X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=88752880345bdce8a48b339f1eb053a962b2fe7e;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=c7e3fd99b64730023f5ac4845cd581c02ba26311;hpb=948b782d6ecd8cfd15aedc2dba66e6c994108629;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c7e3fd9..8875288 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,25 +20,56 @@
*/
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.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
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;
@@ -47,41 +78,40 @@ import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
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.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
/**
- * 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
{
+ /*
+ * 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;
+
+ private final AlignmentPanel ap;
+
+ /*
+ * the sequence under the cursor when clicked
+ * (additional sequences may be selected)
+ */
+ private final SequenceI sequence;
+
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
@@ -92,30 +122,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem modifyConservation = new JMenuItem();
+ protected JRadioButtonMenuItem annotationColour;
- AlignmentPanel ap;
+ protected JMenuItem modifyConservation = new JMenuItem();
JMenu sequenceMenu = new JMenu();
- JMenuItem sequenceName = new JMenuItem();
-
- JMenuItem sequenceDetails = new JMenuItem();
-
- JMenuItem sequenceSelDetails = new JMenuItem();
-
JMenuItem makeReferenceSeq = new JMenuItem();
- JMenuItem chooseAnnotations = new JMenuItem();
-
- SequenceI sequence;
-
JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
- JMenuItem outline = new JMenuItem();
-
JMenu colourMenu = new JMenu();
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
@@ -128,18 +146,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
JMenu editMenu = new JMenu();
- JMenuItem cut = new JMenuItem();
-
- JMenuItem copy = new JMenuItem();
-
JMenuItem upperCase = new JMenuItem();
JMenuItem lowerCase = new JMenuItem();
JMenuItem toggle = new JMenuItem();
- JMenu pdbMenu = new JMenu();
-
JMenu outputMenu = new JMenu();
JMenu seqShowAnnotationsMenu = new JMenu();
@@ -156,52 +168,246 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
JMenuItem groupAddReferenceAnnotations = new JMenuItem(
MessageManager.getString("label.add_reference_annotations"));
- JMenuItem sequenceFeature = new JMenuItem();
-
JMenuItem textColour = new JMenuItem();
- JMenu jMenu1 = new JMenu();
+ JMenu editGroupMenu = new JMenu();
- JMenuItem pdbStructureDialog = new JMenuItem();
+ JMenuItem chooseStructure = new JMenuItem();
JMenu rnaStructureMenu = new JMenu();
- JMenuItem editSequence = 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
+ */
+ protected static JMenu buildLinkMenu(final SequenceI seq,
+ List features)
+ {
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- JMenu groupLinksMenu;
+ List nlinks = null;
+ if (seq != null)
+ {
+ nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ UrlLink.sort(nlinks);
+ }
+ else
+ {
+ nlinks = new ArrayList<>();
+ }
- JMenuItem hideInsertions = new JMenuItem();
+ 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)
+ {
+ Console.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Console.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;
+ }
/**
- * Creates a new PopupMenu object.
+ * 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);
+ }
+
+ /**
+ * Constructor for a PopupMenu for a click in the alignment panel (on a
+ * residue)
*
* @param ap
- * DOCUMENT ME!
+ * the panel in which the mouse is clicked
* @param seq
- * DOCUMENT ME!
+ * the sequence under the mouse
+ * @throws NullPointerException
+ * if seq is null
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, List links)
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
{
- this(ap, seq, links, null);
+ this(false, ap, seq, column, null);
}
/**
+ * Constructor for a PopupMenu for a click in the sequence id panel
*
- * @param ap
+ * @param alignPanel
+ * the panel in which the mouse is clicked
* @param seq
- * @param links
+ * the sequence under the mouse click
* @param groupLinks
+ * templates for sequence external links
+ * @throws NullPointerException
+ * if seq is null
*/
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
- List links, List groupLinks)
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List groupLinks)
{
- // /////////////////////////////////////////////////////////
- // If this is activated from the sequence panel, the user may want to
- // edit or annotate a particular residue. Therefore display the residue menu
- //
- // If from the IDPanel, we must display the sequence menu
- // ////////////////////////////////////////////////////////
- this.ap = ap;
+ this(true, alignPanel, seq, -1, groupLinks);
+ }
+
+ /**
+ * Private constructor that constructs a popup menu for either sequence ID
+ * Panel, or alignment context
+ *
+ * @param fromIdPanel
+ * @param alignPanel
+ * @param seq
+ * @param column
+ * aligned column position (0...)
+ * @param groupLinks
+ */
+ private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
+ final SequenceI seq, final int column, List groupLinks)
+ {
+ Objects.requireNonNull(seq);
+ this.forIdPanel = fromIdPanel;
+ this.ap = alignPanel;
sequence = seq;
for (String ff : FileFormats.getInstance().getWritableFormats(true))
@@ -225,8 +431,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* 'reference annotations' that may be added to the alignment. First for the
* currently selected sequence (if there is one):
*/
- final List selectedSequence = (seq == null ? Collections
- . emptyList() : Arrays.asList(seq));
+ final List selectedSequence = (forIdPanel && seq != null
+ ? Arrays.asList(seq)
+ : Collections. emptyList());
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
@@ -235,9 +442,10 @@ 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 ? Collections
- . emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List selectedGroup = (alignPanel.av
+ .getSelectionGroup() == null
+ ? Collections. emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -251,22 +459,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
e.printStackTrace();
}
- JMenuItem menuItem;
- if (seq != null)
+ if (forIdPanel)
{
+ JMenuItem menuItem;
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);
}
@@ -277,7 +485,7 @@ 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)
{
@@ -290,14 +498,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
*/
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);
@@ -318,15 +526,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
// 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);
@@ -351,12 +559,12 @@ 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[] { seq.getName() }));
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
menuItem.addActionListener(new ActionListener()
{
@Override
@@ -368,12 +576,12 @@ 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"));
@@ -382,10 +590,10 @@ 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();
}
}
});
@@ -393,32 +601,43 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
}
- // for the case when no sequences are even visible
- if (ap.av.hasHiddenRows())
+
+ /*
+ * offer 'Reveal All'
+ * - in the IdPanel (seq not null) if any sequence is hidden
+ * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+ */
+ if (alignPanel.av.hasHiddenRows())
{
+ boolean addOption = seq != null;
+ if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
{
- menuItem = new JMenuItem(
+ addOption = true;
+ }
+ if (addOption)
+ {
+ JMenuItem menuItem = new JMenuItem(
MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
@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();
}
}
});
-
add(menuItem);
}
}
- 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)
{
@@ -452,9 +671,11 @@ 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)
@@ -472,9 +693,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
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;
}
}
@@ -488,81 +709,261 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ editGroupMenu
+ .setText(MessageManager.getString("action.edit_new_group"));
}
else
{
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText(MessageManager.getString("action.edit_group"));
+ editGroupMenu.setText(MessageManager.getString("action.edit_group"));
}
- if (seq == null)
+ if (!forIdPanel)
{
sequenceMenu.setVisible(false);
- pdbStructureDialog.setVisible(false);
+ chooseStructure.setVisible(false);
rnaStructureMenu.setVisible(false);
}
- if (links != null && links.size() > 0)
+ addLinksAndFeatures(seq, column);
+ }
+
+ /**
+ * Adds
+ *
+ * - configured sequence database links (ID panel popup menu)
+ * - non-positional feature links (ID panel popup menu)
+ * - 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.
