X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=8d194f39af0d2719bb47277c3436c2e7747d3ee9;hp=e73679582db90930fa10098d1eb943d84694bd23;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hpb=197359781e7142ec6bcb53740831fc626c4675cd diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index e736795..8d194f3 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,716 +1,1462 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - -import java.awt.image.*; -import javax.swing.*; -import javax.swing.JOptionPane; -import java.awt.event.*; - - -/** - * 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 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.getSequence().charAt(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); - } - - int featureIndex = 0; - boolean amendFeatures(SequenceI[] sequences, - final SequenceFeature [] features, - boolean newFeatures) - { - 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(); - - 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)); - colour.setForeground(getColour(lastFeatureAdded)); - } - else - { - colour.setBackground(new Color(60, 160, 115)); - colour.setForeground(new Color(60, 160, 115)); - } - - } - else if (!newFeatures) - { - featureIndex = 0; - for(int f=0; f 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.gui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; +import java.awt.image.*; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; + +import javax.swing.*; + +import jalview.datamodel.*; +import jalview.schemes.GraduatedColor; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer implements jalview.api.FeatureRenderer +{ + AlignmentPanel ap; + + AlignViewport av; + + Color resBoxColour; + + /** + * global transparency for feature + */ + float transparency = 1.0f; + + FontMetrics fm; + + int charOffset; + + Hashtable featureColours = new Hashtable(); + + // A higher level for grouping features of a + // particular type + Hashtable featureGroups = new Hashtable(); + + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; + + String[] renderOrder; + + PropertyChangeSupport changeSupport = new PropertyChangeSupport(this); + + Vector allfeatures; + + /** + * Creates a new FeatureRenderer object. + * + * @param av + * DOCUMENT ME! + */ + public FeatureRenderer(AlignmentPanel ap) + { + this.ap = ap; + this.av = ap.av; + } + + public class FeatureRendererSettings implements Cloneable + { + String[] renderOrder; + + Hashtable featureGroups; + + Hashtable featureColours; + + float transparency; + + Hashtable featureOrder; + + public FeatureRendererSettings(String[] renderOrder, + Hashtable featureGroups, Hashtable featureColours, + float transparency, Hashtable featureOrder) + { + super(); + this.renderOrder = renderOrder; + this.featureGroups = featureGroups; + this.featureColours = featureColours; + this.transparency = transparency; + this.featureOrder = featureOrder; + } + + /** + * create an independent instance of the feature renderer settings + * + * @param fr + */ + public FeatureRendererSettings(FeatureRenderer fr) + { + renderOrder = null; + featureGroups = new Hashtable(); + featureColours = new Hashtable(); + featureOrder = new Hashtable(); + if (fr.renderOrder != null) + { + this.renderOrder = new String[fr.renderOrder.length]; + System.arraycopy(fr.renderOrder, 0, renderOrder, 0, + renderOrder.length); + } + if (fr.featureGroups != null) + { + this.featureGroups = new Hashtable(fr.featureGroups); + } + if (fr.featureColours != null) + { + this.featureColours = new Hashtable(fr.featureColours); + } + Enumeration en = fr.featureColours.keys(); + while (en.hasMoreElements()) + { + Object next = en.nextElement(); + Object val = featureColours.get(next); + if (val instanceof GraduatedColor) + { + featureColours + .put(next, new GraduatedColor((GraduatedColor) val)); + } + } + this.transparency = fr.transparency; + if (fr.featureOrder != null) + { + this.featureOrder = new Hashtable(fr.featureOrder); + } + } + } + + public FeatureRendererSettings getSettings() + { + return new FeatureRendererSettings(this); + } + + public void transferSettings(FeatureRendererSettings fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = fr.featureOrder; + } + + public void transferSettings(FeatureRenderer fr) + { + FeatureRendererSettings frs = new FeatureRendererSettings(fr); + this.renderOrder = frs.renderOrder; + this.featureGroups = frs.featureGroups; + this.featureColours = frs.featureColours; + this.transparency = frs.transparency; + this.featureOrder = frs.featureOrder; + if (av != null && av!