From 93a27d6137378f64deed4a8dea5c150f4ce4eadd Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 23 Mar 2007 15:39:20 +0000 Subject: [PATCH] lastSeq==null to force refresh of sequencefeature array reference --- src/jalview/gui/FeatureRenderer.java | 1577 +++++++++++++++++----------------- 1 file changed, 789 insertions(+), 788 deletions(-) diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 634dbed..568b945 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,788 +1,789 @@ -/* - * 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 + * 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() + { + lastSeq=null; + 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; + } + } + + } + +} -- 1.7.10.2