/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+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.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;
+
+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.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+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;
/**
- * 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
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
- JMenu groupMenu = new JMenu();
-
- JMenuItem groupName = new JMenuItem();
-
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ /*
+ * maximum length of feature description to include in popup menu item text
+ */
+ private static final int FEATURE_DESC_MAX = 40;
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ /*
+ * true for ID Panel menu, false for alignment panel menu
+ */
+ private final boolean forIdPanel;
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ private final AlignmentPanel ap;
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ /*
+ * the sequence under the cursor when clicked
+ * (additional sequences may be selected)
+ */
+ private final SequenceI sequence;
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ JMenu groupMenu = new JMenu();
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+ JMenuItem groupName = new JMenuItem();
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
- AlignmentPanel ap;
-
- JMenu sequenceMenu = new JMenu();
+ protected JRadioButtonMenuItem annotationColour;
- JMenuItem sequenceName = new JMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
- JMenuItem sequenceDetails = new JMenuItem();
+ JMenu sequenceMenu = new JMenu();
- JMenuItem sequenceSelDetails = new JMenuItem();
+ JMenuItem makeReferenceSeq = new JMenuItem();
- SequenceI sequence;
JMenuItem createGroupMenuItem = new JMenuItem();
- JMenuItem unGroupMenuItem = new JMenuItem();
- JMenuItem outline = new JMenuItem();
-
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+ JMenuItem unGroupMenuItem = new JMenuItem();
JMenu colourMenu = new JMenu();
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();
- JMenuItem pdbFromFile = new JMenuItem();
+ JMenu seqShowAnnotationsMenu = new JMenu();
- JMenuItem enterPDB = new JMenuItem();
+ JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem discoverPDB = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
- JMenu outputMenu = new JMenu();
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
- JMenuItem sequenceFeature = new JMenuItem();
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenuItem textColour = new JMenuItem();
- JMenu jMenu1 = new JMenu();
+ JMenu editGroupMenu = new JMenu();
+
+ JMenuItem chooseStructure = new JMenuItem();
+
+ JMenu rnaStructureMenu = new JMenu();
+
+ /**
+ * 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<SequenceFeature> features)
+ {
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+
+ List<String> nlinks = null;
+ if (seq != null)
+ {
+ nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ UrlLink.sort(nlinks);
+ }
+ else
+ {
+ nlinks = new ArrayList<>();
+ }
+
+ 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<String, List<String>> 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;
+ }
- JMenu structureMenu = new JMenu();
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
- JMenu viewStructureMenu = new JMenu();
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
- // JMenu colStructureMenu = new JMenu();
- JMenuItem editSequence = new JMenuItem();
+ /*
+ * construct menu items for the hyperlinks (still preserving
+ * the order of the sorted templates)
+ */
+ addUrlLinks(linkMenu, linkset.values());
- // JMenuItem annotationMenuItem = new JMenuItem();
+ return linkMenu;
+ }
- JMenu groupLinksMenu;
+ /**
+ * 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<List<String>> linkset)
+ {
+ for (List<String> 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);
+ }
+ }
/**
- * Creates a new PopupMenu object.