=fr.av) + { + // copy over the displayed feature settings + if (fr.av != null) + { + if (fr.av.featuresDisplayed != null) + { + // update display settings + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed); + } + else + { + av.featuresDisplayed.clear(); + Enumeration en = fr.av.featuresDisplayed.keys(); + while (en.hasMoreElements()) + { + av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); + } + + } + } + } + } + } + + 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 synchronized 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) + { + sfSize = sequenceFeatures.length; + } + } + + if (sequenceFeatures != lastSeq.getDatasetSequence() + .getSequenceFeatures()) + { + sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + + if (sequenceFeatures == null || sfSize == 0) + { + return initialCol; + } + + 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; + // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized. + 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; + + /** + * show scores as heights + */ + protected boolean varyHeight = false; + + synchronized 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(); + } + + if (lastSeq == null + || seq != lastSeq + || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures) + { + lastSeq = seq; + sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); + } + + 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); + } + + sfSize = sequenceFeatures.length; + 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[sfindex].type.equals(type)) + { + continue; + } + + if (featureGroups != null + && sequenceFeatures[sfindex].featureGroup != null + && sequenceFeatures[sfindex].featureGroup.length() != 0 + && 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) + { + // this is passed out to the overview and other sequence renderers + // (e.g. molecule viewer) to get displayed colour for rendered + // sequence + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB()); + // used to be retreived from av.featuresDisplayed + // 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, + getColour(sequenceFeatures[sfindex]) + // 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, + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); + + } + else if (showFeature(sequenceFeatures[sfindex])) + { + if (av.showSeqFeaturesHeight + && sequenceFeatures[sfindex].score != Float.NaN) + { + renderScoreFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1, + normaliseScore(sequenceFeatures[sfindex])); + } + else + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1); + } + } + + } + + } + + if (transparency != 1.0f && g != null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + 1.0f)); + } + } + + Hashtable minmax = new Hashtable(); + + /** + * normalise a score against the max/min bounds for the feature type. + * + * @param sequenceFeature + * @return byte[] { signed, normalised signed (-127 to 127) or unsigned + * (0-255) value. + */ + private final byte[] normaliseScore(SequenceFeature sequenceFeature) + { + float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0]; + final byte[] r = new byte[] + { 0, (byte) 255 }; + if (mm != null) + { + if (r[0] != 0 || mm[0] < 0.0) + { + r[0] = 1; + r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1])); + } + else + { + r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1])); + } + } + return r; + } + + 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); + + } + } + } + + void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1, byte[] bs) + { + + 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; + int ystrt = 0, yend = av.charHeight; + if (bs[0] != 0) + { + // signed - zero is always middle of residue line. + if (bs[1] < 128) + { + yend = av.charHeight * (128 - bs[1]) / 512; + ystrt = av.charHeight - yend / 2; + } + else + { + ystrt = av.charHeight / 2; + yend = av.charHeight * (bs[1] - 128) / 512; + } + } + else + { + yend = av.charHeight * bs[1] / 255; + ystrt = av.charHeight - yend; + + } + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + int x = (i - start) * av.charWidth; + g.drawRect(x, y1, av.charWidth, av.charHeight); + g.fillRect(x, y1 + ystrt, av.charWidth, yend); + + if (offscreenRender || !av.validCharWidth) + { + continue; + } + + g.setColor(Color.black); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av.charWidth * (i - start)), pady); + + } + } + } + + boolean newFeatureAdded = false; + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } + + boolean findingFeatures = false; + + /** + * search the alignment for all new features, give them a colour and display + * them. Then fires a PropertyChangeEvent on the changeSupport object. + * + */ + void findAllFeatures() + { + synchronized (firing) + { + if (firing.equals(Boolean.FALSE)) + { + firing = Boolean.TRUE; + findAllFeatures(true); // add all new features as visible + changeSupport.firePropertyChange("changeSupport", null, null); + firing = Boolean.FALSE; + } + } + } + + /** + * Searches alignment for all features and updates colours + * + * @param newMadeVisible + * if true newly added feature types will be rendered immediatly + */ + synchronized void findAllFeatures(boolean newMadeVisible) + { + newFeatureAdded = false; + + if (findingFeatures) + { + newFeatureAdded = true; + return; + } + + findingFeatures = true; + + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(); + } + + allfeatures = new Vector(); + Vector oldfeatures = new Vector(); + if (renderOrder != null) + { + for (int i = 0; i < renderOrder.length; i++) + { + if (renderOrder[i] != null) + { + oldfeatures.addElement(renderOrder[i]); + } + } + } + if (minmax == null) + { + minmax = new Hashtable(); + } + 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 (featureGroups.containsKey(features[index].getType())) + { + boolean visible = ((Boolean) featureGroups + .get(features[index].featureGroup)).booleanValue(); + + if (!visible) + { + index++; + continue; + } + } + + 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 (newMadeVisible + && !oldfeatures.contains(features[index].getType())) + { + // this is a new feature type on the alignment. Mark it for + // display. + av.featuresDisplayed.put(features[index].getType(), + new Integer(getColour(features[index].getType()) + .getRGB())); + setOrder(features[index].getType(), 0); + } + } + } + if (!allfeatures.contains(features[index].getType())) + { + allfeatures.addElement(features[index].getType()); + } + if (features[index].score != Float.NaN) + { + int nonpos = features[index].getBegin() >= 1 ? 0 : 1; + float[][] mm = (float[][]) minmax.get(features[index].getType()); + if (mm == null) + { + mm = new float[][] + { null, null }; + minmax.put(features[index].getType(), mm); + } + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + + } + else + { + if (mm[nonpos][0] > features[index].score) + { + mm[nonpos][0] = features[index].score; + } + if (mm[nonpos][1] < features[index].score) + { + mm[nonpos][1] = features[index].score; + } + } + } + index++; + } + } + updateRenderOrder(allfeatures); + findingFeatures = false; + } + + protected Boolean firing = Boolean.FALSE; + + /** + * replaces the current renderOrder with the unordered features in + * allfeatures. The ordering of any types in both renderOrder and allfeatures + * is preserved, and all new feature types are rendered on top of the existing + * types, in the order given by getOrder or the order given in allFeatures. + * Note. this operates directly on the featureOrder hash for efficiency. TODO: + * eliminate the float storage for computing/recalling the persistent ordering + * New Cability: updates min/max for colourscheme range if its dynamic + * + * @param allFeatures + */ + private void updateRenderOrder(Vector allFeatures) + { + Vector allfeatures = new Vector(allFeatures); + String[] oldRender = renderOrder; + renderOrder = new String[allfeatures.size()]; + Object mmrange, fc = null; + boolean initOrders = (featureOrder == null); + int opos = 0; + if (oldRender != null && oldRender.length > 0) + { + for (int j = 0; j < oldRender.length; j++) + { + if (oldRender[j] != null) + { + if (initOrders) + { + setOrder(oldRender[j], (1 - (1 + (float) j) + / (float) oldRender.length)); + } + if (allfeatures.contains(oldRender[j])) + { + renderOrder[opos++] = oldRender[j]; // existing features always + // appear below new features + allfeatures.removeElement(oldRender[j]); + if (minmax != null) + { + mmrange = minmax.get(oldRender[j]); + if (mmrange != null) + { + fc = featureColours.get(oldRender[j]); + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds( + ((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); + } + } + } + } + } + } + } + if (allfeatures.size() == 0) + { + // no new features - leave order unchanged. + return; + } + int i = allfeatures.size() - 1; + int iSize = i; + boolean sort = false; + String[] newf = new String[allfeatures.size()]; + float[] sortOrder = new float[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + // sort remaining elements + while (en.hasMoreElements()) + { + newf[i] = en.nextElement().toString(); + if (minmax != null) + { + // update from new features minmax if necessary + mmrange = minmax.get(newf[i]); + if (mmrange != null) + { + fc = featureColours.get(newf[i]); + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); + } + } + } + if (initOrders || !featureOrder.containsKey(newf[i])) + { + int denom = initOrders ? allfeatures.size() : featureOrder.size(); + // new unordered feature - compute persistent ordering at head of + // existing features. + setOrder(newf[i], i / (float) denom); + } + // set order from newly found feature from persisted ordering. + sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); + if (i < iSize) + { + // only sort if we need to + sort = sort || sortOrder[i] > sortOrder[i + 1]; + } + i--; + } + if (iSize > 1 && sort) + { + jalview.util.QuickSort.sort(sortOrder, newf); + } + sortOrder = null; + System.arraycopy(newf, 0, renderOrder, opos, newf.length); + } + + /** + * get a feature style object for the given type string. Creates a + * java.awt.Color for a featureType with no existing colourscheme. TODO: + * replace return