X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2034b3fc0938849fa279766da2900f8a39adec38;hb=71c5a29a58e5505aaf7d63a8c9f1bea3ae93d629;hp=2ef71cce5d6fff162391756b1425434754dcce56;hpb=6d06be2714c9cba8c69148d5e2d26b50b7051840;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ef71cc..2034b3f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -24,21 +24,23 @@ import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
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.ResidueCount;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.io.CountReader;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
@@ -47,14 +49,20 @@ 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.StringUtils;
import jalview.util.UrlLink;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
@@ -64,24 +72,38 @@ import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
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.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
/**
- * 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
{
+ /*
+ * 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 +114,18 @@ 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 +138,12 @@ 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();
@@ -156,53 +160,246 @@ 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)
+ {
+ Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ /*
+ * construct menu items for the hyperlinks (still preserving
+ * the order of the sorted templates)
+ */
+ addUrlLinks(linkMenu, linkset.values());
+
+ return linkMenu;
+ }
/**
- * 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
+ * the sequence under the mouse click
+ * @param groupLinks
+ * templates for sequence external links
+ * @throws NullPointerException
+ * if seq is null
+ */
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List groupLinks)
+ {
+ 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 links
+ * @param column
+ * aligned column position (0...)
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
- List links, List groupLinks)
+ private PopupMenu(boolean fromIdPanel,
+ final AlignmentPanel alignPanel,
+ final SequenceI seq, final int column, 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;
+ Objects.requireNonNull(seq);
+ this.forIdPanel = fromIdPanel;
+ this.ap = alignPanel;
sequence = seq;
for (String ff : FileFormats.getInstance().getWritableFormats(true))
@@ -226,9 +423,9 @@ 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,
@@ -237,9 +434,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
/*
* And repeat for the current selection group (if there is one):
*/
- final List selectedGroup = (ap.av.getSelectionGroup() == null
+ final List selectedGroup = (alignPanel.av.getSelectionGroup() == null
? Collections. emptyList()
- : ap.av.getSelectionGroup().getSequences());
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -253,11 +450,11 @@ 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"));
@@ -268,7 +465,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
MessageManager.getString("action.set_as_reference"));
}
- if (!ap.av.getAlignment().isNucleotide())
+ if (!alignPanel.av.getAlignment().isNucleotide())
{
remove(rnaStructureMenu);
}
@@ -279,7 +476,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* add menu items to 2D-render any alignment or sequence secondary
* structure annotation
*/
- AlignmentAnnotation[] aas = ap.av.getAlignment()
+ AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
.getAlignmentAnnotation();
if (aas != null)
{
@@ -299,7 +496,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
@Override
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
@@ -328,7 +525,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
@@ -341,6 +538,36 @@ 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()
@@ -353,8 +580,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
});
add(menuItem);
- if (ap.av.getSelectionGroup() != null
- && ap.av.getSelectionGroup().getSize() > 1)
+ if (alignPanel.av.getSelectionGroup() != null
+ && alignPanel.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager
.formatMessage("label.represent_group_with", new Object[]
@@ -370,12 +597,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
sequenceMenu.add(menuItem);
}
- if (ap.av.hasHiddenRows())
+ if (alignPanel.av.hasHiddenRows())
{
- final int index = ap.av.getAlignment().findIndex(seq);
+ final int index = alignPanel.av.getAlignment().findIndex(seq);
- if (ap.av.adjustForHiddenSeqs(index)
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ if (alignPanel.av.adjustForHiddenSeqs(index)
+ - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
{
menuItem = new JMenuItem(
MessageManager.getString("action.reveal_sequences"));
@@ -384,10 +611,10 @@ 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();
}
}
});
@@ -395,32 +622,42 @@ 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();
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
boolean isDefinedGroup = (sg != null)
- ? ap.av.getAlignment().getGroups().contains(sg)
+ ? alignPanel.av.getAlignment().getGroups().contains(sg)
: false;
if (sg != null && sg.getSize() > 0)
@@ -455,10 +692,11 @@ 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<>();
+ 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)
@@ -492,81 +730,216 @@ 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)
- {
- addFeatureLinks(seq, links);
- }
+ addLinksAndFeatures(seq, column);
}
/**
- * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * 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 links
+ * @param column
*/
- void addFeatureLinks(final SequenceI seq, List links)
+ void addLinksAndFeatures(final SequenceI seq, final int column)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Map> linkset = new LinkedHashMap<>();
+ List features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
+ {
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
+ }
- for (String link : links)
+ addLinks(seq, features);
+
+ if (!forIdPanel)
{
- UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(link);
- } catch (Exception foo)
- {
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
- continue;
- }
+ addFeatureDetails(features, seq, column);
+ }
+ }
- if (!urlLink.isValid())
+ /**
+ * Add a link to show feature details for each sequence feature
+ *
+ * @param features
+ * @param column
+ * @param seq
+ */
+ protected void addFeatureDetails(List features,
+ SequenceI seq, int column)
+ {
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ MappedFeatures mf = null;
+ if (ap.av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
{
- Cache.log.error(urlLink.getInvalidMessage());
- 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);
}
+ }
- urlLink.createLinksFromSeq(seq, linkset);
+ if (features.isEmpty() && mf == null)
+ {
+ /*
+ * no features to show at this position
+ */
+ return;
}
- addshowLinks(linkMenu, linkset.values());
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
- // disable link menu if there are no valid entries
- if (linkMenu.getItemCount() > 0)
+ String name = seq.getName();
+ for (final SequenceFeature sf : features)
{
- linkMenu.setEnabled(true);
+ addFeatureDetailsMenuItem(details, name, sf);
}
- else
+
+ if (mf != null)
{
- linkMenu.setEnabled(false);
+ name = mf.fromSeq == seq ? mf.mapping.getTo().getName()
+ : mf.fromSeq.getName();
+ for (final SequenceFeature sf : mf.features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf);
+ }
}
+ }
- if (sequence != null)
+ /**
+ * A helper method to add one menu item whose action is to show details for one
+ * feature
+ *
+ * @param details
+ * @param seqName
+ * @param sf
+ */
+ void addFeatureDetailsMenuItem(JMenu details, final String seqName,
+ final SequenceFeature sf)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ String desc = null;
+ if (start == end)
{
- sequenceMenu.add(linkMenu);
+ desc = String.format("%s %d", sf.getType(), start);
}
else
{
- add(linkMenu);
+ desc = String.format("%s %d-%d", sf.getType(), start, end);
+ }
+ String tooltip = desc;
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ description = StringUtils.stripHtmlTags(description);
+ if (description.length() > 12)
+ {
+ desc = desc + " " + description.substring(0, 12) + "..";
+ }
+ else
+ {
+ desc = desc + " " + description;
+ }
+ tooltip = tooltip + " " + description;
+ }
+ if (sf.getFeatureGroup() != null)
+ {
+ tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
}
+ JMenuItem item = new JMenuItem(desc);
+ item.setToolTipText(tooltip);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showFeatureDetails(seqName, sf);
+ }
+ });
+ details.add(item);
+ }
+
+ /**
+ * Opens a panel showing a text report of feature dteails
+ *
+ * @param seqName
+ *
+ * @param sf
+ */
+ protected void showFeatureDetails(String seqName, SequenceFeature sf)
+ {
+ 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));
+ 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. 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);
+ }
+ }
}
/**
@@ -706,7 +1079,7 @@ 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,
@@ -846,98 +1219,6 @@ 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!
