X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=ac56590446bbb586fd553c8bc3a512c32cffe75d;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=634dbedae985fed6de65e73ef909d673811aad68;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index 634dbed..ac56590 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,788 +1,571 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; - -import jalview.datamodel.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - Color resBoxColour; - float transparency = 1.0f; - FontMetrics fm; - int charOffset; - - Hashtable featureColours = new Hashtable(); - - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - } - - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - } - - BufferedImage offscreenImage; - boolean offscreenRender = false; - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) - { - return new Color(findFeatureColour(initialCol.getRGB(), - seq, res)); - } - - /** - * This is used by the Molecule Viewer and Overview to - * get the accurate colourof the rendered sequence - */ - public int findFeatureColour(int initialCol, SequenceI seq, int column) - { - if (!av.showSequenceFeatures) - { - return initialCol; - } - - if (seq != lastSeq) - { - lastSeq = seq; - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures == null) - { - return initialCol; - } - - sfSize = sequenceFeatures.length; - } - - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) - { - return Color.white.getRGB(); - } - - //Only bother making an offscreen image if transparency is applied - if (transparency != 1.0f && offscreenImage == null) - { - offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); - } - - currentColour = null; - - offscreenRender = true; - - if (offscreenImage != null) - { - offscreenImage.setRGB(0, 0, initialCol); - drawSequence(offscreenImage.getGraphics(), - lastSeq, - column, column, 0); - - return offscreenImage.getRGB(0, 0); - } - else - { - drawSequence(null, - lastSeq, - lastSeq.findPosition(column), - -1, -1); - - if (currentColour == null) - { - return initialCol; - } - else - { - return ( (Integer) currentColour).intValue(); - } - } - - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param seq DOCUMENT ME! - * @param sg DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * @param x1 DOCUMENT ME! - * @param y1 DOCUMENT ME! - * @param width DOCUMENT ME! - * @param height DOCUMENT ME! - */ - // String type; - // SequenceFeature sf; - SequenceI lastSeq; - SequenceFeature[] sequenceFeatures; - int sfSize, sfindex, spos, epos; - - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) - { - if (seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().length == 0) - { - return; - } - - if (g != null) - { - fm = g.getFontMetrics(); - } - - if (av.featuresDisplayed == null - || renderOrder == null - || newFeatureAdded) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; - } - - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if (lastSeq == null || seq != lastSeq) - { - lastSeq = seq; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if (transparency != 1 && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); - } - - if (!offscreenRender) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - } - - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - - if (type == null || !av.featuresDisplayed.containsKey(type)) - { - continue; - } - - // loop through all features in sequence to find - // current feature to render - for (sfindex = 0; sfindex < sfSize; sfindex++) - { - if (sequenceFeatures.length <= sfindex) - { - continue; - } - if (!sequenceFeatures[sfindex].type.equals(type)) - { - continue; - } - - if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && - featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup) - && - ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex]. - featureGroup)). - booleanValue()) - { - continue; - } - - if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos - || sequenceFeatures[sfindex].getEnd() < spos)) - { - continue; - } - - if (offscreenRender && offscreenImage == null) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) - { - currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); - } - } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) - { - - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - new Color( ( (Integer) av.featuresDisplayed.get( - sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - new Color( ( (Integer) av.featuresDisplayed.get( - sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); - - } - else - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1); - } - - } - - } - - if (transparency != 1.0f && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); - } - } - - char s; - int i; - void renderFeature(Graphics g, SequenceI seq, - int fstart, int fend, Color featureColour, int start, - int end, int y1) - { - - if ( ( (fstart <= end) && (fend >= start))) - { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } - - if (fend >= end) - { - fend = end; - } - int pady = (y1 + av.charHeight) - av.charHeight / 5; - for (i = fstart; i <= fend; i++) - { - s = seq.getCharAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } - - g.setColor(featureColour); - - g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); - - if (offscreenRender || !av.validCharWidth) - { - continue; - } - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (av.charWidth * (i - start)), - pady); - - } - } - } - - boolean newFeatureAdded = false; - - public void featuresAdded() - { - findAllFeatures(); - } - - boolean findingFeatures = false; - synchronized void findAllFeatures() - { - newFeatureAdded = false; - - if (findingFeatures) - { - newFeatureAdded = true; - return; - } - - findingFeatures = true; - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - av.featuresDisplayed.clear(); - - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature[] features - = av.alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) - { - if (!av.featuresDisplayed.containsKey(features[index].getType())) - { - if (! (features[index].begin == 0 && features[index].end == 0)) - { - // If beginning and end are 0, the feature is for the whole sequence - // and we don't want to render the feature in the normal way - - if (getColour(features[index].getType()) == null) - { - featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index]. - getType())); - } - - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index]. - getType()).getRGB())); - allfeatures.addElement(features[index].getType()); - } - } - index++; - } - } - - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size() - 1; - while (en.hasMoreElements()) - { - renderOrder[i] = en.nextElement().toString(); - i--; - } - - findingFeatures = false; - } - - public Color getColour(String featureType) - { - Color colour = (Color) featureColours.get(featureType); - return colour; - } - - static String lastFeatureAdded; - static String lastFeatureGroupAdded; - static String lastDescriptionAdded; - - public boolean createNewFeatures(SequenceI[] sequences, - SequenceFeature[] features) - { - return amendFeatures(sequences, features, true, null); - } - - int featureIndex = 0; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, - boolean newFeatures, - final AlignmentPanel ap) - { - JPanel bigPanel = new JPanel(new BorderLayout()); - final JComboBox name = new JComboBox(); - final JComboBox source = new JComboBox(); - final JTextArea description = new JTextArea(3, 25); - final JSpinner start = new JSpinner(); - final JSpinner end = new JSpinner(); - start.setPreferredSize(new Dimension(80, 20)); - end.setPreferredSize(new Dimension(80, 20)); - final JPanel colour = new JPanel(); - colour.setBorder(BorderFactory.createEtchedBorder()); - colour.setMaximumSize(new Dimension(40, 10)); - colour.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - colour.setBackground( - JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", - colour.getBackground())); - } - }); - - JPanel panel = new JPanel(new GridLayout(3, 2)); - panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT)); - panel.add(name); - panel.add(new JLabel("Feature Group: ", JLabel.RIGHT)); - panel.add(source); - panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT)); - JPanel tmp = new JPanel(); - tmp.add(colour); - colour.setPreferredSize(new Dimension(150, 15)); - panel.add(tmp); - name.setEditable(true); - source.setEditable(true); - - bigPanel.add(panel, BorderLayout.NORTH); - panel = new JPanel(); - panel.add(new JLabel("Description: ", JLabel.RIGHT)); - description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - description.setLineWrap(true); - panel.add(new JScrollPane(description)); - - if (!newFeatures) - { - bigPanel.add(panel, BorderLayout.SOUTH); - - panel = new JPanel(); - panel.add(new JLabel(" Start:", JLabel.RIGHT)); - panel.add(start); - panel.add(new JLabel(" End:", JLabel.RIGHT)); - panel.add(end); - bigPanel.add(panel, BorderLayout.CENTER); - } - else - { - bigPanel.add(panel, BorderLayout.CENTER); - } - - if (lastFeatureAdded == null) - { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else - { - lastFeatureAdded = "feature_1"; - } - } - - if (lastFeatureGroupAdded == null) - { - if (features[0].featureGroup != null) - { - lastFeatureGroupAdded = features[0].featureGroup; - } - else - { - lastFeatureAdded = "Jalview"; - } - } - - Enumeration en; - if (featureGroups != null) - { - en = featureGroups.keys(); - while (en.hasMoreElements()) - { - source.addItem(en.nextElement().toString()); - } - } - - if (newFeatures) - { - if (av.featuresDisplayed != null) - { - en = av.