+ *
+ * @param seq
+ * @param column
+ */
+ void addLinksAndFeatures(final SequenceI seq, final int column)
+ {
+ List features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
{
- addFeatureLinks(seq, links);
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
+ }
+
+ addLinks(seq, features);
+
+ if (!forIdPanel)
+ {
+ addFeatureDetails(features, seq, column);
}
}
/**
- * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * 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 links
+ * @param column
*/
- void addFeatureLinks(final SequenceI seq, List links)
+ protected void addFeatureDetails(List features,
+ final SequenceI seq, final int column)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Map> linkset = new LinkedHashMap>();
-
- for (String link : links)
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ MappedFeatures mf = null;
+ if (ap.av.isShowComplementFeatures())
{
- UrlLink urlLink = null;
- try
+ if (!Comparison.isGap(sequence.getCharAt(column)))
{
- urlLink = new UrlLink(link);
- } catch (Exception foo)
- {
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
- continue;
+ 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 (!urlLink.isValid())
- {
- Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
+ if (features.isEmpty() && mf == null)
+ {
+ /*
+ * no features to show at this position
+ */
+ return;
+ }
- urlLink.createLinksFromSeq(seq, linkset);
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
+
+ String name = seq.getName();
+ for (final SequenceFeature sf : features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, null);
}
- addshowLinks(linkMenu, linkset.values());
+ if (mf != null)
+ {
+ for (final SequenceFeature sf : mf.features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, mf);
+ }
+ }
+ }
- // disable link menu if there are no valid entries
- if (linkMenu.getItemCount() > 0)
+ /**
+ * 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)
{
- linkMenu.setEnabled(true);
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
}
- else
+ StringBuilder desc = new StringBuilder();
+ desc.append(sf.getType()).append(" ").append(String.valueOf(start));
+ if (start != end)
{
- linkMenu.setEnabled(false);
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
}
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ desc.append(" ");
+ description = StringUtils.stripHtmlTags(description);
- if (sequence != null)
+ /*
+ * 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 = description.substring(0, FEATURE_DESC_MAX) + "...";
+ }
+ desc.append(description);
+ }
+ String featureGroup = sf.getFeatureGroup();
+ if (featureGroup != null)
{
- sequenceMenu.add(linkMenu);
+ 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)
+ {
+ showFeatureDetails(sf, seqName, mf);
+ }
+ });
+ details.add(item);
+ }
+
+ /**
+ * Opens a panel showing a text report of feature details
+ *
+ * @param sf
+ * @param seqName
+ * @param mf
+ */
+ protected void showFeatureDetails(SequenceFeature sf, String seqName,
+ MappedFeatures mf)
+ {
+ 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
+ */
{
- add(linkMenu);
+ 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);
+ }
+ /**
+ * 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(forIdPanel ? seq : null, features);
+
+ // only add link menu if it has entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (forIdPanel)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
}
/**
@@ -586,9 +987,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
showMenu.removeAll();
hideMenu.removeAll();
- final List all = Arrays.asList(new String[] { MessageManager
- .getString("label.all") });
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
@@ -603,8 +1006,8 @@ 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);
@@ -700,7 +1103,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(
+ JMenu groupLinksMenu = new JMenu(
MessageManager.getString("action.group_link"));
// three types of url that might be created.
JMenu[] linkMenus = new JMenu[] { null,
@@ -710,12 +1113,12 @@ 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++)
{
- 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
@@ -724,12 +1127,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
sqi = sqi.getDatasetSequence();
}
- DBRefEntry[] dbr = sqi.getDBRefs();
- if (dbr != null && dbr.length > 0)
+ List 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)
{
@@ -742,10 +1147,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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]++;
}
}
@@ -763,20 +1168,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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)
{
@@ -815,9 +1219,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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;
}
@@ -839,96 +1244,6 @@ 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!
