X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureEditor.java;h=844eee4f74c3ccddb2325ed6e6a8bd4e9d1e739d;hb=0e8bd9f4db76c85561be7e65f1e987c2d78b4fd6;hp=a86725b8bcfd40e00b11f0e735db467a23ac7435;hpb=2cc0663ace7adaa36478db77ca96daa736993890;p=jalview.git diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java index a86725b..844eee4 100644 --- a/src/jalview/gui/FeatureEditor.java +++ b/src/jalview/gui/FeatureEditor.java @@ -1,17 +1,25 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.gui; -import jalview.api.FeatureColourI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.gui.JalviewColourChooser.ColourChooserListener; -import jalview.io.FeaturesFile; -import jalview.schemes.FeatureColour; -import jalview.util.ColorUtils; -import jalview.util.MessageManager; -import jalview.util.dialogrunner.RunResponse; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -33,10 +41,24 @@ import javax.swing.JScrollPane; import javax.swing.JSpinner; import javax.swing.JTextArea; import javax.swing.JTextField; +import javax.swing.SpinnerNumberModel; import javax.swing.SwingConstants; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; + /** * Provides a dialog allowing the user to add new features, or amend or delete * existing features @@ -52,7 +74,23 @@ public class FeatureEditor static String lastFeatureGroupAdded = "Jalview"; /* - * index into a list of features if more than one selected for editing + * the sequence(s) with features to be created / amended + */ + final List sequences; + + /* + * the features (or template features) to be created / amended + */ + final List features; + + /* + * true if the dialog is to create a new feature, false if + * for amend or delete of existing feature(s) + */ + final boolean forCreate; + + /* + * index into the list of features */ int featureIndex; @@ -64,50 +102,50 @@ public class FeatureEditor AlignmentPanel ap; + JTextField name; + + JTextField group; + + JTextArea description; + + JSpinner start; + + JSpinner end; + + JPanel mainPanel; + /** * Constructor * * @param alignPanel + * @param seqs + * @param feats + * @param create + * if true create a new feature, else amend or delete an existing + * feature */ - public FeatureEditor(AlignmentPanel alignPanel) + public FeatureEditor(AlignmentPanel alignPanel, List seqs, + List feats, boolean create) { ap = alignPanel; fr = alignPanel.getSeqPanel().seqCanvas.fr; + sequences = seqs; + features = feats; + this.forCreate = create; + + init(); } /** - * Presents a dialog allowing the user to add new features, or amend or delete - * existing features. Currently this can be on - *
    - *
  • double-click on a sequence - Amend/Delete features at position
    • - *
  • Create sequence feature from pop-up menu on selected region
    • - *
  • Create features for pattern matches from Find
    • - *
- * If the supplied feature type is null, show (and update on confirm) the type - * and group of the last new feature created (with initial defaults of - * "feature_1" and "Jalview"). - * - * @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 feature(s) with start/end position set (if creating) - * @param create - * true to create features, false to amend or delete - * @param alignPanel - * @param responseHandler - * boolean true RunResponse is run if features are created + * Initialise the layout and controls */ - public boolean amendFeatures(final List sequences, - final List features, boolean create, - final Runnable responseHandler) + protected void init() { featureIndex = 0; - - final JPanel mainPanel = new JPanel(new BorderLayout()); - - final JTextField name = new JTextField(25); + + mainPanel = new JPanel(new BorderLayout()); + + name = new JTextField(25); name.getDocument().addDocumentListener(new DocumentListener() { @Override @@ -115,21 +153,21 @@ public class FeatureEditor { warnIfTypeHidden(mainPanel, name.getText()); } - + @Override public void removeUpdate(DocumentEvent e) { warnIfTypeHidden(mainPanel, name.getText()); } - + @Override public void changedUpdate(DocumentEvent e) { warnIfTypeHidden(mainPanel, name.getText()); } }); - - final JTextField group = new