+ * 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, Vector 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,
- Vector links, Vector groupLinks)
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List<String> 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<String> groupLinks)
+ {
+ Objects.requireNonNull(seq);
+ this.forIdPanel = fromIdPanel;
+ this.ap = alignPanel;
sequence = seq;
- ButtonGroup colours = new ButtonGroup();
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(abovePIDColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(purinePyrimidineColour);
- // colours.add(covariationColour);
-
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
- JMenuItem item = new JMenuItem(
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(new java.awt.event.ActionListener()
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
+ {
+ JMenuItem item = new JMenuItem(ff);
+
+ item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
outputMenu.add(item);
}
+ /*
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment. First for the
+ * currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (forIdPanel && seq != null
+ ? Arrays.asList(seq)
+ : Collections.<SequenceI> emptyList());
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+
try
{
jbInit();
e.printStackTrace();
}
- JMenuItem menuItem;
- if (seq != null)
+ if (forIdPanel)
{
+ JMenuItem menuItem;
sequenceMenu.setText(sequence.getName());
-
- if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size() > 0)
+ if (seq == alignPanel.av.getAlignment().getSeqrep())
{
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
- .elements();
-
- while (e.hasMoreElements())
- {
- final PDBEntry pdb = (PDBEntry) e.nextElement();
-
- menuItem = new JMenuItem();
- menuItem.setText(pdb.getId());
- menuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- // TODO re JAL-860: optionally open dialog or provide a menu entry
- // allowing user to open just one structure per sequence
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
- { pdb })[0], null, ap);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
- }
-
- });
- viewStructureMenu.add(menuItem);
-
- /*
- * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
- * menuItem.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * colourByStructure(pdb.getId()); } });
- * colStructureMenu.add(menuItem);
- */
- }
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.unmark_as_reference"));
}
else
{
- if (ap.av.getAlignment().isNucleotide() == false)
- {
- structureMenu.remove(viewStructureMenu);
- }
- // structureMenu.remove(colStructureMenu);
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.set_as_reference"));
}
- if (ap.av.getAlignment().isNucleotide() == true)
+ if (!alignPanel.av.getAlignment().isNucleotide())
+ {
+ remove(rnaStructureMenu);
+ }
+ else
{
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ int origCount = rnaStructureMenu.getItemCount();
+ /*
+ * add menu items to 2D-render any alignment or sequence secondary
+ * structure annotation
+ */
+ AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; i < aa.length; i++)
+ if (aas != null)
{
- if (aa[i].getRNAStruc() != null)
+ for (final AlignmentAnnotation aa : aas)
{
- final String rnastruc = aa[i].getRNAStruc();
- final String structureLine = aa[i].label;
- menuItem = new JMenuItem();
- menuItem.setText("2D RNA " + structureLine);
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ if (aa.isValidStruc() && aa.sequenceRef == null)
{
- public void actionPerformed(ActionEvent e)
+ /*
+ * valid alignment RNA secondary structure annotation
+ */
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new Object[]
+ { aa.label }));
+ menuItem.addActionListener(new ActionListener()
{
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),
- rnastruc, seq.getName(), ap);
- }
- });
- viewStructureMenu.add(menuItem);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq, aa, alignPanel);
+ }
+ });
+ rnaStructureMenu.add(menuItem);
+ }
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
-
if (seq.getAnnotation() != null)
{
- AlignmentAnnotation seqAnno[] = seq.getAnnotation();
- for (int i = 0; i < seqAnno.length; i++)
+ AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+ for (final AlignmentAnnotation aa : seqAnns)
{
- if (seqAnno[i].getRNAStruc() != null)
+ if (aa.isValidStruc())
{
- final String rnastruc = seqAnno[i].getRNAStruc();
-
+ /*
+ * valid sequence RNA secondary structure annotation
+ */
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText("2D RNA - " + seq.getName());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.setText(MessageManager.formatMessage(
+ "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.getName() + " structure", seq, seq
- .getSequenceAsString(), rnastruc, seq.getName(),
- ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
- viewStructureMenu.add(menuItem);
+ rnaStructureMenu.add(menuItem);
}
}
}
-
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
}
- menuItem = new JMenuItem("Hide Sequences");
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
+ menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(false);
});