type with object implementing standard abstract colour/style + * interface + * + * @param featureType + * @return java.awt.Color or GraduatedColor + */ + public Object getFeatureStyle(String featureType) + { + Object fc = featureColours.get(featureType); + if (fc == null) + { + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); + Color col = ucs.createColourFromName(featureType); + featureColours.put(featureType, fc = col); + } + return fc; + } + + /** + * return a nominal colour for this feature + * + * @param featureType + * @return standard color, or maximum colour for graduated colourscheme + */ + public Color getColour(String featureType) + { + Object fc = getFeatureStyle(featureType); + + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).getMaxColor(); + } + } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + featureType); + } + + /** + * calculate the render colour for a specific feature using current feature + * settings. + * + * @param feature + * @return render colour for the given feature + */ + public Color getColour(SequenceFeature feature) + { + Object fc = getFeatureStyle(feature.getType()); + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).findColor(feature); + } + } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + feature.getType()); + } + + private boolean showFeature(SequenceFeature sequenceFeature) + { + Object fc = getFeatureStyle(sequenceFeature.type); + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).isColored(sequenceFeature); + } + else + { + return true; + } + } + + // // ///////////// + // // Feature Editing Dialog + // // Will be refactored in next release. + + static String lastFeatureAdded; + + static String lastFeatureGroupAdded; + + static String lastDescriptionAdded; + + Object oldcol, fcol; + + int featureIndex = 0; + + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) + { + + featureIndex = 0; + + final JPanel bigPanel = new JPanel(new BorderLayout()); + final JComboBox overlaps; + final JTextField name = new JTextField(25); + final JTextField source = new JTextField(25); + 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; + + public void mousePressed(MouseEvent evt) + { + if (fcol instanceof Color) + { + Color col = JColorChooser.showDialog(Desktop.desktop, + "Select Feature Colour", ((Color) fcol)); + if (col != null) + { + fcol = col; + updateColourButton(bigPanel, colour, col); + } + } + else + { + + if (fcc == null) + { + final String type = features[featureIndex].getType(); + fcc = new FeatureColourChooser(me, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + + fcc.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + fcol = fcc.getLastColour(); + fcc = null; + setColour(type, fcol); + updateColourButton(bigPanel, colour, fcol); + } + }); + + } + } + } + }); + JPanel tmp = new JPanel(); + JPanel panel = new JPanel(new GridLayout(3, 1)); + + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) + { + panel = new JPanel(new GridLayout(4, 1)); + tmp = new JPanel(); + tmp.add(new JLabel("Select Feature: ")); + overlaps = new JComboBox(); + for (int i = 0; i < features.length; i++) + { + overlaps.addItem(features[i].getType() + "/" + + features[i].getBegin() + "-" + features[i].getEnd() + + " (" + features[i].getFeatureGroup() + ")"); + } + + tmp.add(overlaps); + + overlaps.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + int index = overlaps.getSelectedIndex(); + if (index != -1) + { + featureIndex = index; + name.setText(features[index].getType()); + description.setText(features[index].getDescription()); + source.setText(features[index].getFeatureGroup()); + start.setValue(new Integer(features[index].getBegin())); + end.setValue(new Integer(features[index].getEnd())); + + SearchResults highlight = new SearchResults(); + highlight.addResult(sequences[0], features[index].getBegin(), + features[index].getEnd()); + + ap.seqPanel.seqCanvas.highlightSearchResults(highlight); + + } + Object col = getFeatureStyle(name.getText()); + if (col == null) + { + col = new jalview.schemes.UserColourScheme() + .createColourFromName(name.getText()); + } + oldcol = fcol = col; + updateColourButton(bigPanel, colour, col); + } + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Name: ", JLabel.RIGHT)); + tmp.add(name); + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Group: ", JLabel.RIGHT)); + tmp.add(source); + + tmp = new JPanel(); + panel.add(tmp); + tmp.add(new JLabel("Colour: ", JLabel.RIGHT)); + tmp.