JTextField(25); + + group = new JTextField(25); group.getDocument().addDocumentListener(new DocumentListener() { @Override @@ -137,39 +175,62 @@ public class FeatureEditor { warnIfGroupHidden(mainPanel, group.getText()); } - + @Override public void removeUpdate(DocumentEvent e) { warnIfGroupHidden(mainPanel, group.getText()); } - + @Override public void changedUpdate(DocumentEvent e) { warnIfGroupHidden(mainPanel, group.getText()); } }); - - final JTextArea description = new JTextArea(3, 25); - final JSpinner start = new JSpinner(); - final JSpinner end = new JSpinner(); + + description = new JTextArea(3, 25); + + start = new JSpinner(); + end = new JSpinner(); start.setPreferredSize(new Dimension(80, 20)); end.setPreferredSize(new Dimension(80, 20)); + + /* + * ensure that start can never be more than end + */ + start.addChangeListener(new ChangeListener() + { + @Override + public void stateChanged(ChangeEvent e) + { + Integer startVal = (Integer) start.getValue(); + ((SpinnerNumberModel) end.getModel()).setMinimum(startVal); + } + }); + end.addChangeListener(new ChangeListener() + { + @Override + public void stateChanged(ChangeEvent e) + { + Integer endVal = (Integer) end.getValue(); + ((SpinnerNumberModel) start.getModel()).setMaximum(endVal); + } + }); + final JLabel colour = new JLabel(); colour.setOpaque(true); - // colour.setBorder(BorderFactory.createEtchedBorder()); colour.setMaximumSize(new Dimension(30, 16)); colour.addMouseListener(new MouseAdapter() { - /* - * open colour chooser on click in colour panel - */ @Override public void mousePressed(MouseEvent evt) { if (featureColour.isSimpleColour()) { + /* + * open colour chooser on click in colour panel + */ String title = MessageManager .getString("label.select_feature_colour"); ColourChooserListener listener = new ColourChooserListener() @@ -192,8 +253,7 @@ public class FeatureEditor */ final String ft = features.get(featureIndex).getType(); final String type = ft == null ? lastFeatureAdded : ft; - FeatureTypeSettings fcc = new FeatureTypeSettings( - fr, type); + FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type); fcc.setRequestFocusEnabled(true); fcc.requestFocus(); fcc.addActionListener(new ActionListener() @@ -210,8 +270,8 @@ public class FeatureEditor } }); JPanel gridPanel = new JPanel(new GridLayout(3, 1)); - - if (!create && features.size() > 1) + + if (!forCreate && features.size() > 1) { /* * more than one feature at selected position - @@ -236,7 +296,7 @@ public class FeatureEditor added.add(text); } choosePanel.add(overlaps); - + overlaps.addItemListener(new ItemListener() { @Override @@ -252,13 +312,14 @@ public class FeatureEditor group.setText(sf.getFeatureGroup()); start.setValue(new Integer(sf.getBegin())); end.setValue(new Integer(sf.getEnd())); - + ((SpinnerNumberModel) start.getModel()).setMaximum(sf.getEnd()); + ((SpinnerNumberModel) end.getModel()).setMinimum(sf.getBegin()); + SearchResultsI highlight = new SearchResults(); highlight.addResult(sequences.get(0), sf.getBegin(), sf.getEnd()); - - ap.getSeqPanel().seqCanvas - .highlightSearchResults(highlight, false); + + ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } FeatureColourI col = fr.getFeatureStyle(name.getText()); if (col == null) @@ -270,22 +331,22 @@ public class FeatureEditor updateColourButton(mainPanel, colour, col); } }); - + gridPanel.add(choosePanel); } - + JPanel namePanel = new JPanel(); gridPanel.add(namePanel); namePanel.add(new JLabel(MessageManager.getString("label.name:"), JLabel.RIGHT)); namePanel.add(name); - + JPanel groupPanel = new JPanel(); gridPanel.add(groupPanel); groupPanel.add(new JLabel(MessageManager.getString("label.group:"), JLabel.RIGHT)); groupPanel.add(group); - + JPanel colourPanel = new JPanel(); gridPanel.add(colourPanel); colourPanel.add(new JLabel(MessageManager.getString("label.colour"), @@ -299,18 +360,18 @@ public class FeatureEditor colour.setHorizontalTextPosition(SwingConstants.CENTER); colour.setVerticalTextPosition(SwingConstants.CENTER); mainPanel.add(gridPanel, BorderLayout.NORTH); - + JPanel descriptionPanel = new JPanel(); descriptionPanel.add(new JLabel( MessageManager.getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); descriptionPanel.add(new JScrollPane(description)); - - if (!create) + + if (!forCreate) { mainPanel.add(descriptionPanel, BorderLayout.SOUTH); - + JPanel startEndPanel = new JPanel(); startEndPanel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT)); @@ -324,7 +385,7 @@ public class FeatureEditor { mainPanel.add(descriptionPanel, BorderLayout.CENTER); } - + /* * default feature type and group to that of the first feature supplied, * or to the last feature created if not supplied (null value) @@ -337,156 +398,180 @@ public class FeatureEditor : firstFeature.getFeatureGroup(); name.setText(featureType); group.setText(featureGroup); - + start.setValue(new Integer(firstFeature.getBegin())); end.setValue(new Integer(firstFeature.getEnd())); + ((SpinnerNumberModel) start.getModel()) + .setMaximum(firstFeature.getEnd()); + ((SpinnerNumberModel) end.getModel()) + .setMinimum(firstFeature.getBegin()); + description.setText(firstFeature.getDescription()); featureColour = fr.getFeatureStyle(featureType); oldColour = featureColour; updateColourButton(mainPanel, colour, oldColour); - Object[] options; - if (!create) + } + + /** + * Presents a dialog allowing the user to add new features, or amend or delete + * an existing feature. Currently this can be on + *
    + *
  • double-click on a sequence - Amend/Delete a selected feature at the + * position
    • + *
  • Create sequence feature(s) from pop-up menu on selected region
    • + *
  • Create features for pattern matches from Find
    • + *
+ * If the supplied feature type is null, show (and update on confirm) the type + * and group of the last new feature created (with initial defaults of + * "feature_1" and "Jalview"). + */ + public void showDialog() + { + Runnable okAction = forCreate ? getCreateAction() : getAmendAction(); + Runnable cancelAction = getCancelAction(); + + /* + * set dialog action handlers for OK (create/Amend) and Cancel options + * also for Delete if applicable (when amending features) + */ + JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame) + .setResponseHandler(0, okAction) + .setResponseHandler(2, cancelAction); + if (!forCreate) { - options = new Object[] { MessageManager.getString("label.amend"), - MessageManager.getString("action.delete"), + dialog.setResponseHandler(1, getDeleteAction()); + } + + String title = null; + Object[] options = null; + if (forCreate) + { + title = MessageManager + .getString("label.create_new_sequence_features"); + options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; } else { - options = new Object[] { MessageManager.getString("action.ok"), + title = MessageManager.formatMessage("label.amend_delete_features", + new String[] + { sequences.get(0).getName() }); + options = new Object[] { MessageManager.getString("label.amend"), + MessageManager.getString("action.delete"), MessageManager.getString("action.cancel") }; } - - String title = create - ? MessageManager.getString("label.create_new_sequence_features") - : MessageManager.formatMessage("label.amend_delete_features", - new String[] - { sequences.get(0).getName() }); - - /* - * register responses and show the dialog - */ - JvOptionPane.newOptionDialog(Desktop.desktop).response( - - new RunResponse(JvOptionPane.OK_OPTION) - { - public void run() - { - final String enteredType = name.getText().trim(); - final String enteredGroup = group.getText().trim(); - final String enteredDescription = description.getText() - .replaceAll("\n", " "); - if (enteredType.length() > 0) - - { - /* - * update default values only if creating using default values - */ - if (useLastDefaults) - { - lastFeatureAdded = enteredType; - lastFeatureGroupAdded = enteredGroup; - // TODO: determine if the null feature group is valid - if (lastFeatureGroupAdded.length() < 1) - { - lastFeatureGroupAdded = null; - } - } - } - - if (create) - { - // NEW FEATURES ADDED - if (enteredType.length() > 0) - { - for (int i = 0; i < sequences.size(); i++) - { - SequenceFeature sf = features.get(i); - SequenceFeature sf2 = new SequenceFeature(enteredType, - enteredDescription, sf.getBegin(), - sf.getEnd(), enteredGroup); - new