X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=26c27599a290141feef005373d2fd918dbc16a29;hb=0eecb83722155f32d5eade88a5e8b4a5caca1a67;hp=40f576497ea39071878ee0d858a0d7e7c846b6bd;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 40f5764..26c2759 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; @@ -49,7 +50,9 @@ import jalview.schemes.PIDColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; +import jalview.util.StringUtils; import jalview.util.UrlLink; +import jalview.util.dialogrunner.RunResponse; import java.awt.Color; import java.awt.event.ActionEvent; @@ -68,7 +71,6 @@ import java.util.TreeMap; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; @@ -549,23 +551,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { desc = String.format("%s %d-%d", sf.getType(), start, end); } + String tooltip = desc; String description = sf.getDescription(); if (description != null) { - if (description.length() <= 6) + description = StringUtils.stripHtmlTags(description); + if (description.length() > 12) { - desc = desc + " " + description; + desc = desc + " " + description.substring(0, 12) + ".."; } else { - desc = desc + " " + description.substring(0, 6) + ".."; + desc = desc + " " + description; } + tooltip = tooltip + " " + description; } if (sf.getFeatureGroup() != null) { - desc = desc + " (" + sf.getFeatureGroup() + ")"; + tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")"); } JMenuItem item = new JMenuItem(desc); + item.setToolTipText(tooltip); item.addActionListener(new ActionListener() { @Override @@ -585,8 +591,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ protected void showFeatureDetails(SequenceFeature sf) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); + 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); } @@ -1261,7 +1271,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent actionEvent) { - editSequence_actionPerformed(actionEvent); + editSequence_actionPerformed(); } }); makeReferenceSeq.setText( @@ -1552,15 +1562,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - - HiddenColumns hidden = new HiddenColumns(); - BitSet inserts = new BitSet(), mask = new BitSet(); - - // set mask to preserve existing hidden columns outside selected group - if (ap.av.hasHiddenColumns()) - { - ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask); - } + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + BitSet inserts = new BitSet(); boolean markedPopup = false; // mark inserts in current selection @@ -1568,10 +1571,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { // mark just the columns in the selection group to be hidden inserts.set(ap.av.getSelectionGroup().getStartRes(), - ap.av.getSelectionGroup().getEndRes() + 1); - - // and clear that part of the mask - mask.andNot(inserts); + ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1? // now clear columns without gaps for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) @@ -1582,29 +1582,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } inserts.and(sq.getInsertionsAsBits()); } - } - else - { - // initially, mark all columns to be hidden - inserts.set(0, ap.av.getAlignment().getWidth()); - - // and clear out old hidden regions completely - mask.clear(); + hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes()); } // now mark for sequence under popup if we haven't already done it - if (!markedPopup && sequence != null) + else if (!markedPopup && sequence != null) { - inserts.and(sequence.getInsertionsAsBits()); - } - - // finally, preserve hidden regions outside selection - inserts.or(mask); + inserts.or(sequence.getInsertionsAsBits()); - // and set hidden columns accordingly - hidden.hideMarkedBits(inserts); - - ap.av.getAlignment().setHiddenColumns(hidden); + // and set hidden columns accordingly + hidden.hideColumns(inserts); + } refresh(); } @@ -1629,10 +1618,7 @@ 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() + ""); @@ -1764,30 +1750,27 @@ 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 RunResponse(JvOptionPane.OK_OPTION) + { + @Override + public void run() + { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + }); } /** @@ -1808,48 +1791,41 @@ 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, false); - } - - sequence.setDescription(dialog.getDescription()); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - + new RunResponse(JvOptionPane.OK_OPTION) + { + @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()); + } + }); } /** @@ -1874,24 +1850,23 @@ 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); } /** @@ -2054,13 +2029,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ if (!seqs.isEmpty()) { - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .amendFeatures(seqs, features, true, ap)) + new FeatureEditor(ap).createFeatures(seqs, features, new Runnable() { - ap.alignFrame.setShowSeqFeatures(true); - ap.av.setSearchResults(null); // clear highlighting - ap.repaint(); // draw new/amended features - } + public void run() + { + ap.alignFrame.setShowSeqFeatures(true); + ap.av.setSearchResults(null); // clear highlighting + ap.repaint(); // draw new/amended features + } + }); } } @@ -2092,7 +2069,12 @@ 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(); @@ -2106,24 +2088,28 @@ 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 RunResponse(JvOptionPane.OK_OPTION) + { + @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()); + } + }); } }