X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3c32180ed65672a53b5ca215ae77487d7b7fdb9f;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=6903034f1ca18d5f08e7adff8fb5b85e9040b3b6;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6903034..3c32180 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -66,11 +66,13 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; +import jalview.datamodel.ResidueCount; 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.CountReader; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; @@ -89,6 +91,8 @@ import jalview.util.StringUtils; import jalview.util.UrlLink; import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import java.io.IOException; +import java.net.MalformedURLException; /** * The popup menu that is displayed on right-click on a sequence id, or in the * sequence alignment. @@ -303,7 +307,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE); @@ -359,15 +363,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * 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 + * the panel in which the mouse is clicked * @param seq - * the sequence under the mouse + * the sequence under the mouse * @throws NullPointerException - * if seq is null + * if seq is null */ public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column) { @@ -378,13 +381,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * Constructor for a PopupMenu for a click in the sequence id panel * * @param alignPanel - * the panel in which the mouse is clicked + * the panel in which the mouse is clicked * @param seq - * the sequence under the mouse click + * the sequence under the mouse click * @param groupLinks - * templates for sequence external links + * templates for sequence external links * @throws NullPointerException - * if seq is null + * if seq is null */ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, List groupLinks) @@ -400,10 +403,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * @param alignPanel * @param seq * @param column - * aligned column position (0...) + * aligned column position (0...) * @param groupLinks */ - private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel, + private PopupMenu(boolean fromIdPanel, + final AlignmentPanel alignPanel, final SequenceI seq, final int column, List groupLinks) { Objects.requireNonNull(seq); @@ -443,10 +447,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (alignPanel.av - .getSelectionGroup() == null - ? Collections. emptyList() - : alignPanel.av.getSelectionGroup().getSequences()); + final List selectedGroup = (alignPanel.av.getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -548,6 +551,35 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } + if (seq.hasHMMProfile()) + { + menuItem = new JMenuItem(MessageManager + .getString("action.add_background_frequencies")); + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + ResidueCount counts = CountReader.getBackgroundFrequencies(ap, + seq); + if (counts != null) + { + seq.getHMM().setBackgroundFrequencies(counts); + ap.alignFrame.buildColourMenu(); + } + } catch (MalformedURLException e1) + { + e1.printStackTrace(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + add(menuItem); + } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new ActionListener() @@ -671,9 +703,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { buildGroupURLMenu(sg, groupLinks); } + // TODO REMOVE FOR 2.12 ? // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable<>(), - reppdb = new Hashtable<>(); + Hashtable pdbe = new Hashtable<>(); + Hashtable reppdb = new Hashtable<>(); SequenceI sqass = null; for (SequenceI sq : alignPanel.av.getSequenceSelection()) @@ -710,8 +743,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); - editGroupMenu - .setText(MessageManager.getString("action.edit_new_group")); + editGroupMenu.setText(MessageManager.getString("action.edit_new_group")); } else { @@ -738,8 +770,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener *
  • positional feature links (alignment panel popup menu)
    • *
  • feature details links (alignment panel popup menu)
    • * - * If this panel is also showed complementary (CDS/protein) features, then - * links to their feature details are also added. + * If this panel is also showed complementary (CDS/protein) features, then links + * to their feature details are also added. * * @param seq * @param column @@ -1147,8 +1179,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (((String[]) sarray[1])[sq] == null) { - if (!e.hasMap() - || (e.getMap().locateMappedRange(start, end) != null)) + if (!e.hasMap() || (e.getMap() + .locateMappedRange(start, end) != null)) { ((String[]) sarray[1])[sq] = e.getAccessionId(); ((int[]) sarray[0])[0]++; @@ -1787,8 +1819,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } inserts.and(sq.getInsertionsAsBits()); } - hidden.clearAndHideColumns(inserts, - ap.av.getSelectionGroup().getStartRes(), + hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), ap.av.getSelectionGroup().getEndRes()); } @@ -2018,8 +2049,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /** * 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() { @@ -2027,8 +2058,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequence.getDescription(), MessageManager.getString("label.sequence_name"), MessageManager.getString("label.sequence_description")); - dialog.showDialog(ap.alignFrame, MessageManager.getString( - "label.edit_sequence_name_description"), new Runnable() + dialog.showDialog(ap.alignFrame, + MessageManager.getString( + "label.edit_sequence_name_description"), + new Runnable() { @Override public void run() @@ -2048,8 +2081,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener ap.paintAlignment(false, false); } sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); } @@ -2080,7 +2112,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ protected void outline_actionPerformed() { - String title = MessageManager.getString("label.select_outline_colour"); + String title = MessageManager + .getString("label.select_outline_colour"); ColourChooserListener listener = new ColourChooserListener() { @Override @@ -2090,8 +2123,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title, - Color.BLUE, listener); + JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), + title, Color.BLUE, listener); } /** @@ -2179,9 +2212,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); + ap.av.notifyAlignment(); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); } } @@ -2288,8 +2320,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); }