X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=37defd0900a1af7bb5b6ffd7e2d80f6735bdf8fa;hb=91dd5d379e0624f6cd4be02c17187ec1a630d693;hp=2bcd229e093f4a9dd4995c86d2a60112e95d2181;hpb=71ca5630223ddd30ab463e4f736fac9667e9cb18;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 2bcd229..37defd0 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -47,12 +47,13 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.util.StringUtils; import jalview.util.UrlLink; -import jalview.util.dialogrunner.RunResponse; import java.awt.BorderLayout; import java.awt.Color; @@ -71,6 +72,7 @@ import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; +import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JLabel; @@ -78,7 +80,8 @@ import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; -import javax.swing.JTextArea; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; /** * DOCUMENT ME! @@ -98,6 +101,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem annotationColour; + protected JMenuItem modifyConservation = new JMenuItem(); AlignmentPanel ap; @@ -407,9 +412,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } } - // for the case when no sequences are even visible + + /* + * 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")); @@ -425,7 +441,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } }); - add(menuItem); } } @@ -597,23 +612,28 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void showFeatureDetails(SequenceFeature sf) { JInternalFrame details; - if (/** @j2sNative true || */ false) + if (Platform.isJS())// ** @j2sNative true || */ false) { details = new JInternalFrame(); JPanel panel = new JPanel(new BorderLayout()); panel.setOpaque(true); panel.setBackground(Color.white); // TODO JAL-3026 set style of table correctly for feature details - JLabel reprt = new JLabel(MessageManager.formatMessage("label.html_content", - new Object[] - { sf.getDetailsReport()})); + JLabel reprt = new JLabel(MessageManager + .formatMessage("label.html_content", new Object[] + { sf.getDetailsReport() })); reprt.setBackground(Color.WHITE); reprt.setOpaque(true); - panel.add(reprt,BorderLayout.CENTER); + panel.add(reprt, BorderLayout.CENTER); details.setContentPane(panel); details.pack(); } else + /** + * Java only + * + * @j2sNative + */ { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); // it appears Java's CSS does not support border-collaps :-( @@ -864,12 +884,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRefs(); - if (dbr != null && dbr.length > 0) + List dbr = sqi.getDBRefs(); + int nd; + if (dbr != null && (nd = dbr.size()) > 0) { - for (int d = 0; d < dbr.length; d++) + for (int d = 0; d < nd; d++) { - String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + DBRefEntry e = dbr.get(d); + String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); Object[] sarray = commonDbrefs.get(src); if (sarray == null) { @@ -882,10 +904,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (((String[]) sarray[1])[sq] == null) { - if (!dbr[d].hasMap() || (dbr[d].getMap() + if (!e.hasMap() || (e.getMap() .locateMappedRange(start, end) != null)) { - ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); + ((String[]) sarray[1])[sq] = e.getAccessionId(); ((int[]) sarray[0])[0]++; } } @@ -1427,6 +1449,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); + annotationColour = new JRadioButtonMenuItem( + MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); + annotationColour.setEnabled(false); + annotationColour.setToolTipText( + MessageManager.getString("label.by_annotation_tooltip")); + modifyConservation.setText(MessageManager .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(new ActionListener() @@ -1457,7 +1486,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, + false); + bg.add(annotationColour); + colourMenu.add(annotationColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1634,8 +1666,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener public void createSequenceDetailsReport(SequenceI[] sequences) { - CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); StringBuilder contents = new StringBuilder(128); + contents.append(""); for (SequenceI seq : sequences) { contents.append("

" + MessageManager.formatMessage( @@ -1646,9 +1678,35 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } - cap.setText("" + contents.toString() + ""); + contents.append(""); + String report = contents.toString(); + + JInternalFrame frame; + if (Platform.isJS()) + { + JLabel textLabel = new JLabel(); + textLabel.setText(report); + textLabel.setBackground(Color.WHITE); + JPanel pane = new JPanel(new BorderLayout()); + pane.setOpaque(true); + pane.setBackground(Color.WHITE); + pane.add(textLabel, BorderLayout.NORTH); + frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(pane)); + } + else + /** + * Java only + * + * @j2sNative + */ + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + cap.setText(report); + frame = cap; + } - Desktop.addInternalFrame(cap, + Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.sequence_details_for", (sequences.length == 1 ? new Object[] { sequences[0].getDisplayId(true) } @@ -1656,7 +1714,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { MessageManager .getString("label.selection") })), 500, 400); - } protected void showNonconserved_actionPerformed() @@ -1786,7 +1843,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("label.group_description")); dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - new RunResponse(JvOptionPane.OK_OPTION) + new Runnable() { @Override public void run() @@ -1827,7 +1884,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener dialog.showDialog(ap.alignFrame, MessageManager.getString( "label.edit_sequence_name_description"), - new RunResponse(JvOptionPane.OK_OPTION) + new Runnable() { @Override public void run() @@ -1953,12 +2010,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener public void copy_actionPerformed() { - ap.alignFrame.copy_actionPerformed(null); + ap.alignFrame.copy_actionPerformed(); } public void cut_actionPerformed() { - ap.alignFrame.cut_actionPerformed(null); + ap.alignFrame.cut_actionPerformed(); } void changeCase(ActionEvent e) @@ -2054,15 +2111,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ if (!seqs.isEmpty()) { - new FeatureEditor(ap).createFeatures(seqs, features, new Runnable() - { - public void run() - { - ap.alignFrame.setShowSeqFeatures(true); - ap.av.setSearchResults(null); // clear highlighting - ap.repaint(); // draw new/amended features - } - }); + new FeatureEditor(ap, seqs, features, true).showDialog(); } } @@ -2116,7 +2165,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener null, MessageManager.getString("label.edit_sequence"), null); dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_sequence"), - new RunResponse(JvOptionPane.OK_OPTION) + new Runnable() { @Override public void run() @@ -2152,7 +2201,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * switch to the chosen colour scheme (or null for None) */ ColourSchemeI colourScheme = ColourSchemes.getInstance() - .getColourScheme(colourSchemeName, sg, + .getColourScheme(colourSchemeName, ap.av, sg, ap.av.getHiddenRepSequences()); sg.setColourScheme(colourScheme); if (colourScheme instanceof Blosum62ColourScheme