FeaturesFile().parseDescriptionHTML(sf2, false); - sequences.get(i).addSequenceFeature(sf2); - } - - fr.setColour(enteredType, featureColour); - - fr.featuresAdded(); - - responseHandler.run(); - } - } else { - SequenceFeature sf = features.get(featureIndex); - /* - * Feature amended - YES_OPTION corresponds to the Amend button - * need to refresh Feature Settings if type, group or colour changed; - * note we don't force the feature to be visible - the user has been - * warned if a hidden feature type or group was entered - */ - boolean refreshSettings = (!featureType.equals(enteredType) - || !featureGroup.equals(enteredGroup)); - refreshSettings |= (featureColour != oldColour); - fr.setColour(enteredType, featureColour); - int newBegin = sf.begin; - int newEnd = sf.end; - try - { - newBegin = ((Integer) start.getValue()).intValue(); - newEnd = ((Integer) end.getValue()).intValue(); - } catch (NumberFormatException ex) - { - // JSpinner doesn't accept invalid format data :-) - } - - /* - * replace the feature by deleting it and adding a new one - * (to ensure integrity of SequenceFeatures data store) - */ - sequences.get(0).deleteFeature(sf); - SequenceFeature newSf = new SequenceFeature(sf, enteredType, - newBegin, newEnd, enteredGroup, sf.getScore()); - newSf.setDescription(enteredDescription); - new FeaturesFile().parseDescriptionHTML(newSf, false); - // amend features dialog only updates one sequence at a time - sequences.get(0).addSequenceFeature(newSf); - - if (refreshSettings) - { - fr.featuresAdded(); - } - } - ap.getSeqPanel().seqCanvas.highlightSearchResults(null, - false); - ap.paintAlignment(true, true); - } - }).response(new RunResponse(JvOptionPane.NO_OPTION) - { - public void run() - { - SequenceFeature sf = features.get(featureIndex); - /* - * NO_OPTION corresponds to the Delete button - */ - sequences.get(0).getDatasetSequence().deleteFeature(sf); - // update Feature Settings for removal of feature / group - fr.featuresAdded(); - ap.getSeqPanel().seqCanvas.highlightSearchResults(null, - false); - ap.paintAlignment(true, true); - } - }).defaultResponse(new Runnable() + + dialog.showInternalDialog(mainPanel, title, + JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, + null, options, MessageManager.getString("action.ok")); + } + + /** + * Answers an action to run on Cancel in the dialog. This is just to remove + * any feature highlighting from the display. Changes in the dialog are not + * applied until it is dismissed with OK, Amend or Delete, so there are no + * updates to reset on Cancel. + * + * @return + */ + protected Runnable getCancelAction() + { + Runnable okAction = new Runnable() + { + @Override + public void run() + { + ap.highlightSearchResults(null); + ap.paintAlignment(false, false); + } + }; + return okAction; + } + + /** + * Returns the action to be run on OK in the dialog when creating one or more + * sequence features. Note these may have a pre-supplied feature type (such as + * a Find pattern), or none, in which case the feature type and group default + * to those last added through this dialog. The action includes refreshing the + * Feature Settings panel (if it is open), to show any new feature type, or + * amended colour for an existing type. + * + * @return + */ + protected Runnable getCreateAction() + { + Runnable okAction = new Runnable() + { + boolean useLastDefaults = features.get(0).getType() == null; + + @Override + public void run() + { + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText() + .replaceAll("\n", " "); + if (enteredType.length() > 0) + { + /* + * update default values only if creating using default values + */ + if (useLastDefaults) + { + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) { - public void run() - { - ap.getSeqPanel().seqCanvas.highlightSearchResults(null, - false); - ap.paintAlignment(true, true); - } - }).showInternalDialog(mainPanel, title, - JvOptionPane.YES_NO_CANCEL_OPTION, - JvOptionPane.QUESTION_MESSAGE, null, options, - MessageManager.getString("action.ok")); - return true; + lastFeatureGroupAdded = null; + } + } + } + + if (enteredType.length() > 0) + { + for (int i = 0; i < sequences.size(); i++) + { + SequenceFeature sf = features.get(i); + SequenceFeature sf2 = new SequenceFeature(enteredType, + enteredDescription, sf.getBegin(), sf.getEnd(), + enteredGroup); + new FeaturesFile().parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); + } + + fr.setColour(enteredType, featureColour); + fr.featuresAdded(); + + repaintPanel(); + } + } + }; + return okAction; + } + + /** + * Answers the action to run on Delete in the dialog. Note this includes + * refreshing the Feature Settings (if open) in case the only instance of a + * feature type or group has been deleted. + * + * @return + */ + protected Runnable getDeleteAction() + { + Runnable deleteAction = new Runnable() + { + @Override + public void run() + { + SequenceFeature sf = features.get(featureIndex); + sequences.get(0).getDatasetSequence().deleteFeature(sf); + fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.highlightSearchResults(null); + ap.paintAlignment(true, true); + } + }; + return deleteAction; } /** @@ -501,17 +586,18 @@ public class FeatureEditor { colour.removeAll(); colour.setIcon(null); - colour.setToolTipText(null); colour.setText(""); - + if (col.isSimpleColour()) { + colour.setToolTipText(null); colour.setBackground(col.getColour()); } else { colour.setBackground(bigPanel.getBackground()); colour.setForeground(Color.black); + colour.setToolTipText(FeatureSettings.getColorTooltip(col, false)); FeatureSettings.renderGraduatedColor(colour, col); } } @@ -553,4 +639,104 @@ public class FeatureEditor } } + /** + * On closing the dialog - ensure feature display is turned on, to show any + * new features - remove highlighting of the last selected feature - repaint + * the panel to show any changes + */ + protected void repaintPanel() + { + ap.alignFrame.showSeqFeatures.setSelected(true); + ap.av.setShowSequenceFeatures(true); + ap.av.setSearchResults(null); + ap.paintAlignment(true, true); + } + + /** + * Returns the action to be run on OK in the dialog when amending a feature. + * Note this may include refreshing the Feature Settings panel (if it is + * open), if feature type, group or colour has changed (but not for + * description or extent). + * + * @return + */ + protected Runnable getAmendAction() + { + Runnable okAction = new Runnable() + { + boolean useLastDefaults = features.get(0).getType() == null; + + String featureType = name.getText(); + + String featureGroup = group.getText(); + + @Override + public void run() + { + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText() + .replaceAll("\n", " "); + if (enteredType.length() > 0) + + { + /* + * update default values only if creating using default values + */ + if (useLastDefaults) + { + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + { + lastFeatureGroupAdded = null; + } + } + } + + SequenceFeature sf = features.get(featureIndex); + + /* + * Need to refresh Feature Settings if type, group or colour changed; + * note we don't force the feature to be visible - the user has been + * warned if a hidden feature type or group was entered + */ + boolean refreshSettings = (!featureType.equals(enteredType) + || !featureGroup.equals(enteredGroup)); + refreshSettings |= (featureColour != oldColour); + fr.setColour(enteredType, featureColour); + int newBegin = sf.begin; + int newEnd = sf.end; + try + { + newBegin = ((Integer) start.getValue()).intValue(); + newEnd = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { + // JSpinner doesn't accept invalid format data :-) + } + + /* + * 'amend' the feature by deleting it and adding a new one + * (to ensure integrity of SequenceFeatures data store) + * note this dialog only updates one sequence at a time + */ + sequences.get(0).deleteFeature(sf); + SequenceFeature newSf = new SequenceFeature(sf, enteredType, + newBegin, newEnd, enteredGroup, sf.getScore()); + newSf.setDescription(enteredDescription); + new FeaturesFile().parseDescriptionHTML(newSf, false); + sequences.get(0).addSequenceFeature(newSf); + + if (refreshSettings) + { + fr.featuresAdded(); + } + repaintPanel(); + } + }; + return okAction; + } + }