*
@@ -948,8 +1263,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager
- .getString("label.edit_name_description"));
+
+ JMenuItem sequenceName = new JMenuItem(
+ MessageManager.getString("label.edit_name_description"));
sequenceName.addActionListener(new ActionListener()
{
@Override
@@ -958,8 +1274,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
sequenceName_actionPerformed();
}
});
- chooseAnnotations.setText(MessageManager
- .getString("action.choose_annotations"));
+ JMenuItem chooseAnnotations = new JMenuItem(
+ MessageManager.getString("action.choose_annotations"));
chooseAnnotations.addActionListener(new ActionListener()
{
@Override
@@ -968,24 +1284,24 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
chooseAnnotations_actionPerformed(e);
}
});
- sequenceDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ JMenuItem sequenceDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
sequenceDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- sequenceDetails_actionPerformed();
+ createSequenceDetailsReport(new SequenceI[] { sequence });
}
});
- sequenceSelDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ JMenuItem sequenceSelDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
sequenceSelDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- sequenceSelectionDetails_actionPerformed();
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
}
});
@@ -999,8 +1315,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager
- .getString("action.create_group"));
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
@@ -1010,7 +1326,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- outline.setText(MessageManager.getString("action.border_colour"));
+ JMenuItem outline = new JMenuItem(
+ MessageManager.getString("action.border_colour"));
outline.addActionListener(new ActionListener()
{
@Override
@@ -1048,8 +1365,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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()
{
@@ -1060,7 +1377,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
editMenu.setText(MessageManager.getString("action.edit"));
- cut.setText(MessageManager.getString("action.cut"));
+ JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
@Override
@@ -1078,7 +1395,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
changeCase(e);
}
});
- copy.setText(MessageManager.getString("action.copy"));
+ JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
@Override
@@ -1105,18 +1422,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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"));
+ JMenuItem sequenceFeature = new JMenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
@@ -1125,10 +1442,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
sequenceFeature_actionPerformed();
}
});
- jMenu1.setText(MessageManager.getString("label.group"));
- pdbStructureDialog.setText(MessageManager
- .getString("label.show_pdbstruct_dialog"));
- pdbStructureDialog.addActionListener(new ActionListener()
+ editGroupMenu.setText(MessageManager.getString("label.group"));
+ chooseStructure.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ chooseStructure.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
@@ -1142,22 +1459,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- 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")
- + "...");
+ JMenuItem editSequence = new JMenuItem(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- editSequence_actionPerformed(actionEvent);
+ editSequence_actionPerformed();
}
});
- makeReferenceSeq.setText(MessageManager
- .getString("label.mark_as_representative"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
@@ -1168,25 +1485,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- hideInsertions.setText(MessageManager
- .getString("label.hide_insertions"));
- hideInsertions.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hideInsertions_actionPerformed(e);
- }
- });
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
add(rnaStructureMenu);
- add(pdbStructureDialog);
- if (sequence != null)
+ add(chooseStructure);
+ if (forIdPanel)
{
+ JMenuItem hideInsertions = new JMenuItem(
+ MessageManager.getString("label.hide_insertions"));
+ hideInsertions.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
add(hideInsertions);
}
// annotations configuration panel suppressed for now
@@ -1207,7 +1524,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
groupMenu.add(sequenceFeature);
groupMenu.add(createGroupMenuItem);
groupMenu.add(unGroupMenuItem);
- groupMenu.add(jMenu1);
+ groupMenu.add(editGroupMenu);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
@@ -1221,19 +1538,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
- // JBPNote: These shouldn't be added here - should appear in a generic
- // 'apply web service to this sequence menu'
- // pdbMenu.add(RNAFold);
- // pdbMenu.add(ContraFold);
- jMenu1.add(groupName);
- jMenu1.add(colourMenu);
- jMenu1.add(showBoxes);
- jMenu1.add(showText);
- jMenu1.add(showColourText);
- jMenu1.add(outline);
- jMenu1.add(displayNonconserved);
+ editGroupMenu.add(groupName);
+ editGroupMenu.add(colourMenu);
+ editGroupMenu.add(showBoxes);
+ editGroupMenu.add(showText);
+ editGroupMenu.add(showColourText);
+ editGroupMenu.add(outline);
+ editGroupMenu.add(displayNonconserved);
}
-
+
/**
* Constructs the entries for the colour menu
*/
@@ -1250,8 +1563,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- abovePIDColour.setText(MessageManager
- .getString("label.above_identity_threshold"));
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
@@ -1261,8 +1574,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_threshold"));
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
@@ -1272,18 +1585,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
- 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());
}
});
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.setEnabled(false);
+ annotationColour.setToolTipText(
+ MessageManager.getString("label.by_annotation_tooltip"));
+
modifyConservation.setText(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
@@ -1314,7 +1634,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
@@ -1341,8 +1664,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
// 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();
}
}
@@ -1369,11 +1691,11 @@ 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);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
@@ -1413,10 +1735,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected void addReferenceAnnotations_actionPerformed(
Map> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
- AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
refresh();
}
@@ -1445,14 +1765,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
- HiddenColumns hidden = new HiddenColumns();
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
BitSet inserts = new BitSet();
- inserts.set(0, ap.av.getAlignment().getWidth());
boolean markedPopup = false;
// mark inserts in current selection
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); // TODO why +1?
+
+ // now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
{
if (sq == sequence)
@@ -1461,17 +1785,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
inserts.and(sq.getInsertionsAsBits());
}
+ 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());
- }
+ inserts.or(sequence.getInsertionsAsBits());
- // finally, hide and set hidden columns
- hidden.hideMarkedBits(inserts);
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
@@ -1480,42 +1806,57 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
createSequenceDetailsReport(ap.av.getSequenceSelection());
}
- protected void sequenceDetails_actionPerformed()
- {
- createSequenceDetailsReport(new SequenceI[] { sequence });
- }
-
public void createSequenceDetailsReport(SequenceI[] sequences)
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
StringBuilder contents = new StringBuilder(128);
+ contents.append("");
for (SequenceI seq : sequences)
{
- contents.append(""
- + MessageManager
- .formatMessage(
- "label.create_sequence_details_report_annotation_for",
- 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.append("
" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "
\n");
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("
");
}
- cap.setText("" + contents.toString() + "");
-
- 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);
+ contents.append("");
+ 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(frame,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
}
protected void showNonconserved_actionPerformed()
@@ -1530,7 +1871,9 @@ 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());
}
@@ -1562,8 +1905,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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());
@@ -1609,9 +1951,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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());
@@ -1633,30 +1975,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
/**
- * 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") + " ",
+ sg.getDescription(),
+ 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();
+ });
}
/**
@@ -1677,50 +2011,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * 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.
*/
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;
- }
-
- if (dialog.getName() != null)
- {
- 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);
- }
-
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(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());
+ });
}
/**
@@ -1745,24 +2070,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
/**
- * 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);
}
/**
@@ -1801,22 +2124,6 @@ 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);
@@ -1824,12 +2131,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
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)
@@ -1867,8 +2174,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
@@ -1877,18 +2184,21 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
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;
- 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
- 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()
@@ -1899,8 +2209,8 @@ 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,
@@ -1914,15 +2224,16 @@ 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));
}
}
- if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
{
- ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+ new FeatureEditor(ap, seqs, features, true).showDialog();
}
}
@@ -1935,57 +2246,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
- public void colourByStructure(String pdbid)
- {
- Annotation[] anots = ap.av.getStructureSelectionManager()
- .colourSequenceFromStructure(sequence, pdbid);
-
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",
- "Coloured by " + pdbid, anots);
-
- ap.av.getAlignment().addAnnotation(an);
- an.createSequenceMapping(sequence, 0, true);
- // an.adjustForAlignment();
- ap.av.getAlignment().setAnnotationIndex(an, 0);
-
- ap.adjustAnnotationHeight();
-
- sequence.addAlignmentAnnotation(an);
-
- }
-
- 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();
+ SequenceI seq = sequence;
if (sg != null)
{
- if (sequence == null)
+ if (seq == null)
{
- sequence = sg.getSequenceAt(0);
+ seq = sg.getSequenceAt(0);
}
EditNameDialog dialog = new EditNameDialog(
- sequence.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());
+ });
}
}
@@ -2003,7 +2298,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* switch to the chosen colour scheme (or null for None)
*/
ColourSchemeI colourScheme = ColourSchemes.getInstance()
- .getColourScheme(colourSchemeName, sg,
+ .getColourScheme(colourSchemeName, ap.av, sg,
ap.av.getHiddenRepSequences());
sg.setColourScheme(colourScheme);
if (colourScheme instanceof Blosum62ColourScheme