From 651ed4273f899e80f4931bed82714355e16fd837 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 May 2017 15:56:32 +0100 Subject: [PATCH] JAL-2504 allow feature type to be specified for Create Features dialog --- src/jalview/appletgui/APopupMenu.java | 2 +- src/jalview/appletgui/FeatureRenderer.java | 46 ++++-- src/jalview/appletgui/Finder.java | 5 +- src/jalview/appletgui/SeqPanel.java | 2 +- src/jalview/gui/FeatureRenderer.java | 243 ++++++++++++++++------------ src/jalview/gui/Finder.java | 64 ++++---- src/jalview/gui/PopupMenu.java | 27 ++-- src/jalview/gui/SeqPanel.java | 25 ++- src/jalview/jbgui/GFinder.java | 18 +-- 9 files changed, 252 insertions(+), 180 deletions(-) diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 8fd317a..cd49f63 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -843,7 +843,7 @@ public class APopupMenu extends java.awt.PopupMenu implements seqs = rseqs; if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + features, true, ap, null)) { ap.alignFrame.sequenceFeatures.setState(true); ap.av.setShowSequenceFeatures(true); diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index b88a1dc..be027ec 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -165,9 +165,20 @@ public class FeatureRenderer extends } + /** + * Shows a dialog allowing the user to create, or amend or delete, sequence + * features. + * + * @param sequences + * @param features + * @param create + * @param ap + * @param featureType + * @return + */ boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, - final AlignmentPanel ap) + final SequenceFeature[] features, boolean create, + final AlignmentPanel ap, String featureType) { Panel bigPanel = new Panel(new BorderLayout()); final TextField name = new TextField(16); @@ -190,7 +201,7 @@ public class FeatureRenderer extends // ///////////////////////////////////// // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!newFeatures && features.length > 1) + if (!create && features.length > 1) { panel = new Panel(new GridLayout(4, 1)); tmp = new Panel(); @@ -272,7 +283,7 @@ public class FeatureRenderer extends Label.RIGHT)); panel.add(new ScrollPane().add(description)); - if (!newFeatures) + if (!create) { bigPanel.add(panel, BorderLayout.SOUTH); @@ -290,15 +301,22 @@ public class FeatureRenderer extends bigPanel.add(panel, BorderLayout.CENTER); } - if (lastFeatureAdded == null) + if (featureType != null) { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else + lastFeatureAdded = featureType; + } + else + { + if (lastFeatureAdded == null) { - lastFeatureAdded = "feature_1"; + if (features[0].type != null) + { + lastFeatureAdded = features[0].type; + } + else + { + lastFeatureAdded = "feature_1"; + } } } @@ -314,7 +332,7 @@ public class FeatureRenderer extends } } - String title = newFeatures ? MessageManager + String title = create ? MessageManager .getString("label.create_new_sequence_features") : MessageManager.formatMessage("label.amend_delete_features", new String[] { sequences[0].getName() }); @@ -324,7 +342,7 @@ public class FeatureRenderer extends dialog.setMainPanel(bigPanel); - if (newFeatures) + if (create) { name.setText(lastFeatureAdded); source.setText(lastFeatureGroupAdded); @@ -387,7 +405,7 @@ public class FeatureRenderer extends lastFeatureGroupAdded = null; } - if (!newFeatures) + if (!create) { SequenceFeature sf = features[featureIndex]; diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index d2fe69c..2579d91 100644 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -116,20 +116,21 @@ public class Finder extends Panel implements ActionListener SequenceI[] seqs = new SequenceI[searchResults.getSize()]; SequenceFeature[] features = new SequenceFeature[searchResults .getSize()]; + String searchString = textfield.getText().trim(); int i = 0; for (SearchResultMatchI match : searchResults.getResults()) { seqs[i] = match.getSequence().getDatasetSequence(); - features[i] = new SequenceFeature(textfield.getText().trim(), + features[i] = new SequenceFeature(searchString, "Search Results", null, match.getStart(), match.getEnd(), "Search Results"); i++; } if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + features, true, ap, searchString)) { ap.alignFrame.sequenceFeatures.setState(true); av.setShowSequenceFeatures(true); diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 0e12703..60c53dd 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -570,7 +570,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (features != null && features.length > 0) { seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, features, false, ap); + new SequenceI[] { sequence }, features, false, ap, null); seqCanvas.highlightSearchResults(null); } diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index f519f99..e608552 