*
@@ -957,7 +1238,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(
+
+ JMenuItem sequenceName = new JMenuItem(
MessageManager.getString("label.edit_name_description"));
sequenceName.addActionListener(new ActionListener()
{
@@ -967,8 +1249,8 @@ 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
@@ -977,24 +1259,24 @@ 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());
}
});
@@ -1019,7 +1301,8 @@ 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
@@ -1069,7 +1352,7 @@ 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
@@ -1087,7 +1370,7 @@ 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
@@ -1124,7 +1407,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
.setText(MessageManager.getString("label.show_annotations"));
groupHideAnnotationsMenu
.setText(MessageManager.getString("label.hide_annotations"));
- sequenceFeature.setText(
+ JMenuItem sequenceFeature = new JMenuItem(
MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@@ -1134,10 +1417,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
sequenceFeature_actionPerformed();
}
});
- jMenu1.setText(MessageManager.getString("label.group"));
- pdbStructureDialog.setText(
+ editGroupMenu.setText(MessageManager.getString("label.group"));
+ chooseStructure.setText(
MessageManager.getString("label.show_pdbstruct_dialog"));
- pdbStructureDialog.addActionListener(new ActionListener()
+ chooseStructure.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
@@ -1155,7 +1438,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
.setText(MessageManager.getString("label.view_rna_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(
+ JMenuItem editSequence = new JMenuItem(
MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@@ -1177,25 +1460,25 @@ 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
@@ -1216,7 +1499,7 @@ 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);
@@ -1230,17 +1513,13 @@ 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);
}
/**
@@ -1293,6 +1572,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
});
+ 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()
@@ -1323,7 +1609,10 @@ 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);
@@ -1453,15 +1742,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
-
- HiddenColumns hidden = new HiddenColumns();
- BitSet inserts = new BitSet(), mask = new BitSet();
-
- // set mask to preserve existing hidden columns outside selected group
- if (ap.av.hasHiddenColumns())
- {
- ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
- }
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
@@ -1469,10 +1751,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
- ap.av.getSelectionGroup().getEndRes() + 1);
-
- // and clear that part of the mask
- mask.andNot(inserts);
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
@@ -1483,29 +1762,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
inserts.and(sq.getInsertionsAsBits());
}
- }
- else
- {
- // initially, mark all columns to be hidden
- inserts.set(0, ap.av.getAlignment().getWidth());
-
- // and clear out old hidden regions completely
- mask.clear();
+ hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
- if (!markedPopup && sequence != null)
+ else if (!markedPopup && sequence != null)
{
- inserts.and(sequence.getInsertionsAsBits());
- }
-
- // finally, preserve hidden regions outside selection
- inserts.or(mask);
+ inserts.or(sequence.getInsertionsAsBits());
- // and set hidden columns accordingly
- hidden.hideMarkedBits(inserts);
-
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
@@ -1514,11 +1782,6 @@ 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();
@@ -1530,10 +1793,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
new Object[]
{ seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents, seq, true, true,
- (ap.getSeqPanel().seqCanvas.fr != null)
- ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
- : null);
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("
");
}
cap.setText("" + contents.toString() + "");
@@ -1709,10 +1969,9 @@ 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()
{
@@ -1730,9 +1989,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
return;
}
- if (dialog.getName() != null)
+ String name = dialog.getName();
+ if (name != null)
{
- if (dialog.getName().indexOf(" ") > -1)
+ if (name.indexOf(" ") > -1)
{
JvOptionPane.showMessageDialog(ap,
MessageManager
@@ -1740,10 +2000,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
MessageManager
.getString("label.no_spaces_allowed_sequence_name"),
JvOptionPane.WARNING_MESSAGE);
+ name = name.replace(' ', '_');
}
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
+ sequence.setName(name);
+ ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
@@ -1831,22 +2092,6 @@ 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);
@@ -1946,8 +2191,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
- features.add(
- new SequenceFeature(null, null, null, start, end, null));
+ features.add(new SequenceFeature(null, null, start, end, null));
}
}
@@ -1960,7 +2204,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
.amendFeatures(seqs, features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
}
}
}
@@ -1974,38 +2219,20 @@ 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)
{
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(),
+ seq.getSequenceAsString(sg.getStartRes(),
sg.getEndRes() + 1),
null, MessageManager.getString("label.edit_sequence"), null,
MessageManager.getString("label.edit_sequence"),
@@ -2042,7 +2269,7 @@ 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