X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f50b72b206c9da5fbe942c7e3698910a93d34dcc;hb=265e81c0b3599a09c312f17188e3a892e9d96c4e;hp=d1e8e32b83e4ea302c39a1ee81bf084499263970;hpb=0913cb6ee2033d714c0aa6eb3e152da7485b21a4;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d1e8e32..f50b72b 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,8 +20,6 @@
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
@@ -34,6 +32,7 @@ import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.SortedMap;
@@ -56,7 +55,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
@@ -88,6 +87,8 @@ import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.viewmodel.seqfeatures.IdColumn;
+import jalview.viewmodel.seqfeatures.IdColumns;
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
@@ -230,13 +231,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ Console.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
@@ -359,14 +360,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
/**
- * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
+ * Constructor for a PopupMenu for a click in the alignment panel (on a
+ * residue)
*
* @param ap
- * the panel in which the mouse is clicked
+ * the panel in which the mouse is clicked
* @param seq
- * the sequence under the mouse
+ * the sequence under the mouse
* @throws NullPointerException
- * if seq is null
+ * if seq is null
*/
public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
{
@@ -377,13 +379,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
* Constructor for a PopupMenu for a click in the sequence id panel
*
* @param alignPanel
- * the panel in which the mouse is clicked
+ * the panel in which the mouse is clicked
* @param seq
- * the sequence under the mouse click
+ * the sequence under the mouse click
* @param groupLinks
- * templates for sequence external links
+ * templates for sequence external links
* @throws NullPointerException
- * if seq is null
+ * if seq is null
*/
public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
List
@@ -735,8 +768,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
*
- * If this panel is also showed complementary (CDS/protein) features, then links
- * to their feature details are also added.
+ * If this panel is also showed complementary (CDS/protein) features, then
+ * links to their feature details are also added.
*
* @param seq
* @param column
@@ -842,6 +875,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
int[] localRange = mf.getMappedPositions(start, end);
if (localRange == null)
{
+ // e.g. variant extending to stop codon so not mappable
return;
}
start = localRange[0];
@@ -1143,8 +1177,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
if (((String[]) sarray[1])[sq] == null)
{
- if (!e.hasMap() || (e.getMap()
- .locateMappedRange(start, end) != null))
+ if (!e.hasMap()
+ || (e.getMap().locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = e.getAccessionId();
((int[]) sarray[0])[0]++;
@@ -1164,12 +1198,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ Console.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
@@ -1783,7 +1817,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
}
inserts.and(sq.getInsertionsAsBits());
}
- hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ hidden.clearAndHideColumns(inserts,
+ ap.av.getSelectionGroup().getStartRes(),
ap.av.getSelectionGroup().getEndRes());
}
@@ -1812,7 +1847,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
contents.append("" + MessageManager.formatMessage(
"label.create_sequence_details_report_annotation_for",
new Object[]
- { seq.getDisplayId(true) }) + "
"); + { seq.getDisplayId(true) }) + "
\n"); new SequenceAnnotationReport(false).createSequenceAnnotationReport( contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("
"); @@ -1982,15 +2017,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("label.group_description")); dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - new Runnable() - { - @Override - public void run() - { - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); - } + () -> { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + return null; }); } @@ -2013,8 +2044,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /** * Shows a dialog where the sequence name and description may be edited. If a - * name containing spaces is entered, these are converted to underscores, with a - * warning message. + * name containing spaces is entered, these are converted to underscores, with + * a warning message. */ void sequenceName_actionPerformed() { @@ -2022,32 +2053,26 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequence.getDescription(), MessageManager.getString("label.sequence_name"), MessageManager.getString("label.sequence_description")); - dialog.showDialog(ap.alignFrame, - MessageManager.getString( - "label.edit_sequence_name_description"), - new Runnable() - { - @Override - public void run() + dialog.showDialog(ap.alignFrame, MessageManager + .getString("label.edit_sequence_name_description"), () -> { + if (dialog.getName() != null) { - if (dialog.getName() != null) + if (dialog.getName().indexOf(" ") > -1) { - 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); + JvOptionPane.showMessageDialog(ap, + MessageManager.getString( + "label.spaces_converted_to_underscores"), + MessageManager.getString( + "label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); } - sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + return null; }); } @@ -2077,8 +2102,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ protected void outline_actionPerformed() { - String title = MessageManager - .getString("label.select_outline_colour"); + String title = MessageManager.getString("label.select_outline_colour"); ColourChooserListener listener = new ColourChooserListener() { @Override @@ -2088,8 +2112,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), - title, Color.BLUE, listener); + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title, + Color.BLUE, listener); } /** @@ -2270,25 +2294,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null); dialog.showDialog(ap.alignFrame, - MessageManager.getString("label.edit_sequence"), - 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()); - } + MessageManager.getString("label.edit_sequence"), () -> { + 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()); + return null; }); } }