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -25,6 +25,7 @@ import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; import jalview.schemes.FeatureColour; import jalview.util.ColorUtils; import jalview.util.MessageManager; @@ -42,6 +43,7 @@ import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Arrays; import java.util.Comparator; +import java.util.List; import javax.swing.JColorChooser; import javax.swing.JComboBox; @@ -67,20 +69,19 @@ public class FeatureRenderer extends AlignmentPanel ap; /** - * Creates a new FeatureRenderer object. + * Creates a new FeatureRenderer object * - * @param av - * DOCUMENT ME! + * @param alignPanel */ - public FeatureRenderer(AlignmentPanel ap) + public FeatureRenderer(AlignmentPanel alignPanel) { - super(ap.av); - this.ap = ap; - if (ap != null && ap.getSeqPanel() != null - && ap.getSeqPanel().seqCanvas != null - && ap.getSeqPanel().seqCanvas.fr != null) + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) { - transferSettings(ap.getSeqPanel().seqCanvas.fr); + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); } } @@ -98,15 +99,38 @@ public class FeatureRenderer extends int featureIndex = 0; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, - final AlignmentPanel ap) + /** + * Presents a dialog allowing the user to add new features, or amend or delete + * existing features. Currently this can be on + * + * + * @param sequences + * the sequences features are to be created on (if creating + * features), or a single sequence (if amending features) + * @param features + * the current features at the position (if amending), or template + * new features with start/end position set (if creating) + * @param create + * true to create features, false to amend or delete + * @param featureType + * the feature type to set on new features; if null, defaults to the + * type of the last new feature created if any, failing that to + * "feature_1" + * @param alignPanel + * @return + */ + protected boolean amendFeatures(final List sequences, + final List features, boolean create, + final AlignmentPanel alignPanel, String featureType) { featureIndex = 0; - final JPanel bigPanel = new JPanel(new BorderLayout()); - final JComboBox overlaps; + final JPanel mainPanel = new JPanel(new BorderLayout()); final JTextField name = new JTextField(25); final JTextField source = new JTextField(25); final JTextArea description = new JTextArea(3, 25); @@ -134,14 +158,14 @@ public class FeatureRenderer extends if (col != null) { fcol = new FeatureColour(col); - updateColourButton(bigPanel, colour, new FeatureColour(col)); + updateColourButton(mainPanel, colour, new FeatureColour(col)); } } else { if (fcc == null) { - final String type = features[featureIndex].getType(); + final String type = features.get(featureIndex).getType(); fcc = new FeatureColourChooser(me, type); fcc.setRequestFocusEnabled(true); fcc.requestFocus(); @@ -155,7 +179,7 @@ public class FeatureRenderer extends fcol = fcc.getLastColour(); fcc = null; setColour(type, fcol); - updateColourButton(bigPanel, colour, fcol); + updateColourButton(mainPanel, colour, fcol); } }); @@ -163,26 +187,27 @@ public class FeatureRenderer extends } } }); - JPanel tmp = new JPanel(); - JPanel panel = new JPanel(new GridLayout(3, 1)); + JPanel gridPanel = new JPanel(new GridLayout(3, 1)); - // ///////////////////////////////////// - // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!newFeatures && features.length > 1) + if (!create && features.size() > 1) { - panel = new JPanel(new GridLayout(4, 1)); - tmp = new JPanel(); - tmp.add(new JLabel(MessageManager.getString("label.select_feature") + /* + * more than one feature at selected position - add a drop-down + * to choose the feature to amend + */ + gridPanel = new JPanel(new GridLayout(4, 1)); + JPanel choosePanel = new JPanel(); + choosePanel.add(new JLabel(MessageManager + .getString("label.select_feature") + ":")); - overlaps = new JComboBox(); - for (int i = 0; i < features.length; i++) + final JComboBox overlaps = new JComboBox(); + for (SequenceFeature sf : features) { - overlaps.addItem(features[i].getType() + "/" - + features[i].getBegin() + "-" + features[i].getEnd() - + " (" + features[i].getFeatureGroup() + ")"); + String text = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; + overlaps.addItem(text); } - - tmp.add(overlaps); + choosePanel.add(overlaps); overlaps.addItemListener(new ItemListener() { @@ -193,17 +218,18 @@ public class FeatureRenderer extends if (index != -1) { featureIndex = index; - name.setText(features[index].getType()); - description.setText(features[index].getDescription()); - source.setText(features[index].getFeatureGroup()); - start.setValue(new Integer(features[index].getBegin())); - end.setValue(new Integer(features[index].getEnd())); + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + source.setText(sf.getFeatureGroup()); + start.setValue(new Integer(sf.getBegin())); + end.setValue(new Integer(sf.getEnd())); SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequences[0], features[index].getBegin(), - features[index].getEnd()); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); - ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } FeatureColourI col = getFeatureStyle(name.getText()); @@ -213,32 +239,32 @@ public class FeatureRenderer extends .createColourFromName(name.getText())); } oldcol = fcol = col; - updateColourButton(bigPanel, colour, col); + updateColourButton(mainPanel, colour, col); } }); - panel.add(tmp); + gridPanel.add(choosePanel); } // //////// // //////////////////////////////////// - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.name:"), + JPanel namePanel = new JPanel(); + gridPanel.add(namePanel); + namePanel.add(new JLabel(MessageManager.getString("label.name:"), JLabel.RIGHT)); - tmp.add(name); + namePanel.add(name); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.group:"), + JPanel groupPanel = new JPanel(); + gridPanel.add(groupPanel); + groupPanel.add(new JLabel(MessageManager.getString("label.group:"), JLabel.RIGHT)); - tmp.add(source); + groupPanel.add(source); - tmp = new JPanel(); - panel.add(tmp); - tmp.add(new JLabel(MessageManager.getString("label.colour"), + JPanel colourPanel = new JPanel(); + gridPanel.add(colourPanel); + colourPanel.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT)); - tmp.add(colour); + colourPanel.add(colour); colour.setPreferredSize(new Dimension(150, 15)); colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); colour.setForeground(Color.black); @@ -246,50 +272,59 @@ public class FeatureRenderer extends colour.setVerticalAlignment(SwingConstants.CENTER); colour.setHorizontalTextPosition(SwingConstants.CENTER); colour.setVerticalTextPosition(SwingConstants.CENTER); - bigPanel.add(panel, BorderLayout.NORTH); + mainPanel.add(gridPanel, BorderLayout.NORTH); - panel = new JPanel(); - panel.add(new JLabel(MessageManager.getString("label.description:"), + JPanel descriptionPanel = new JPanel(); + descriptionPanel.add(new JLabel(MessageManager + .getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); - panel.add(new JScrollPane(description)); + descriptionPanel.add(new JScrollPane(description)); - if (!newFeatures) + if (!create) { - bigPanel.add(panel, BorderLayout.SOUTH); + mainPanel.add(descriptionPanel, BorderLayout.SOUTH); - panel = new JPanel(); - panel.add(new JLabel(MessageManager.getString("label.start"), + JPanel startEndPanel = new JPanel(); + startEndPanel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT)); - panel.add(start); - panel.add(new JLabel(MessageManager.getString("label.end"), + startEndPanel.add(start); + startEndPanel.add(new JLabel(MessageManager.getString("label.end"), JLabel.RIGHT)); - panel.add(end); - bigPanel.add(panel, BorderLayout.CENTER); + startEndPanel.add(end); + mainPanel.add(startEndPanel, BorderLayout.CENTER); } else { - bigPanel.add(panel, BorderLayout.CENTER); + mainPanel.add(descriptionPanel, BorderLayout.CENTER); } - if (lastFeatureAdded == null) + SequenceFeature firstFeature = features.get(0); + if (featureType != null) { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else + lastFeatureAdded = featureType; + } + else + { + if (lastFeatureAdded == null) { - lastFeatureAdded = "feature_1"; + if (firstFeature.type != null) + { + lastFeatureAdded = firstFeature.type; + } + else + { + lastFeatureAdded = "feature_1"; + } } } if (lastFeatureGroupAdded == null) { - if (features[0].featureGroup != null) + if (firstFeature.featureGroup != null) { - lastFeatureGroupAdded = features[0].featureGroup; + lastFeatureGroupAdded = firstFeature.featureGroup; } else { @@ -297,43 +332,46 @@ public class FeatureRenderer extends } } - if (newFeatures) + if (create) { name.setText(lastFeatureAdded); source.setText(lastFeatureGroupAdded); } else { - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); + name.setText(firstFeature.getType()); + source.setText(firstFeature.getFeatureGroup()); } - start.setValue(new Integer(features[0].getBegin())); - end.setValue(new Integer(features[0].getEnd())); - description.setText(features[0].getDescription()); - updateColourButton(bigPanel, colour, + start.setValue(new Integer(firstFeature.getBegin())); + end.setValue(new Integer(firstFeature.getEnd())); + description.setText(firstFeature.getDescription()); + updateColourButton(mainPanel, colour, (oldcol = fcol = getFeatureStyle(name.getText()))); Object[] options; - if (!newFeatures) + if (!create) { - options = new Object[] { "Amend", "Delete", "Cancel" }; + options = new Object[] { MessageManager.getString("label.amend"), + MessageManager.getString("action.delete"), + MessageManager.getString("action.cancel") }; } else { - options = new Object[] { "OK", "Cancel" }; + options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; } - String title = newFeatures ? MessageManager + String title = create ? MessageManager .getString("label.create_new_sequence_features") : MessageManager.formatMessage("label.amend_delete_features", - new String[] { sequences[0].getName() }); + new String[] { sequences.get(0).getName() }); int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, + mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok")); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0) { @@ -347,13 +385,13 @@ public class FeatureRenderer extends } } - if (!newFeatures) + if (!create) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); if (reply == JvOptionPane.NO_OPTION) { - sequences[0].getDatasetSequence().deleteFeature(sf); + sequences.get(0).getDatasetSequence().deleteFeature(sf); } else if (reply == JvOptionPane.YES_OPTION) { @@ -380,14 +418,15 @@ public class FeatureRenderer extends { if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); i++) { - features[i].type = lastFeatureAdded; + SequenceFeature sf = features.get(i); + sf.type = lastFeatureAdded; // fix for JAL-1538 - always set feature group here - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + sequences.get(i).addSequenceFeature(sf); + ffile.parseDescriptionHTML(sf, false); } if (lastFeatureGroupAdded != null) @@ -399,7 +438,7 @@ public class FeatureRenderer extends findAllFeatures(false); - ap.paintAlignment(true); + alignPanel.paintAlignment(true); return true; } @@ -409,7 +448,7 @@ public class FeatureRenderer extends } } - ap.paintAlignment(true); + alignPanel.paintAlignment(true); return true; } diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index e44c956..21c6c8a 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -31,6 +31,8 @@ import jalview.viewmodel.AlignmentViewport; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; +import java.util.ArrayList; +import java.util.List; import java.util.Vector; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -54,9 +56,9 @@ import javax.swing.KeyStroke; */ public class Finder extends GFinder { - private static final int HEIGHT = 120; + private static final int MY_HEIGHT = 120; - private static final int WIDTH = 400; + private static final int MY_WIDTH = 400; AlignmentViewport av; @@ -100,7 +102,7 @@ public class Finder extends GFinder frame.setLayer(JLayeredPane.PALETTE_LAYER); addEscapeHandler(); Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - WIDTH, HEIGHT); + MY_WIDTH, MY_HEIGHT); frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); textfield.requestFocus(); } @@ -189,11 +191,11 @@ public class Finder extends GFinder JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int f = 0; f < frames.length; f++) { - JInternalFrame frame = frames[f]; - if (frame != null && frame instanceof AlignFrame) + JInternalFrame alignFrame = frames[f]; + if (alignFrame != null && alignFrame instanceof AlignFrame) { - av = ((AlignFrame) frame).viewport; - ap = ((AlignFrame) frame).alignPanel; + av = ((AlignFrame) alignFrame).viewport; + ap = ((AlignFrame) alignFrame).alignPanel; return true; } } @@ -201,32 +203,36 @@ public class Finder extends GFinder } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Opens a dialog that allows the user to create sequence features for the + * find match results. */ @Override - public void createNewGroup_actionPerformed(ActionEvent e) + public void createFeatures_actionPerformed() { - SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[searchResults - .getSize()]; + List seqs = new ArrayList(); + List features = new ArrayList(); - int i = 0; + String searchString = textfield.getText().trim(); + String desc = "Search Results"; + + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ for (SearchResultMatchI match : searchResults.getResults()) { - seqs[i] = match.getSequence().getDatasetSequence(); - - features[i] = new SequenceFeature(textfield.getText().trim(), - "Search Results", null, match.getStart(), match.getEnd(), - "Search Results"); - i++; + seqs.add(match.getSequence().getDatasetSequence()); + features.add(new SequenceFeature(searchString, desc, null, match + .getStart(), match.getEnd(), desc)); } if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + features, true, ap, searchString)) { + /* + * ensure feature display is turned on to show the new features, + * and remove them as highlighted regions + */ ap.alignFrame.showSeqFeatures.setSelected(true); av.setShowSequenceFeatures(true); ap.highlightSearchResults(null); @@ -237,11 +243,11 @@ public class Finder extends GFinder * Search the alignment for the next or all matches. If 'all matches', a * dialog is shown with