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("Represent Group with " + seq.getName());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
+ menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(true);
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("Reveal Sequences");
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- ap.av.showSequence(index);
- if (ap.overviewPanel != null)
+ alignPanel.av.showSequence(index);
+ if (alignPanel.overviewPanel != null)
{
- ap.overviewPanel.updateOverviewImage();
+ alignPanel.overviewPanel.updateOverviewImage();
}
}
});
}
}
}
- // for the case when no sequences are even visible
- if (ap.av.hasHiddenRows())
+
+ /*
+ * 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)
+ {
+ addOption = true;
+ }
+ if (addOption)
{
- menuItem = new JMenuItem("Reveal All");
+ 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)
- {
- groupName.setText("Name: " + sg.getName());
- groupName.setText("Edit name and description of current group.");
+ {
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
- if (sg.cs instanceof ZappoColourScheme)
- {
- zappoColour.setSelected(true);
- }
- else if (sg.cs instanceof TaylorColourScheme)
- {
- taylorColour.setSelected(true);
- }
- else if (sg.cs instanceof PIDColourScheme)
- {
- PIDColour.setSelected(true);
- }
- else if (sg.cs instanceof Blosum62ColourScheme)
- {
- BLOSUM62Colour.setSelected(true);
- }
- else if (sg.cs instanceof UserColourScheme)
- {
- userDefinedColour.setSelected(true);
- }
- else if (sg.cs instanceof HydrophobicColourScheme)
- {
- hydrophobicityColour.setSelected(true);
- }
- else if (sg.cs instanceof HelixColourScheme)
- {
- helixColour.setSelected(true);
- }
- else if (sg.cs instanceof StrandColourScheme)
- {
- strandColour.setSelected(true);
- }
- else if (sg.cs instanceof TurnColourScheme)
- {
- turnColour.setSelected(true);
- }
- else if (sg.cs instanceof BuriedColourScheme)
- {
- buriedColour.setSelected(true);
- }
- else if (sg.cs instanceof ClustalxColourScheme)
- {
- clustalColour.setSelected(true);
- }
- else if (sg.cs instanceof PurinePyrimidineColourScheme)
- {
- purinePyrimidineColour.setSelected(true);
- }
- /*
- * else if (sg.cs instanceof CovariationColourScheme) {
- * covariationColour.setSelected(true); }
- */
- else
- {
- noColourmenuItem.setSelected(true);
- }
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
- if (sg.cs != null && sg.cs.conservationApplied())
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
+
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
+ modifyPID.setEnabled(abovePIDColour.isSelected());
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+
SequenceI sqass = null;
- for (SequenceI sq : ap.av.getSequenceSelection())
+ for (SequenceI sq : alignPanel.av.getSequenceSelection())
{
- Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
- .getPDBId();
- if (pes != null)
+ Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
+ if (pes != null && pes.size() > 0)
{
+ reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
}
if (pdbe.size() > 0)
{
- final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]);
- final JMenuItem gpdbview;
- if (pdbe.size() == 1)
- {
- structureMenu.add(gpdbview = new JMenuItem("View structure for "
- + sqass.getDisplayId(false)));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem("View all "
- + pdbe.size() + " structures."));
- }
- gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
- gpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));
- }
- });
+ final PDBEntry[] pe = pdbe.values()
+ .toArray(new PDBEntry[pdbe.size()]),
+ pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
}
}
else
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText("Edit New Group");
- } else {
+ editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText("Edit Group");
+ editGroupMenu.setText(MessageManager.getString("action.edit_group"));
}
- if (seq == null)
+ if (!forIdPanel)
{
sequenceMenu.setVisible(false);
- structureMenu.setVisible(false);
+ chooseStructure.setVisible(false);
+ rnaStructureMenu.setVisible(false);
+ }
+
+ addLinksAndFeatures(seq, column);
+ }
+
+ /**
+ * Adds
+ * <ul>
+ * <li>configured sequence database links (ID panel popup menu)</li>
+ * <li>non-positional feature links (ID panel popup menu)</li>
+ * <li>positional feature links (alignment panel popup menu)</li>
+ * <li>feature details links (alignment panel popup menu)</li>
+ * </ul>
+ * 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<SequenceFeature> features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
+ {
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
}
- if (links != null && links.size() > 0)
+ addLinks(seq, features);
+
+ if (!forIdPanel)
{
+ addFeatureDetails(features, seq, column);
+ }
+ }
- JMenu linkMenu = new JMenu("Link");
- Vector linkset = new Vector();
- for (int i = 0; i < links.size(); i++)
+ /**
+ * 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 column
+ */
+ protected void addFeatureDetails(List<SequenceFeature> features,
+ final SequenceI seq, final 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)))
{
- String link = links.elementAt(i).toString();
- UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for URLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ int seqPos = sequence.findPosition(column);
+ mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
+ }
+ }
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- { urlLink.getTarget() });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
+ if (features.isEmpty() && mf == null)
+ {
+ /*
+ * no features to show at this position
+ */
+ return;
+ }
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
- true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label + "|" + urls[u],
- urls[u + 1]);
- }
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- }
- else
- {
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.addElement(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
- }
+ 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);
+ }
+
+ if (mf != null)
+ {
+ for (final SequenceFeature sf : mf.features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, mf);
}
- if (sequence != null)
+ }
+ }
+
+ /**
+ * 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)
+ {
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] beginRange = mf.getMappedPositions(start, start);
+ int[] endRange = mf.getMappedPositions(end, end);
+ if (beginRange == null || endRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = beginRange[0];
+ end = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
+ }
+ StringBuilder desc = new StringBuilder();
+ desc.append(sf.getType()).append(" ").append(String.valueOf(start));
+ if (start != end)
+ {
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ desc.append(" ");
+ description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * 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)
+ {
+ 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)
+ {
+ 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));
+
+ 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<SequenceFeature> 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);
+ add(linkMenu);
+ }
+ }
+ }
+
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ * <p>
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
+ *
+ * @param seq
+ * @return
+ */
+ protected List<SequenceI> getSequenceScope(SequenceI seq)
+ {
+ List<SequenceI> forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
+ {
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq);
+ }
+ return forSequences;
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1); // a, b, c
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
}
- }
+ });
+ showOrHideMenu.add(item);
}
- private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+ private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
{
// TODO: usability: thread off the generation of group url content so root
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
- JMenu[] linkMenus = new JMenu[]
- { null, new JMenu("IDS"), new JMenu("Sequences"),
- new JMenu("IDS and Sequences") }; // three types of url that might be
- // created.
+ JMenu groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ // three types of url that might be created.
+ JMenu[] linkMenus = new JMenu[] { null,
+ new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable commonDbrefs = new Hashtable();
+ Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
- .findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
// just collect ids from dataset sequence
// TODO: check if IDs collected from selecton group intersects with the
// current selection, too
{
sqi = sqi.getDatasetSequence();
}
- DBRefEntry[] dbr = sqi.getDBRef();
+ DBRefEntry[] dbr = sqi.getDBRefs();
if (dbr != null && dbr.length > 0)
{
for (int d = 0; d < dbr.length; d++)
{
String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
- Object[] sarray = (Object[]) commonDbrefs.get(src);
+ Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
sarray = new Object[2];
- sarray[0] = new int[]
- { 0 };
+ sarray[0] = new int[] { 0 };
sarray[1] = new String[seqs.length];
commonDbrefs.put(src, sarray);
if (((String[]) sarray[1])[sq] == null)
{
- if (!dbr[d].hasMap()
- || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ if (!dbr[d].hasMap() || (dbr[d].getMap()
+ .locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
((int[]) sarray[0])[0]++;
// now create group links for all distinct ID/sequence sets.
boolean addMenu = false; // indicates if there are any group links to give
// to user
- for (int i = 0; i < groupLinks.size(); i++)
+ for (String link : groupLinks)
{
- String link = groupLinks.elementAt(i).toString();
GroupUrlLink urlLink = null;
try
{
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
+ Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
;
if (!urlLink.isValid())
{
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ Cache.log.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 = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
// 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;
}
}
if (addMenu)
{
- groupLinksMenu = new JMenu("Group Links");
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
}
/**
- * add a show URL menu item to the given linkMenu
+ * DOCUMENT ME!
*
- * @param linkMenu
- * @param label
- * - menu label string
- * @param url
- * - url to open
+ * @throws Exception
+ * DOCUMENT ME!
*/
- private void addshowLink(JMenu linkMenu, String label, final String url)
+ private void jbInit() throws Exception
{
- JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + url);
- item.addActionListener(new java.awt.event.ActionListener()
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
+ groupName.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new Thread(new Runnable()
- {
-
- public void run()
- {
- showLink(url);
- }
-
- }).start();
+ groupName_actionPerformed();
}
});
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
- 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("open URL (" + urlgenerator.getUrl_prefix()
- + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
- // put
- // in
- // info
- // about
- // what
- // is
- // being
- // sent.
- item.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sequenceName = new JMenuItem(
+ MessageManager.getString("label.edit_name_description"));
+ sequenceName.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new Thread(new Runnable()
- {
-
- public void run()
- {
- try
- {
- showLink(urlgenerator.constructFrom(urlstub));
- } catch (UrlStringTooLongException e)
- {
- }
- }
-
- }).start();
+ sequenceName_actionPerformed();
}
});
-
- linkMenu.add(item);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @throws Exception
- * DOCUMENT ME!
- */
- private void jbInit() throws Exception
- {
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
- groupName.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem chooseAnnotations = new JMenuItem(
+ MessageManager.getString("action.choose_annotations"));
+ chooseAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- groupName_actionPerformed();
+ chooseAnnotations_actionPerformed(e);
}
});
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
- sequenceName.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sequenceDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceDetails.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sequenceName_actionPerformed();
+ createSequenceDetailsReport(new SequenceI[] { sequence });
}
});
- sequenceDetails.setText("Sequence Details ...");
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sequenceSelDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceSelDetails.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sequenceDetails_actionPerformed();
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
}
});
- sequenceSelDetails.setText("Sequence Details ...");
- sequenceSelDetails
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText("Create Group");
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createGroupMenuItem_actionPerformed();
}
});
- outline.setText("Border colour");
- outline.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem outline = new JMenuItem(
+ MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText("Nucleotide");
- nucleotideMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed();
- }
- });
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
- upperCase.setText("To Upper Case");
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- copy.setText("Copy");
+ JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
- lowerCase.setText("To Lower Case");
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- toggle.setText("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
- pdbFromFile.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- pdbFromFile_actionPerformed();
- }
- });
- enterPDB.setText("Enter PDB Id");
- enterPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- enterPDB_actionPerformed();
- }
- });
- discoverPDB.setText("Discover PDB ids");
- discoverPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- discoverPDB_actionPerformed();
- }
- });
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("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
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
- textColour.addActionListener(new ActionListener()
+ editGroupMenu.setText(MessageManager.getString("label.group"));
+ chooseStructure.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ chooseStructure.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
{
- textColour_actionPerformed();
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
}
});
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
+
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
+
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
+ JMenuItem editSequence = new JMenuItem(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
}
});
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
+ makeReferenceSeq.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ makeReferenceSeq_actionPerformed(actionEvent);
+
+ }
+ });
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
- this.add(structureMenu);
+ add(rnaStructureMenu);
+ 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
+ // groupMenu.add(chooseAnnotations);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(createGroupMenuItem);
groupMenu.add(unGroupMenuItem);
- groupMenu.add(jMenu1);
+ groupMenu.add(editGroupMenu);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
- colourMenu.add(textColour);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide())
- {
- colourMenu.add(purinePyrimidineColour);
- }
- // colourMenu.add(covariationColour);
- colourMenu.add(userDefinedColour);
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
+ sequenceMenu.add(makeReferenceSeq);
- while (userColours.hasMoreElements())
- {
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- }
- }
+ initColourMenu();
+ buildColourMenu();
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
- pdbMenu.add(pdbFromFile);
- pdbMenu.add(enterPDB);
- pdbMenu.add(discoverPDB);
- jMenu1.add(groupName);
- jMenu1.add(colourMenu);
- jMenu1.add(showBoxes);
- jMenu1.add(showText);
- jMenu1.add(showColourText);
- jMenu1.add(outline);
- jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
+ editGroupMenu.add(groupName);
+ editGroupMenu.add(colourMenu);
+ editGroupMenu.add(showBoxes);
+ editGroupMenu.add(showText);
+ editGroupMenu.add(showColourText);
+ editGroupMenu.add(outline);
+ editGroupMenu.add(displayNonconserved);
+ }
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed();
+ textColour_actionPerformed();
}
});
- abovePIDColour.setText("Above % Identity");
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
- userDefinedColour.setText("User Defined...");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ modifyPID_actionPerformed();
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- PIDColour_actionPerformed();
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
- BLOSUM62Colour.setText("BLOSUM62");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- BLOSUM62Colour_actionPerformed();
+ modifyConservation_actionPerformed();
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
- /*
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
-
- conservationMenuItem.setText("Conservation");
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
- }
-
- protected void sequenceSelectionDetails_actionPerformed()
- {
- createSequenceDetailsReport(ap.av.getSequenceSelection());
- }
-
- protected void sequenceDetails_actionPerformed()
- {
- createSequenceDetailsReport(new SequenceI[]
- { sequence });
}
- public void createSequenceDetailsReport(SequenceI[] sequences)
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- StringBuffer contents = new StringBuffer();
- for (SequenceI seq : sequences)
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
{
- contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
- + "</h2></p><p>");
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
- : null);
- contents.append("</p>");
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
}
- cap.setText("<html>" + contents.toString() + "</html>");
-
- Desktop.instance.addInternalFrame(cap, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 500, 400);
-
- }
-
- protected void showNonconserved_actionPerformed()
- {
- getGroup().setShowNonconserved(displayNonconserved.isSelected());
- refresh();
- }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
- /**
- * call to refresh view after settings change
- */
- void refresh()
- {
- ap.updateAnnotation();
- ap.paintAlignment(true);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
+ protected void modifyConservation_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
+ protected void modifyPID_actionPerformed()
{
- getGroup().cs = new ZappoColourScheme();
- refresh();
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+ SliderPanel.showPIDSlider();
+ }
}
/**
- * DOCUMENT ME!
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
*
- * @param e
- * DOCUMENT ME!
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
+ *
+ * @param menuItem
+ * @param forSequences
*/
- protected void taylorColour_actionPerformed()
+ protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+ List<SequenceI> forSequences)
{
- getGroup().cs = new TaylorColourScheme();
- refresh();
+ menuItem.setEnabled(false);
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
}
/**
- * DOCUMENT ME!
+ * Add annotations to the sequences and to the alignment.
*
- * @param e
- * DOCUMENT ME!
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
*/
- protected void hydrophobicityColour_actionPerformed()
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- getGroup().cs = new HydrophobicColourScheme();
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
refresh();
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
+ protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
- getGroup().cs = new HelixColourScheme();
+ if (!ap.av.getAlignment().hasSeqrep())
+ {
+ // initialise the display flags so the user sees something happen
+ ap.av.setDisplayReferenceSeq(true);
+ ap.av.setColourByReferenceSeq(true);
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == sequence)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ }
refresh();
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
+ protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
- getGroup().cs = new StrandColourScheme();
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
+
+ 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)
+ {
+ markedPopup = true;
+ }
+ 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
+ else if (!markedPopup && sequence != null)
+ {
+ inserts.or(sequence.getInsertionsAsBits());
+
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
+ protected void sequenceSelectionDetails_actionPerformed()
{
- getGroup().cs = new TurnColourScheme();
- refresh();
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
+ public void createSequenceDetailsReport(SequenceI[] sequences)
{
- getGroup().cs = new BuriedColourScheme();
- refresh();
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuilder contents = new StringBuilder(128);
+ for (SequenceI seq : sequences)
+ {
+ contents.append("<p><h2>" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "</h2></p><p>");
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
+ contents.append("</p>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
+ Desktop.addInternalFrame(cap,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
+
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
+ protected void showNonconserved_actionPerformed()
{
- getGroup().cs = new NucleotideColourScheme();
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
refresh();
}
- protected void purinePyrimidineColour_actionPerformed()
+ /**
+ * call to refresh view after settings change
+ */
+ void refresh()
{
- getGroup().cs = new PurinePyrimidineColourScheme();
- refresh();
+ ap.updateAnnotation();
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
/*
/**
* DOCUMENT ME!
