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;
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;
* 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))
* 'reference annotations' that may be added to the alignment. First for the
* currently selected sequence (if there is one):
*/
- final List<SequenceI> selectedSequence = (seq == null ? Collections
- .<SequenceI> emptyList() : Arrays.asList(seq));
+ final List<SequenceI> selectedSequence = (seq == null
+ ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq));
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
/*
* And repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- .<SequenceI> emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : 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"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.unmark_as_reference"));
}
else
{
- makeReferenceSeq.setText(MessageManager
- .getString("action.set_as_reference"));
+ makeReferenceSeq.setText(
+ 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)
{
*/
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line",
- new Object[] { aa.label }));
+ "label.2d_rna_structure_line", new Object[]
+ { aa.label }));
menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name",
- new Object[] { seq.getName() }));
+ "label.2d_rna_sequence_name", new Object[]
+ { seq.getName() }));
menuItem.addActionListener(new ActionListener()
{
@Override
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[] { seq.getName() }));
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
menuItem.addActionListener(new ActionListener()
{
@Override
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();
- boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
- .getGroups().contains(sg) : false;
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg != null)
+ ? 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)
}
if (pdbe.size() > 0)
{
- final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
+ final PDBEntry[] pe = pdbe.values()
+ .toArray(new PDBEntry[pdbe.size()]),
+ pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
}
}
rnaStructureMenu.setVisible(false);
}
- if (links != null && links.size() > 0)
+ addLinks(seq, features);
+
+ if (seq == null)
{
- addFeatureLinks(seq, links);
+ 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)
+ {
+ 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)
+ {
+ description = StringUtils.stripHtmlTags(description);
+ 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)
+ {
+ 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());
+
+ 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);
+ }
}
-
}
/**
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(new String[] { MessageManager
- .getString("label.all") });
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List<String> all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
* 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++)
{
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
- .findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
// just collect ids from dataset sequence
// TODO: check if IDs collected from selecton group intersects with the
// current selection, too
if (((String[]) sarray[1])[sq] == null)
{
- if (!dbr[d].hasMap()
- || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ if (!dbr[d].hasMap() || (dbr[d].getMap()
+ .locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
((int[]) sarray[0])[0]++;
int type = urlLink.getGroupURLType() & 3;
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label
- + (((type & 1) == 1) ? ("("
- + (usingNames ? "Names" : ltarget) + ")") : ""),
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
urlLink, urlset);
addMenu = true;
}
}
}
- private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+ private void addshowLinks(JMenu linkMenu,
+ Collection<List<String>> linkset)
{
for (List<String> linkstrset : linkset)
{
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.setToolTipText(MessageManager.formatMessage("label.open_url_param",
+ new Object[]
+ { url }));
item.addActionListener(new ActionListener()
{
@Override
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(),
+ 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()
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager
- .getString("label.edit_name_description"));
+ sequenceName.setText(
+ MessageManager.getString("label.edit_name_description"));
sequenceName.addActionListener(new ActionListener()
{
@Override
sequenceName_actionPerformed();
}
});
- chooseAnnotations.setText(MessageManager
- .getString("action.choose_annotations"));
+ chooseAnnotations
+ .setText(MessageManager.getString("action.choose_annotations"));
chooseAnnotations.addActionListener(new ActionListener()
{
@Override
chooseAnnotations_actionPerformed(e);
}
});
- sequenceDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ sequenceDetails
+ .setText(MessageManager.getString("label.sequence_details"));
sequenceDetails.addActionListener(new ActionListener()
{
@Override
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ sequenceSelDetails
+ .setText(MessageManager.getString("label.sequence_details"));
sequenceSelDetails.addActionListener(new ActionListener()
{
@Override
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager
- .getString("action.create_group"));
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager
- .getString("label.show_non_conserved"));
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
changeCase(e);
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox")
- + "...");
- seqShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- seqHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- groupShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- groupHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- sequenceFeature.setText(MessageManager
- .getString("label.create_sequence_feature"));
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ sequenceFeature.setText(
+ MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- pdbStructureDialog.setText(MessageManager
- .getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
pdbStructureDialog.addActionListener(new ActionListener()
{
@Override
}
});
- rnaStructureMenu.setText(MessageManager
- .getString("label.view_rna_structure"));
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence")
- + "...");
+ editSequence.setText(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@Override
editSequence_actionPerformed(actionEvent);
}
});
- makeReferenceSeq.setText(MessageManager
- .getString("label.mark_as_representative"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
}
});
- hideInsertions.setText(MessageManager
- .getString("label.hide_insertions"));
+ hideInsertions
+ .setText(MessageManager.getString("label.hide_insertions"));
hideInsertions.addActionListener(new ActionListener()
{
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
}
-
+
/**
* Constructs the entries for the colour menu
*/
}
});
- abovePIDColour.setText(MessageManager
- .getString("label.above_identity_threshold"));
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
}
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_threshold"));
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
}
});
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(conservationMenuItem
- .isSelected());
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
// int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
// .getName());
// sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
- SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
SliderPanel.showPIDSlider();
}
}
* 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);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
if (ap.av.getSelectionGroup() != null)
{
// mark just the columns in the selection group to be hidden
- inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av
- .getSelectionGroup().getEndRes() + 1);
+ inserts.set(ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes() + 1);
// and clear that part of the mask
mask.andNot(inserts);
StringBuilder contents = new StringBuilder(128);
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(
- contents,
- seq,
- true,
- true,
- (ap.getSeqPanel().seqCanvas.fr != null) ? ap
- .getSeqPanel().seqCanvas.fr.getMinMax()
- : null);
+ 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(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("</p>");
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequence_details_for",
- (sequences.length == 1 ? new Object[] { sequences[0]
- .getDisplayId(true) } : new Object[] { MessageManager
- .getString("label.selection") })), 500, 400);
+ Desktop.addInternalFrame(cap,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
}
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());
}
sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap,
- sg.getGroupColourScheme(), getGroup()
- .getName());
+ sg.getGroupColourScheme(), getGroup().getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
- Conservation c = new Conservation("Group", sg.getSequences(ap.av
- .getHiddenRepSequences()), sg.getStartRes(),
- sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group",
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " "
- + MessageManager.getString("label.group_name") + " ",
+ sg.getDescription(),
+ " " + MessageManager.getString("label.group_name") + " ",
MessageManager.getString("label.group_description") + " ",
MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
" " + MessageManager.getString("label.sequence_name")
+ " ",
MessageManager.getString("label.sequence_description") + " ",
- MessageManager
- .getString("label.edit_sequence_name_description"),
+ MessageManager.getString(
+ "label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
if (dialog.getName().indexOf(" ") > -1)
{
- JvOptionPane
- .showMessageDialog(
- ap,
- MessageManager
- .getString("label.spaces_converted_to_backslashes"),
- MessageManager
- .getString("label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
// or we simply trust the user wants
// wysiwig behaviour
- FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
- cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()
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,
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));
}
}
*/
if (!seqs.isEmpty())
{
- if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
- seqs, features, true, ap))
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .amendFeatures(seqs, features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
}
}
}
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null,
- MessageManager.getString("label.edit_sequence"), null,
+ sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null,
MessageManager.getString("label.edit_sequence"),
ap.alignFrame);
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- Action.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ 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());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}