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); + bigPanel.add(panel, BorderLayout.NORTH); + + panel = new JPanel(); + panel.add(new JLabel("Description: ", JLabel.RIGHT)); + description.setFont(JvSwingUtils.getTextAreaFont()); + 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 + { + lastFeatureGroupAdded = "Jalview"; + } + } + + if (newFeatures) + { + name.setText(lastFeatureAdded); + source.setText(lastFeatureGroupAdded); + } + else + { + name.setText(features[0].getType()); + source.setText(features[0].getFeatureGroup()); + } + + start.setValue(new Integer(features[0].getBegin())); + end.setValue(new Integer(features[0].getEnd())); + description.setText(features[0].getDescription()); + updateColourButton(bigPanel, colour, + (oldcol = fcol = getFeatureStyle(name.getText()))); + 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.getText().length() > 0) + { + // This ensures that the last sequence + // is refreshed and new features are rendered + lastSeq = null; + lastFeatureAdded = name.getText().trim(); + lastFeatureGroupAdded = source.getText().trim(); + lastDescriptionAdded = description.getText().replaceAll("\n", " "); + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + lastFeatureGroupAdded = null; + } + + 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, fcol); + av.featuresDisplayed.put(sf.type, getColour(sf.type)); + + try + { + sf.begin = ((Integer) start.getValue()).intValue(); + sf.end = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { + } + + ffile.parseDescriptionHTML(sf, false); + } + } + else + // NEW FEATURES ADDED + { + if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + { + for (int i = 0; i < sequences.length; i++) + { + features[i].type = lastFeatureAdded; + if (lastFeatureGroupAdded != null) + 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 (lastFeatureGroupAdded != null) + { + if (featureGroups == null) + featureGroups = new Hashtable(); + featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + } + setColour(lastFeatureAdded, fcol); + av.featuresDisplayed.put(lastFeatureAdded, + getColour(lastFeatureAdded)); + + findAllFeatures(false); + + ap.paintAlignment(true); + + return true; + } + else + { + return false; + } + } + + ap.paintAlignment(true); + + return true; + } + + /** + * update the amend feature button dependent on the given style + * + * @param bigPanel + * @param col + * @param col2 + */ + protected void updateColourButton(JPanel bigPanel, JLabel colour, + Object col2) + { + colour.removeAll(); + colour.setIcon(null); + colour.setToolTipText(null); + colour.setText(""); + + if (col2 instanceof Color) + { + colour.setBackground((Color) col2); + } + else + { + colour.setBackground(bigPanel.getBackground()); + colour.setForeground(Color.black); + FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2); + // colour.setForeground(colour.getBackground()); + } + } + + public void setColour(String featureType, Object col) + { + // overwrite + // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof + // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; + // Object c = featureColours.get(featureType); + // if (c == null || c instanceof Color || (c instanceof GraduatedColor && + // !((GraduatedColor)c).getMaxColor().equals(_col))) + { + featureColours.put(featureType, col); + } + } + + public void setTransparency(float value) + { + transparency = value; + } + + public float getTransparency() + { + return transparency; + } + + /** + * Replace current ordering with new ordering + * + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } + */ + public void setFeaturePriority(Object[][] data) + { + setFeaturePriority(data, true); + } + + /** + * + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } + * @param visibleNew + * when true current featureDisplay list will be cleared + */ + public void setFeaturePriority(Object[][] data, boolean visibleNew) + { + if (visibleNew) + { + if (av.featuresDisplayed != null) + { + av.featuresDisplayed.clear(); + } + else + { + av.featuresDisplayed = new Hashtable(); + } + } + if (data == null) + { + return; + } + + // 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 + 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, data[i][1]); // todo : typesafety - feature color + // interface object + if (((Boolean) data[i][2]).booleanValue()) + { + av.featuresDisplayed.put(type, new Integer(getColour(type) + .getRGB())); + } + + renderOrder[data.length - i - 1] = type; + } + } + + } + + Hashtable featureOrder = null; + + /** + * analogous to colour - store a normalized ordering for all feature types in + * this rendering context. + * + * @param type + * Feature type string + * @param position + * normalized priority - 0 means always appears on top, 1 means + * always last. + */ + public float setOrder(String type, float position) + { + if (featureOrder == null) + { + featureOrder = new Hashtable(); + } + featureOrder.put(type, new Float(position)); + return position; + } + + /** + * get the global priority (0 (top) to 1 (bottom)) + * + * @param type + * @return [0,1] or -1 for a type without a priority + */ + public float getOrder(String type) + { + if (featureOrder != null) + { + if (featureOrder.containsKey(type)) + { + return ((Float) featureOrder.get(type)).floatValue(); + } + } + return -1; + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } +}