X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=7ab60222127c17c8920b5d8cb8e47f54e78e12ea;hb=a82f1e47eef845557e95e61116e6b34bdd3242f3;hp=ad3d6af347997305f9483e80c07b1b5dbf1e490d;hpb=e373651097c72eb6c9ca6009fb70d47341e8f405;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ad3d6af..8c87aa0 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,113 +20,86 @@
*/
package jalview.gui;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-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.JOptionPane;
-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.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.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
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;
import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.util.UrlLink;
+import java.awt.Color;
+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;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.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
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
- private static final String ALL_ANNOTATIONS = "All";
-
- private static final String COMMA = ",";
-
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem annotationColour;
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
AlignmentPanel ap;
@@ -137,7 +110,7 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceDetails = new JMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
-
+
JMenuItem makeReferenceSeq = new JMenuItem();
JMenuItem chooseAnnotations = new JMenuItem();
@@ -150,8 +123,6 @@ public class PopupMenu extends JPopupMenu
JMenuItem outline = new JMenuItem();
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
-
JMenu colourMenu = new JMenu();
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
@@ -176,12 +147,6 @@ public class PopupMenu extends JPopupMenu
JMenu pdbMenu = new JMenu();
- JMenuItem pdbFromFile = new JMenuItem();
-
- JMenuItem enterPDB = new JMenuItem();
-
- JMenuItem discoverPDB = new JMenuItem();
-
JMenu outputMenu = new JMenu();
JMenu seqShowAnnotationsMenu = new JMenu();
@@ -200,11 +165,12 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceFeature = new JMenuItem();
+
JMenuItem textColour = new JMenuItem();
JMenu jMenu1 = new JMenu();
- JMenuItem proteinStructureMenu = new JMenuItem();
+ JMenuItem pdbStructureDialog = new JMenuItem();
JMenu rnaStructureMenu = new JMenu();
@@ -215,27 +181,215 @@ public class PopupMenu extends JPopupMenu
JMenuItem hideInsertions = 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
+ */
+ static JMenu buildLinkMenu(final SequenceI seq,
+ List features)
+ {
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+
+ List 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> 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;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
* Creates a new PopupMenu object.
*
* @param ap
- * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * @param features
+ * non-positional features (for seq not null), or positional features
+ * at residue (for seq equal to null)
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq,
+ List features)
{
- this(ap, seq, links, null);
+ this(ap, seq, features, null);
}
/**
+ * Constructor
*
- * @param ap
+ * @param alignPanel
* @param seq
- * @param links
+ * the sequence under the cursor if in the Id panel, null if in the
+ * sequence panel
+ * @param features
+ * non-positional features if in the Id panel, features at the
+ * clicked residue if in the sequence panel
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
- Vector links, Vector groupLinks)
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List features, List groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
@@ -243,32 +397,14 @@ public class PopupMenu extends JPopupMenu
//
// If from the IDPanel, we must display the sequence menu
// ////////////////////////////////////////////////////////
- this.ap = ap;
+ 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(RNAInteractionColour);
-
- 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)
@@ -285,8 +421,9 @@ public class PopupMenu extends JPopupMenu
* '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 = (seq == null
+ ? Collections. emptyList() : Arrays.asList(seq));
+
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
@@ -295,9 +432,9 @@ public class PopupMenu extends JPopupMenu
/*
* And repeat for the current selection group (if there is one):
*/
- final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- . emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List selectedGroup = (alignPanel.av.getSelectionGroup() == null
+ ? Collections. emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -315,24 +452,29 @@ public class PopupMenu extends JPopupMenu
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- if (seq == ap.av.getAlignment().getSeqrep())
+ if (seq == alignPanel.av.getAlignment().getSeqrep())
+ {
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.unmark_as_reference"));
+ }
+ else
{
- makeReferenceSeq.setText("Unmark representative");
- } else {
- makeReferenceSeq.setText("Mark as representative");
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.set_as_reference"));
}
- if (!ap.av.getAlignment().isNucleotide())
+ if (!alignPanel.av.getAlignment().isNucleotide())
{
remove(rnaStructureMenu);
}
else
{
+ int origCount = rnaStructureMenu.getItemCount();
/*
* 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)
{
@@ -347,12 +489,12 @@ public class PopupMenu extends JPopupMenu
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_structure_line", new Object[]
{ aa.label }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
@@ -375,24 +517,58 @@ public class PopupMenu extends JPopupMenu
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_sequence_name", new Object[]
{ seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
- new AppVarna(seq, aa, ap);
+ new AppVarna(seq, aa, alignPanel);
}
});
rnaStructureMenu.add(menuItem);
}
}
}
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
+ }
+
+ 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 java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -402,13 +578,13 @@ public class PopupMenu extends JPopupMenu
});
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[]
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
{ seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -419,12 +595,12 @@ public class PopupMenu extends JPopupMenu
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"));
@@ -433,10 +609,10 @@ public class PopupMenu extends JPopupMenu
@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();
}
}
});
@@ -444,9 +620,20 @@ public class PopupMenu extends JPopupMenu
}
}
}
- // 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(
MessageManager.getString("action.reveal_all"));
@@ -455,93 +642,44 @@ public class PopupMenu extends JPopupMenu
@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(MessageManager.formatMessage("label.name_param",
- new Object[]
- { sg.getName() }));
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);
- }
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
- /*
- * else if (sg.cs instanceof CovariationColourScheme) {
- * covariationColour.setSelected(true); }
- */
- else
- {
- noColourmenuItem.setSelected(true);
- }
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
- if (sg.cs != null && sg.cs.conservationApplied())
+ 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());
@@ -552,11 +690,13 @@ public class PopupMenu extends JPopupMenu
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().getPDBId();
+ Vector pes = sq.getDatasetSequence().getAllPDBEntries();
if (pes != null && pes.size() > 0)
{
reppdb.put(pes.get(0).getId(), pes.get(0));
@@ -572,9 +712,9 @@ public class PopupMenu extends JPopupMenu
}
if (pdbe.size() > 0)
{
- final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
+ final PDBEntry[] pe = pdbe.values()
+ .toArray(new PDBEntry[pdbe.size()]),
+ pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
}
}
@@ -600,122 +740,113 @@ public class PopupMenu extends JPopupMenu
if (seq == null)
{
sequenceMenu.setVisible(false);
- proteinStructureMenu.setVisible(false);
+ pdbStructureDialog.setVisible(false);
rnaStructureMenu.setVisible(false);
}
- if (links != null && links.size() > 0)
+ addLinks(seq, features);
+
+ if (seq == null)
{
+ addFeatureDetails(features);
+ }
+ }
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Vector linkset = new Vector();
- for (int i = 0; i < links.size(); i++)
+ /**
+ * Add a link to show feature details for each sequence feature
+ *
+ * @param features
+ */
+ protected void addFeatureDetails(List features)
+ {
+ if (features == null || features.isEmpty())
+ {
+ return;
+ }
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
+
+ for (final SequenceFeature sf : features)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ String desc = null;
+ if (start == end)
{
- 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())
+ desc = String.format("%s %d", sf.getType(), start);
+ }
+ else
+ {
+ 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)
{
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
+ desc = desc + " " + description.substring(0, 12) + "..";
}
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
+ else
{
-
- // 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 (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]);
- }
- }
- }
- }
+ desc = desc + " " + description;
}
- else
+ 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)
{
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.addElement(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
+ showFeatureDetails(sf);
}
- }
+ });
+ details.add(item);
+ }
+ }
+
+ /**
+ * Opens a panel showing a text report of feature dteails
+ *
+ * @param sf
+ */
+ protected void showFeatureDetails(SequenceFeature sf)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collaps :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+ cap.setText(sf.getDetailsReport());
+
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.feature_details"), 500, 500);
+ }
+
+ /**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * When seq is not null, these are links for the sequence id, which may be to
+ * external web sites for the sequence accession, and/or links embedded in
+ * non-positional features. When seq is null, only links embedded in the
+ * provided features are added. If no links are found, the menu is not added.
+ *
+ * @param seq
+ * @param features
+ */
+ void addLinks(final SequenceI seq, List features)
+ {
+ JMenu linkMenu = buildLinkMenu(seq, features);
+
+ // only add link menu if it has entries
+ if (linkMenu.getItemCount() > 0)
+ {
if (sequence != null)
{
sequenceMenu.add(linkMenu);
@@ -748,8 +879,11 @@ public class PopupMenu extends JPopupMenu
showMenu.removeAll();
hideMenu.removeAll();
- final List all = Arrays.asList(ALL_ANNOTATIONS);
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
@@ -764,19 +898,17 @@ public class PopupMenu extends JPopupMenu
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map>> shownTypes = new LinkedHashMap>>();
- Map>> hiddenTypes = new LinkedHashMap>>();
- AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
- hiddenTypes,
- AlignmentAnnotationUtils.asList(annotations),
- forSequences);
+ Map>> shownTypes = new LinkedHashMap<>();
+ Map>> hiddenTypes = new LinkedHashMap<>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
for (String calcId : hiddenTypes.keySet())
{
for (List type : hiddenTypes.get(calcId))
{
- addAnnotationTypeToShowHide(showMenu, forSequences,
- calcId, type, false, true);
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
}
}
// grey out 'show annotations' if none are hidden
@@ -786,8 +918,8 @@ public class PopupMenu extends JPopupMenu
{
for (List type : shownTypes.get(calcId))
{
- addAnnotationTypeToShowHide(hideMenu, forSequences,
- calcId, type, false, false);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
}
}
// grey out 'hide annotations' if none are shown
@@ -843,20 +975,20 @@ public class PopupMenu extends JPopupMenu
label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
- forSequences, allTypes, actionIsShow);
+ 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 groupLinks)
{
// TODO: usability: thread off the generation of group url content so root
@@ -865,24 +997,20 @@ public class PopupMenu extends JPopupMenu
// ID/regex match URLs
groupLinksMenu = new JMenu(
MessageManager.getString("action.group_link"));
- JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")),
+ // 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")) }; // three
- // types
- // of url
- // that
- // might
- // be
- // created.
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable commonDbrefs = new Hashtable();
+ Hashtable commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
- .findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
// just collect ids from dataset sequence
// TODO: check if IDs collected from selecton group intersects with the
// current selection, too
@@ -891,18 +1019,17 @@ public class PopupMenu extends JPopupMenu
{
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);
@@ -910,8 +1037,8 @@ public class PopupMenu extends JPopupMenu
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]++;
@@ -923,30 +1050,28 @@ public class PopupMenu extends JPopupMenu
// 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)
{
@@ -985,9 +1110,10 @@ public class PopupMenu extends JPopupMenu
int type = urlLink.getGroupURLType() & 3;
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label
- + (((type & 1) == 1) ? ("("
- + (usingNames ? "Names" : ltarget) + ")") : ""),
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
urlLink, urlset);
addMenu = true;
}
@@ -1010,89 +1136,6 @@ public class PopupMenu extends JPopupMenu
}
/**
- * 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 java.awt.event.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 java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- try
- {
- showLink(urlgenerator.constructFrom(urlstub));
- } catch (UrlStringTooLongException e)
- {
- }
- }
-
- }).start();
- }
- });
-
- linkMenu.add(item);
- }
-
- /**
* DOCUMENT ME!
