X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=696f03db15a06b49d4ad2a1a71e9fe640195aa88;hb=94379c810f9115b8564ee7bac46ed119218d5fd2;hp=4d9dc4d670e789030d7ec3a79373d2ed77f3fbf1;hpb=74b531f56bbaad5c5e06a4744980256fe8110923;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4d9dc4d..696f03d 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -46,33 +46,36 @@ import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.JalviewColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; -import jalview.util.DBRefUtils; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; import java.awt.Color; +import java.awt.Component; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.ArrayList; import java.util.Arrays; +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; @@ -81,7 +84,6 @@ 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; @@ -121,9 +123,13 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem RNAInteractionColour; JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -151,8 +157,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -241,28 +245,11 @@ public class PopupMenu extends JPopupMenu this.ap = ap; 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 (String ff : FileFormat.getWritableFormats()) + for (String ff : FileFormat.getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -346,7 +333,7 @@ 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) @@ -374,7 +361,7 @@ 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) @@ -395,7 +382,7 @@ public class PopupMenu extends JPopupMenu 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) @@ -411,7 +398,7 @@ public class PopupMenu extends JPopupMenu 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) @@ -480,63 +467,7 @@ public class PopupMenu extends JPopupMenu 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); - } + setColourSelected(sg.cs); if (sg.cs != null && sg.cs.conservationApplied()) { @@ -619,7 +550,8 @@ public class PopupMenu extends JPopupMenu void addFeatureLinks(final SequenceI seq, List links) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - List linkset = new ArrayList(); + Map> linkset = new LinkedHashMap>(); + for (String link : links) { UrlLink urlLink = null; @@ -631,97 +563,28 @@ public class PopupMenu extends JPopupMenu Cache.log.error("Exception for URLLink '" + link + "'", foo); continue; } - ; + if (!urlLink.isValid()) { Cache.log.error(urlLink.getInvalidMessage()); continue; } - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - // collect matching db-refs - DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(), - new String[] { urlLink.getTarget() }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } + urlLink.createLinksFromSeq(seq, linkset); + } - 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 URL - 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.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); - } - } - } - } - } - if (id != null) - { - // create Bare ID link for this URL - 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.add(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.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - } - else - { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.add(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } - } + addshowLinks(linkMenu, linkset.values()); + + // disable link menu if there are no valid entries + if (linkMenu.getItemCount() > 0) + { + linkMenu.setEnabled(true); } + else + { + linkMenu.setEnabled(false); + } + if (sequence != null) { sequenceMenu.add(linkMenu); @@ -730,8 +593,11 @@ public class PopupMenu extends JPopupMenu { 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 @@ -847,7 +713,7 @@ 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) @@ -930,8 +796,7 @@ public class PopupMenu extends JPopupMenu urlLink = new GroupUrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for GroupURLLink '" + link - + "'", foo); + Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; @@ -1007,6 +872,15 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, Collection> linkset) + { + for (List linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3)); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1021,7 +895,7 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_param", new Object[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1098,7 +972,7 @@ public class PopupMenu extends JPopupMenu { 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) @@ -1109,7 +983,7 @@ 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.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1119,7 +993,7 @@ public class PopupMenu extends JPopupMenu }); chooseAnnotations.setText(MessageManager .getString("action.choose_annotations")); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1129,7 +1003,7 @@ public class PopupMenu extends JPopupMenu }); sequenceDetails.setText(MessageManager .getString("label.sequence_details")); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1140,7 +1014,7 @@ public class PopupMenu extends JPopupMenu sequenceSelDetails.setText(MessageManager .getString("label.sequence_details")); sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() +.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1151,7 +1025,7 @@ public class PopupMenu extends JPopupMenu PIDColour.setFocusPainted(false); unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1162,7 +1036,7 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem.setText(MessageManager .getString("action.create_group")); createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() +.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1172,7 +1046,7 @@ public class PopupMenu extends JPopupMenu }); outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + outline.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1180,17 +1054,6 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem - .setText(MessageManager.getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - nucleotideMenuItem_actionPerformed(); - } - }); - colourMenu.setText(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() @@ -1221,7 +1084,7 @@ public class PopupMenu extends JPopupMenu } }); displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1297,15 +1160,6 @@ 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")); pdbStructureDialog.setText(MessageManager .getString("label.show_pdbstruct_dialog")); @@ -1397,49 +1251,9 @@ 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(); + buildColourMenu(); - 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); - } - } - - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1457,8 +1271,27 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); + + initColourMenu(); + } + + /** + * 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) + { + textColour_actionPerformed(); + } + }); noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + noColourmenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1468,8 +1301,9 @@ public class PopupMenu extends JPopupMenu }); clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() + .getString("label.colourScheme_clustal")); + clustalColour.setName(JalviewColourScheme.Clustal.toString()); + clustalColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1477,8 +1311,10 @@ public class PopupMenu extends JPopupMenu clustalColour_actionPerformed(); } }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() + zappoColour.setText(MessageManager + .getString("label.colourScheme_zappo")); + zappoColour.setName(JalviewColourScheme.Zappo.toString()); + zappoColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1486,8 +1322,10 @@ public class PopupMenu extends JPopupMenu zappoColour_actionPerformed(); } }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() + taylorColour.setText(MessageManager + .getString("label.colourScheme_taylor")); + taylorColour.setName(JalviewColourScheme.Taylor.toString()); + taylorColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1496,18 +1334,21 @@ public class PopupMenu extends JPopupMenu } }); hydrophobicityColour.setText(MessageManager - .getString("label.hydrophobicity")); + .getString("label.colourScheme_hydrophobic")); 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() + .setName(JalviewColourScheme.Hydrophobic.toString()); + hydrophobicityColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); + helixColour.setText(MessageManager + .getString("label.colourScheme_helix_propensity")); + helixColour.setName(JalviewColourScheme.Helix.toString()); + helixColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1516,8 +1357,9 @@ public class PopupMenu extends JPopupMenu } }); strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() + .getString("label.colourScheme_strand_propensity")); + strandColour.setName(JalviewColourScheme.Strand.toString()); + strandColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1525,8 +1367,10 @@ public class PopupMenu extends JPopupMenu strandColour_actionPerformed(); } }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() + turnColour.setText(MessageManager + .getString("label.colourScheme_turn_propensity")); + turnColour.setName(JalviewColourScheme.Turn.toString()); + turnColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1534,8 +1378,10 @@ public class PopupMenu extends JPopupMenu turnColour_actionPerformed(); } }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + buriedColour.setText(MessageManager + .getString("label.colourScheme_buried_index")); + buriedColour.setName(JalviewColourScheme.Buried.toString()); + buriedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1544,8 +1390,8 @@ public class PopupMenu extends JPopupMenu } }); abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + .getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1555,7 +1401,7 @@ public class PopupMenu extends JPopupMenu }); userDefinedColour.setText(MessageManager .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + userDefinedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1564,8 +1410,10 @@ public class PopupMenu extends JPopupMenu } }); PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() +.setText(MessageManager + .getString("label.colourScheme_%_identity")); + PIDColour.setName(JalviewColourScheme.PID.toString()); + PIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1573,8 +1421,11 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + BLOSUM62Colour +.setText(MessageManager + .getString("label.colourScheme_blosum62")); + BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString()); + BLOSUM62Colour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1582,38 +1433,162 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + nucleotideColour.setText(MessageManager + .getString("label.colourScheme_nucleotide")); + nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString()); + nucleotideColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(); + } + }); purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + .getString("label.colourScheme_purine/pyrimidine")); + purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine + .toString()); + purinePyrimidineColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + + tcoffeeColour.setText(MessageManager + .getString("label.colourScheme_t-coffee_scores")); + tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString()); + tcoffeeColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + tcoffeeColorScheme_actionPerformed(); + } + }); /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * covariationColour.addActionListener(new ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); + .getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); } }); } /** + * 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 = getGroup(); + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + // in Java 8, isApplicableTo can be a static method on the interface + clustalColour.setEnabled(new ClustalxColourScheme(sg, null) + .isApplicableTo(sg)); + colourMenu.add(BLOSUM62Colour); + BLOSUM62Colour + .setEnabled(new Blosum62ColourScheme().isApplicableTo(sg)); + colourMenu.add(PIDColour); + PIDColour.setEnabled(new PIDColourScheme().isApplicableTo(sg)); + colourMenu.add(zappoColour); + zappoColour.setEnabled(new ZappoColourScheme().isApplicableTo(sg)); + colourMenu.add(taylorColour); + taylorColour.setEnabled(new TaylorColourScheme().isApplicableTo(sg)); + colourMenu.add(hydrophobicityColour); + hydrophobicityColour.setEnabled(new HydrophobicColourScheme() + .isApplicableTo(sg)); + colourMenu.add(helixColour); + helixColour.setEnabled(new HelixColourScheme().isApplicableTo(sg)); + colourMenu.add(strandColour); + strandColour.setEnabled(new StrandColourScheme().isApplicableTo(sg)); + colourMenu.add(turnColour); + turnColour.setEnabled(new TurnColourScheme().isApplicableTo(sg)); + colourMenu.add(buriedColour); + buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(sg)); + colourMenu.add(nucleotideColour); + nucleotideColour.setEnabled(new NucleotideColourScheme() + .isApplicableTo(sg)); + colourMenu.add(purinePyrimidineColour); + purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme() + .isApplicableTo(sg)); + colourMenu.add(tcoffeeColour); + tcoffeeColour + .setEnabled(new TCoffeeColourScheme(sg).isApplicableTo(sg)); + + /* + * add some of these items to a ButtonGroup so their + * selection is mutually exclusive + */ + ButtonGroup colours = new ButtonGroup(); + + /* + * add any user-defined colours loaded on startup or + * during the application session + */ + SortedMap userColourSchemes = UserDefinedColours + .getUserColourSchemes(); + if (userColourSchemes != null) + { + for (String userColour : userColourSchemes.keySet()) + { + JRadioButtonMenuItem item = new JRadioButtonMenuItem(userColour); + item.setName(userColour); // button name identifies selected colour + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + colours.add(item); + } + } + colourMenu.add(userDefinedColour); + + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(abovePIDColour); + + colours.add(noColourmenuItem); + colours.add(clustalColour); + colours.add(BLOSUM62Colour); + colours.add(PIDColour); + colours.add(zappoColour); + colours.add(taylorColour); + colours.add(hydrophobicityColour); + colours.add(helixColour); + colours.add(strandColour); + colours.add(turnColour); + colours.add(buriedColour); + colours.add(purinePyrimidineColour); + colours.add(tcoffeeColour); + colours.add(nucleotideColour); + colours.add(userDefinedColour); + colours.add(abovePIDColour); + // colours.add(RNAInteractionColour); + + } + + /** * 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 @@ -1635,7 +1610,7 @@ 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(); + SortedMap tipEntries = new TreeMap(); final Map> candidates = new LinkedHashMap>(); AlignmentI al = this.ap.av.getAlignment(); AlignmentUtils.findAddableReferenceAnnotations(forSequences, @@ -1737,7 +1712,7 @@ public class PopupMenu extends JPopupMenu public void createSequenceDetailsReport(SequenceI[] sequences) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - StringBuffer contents = new StringBuffer(); + StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { contents.append("

" @@ -1752,7 +1727,6 @@ public class PopupMenu extends JPopupMenu seq, true, true, - false, (ap.getSeqPanel().seqCanvas.fr != null) ? ap .getSeqPanel().seqCanvas.fr.getMinMax() : null); @@ -1900,6 +1874,12 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void tcoffeeColorScheme_actionPerformed() + { + getGroup().cs = new TCoffeeColourScheme(getGroup()); + refresh(); + } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1956,7 +1936,7 @@ public class PopupMenu extends JPopupMenu } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours + UserColourScheme udc = UserDefinedColours .getUserColourSchemes().get(e.getActionCommand()); sg.cs = udc; @@ -2040,9 +2020,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), + Conservation c = new Conservation("Group", sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -2150,14 +2129,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane + JvOptionPane .showMessageDialog( ap, MessageManager .getString("label.spaces_converted_to_backslashes"), MessageManager .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2256,10 +2235,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2440,4 +2419,36 @@ public class PopupMenu extends JPopupMenu } } + /** + * Marks as selected the colour menu item matching the given name, or the + * first item ('None') if no match is found + * + * @param cs + */ + protected void setColourSelected(ColourSchemeI cs) + { + noColourmenuItem.setSelected(true); + if (cs == null) + { + return; + } + + String schemeName = cs.getSchemeName(); + /* + * look for a radio button with a name that matches the colour name + * (note the button text may not as it may be internationalised) + */ + for (Component menuItem : colourMenu.getMenuComponents()) + { + if (menuItem instanceof JRadioButtonMenuItem) + { + if (schemeName.equals(((JRadioButtonMenuItem) menuItem).getName())) + { + ((JRadioButtonMenuItem) menuItem).setSelected(true); + return; + } + } + } + } + }