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - name.addItem(en.nextElement().toString()); - } - } - - name.setSelectedItem(lastFeatureAdded); - source.setSelectedItem(lastFeatureGroupAdded); - description.setText( - lastDescriptionAdded == null ? - features[0].description : lastDescriptionAdded); - - if (getColour(lastFeatureAdded) != null) - { - colour.setBackground(getColour(lastFeatureAdded)); - } - else - { - colour.setBackground(new Color(60, 160, 115)); - } - - } - else if (!newFeatures) - { - featureIndex = 0; - for (int f = 0; f < features.length; f++) - { - name.addItem(features[f].getType().toString()); - } - - description.setText(features[0].getDescription()); - source.setSelectedItem(features[0].getFeatureGroup()); - start.setValue(new Integer(features[0].getBegin())); - end.setValue(new Integer(features[0].getEnd())); - colour.setBackground( - getColour(name.getSelectedItem().toString())); - name.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - int index = name.getSelectedIndex(); - if (index != -1) - { - featureIndex = index; - description.setText(features[index].getDescription()); - source.setSelectedItem(features[index].getFeatureGroup()); - start.setValue(new Integer(features[index].getBegin())); - end.setValue(new Integer(features[index].getEnd())); - colour.setBackground( - getColour(name.getSelectedItem().toString())); - - SearchResults highlight = new SearchResults(); - highlight.addResult(sequences[0], - features[index].getBegin(), - features[index].getEnd()); - - ap.seqPanel.seqCanvas.highlightSearchResults(highlight); - - } - Color col = getColour(name.getSelectedItem().toString()); - if (col == null) - { - col = new - jalview.schemes.UserColourScheme() - .createColourFromName(name.getSelectedItem().toString()); - } - - colour.setBackground(col); - } - }); - - } - - Object[] options; - if (!newFeatures) - { - options = new Object[] - { - "Amend", "Delete", "Cancel"}; - } - else - { - options = new Object[] - { - "OK", "Cancel"}; - } - - String title = newFeatures ? "Create New Sequence Feature(s)" : - "Amend/Delete Features for " - + sequences[0].getName(); - - int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, - title, - JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, - null, - options, "OK"); - - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); - - if (reply == JOptionPane.OK_OPTION - && name.getSelectedItem() != null - && source.getSelectedItem() != null) - { - //This ensures that the last sequence - //is refreshed and new features are rendered - lastSeq = null; - lastFeatureAdded = name.getSelectedItem().toString(); - lastFeatureGroupAdded = source.getSelectedItem().toString(); - lastDescriptionAdded = description.getText().replaceAll("\n", " "); - } - - if (!newFeatures) - { - SequenceFeature sf = features[featureIndex]; - - if (reply == JOptionPane.NO_OPTION) - { - sequences[0].getDatasetSequence().deleteFeature(sf); - } - else if (reply == JOptionPane.YES_OPTION) - { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; - setColour(sf.type, colour.getBackground()); - try - { - sf.begin = ( (Integer) start.getValue()).intValue(); - sf.end = ( (Integer) end.getValue()).intValue(); - } - catch (NumberFormatException ex) - {} - - ffile.parseDescriptionHTML(sf, false); - } - } - else - { - if (reply == JOptionPane.OK_OPTION - && name.getSelectedItem() != null - && source.getSelectedItem() != null) - { - for (int i = 0; i < sequences.length; i++) - { - features[i].type = lastFeatureAdded; - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); - } - - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - if (featureGroups == null) - { - featureGroups = new Hashtable(); - } - - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - - Color col = colour.getBackground(); - setColour(lastFeatureAdded, colour.getBackground()); - - av.featuresDisplayed.put(lastFeatureGroupAdded, - new Integer(col.getRGB())); - - findAllFeatures(); - - return true; - } - else - { - return false; - } - } - - if (name.getSelectedIndex() == -1) - { - findAllFeatures(); - } - - return true; - } - - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - public void setTransparency(float value) - { - transparency = value; - } - - public float getTransparency() - { - return transparency; - } - - public void setFeaturePriority(Object[][] data) - { - // The feature table will display high priority - // features at the top, but theses are the ones - // we need to render last, so invert the data - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - - renderOrder = new String[data.length]; - - if (data.length > 0) - { - for (int i = 0; i < data.length; i++) - { - String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); - if ( ( (Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } - } - - } - -} +/* + * 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.