*
* @throws Exception
@@ -1100,10 +1143,9 @@ public class PopupMenu extends JPopupMenu
*/
private void jbInit() throws Exception
{
- groupMenu.setText(MessageManager.getString("label.group"));
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
- groupName.addActionListener(new java.awt.event.ActionListener()
+ groupName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -1112,9 +1154,9 @@ public class PopupMenu extends JPopupMenu
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager
- .getString("label.edit_name_description"));
- sequenceName.addActionListener(new java.awt.event.ActionListener()
+ sequenceName.setText(
+ MessageManager.getString("label.edit_name_description"));
+ sequenceName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -1122,9 +1164,9 @@ public class PopupMenu extends JPopupMenu
sequenceName_actionPerformed();
}
});
- chooseAnnotations.setText(MessageManager
- .getString("label.choose_annotations") + "...");
- chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+ chooseAnnotations
+ .setText(MessageManager.getString("action.choose_annotations"));
+ chooseAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -1132,9 +1174,9 @@ public class PopupMenu extends JPopupMenu
chooseAnnotations_actionPerformed(e);
}
});
- sequenceDetails.setText(MessageManager
- .getString("label.sequence_details") + "...");
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ sequenceDetails
+ .setText(MessageManager.getString("label.sequence_details"));
+ sequenceDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -1142,21 +1184,20 @@ public class PopupMenu extends JPopupMenu
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager
- .getString("label.sequence_details") + "...");
sequenceSelDetails
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
+ .setText(MessageManager.getString("label.sequence_details"));
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
+
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ unGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -1164,38 +1205,26 @@ public class PopupMenu extends JPopupMenu
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager
- .getString("action.create_group"));
createGroupMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
-
- outline.setText(MessageManager.getString("action.border_colour"));
- outline.addActionListener(new java.awt.event.ActionListener()
+ .setText(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- outline_actionPerformed();
+ createGroupMenuItem_actionPerformed();
}
});
- nucleotideMenuItem
- .setText(MessageManager.getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(new ActionListener()
+
+ outline.setText(MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- nucleotideMenuItem_actionPerformed();
+ outline_actionPerformed();
}
});
- colourMenu.setText(MessageManager.getString("label.group_colour"));
showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
@@ -1225,8 +1254,8 @@ public class PopupMenu extends JPopupMenu
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager
- .getString("label.show_non_conversed"));
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
@@ -1282,48 +1311,18 @@ public class PopupMenu extends JPopupMenu
changeCase(e);
}
});
- pdbMenu.setText(MessageManager
- .getString("label.associate_structure_with_sequence"));
- pdbFromFile.setText(MessageManager.getString("label.from_file"));
- pdbFromFile.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- pdbFromFile_actionPerformed();
- }
- });
-
- enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
- enterPDB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- enterPDB_actionPerformed();
- }
- });
- discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
- discoverPDB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- discoverPDB_actionPerformed();
- }
- });
- outputMenu.setText(MessageManager.getString("label.out_to_textbox")
- + "...");
- seqShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- seqHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- groupShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- groupHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- sequenceFeature.setText(MessageManager
- .getString("label.create_sequence_feature"));
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ sequenceFeature.setText(
+ MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
@@ -1332,25 +1331,15 @@ public class PopupMenu extends JPopupMenu
sequenceFeature_actionPerformed();
}
});
- textColour.setText(MessageManager.getString("label.text_colour"));
- textColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed();
- }
- });
jMenu1.setText(MessageManager.getString("label.group"));
- proteinStructureMenu.setText(MessageManager
- .getString("label.view_protein_structure"));
- proteinStructureMenu.addActionListener(new ActionListener()
+ pdbStructureDialog.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- SequenceI[] selectedSeqs = new SequenceI[]
- { sequence };
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
if (ap.av.getSelectionGroup() != null)
{
selectedSeqs = ap.av.getSequenceSelection();
@@ -1359,12 +1348,12 @@ public class PopupMenu extends JPopupMenu
}
});
- rnaStructureMenu.setText(MessageManager
- .getString("label.view_rna_structure"));
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence")
- + "...");
+ editSequence.setText(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@Override
@@ -1373,19 +1362,20 @@ public class PopupMenu extends JPopupMenu
editSequence_actionPerformed(actionEvent);
}
});
- makeReferenceSeq.setText(MessageManager
- .getString("label.mark_as_representative"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent actionEvent)
{
makeReferenceSeq_actionPerformed(actionEvent);
-
+
}
});
- hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
+ hideInsertions
+ .setText(MessageManager.getString("label.hide_insertions"));
hideInsertions.addActionListener(new ActionListener()
{
@@ -1395,18 +1385,13 @@ public class PopupMenu extends JPopupMenu
hideInsertions_actionPerformed(e);
}
});
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
+
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
add(rnaStructureMenu);
- add(proteinStructureMenu);
- if (sequence!=null)
+ add(pdbStructureDialog);
+ if (sequence != null)
{
add(hideInsertions);
}
@@ -1432,62 +1417,20 @@ public class PopupMenu extends JPopupMenu
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
- 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())
- {
- // JBPNote - commented since the colourscheme isn't functional
- colourMenu.add(purinePyrimidineColour);
- }
- colourMenu.add(userDefinedColour);
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
- while (userColours.hasMoreElements())
- {
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- }
- }
+ initColourMenu();
+ buildColourMenu();
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
- pdbMenu.add(pdbFromFile);
// 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);
- pdbMenu.add(enterPDB);
- pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
@@ -1495,160 +1438,128 @@ public class PopupMenu extends JPopupMenu
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
+ }
- clustalColour.setText(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.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)
{
- turnColour_actionPerformed();
+ textColour_actionPerformed();
}
});
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
- abovePIDColour.setText(MessageManager
- .getString("label.above_identity_percentage"));
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_actionPerformed();
+ modifyPID_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.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)
{
- PIDColour_actionPerformed();
+ modifyConservation_actionPerformed();
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ }
+
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
- /*
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
- conservationMenuItem.setText(MessageManager
- .getString("label.conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ 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();
+ }
}
/**
@@ -1664,8 +1575,8 @@ public class PopupMenu extends JPopupMenu
* @param menuItem
* @param forSequences
*/
- protected void configureReferenceAnnotationsMenu(
- JMenuItem menuItem, List forSequences)
+ protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+ List forSequences)
{
menuItem.setEnabled(false);
@@ -1673,11 +1584,11 @@ public class PopupMenu extends JPopupMenu
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- Map tipEntries = new TreeMap();
- final Map> candidates = new LinkedHashMap>();
+ SortedMap tipEntries = new TreeMap<>();
+ final Map> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
- AlignmentUtils.findAddableReferenceAnnotations(forSequences,
- tipEntries, candidates, al);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
@@ -1749,18 +1660,41 @@ public class PopupMenu extends JPopupMenu
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
- if (sequence != null)
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
+
+ boolean markedPopup = false;
+ // mark inserts in current selection
+ if (ap.av.getSelectionGroup() != null)
{
- ColumnSelection cs = ap.av.getColumnSelection();
- if (cs == 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())
{
- cs = new ColumnSelection();
+ if (sq == sequence)
+ {
+ markedPopup = true;
+ }
+ inserts.and(sq.getInsertionsAsBits());
}
- cs.hideInsertionsFor(sequence);
- ap.av.setColumnSelection(cs);
+ 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();
}
+
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
@@ -1768,42 +1702,33 @@ public class PopupMenu extends JPopupMenu
protected void sequenceDetails_actionPerformed()
{
- createSequenceDetailsReport(new SequenceI[]
- { sequence });
+ createSequenceDetailsReport(new SequenceI[] { sequence });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- StringBuffer contents = new StringBuffer();
+ StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
- contents.append(""
- + MessageManager
- .formatMessage(
- "label.create_sequence_details_report_annotation_for",
- new Object[]
- { seq.getDisplayId(true) }) + "
");
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.getSeqPanel().seqCanvas.fr != null) ? ap
- .getSeqPanel().seqCanvas.fr
- .getMinMax()
- : null);
+ contents.append("
" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "
");
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("
");
}
cap.setText("" + contents.toString() + "");
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequence_details_for",
- (sequences.length == 1 ? new Object[]
- { sequences[0].getDisplayId(true) } : new Object[]
- { MessageManager.getString("label.selection") })), 500, 400);
+ 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);
}
@@ -1819,126 +1744,13 @@ public class PopupMenu extends JPopupMenu
void refresh()
{
ap.updateAnnotation();
- ap.paintAlignment(true);
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void purinePyrimidineColour_actionPerformed()
- {
- getGroup().cs = new PurinePyrimidineColourScheme();
- refresh();
- }
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1946,10 +1758,12 @@ public class PopupMenu extends JPopupMenu
/**
* 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)
@@ -1957,14 +1771,14 @@ public class PopupMenu extends JPopupMenu
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.isIgnoreGapsConsensus());
@@ -1974,36 +1788,14 @@ public class PopupMenu extends JPopupMenu
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
}
+ modifyPID.setEnabled(selected);
refresh();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getSource().equals(userDefinedColour))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
- }
- refresh();
- }
-
- /**
* Open a panel where the user can choose which types of sequence annotation
* to show or hide.
*
@@ -2021,54 +1813,7 @@ public class PopupMenu extends JPopupMenu
* @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));
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
@@ -2076,45 +1821,28 @@ public class PopupMenu extends JPopupMenu
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();
}
@@ -2130,8 +1858,8 @@ public class PopupMenu extends JPopupMenu
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " "
- + MessageManager.getString("label.group_name") + " ",
+ sg.getDescription(),
+ " " + MessageManager.getString("label.group_name") + " ",
MessageManager.getString("label.group_description") + " ",
MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
@@ -2176,8 +1904,8 @@ public class PopupMenu extends JPopupMenu
" " + MessageManager.getString("label.sequence_name")
+ " ",
MessageManager.getString("label.sequence_description") + " ",
- MessageManager
- .getString("label.edit_sequence_name_description"),
+ MessageManager.getString(
+ "label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -2189,24 +1917,22 @@ public class PopupMenu extends JPopupMenu
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane
- .showMessageDialog(
- ap,
- MessageManager
- .getString("label.spaces_converted_to_backslashes"),
- MessageManager
- .getString("label.no_spaces_allowed_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);
}
sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
@@ -2288,47 +2014,9 @@ public class PopupMenu extends JPopupMenu
refresh();
}
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.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 = sg.getSequences().toArray(new SequenceI[gsize]);
-
- ap.av.hideSequence(hseqs);
- // refresh(); TODO: ? needed ?
- ap.av.sendSelection();
+ ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
@@ -2349,8 +2037,7 @@ public class PopupMenu extends JPopupMenu
if (sg != null)
{
List startEnd = ap.av.getVisibleRegionBoundaries(
- sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
@@ -2377,8 +2064,8 @@ public class PopupMenu extends JPopupMenu
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
@@ -2387,8 +2074,8 @@ public class PopupMenu extends JPopupMenu
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
@@ -2397,69 +2084,10 @@ public class PopupMenu extends JPopupMenu
// or we simply trust the user wants
// wysiwig behaviour
- cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
- ap, true));
- }
-
- 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(MessageManager.formatMessage(
- "label.select_pdb_file_for", new Object[]
- { sequence.getDisplayId(false) }));
- chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new Object[]
- { 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,
- Desktop.instance);
- }
-
- }
-
-
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"),
- MessageManager.getString("label.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()
- {
- @Override
- 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()
@@ -2470,33 +2098,37 @@ public class PopupMenu extends JPopupMenu
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ List seqs = new ArrayList<>();
+ List 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.getSeqPanel().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
+ }
}
}
@@ -2541,8 +2173,8 @@ public class PopupMenu extends JPopupMenu
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null,
- MessageManager.getString("label.edit_sequence"), null,
+ sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null,
MessageManager.getString("label.edit_sequence"),
ap.alignFrame);
@@ -2550,17 +2182,45 @@ public class PopupMenu extends JPopupMenu
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- Action.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ Action.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
+ /**
+ * 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();
+ }
+
}