLinks(linkMenu, linkset.values());
- // disable link menu if there are no valid entries
+ // only add link menu if it has entries
if (linkMenu.getItemCount() > 0)
{
- linkMenu.setEnabled(true);
- }
- else
- {
- linkMenu.setEnabled(false);
- }
-
- if (sequence != null)
- {
- sequenceMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
}
-
}
/**
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+ Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap<String, String> tipEntries = new TreeMap<String, String>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
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());
}
}
sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
return;
}
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
/*
* assemble dataset sequences, and template new sequence features,
git://source.jalview.org / jalview.git / blobdiff