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +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; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer +{ + /* + * defaults for creating a new feature are the last created + * feature type and group + */ + static String lastFeatureAdded = "feature_1"; + + static String lastFeatureGroupAdded = "Jalview"; + + Color resBoxColour; + + AlignmentPanel ap; + + /** + * Creates a new FeatureRenderer object + * + * @param alignPanel + */ + public FeatureRenderer(AlignmentPanel alignPanel) + { + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) + { + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); + } + } + + FeatureColourI oldcol, fcol; + + int featureIndex = 0; + + /** + * Presents a dialog allowing the user to add new features, or amend or delete + * existing features. Currently this can be on + * + * 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 + * @return + */ + protected boolean amendFeatures(final List sequences, + final List features, boolean create, + final AlignmentPanel alignPanel) + { + featureIndex = 0; + + final JPanel mainPanel = new JPanel(new BorderLayout()); + + final JTextField name = new JTextField(25); + name.getDocument().addDocumentListener(new DocumentListener() + { + @Override + public void insertUpdate(DocumentEvent e) + { + 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.getDocument().addDocumentListener(new DocumentListener() + { + @Override + public void insertUpdate(DocumentEvent e) + { + 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(); + start.setPreferredSize(new Dimension(80, 20)); + end.setPreferredSize(new Dimension(80, 20)); + final FeatureRenderer me = this; + final JLabel colour = new JLabel(); + colour.setOpaque(true); + // colour.setBorder(BorderFactory.createEtchedBorder()); + colour.setMaximumSize(new Dimension(30, 16)); + colour.addMouseListener(new MouseAdapter() + { + FeatureColourChooser fcc = null; + + @Override + public void mousePressed(MouseEvent evt) + { + if (fcol.isSimpleColour()) + { + Color col = JColorChooser.showDialog(Desktop.desktop, + MessageManager.getString("label.select_feature_colour"), + fcol.getColour()); + if (col != null) + { + fcol = new FeatureColour(col); + updateColourButton(mainPanel, colour, fcol); + } + } + else + { + if (fcc == null) + { + final String ft = features.get(featureIndex).getType(); + final String type = ft == null ? lastFeatureAdded : ft; + fcc = new FeatureColourChooser(me, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + + fcc.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + fcol = fcc.getLastColour(); + fcc = null; + setColour(type, fcol); + updateColourButton(mainPanel, colour, fcol); + } + }); + + } + } + } + }); + JPanel gridPanel = new JPanel(new GridLayout(3, 1)); + + if (!create && features.size() > 1) + { + /* + * 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") + + ":")); + final JComboBox overlaps = new JComboBox(); + for (SequenceFeature sf : features) + { + String text = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; + overlaps.addItem(text); + } + choosePanel.add(overlaps); + + overlaps.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + int index = overlaps.getSelectedIndex(); + if (index != -1) + { + featureIndex = index; + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + group.setText(sf.getFeatureGroup()); + start.setValue(new Integer(sf.getBegin())); + end.setValue(new Integer(sf.getEnd())); + + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); + + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight); + + } + FeatureColourI col = getFeatureStyle(name.getText()); + if (col == null) + { + col = new FeatureColour(ColorUtils + .createColourFromName(name.getText())); + } + oldcol = fcol = col; + 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"), + JLabel.RIGHT)); + colourPanel.add(colour); + colour.setPreferredSize(new Dimension(150, 15)); + colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); + colour.setForeground(Color.black); + colour.setHorizontalAlignment(SwingConstants.CENTER); + colour.setVerticalAlignment(SwingConstants.CENTER); + 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) + { + mainPanel.add(descriptionPanel, BorderLayout.SOUTH); + + JPanel startEndPanel = new JPanel(); + startEndPanel.add(new JLabel(MessageManager.getString("label.start"), + JLabel.RIGHT)); + startEndPanel.add(start); + startEndPanel.add(new JLabel(MessageManager.getString("label.end"), + JLabel.RIGHT)); + startEndPanel.add(end); + mainPanel.add(startEndPanel, BorderLayout.CENTER); + } + else + { + 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) + */ + SequenceFeature firstFeature = features.get(0); + boolean useLastDefaults = firstFeature.getType() == null; + final String featureType = useLastDefaults ? lastFeatureAdded + : firstFeature.getType(); + final String featureGroup = useLastDefaults ? lastFeatureGroupAdded + : firstFeature.getFeatureGroup(); + name.setText(featureType); + group.setText(featureGroup); + + start.setValue(new Integer(firstFeature.getBegin())); + end.setValue(new Integer(firstFeature.getEnd())); + description.setText(firstFeature.getDescription()); + updateColourButton(mainPanel, colour, + (oldcol = fcol = getFeatureStyle(featureType))); + Object[] options; + if (!create) + { + options = new Object[] { MessageManager.getString("label.amend"), + MessageManager.getString("action.delete"), + MessageManager.getString("action.cancel") }; + } + else + { + options = new Object[] { MessageManager.getString("action.ok"), + 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() }); + + /* + * show the dialog + */ + int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop, + mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.QUESTION_MESSAGE, null, options, + MessageManager.getString("action.ok")); + + FeaturesFile ffile = new FeaturesFile(); + + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText().replaceAll("\n", " "); + + if (reply == JvOptionPane.OK_OPTION && 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) + { + SequenceFeature sf = features.get(featureIndex); + + if (reply == JvOptionPane.NO_OPTION) + { + /* + * NO_OPTION corresponds to the Delete button + */ + sequences.get(0).getDatasetSequence().deleteFeature(sf); + // update Feature Settings for removal of feature / group + featuresAdded(); + } + else if (reply == JvOptionPane.YES_OPTION) + { + /* + * 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 |= (fcol != oldcol); + setColour(enteredType, fcol); + 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, newBegin, newEnd, + enteredGroup, sf.getScore()); + sf.setDescription(enteredDescription); + ffile.parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + + if (refreshSettings) + { + featuresAdded(); + } + } + } + else + // NEW FEATURES ADDED + { + if (reply == JvOptionPane.OK_OPTION && 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); + ffile.parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); + } + + setColour(enteredType, fcol); + + featuresAdded(); + + alignPanel.paintAlignment(true); + + return true; + } + else + { + return false; + } + } + + alignPanel.paintAlignment(true); + + return true; + } + + /** + * Show a warning message if the entered type is one that is currently hidden + * + * @param panel + * @param type + */ + protected void warnIfTypeHidden(JPanel panel, String type) + { + if (getRenderOrder().contains(type)) + { + if (!showFeatureOfType(type)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); + } + } + } + + /** + * Show a warning message if the entered group is one that is currently hidden + * + * @param panel + * @param group + */ + protected void warnIfGroupHidden(JPanel panel, String group) + { + if (featureGroups.containsKey(group) && !featureGroups.get(group)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION); + } + } + + /** + * update the amend feature button dependent on the given style + * + * @param bigPanel + * @param col + * @param col + */ + protected void updateColourButton(JPanel bigPanel, JLabel colour, + FeatureColourI col) + { + colour.removeAll(); + colour.setIcon(null); + colour.setToolTipText(null); + colour.setText(""); + + if (col.isSimpleColour()) + { + colour.setBackground(col.getColour()); + } + else + { + colour.setBackground(bigPanel.getBackground()); + colour.setForeground(Color.black); + FeatureSettings.renderGraduatedColor(colour, col); + } + } + + /** + * Orders features in render precedence (last in order is last to render, so + * displayed on top of other features) + * + * @param order + */ + public void orderFeatures(Comparator order) + { + Arrays.sort(renderOrder, order); + } +}