*
+ * @param selected
+ *
* @param e
* DOCUMENT ME!
*/
- protected void abovePIDColour_actionPerformed()
+ public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (abovePIDColour.isSelected())
+ if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup().getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
- }
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
}
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void PIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
+ modifyPID.setEnabled(selected);
refresh();
}
/**
- * DOCUMENT ME!
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
*
* @param e
- * DOCUMENT ME!
*/
- protected void noColourmenuItem_actionPerformed()
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
{
- getGroup().cs = null;
- refresh();
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
}
/**
* @param e
* DOCUMENT ME!
*/
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (conservationMenuItem.isSelected())
+ if (selected)
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(ap.av
- .getHiddenRepSequences()), sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
-
sg.cs.setConservation(c);
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
}
-
- refresh();
- }
-
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = getGroup();
- if (sg == null)
- {
- return;
- }
-
- AnnotationColourGradient acg = new AnnotationColourGradient(
- sequence.getAnnotation()[0], null,
- AnnotationColourGradient.NO_THRESHOLD);
-
- acg.setPredefinedColours(true);
- sg.cs = acg;
+ modifyConservation.setEnabled(selected);
refresh();
}
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " Group Name ",
- "Group Description ", "Edit Group Name/Description",
+ sg.getDescription(),
+ " " + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
}
/**
- * 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(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description",
+ 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)
+ String name = dialog.getName();
+ if (name != null)
{
- if (dialog.getName().indexOf(" ") > -1)
+ if (name.indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ 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());
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
ap.av.setSelectionGroup(null);
refresh();
}
+
void createGroupMenuItem_actionPerformed()
{
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
refresh();
}
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
refresh();
}
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[]
- { sequence });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(sequence, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- // refresh(); TODO: ? needed ?
- ap.av.sendSelection();
+ ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
- sg.getEndRes() + 1);
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
if (source == toggle)
{
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- "Alignment output - " + 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
// or we simply trust the user wants
// wysiwig behaviour
- SequenceGroup sg = ap.av.getSelectionGroup();
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
- omitHidden = ap.av.getViewAsString(true);
- Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
- {
- for (int i = 0; i < nala.length; i++)
- {
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
- }
- }
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
- }
-
- public void pdbFromFile_actionPerformed()
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file for "
- + sequence.getDisplayId(false));
- chooser.setToolTipText("Load a PDB file and associate it with sequence '"
- + sequence.getDisplayId(false) + "'");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true);
- }
-
- }
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
-
- if (id != null && id.length() > 0)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
- }
- }
-
- public void discoverPDB_actionPerformed()
- {
-
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- Thread discpdb = new Thread(new Runnable()
- {
- public void run()
- {
-
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
- }
-
- });
- discpdb.start();
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ int gSize = sg.getSize();
for (int i = 0; i < gSize; i++)
{
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
- features[rsize] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+ features.add(new SequenceFeature(null, null, start, end, null));
}
}
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
- {
- ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
+ {
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .amendFeatures(seqs, features, true, ap))
+ {
+ ap.alignFrame.setShowSeqFeatures(true);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
+ }
}
}
}
}
- 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)
- sequence = (Sequence) sg.getSequenceAt(0);
+ if (seq == null)
+ {
+ seq = sg.getSequenceAt(0);
+ }
EditNameDialog dialog = new EditNameDialog(
- sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, "Edit Sequence ", null,
- "Edit Sequence", ap.alignFrame);
+ seq.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("Edit Sequences",
- EditCommand.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ 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());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
+ /**
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
+ *
+ * @return
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ SequenceGroup sg = getGroup();
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, ap.av, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
+
+ refresh();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff