X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e78eaf2d4d3a48ea4c620676adcee99b8211ca4b;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=b574dddd50d0fe7d608473cf31b800bf8d129080;hpb=ec335385cbf75abd45251dd673f99fb023c5fd43;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index b574ddd..e78eaf2 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,7 @@ import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
@@ -46,11 +47,15 @@ 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 java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -67,11 +72,16 @@ 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.JInternalFrame;
+import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPanel;
import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
/**
* DOCUMENT ME!
@@ -91,6 +101,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem annotationColour;
+
protected JMenuItem modifyConservation = new JMenuItem();
AlignmentPanel ap;
@@ -400,9 +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"));
@@ -418,7 +441,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
}
});
-
add(menuItem);
}
}
@@ -528,7 +550,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
*/
protected void addFeatureDetails(List" + MessageManager.formatMessage(
@@ -1617,15 +1670,33 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
new Object[]
{ seq.getDisplayId(true) }) + "
"); new SequenceAnnotationReport(null).createSequenceAnnotationReport( - contents, seq, true, true, - (ap.getSeqPanel().seqCanvas.fr != null) - ? ap.getSeqPanel().seqCanvas.fr.getMinMax() - : null); + contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("
"); } - cap.setText("" + contents.toString() + ""); + 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()); + ((JPanel) pane).setOpaque(true); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); + frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(pane)); + } + else + { + 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) } @@ -1633,7 +1704,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { MessageManager .getString("label.selection") })), 500, 400); - } protected void showNonconserved_actionPerformed() @@ -1752,30 +1822,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where group name and description may be edited */ protected void groupName_actionPerformed() { - SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), sg.getDescription(), - " " + MessageManager.getString("label.group_name") + " ", - MessageManager.getString("label.group_description") + " ", + MessageManager.getString("label.group_name"), + MessageManager.getString("label.group_description")); + dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - ap.alignFrame); - - if (!dialog.accept) - { - return; - } - - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); + new Runnable() + { + @Override + public void run() + { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + }); } /** @@ -1796,48 +1863,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where sequence name and description may be edited */ void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence.getDescription(), - " " + MessageManager.getString("label.sequence_name") - + " ", - MessageManager.getString("label.sequence_description") + " ", + MessageManager.getString("label.sequence_name"), + MessageManager.getString("label.sequence_description")); + dialog.showDialog(ap.alignFrame, MessageManager.getString( "label.edit_sequence_name_description"), - ap.alignFrame); - - if (!dialog.accept) - { - return; - } - - if (dialog.getName() != null) - { - if (dialog.getName().indexOf(" ") > -1) - { - 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); - } - - sequence.setDescription(dialog.getDescription()); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - + new Runnable() + { + @Override + public void run() + { + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JvOptionPane.showMessageDialog(ap, + MessageManager.getString( + "label.spaces_converted_to_underscores"), + MessageManager.getString( + "label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); + } + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); + } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + }); } /** @@ -1862,24 +1922,23 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Offers a colour chooser and sets the selected colour as the group outline */ protected void outline_actionPerformed() { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_outline_colour"), - Color.BLUE); - - if (col != null) + String title = MessageManager + .getString("label.select_outline_colour"); + ColourChooserListener listener = new ColourChooserListener() { - sg.setOutlineColour(col); - } - - refresh(); + @Override + public void colourSelected(Color c) + { + getGroup().setOutlineColour(c); + refresh(); + }; + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), + title, Color.BLUE, listener); } /** @@ -1941,12 +2000,12 @@ 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) @@ -2042,13 +2101,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ 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 - } + new FeatureEditor(ap, seqs, features, true).showDialog(); } } @@ -2080,7 +2133,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } - public void editSequence_actionPerformed(ActionEvent actionEvent) + /** + * Shows a dialog where sequence characters may be edited. Any changes are + * applied, and added as an available 'Undo' item in the edit commands + * history. + */ + public void editSequence_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); @@ -2094,24 +2152,28 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, MessageManager.getString("label.edit_sequence"), null, + null, MessageManager.getString("label.edit_sequence"), null); + dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_sequence"), - ap.alignFrame); - - if (dialog.accept) - { - EditCommand editCommand = new EditCommand( - MessageManager.getString("label.edit_sequences"), - Action.REPLACE, - dialog.getName().replace(' ', ap.av.getGapCharacter()), - sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); - - ap.alignFrame.addHistoryItem(editCommand); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } + new Runnable() + { + @Override + public void run() + { + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), + Action.REPLACE, + dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray( + ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); + ap.alignFrame.addHistoryItem(editCommand); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + }); } } @@ -2129,7 +2191,7 @@ 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