the number of sequence ids and subsequences matched. * - * @param findAll + * @param doFindAll */ - void doSearch(boolean findAll) + void doSearch(boolean doFindAll) { - createNewGroup.setEnabled(false); + createFeatures.setEnabled(false); String searchString = textfield.getText().trim(); @@ -258,7 +264,7 @@ public class Finder extends GFinder finder.setCaseSensitive(caseSensitive.isSelected()); finder.setIncludeDescription(searchDescription.isSelected()); - finder.setFindAll(findAll); + finder.setFindAll(doFindAll); finder.find(searchString); // returns true if anything was actually found @@ -283,7 +289,7 @@ public class Finder extends GFinder if (searchResults.getSize() > 0) { haveResults = true; - createNewGroup.setEnabled(true); + createFeatures.setEnabled(true); } else { @@ -305,7 +311,7 @@ public class Finder extends GFinder } else { - if (findAll) + if (doFindAll) { // then we report the matches that were found String message = (idMatch.size() > 0) ? "" + idMatch.size() diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 660c651..1685721 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -55,6 +55,7 @@ import jalview.util.UrlLink; import java.awt.Color; 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; @@ -1880,30 +1881,28 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList(); + List features = new ArrayList(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, null, start, end, + "Jalview")); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + features, true, ap, null)) { ap.alignFrame.setShowSeqFeatures(true); ap.highlightSearchResults(null); diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index db7aa36..95fe381 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -59,6 +59,7 @@ import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.util.ArrayList; +import java.util.Collections; import java.util.List; import javax.swing.JPanel; @@ -1484,6 +1485,11 @@ public class SeqPanel extends JPanel implements MouseListener, } } + /** + * Handler for double-click on a position with one or more sequence features. + * Opens the Amend Features dialog to allow feature details to be amended, or + * the feature deleted. + */ @Override public void mouseClicked(MouseEvent evt) { @@ -1502,20 +1508,23 @@ public class SeqPanel extends JPanel implements MouseListener, .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.size() > 0) + if (!features.isEmpty()) { + /* + * highlight the first feature at the position on the alignment + */ SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.size() > 0) - { - seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, - features.toArray(new SequenceFeature[features.size()]), - false, ap); + /* + * open the Amend Features dialog; clear highlighting afterwards, + * whether changes were made or not + */ + List seqs = Collections.singletonList(sequence); + seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, + ap, null); seqCanvas.highlightSearchResults(null); } } diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java index fef4568..7e9fc30 100755 --- a/src/jalview/jbgui/GFinder.java +++ b/src/jalview/jbgui/GFinder.java @@ -57,7 +57,7 @@ public class GFinder extends JPanel GridLayout gridLayout1 = new GridLayout(); - protected JButton createNewGroup = new JButton(); + protected JButton createFeatures = new JButton(); JScrollPane jScrollPane1 = new JScrollPane(); @@ -121,16 +121,16 @@ public class GFinder extends JPanel gridLayout1.setHgap(0); gridLayout1.setRows(3); gridLayout1.setVgap(2); - createNewGroup.setEnabled(false); - createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12)); - createNewGroup.setMargin(new Insets(0, 0, 0, 0)); - createNewGroup.setText(MessageManager.getString("label.new_feature")); - createNewGroup.addActionListener(new java.awt.event.ActionListener() + createFeatures.setEnabled(false); + createFeatures.setFont(new java.awt.Font("Verdana", 0, 12)); + createFeatures.setMargin(new Insets(0, 0, 0, 0)); + createFeatures.setText(MessageManager.getString("label.new_feature")); + createFeatures.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - createNewGroup_actionPerformed(e); + createFeatures_actionPerformed(); } }); textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12)); @@ -166,7 +166,7 @@ public class GFinder extends JPanel actionsPanel.add(findNext, null); actionsPanel.add(findAll, null); - actionsPanel.add(createNewGroup, null); + actionsPanel.add(createFeatures, null); this.add(jLabelFind, java.awt.BorderLayout.WEST); this.add(actionsPanel, java.awt.BorderLayout.EAST); this.add(jPanel2, java.awt.BorderLayout.SOUTH); @@ -204,7 +204,7 @@ public class GFinder extends JPanel } } - public void createNewGroup_actionPerformed(ActionEvent e) + public void createFeatures_actionPerformed() { } -- 1.7.10.2