X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=244b650a13306cf81f8fe34282fdd638f9bce1e7;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=551dea7d93d6e77bcbdc7e59104324b7af3f0d69;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 551dea7..244b650 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,412 +1,1266 @@ - -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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.appletgui; - -import jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - - Hashtable featureColours = new Hashtable(); - - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; - - // Holds web links for feature groups and feature types - // in the form label|link - Hashtable featureLinks = null; - - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String [] renderOrder; - - FontMetrics fm; - int charOffset; - - float transparency = 1f; - - TransparencySetter transparencySetter = null; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - - if(!System.getProperty("java.version").startsWith("1.1")) - transparencySetter = new TransparencySetter(); - } - - - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - } - - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - overview = true; - if(!av.showSequenceFeatures) - return initialCol; - - lastSequence = seq; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) - return Color.white; - - currentColour = null; - - drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1); - - if(currentColour==null) - return initialCol; - - return new Color( ((Integer)currentColour).intValue() ); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - boolean overview = false; - - int white = Color.white.getRGB(); - public int findFeatureColour(int initialCol, int seqIndex, int column) - { - if(!av.showSequenceFeatures) - return initialCol; - - if(seqIndex!=lastSequenceIndex) - { - lastSequence = av.alignment.getSequenceAt(seqIndex); - lastSequenceIndex = seqIndex; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if(sequenceFeatures==null) - return initialCol; - - sfSize = sequenceFeatures.length; - } - - - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) - return Color.white.getRGB(); - - currentColour = null; - - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); - - if(currentColour==null) - return initialCol; - - 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; - int lastSequenceIndex=-1; - SequenceI lastSequence; - SequenceFeature [] sequenceFeatures; - int sfSize, sfindex, spos, epos; - - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1, int width, int height) - { - if ( seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length==0) - return; - - if(transparencySetter!=null && g!=null) - { - transparencySetter.setTransparency(g, transparency); - } - - if (av.featuresDisplayed == null || renderOrder==null) - { - findAllFeatures(); - if(av.featuresDisplayed.size()<1) - return; - - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - if(lastSequence==null || seq!=lastSequence) - { - lastSequence = seq; - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - if(!overview) - { - spos = lastSequence.findPosition(start); - epos = lastSequence.findPosition(end); - if(g!=null) - fm = g.getFontMetrics(); - } - String type; - for(int renderIndex=0; renderIndex epos - || sequenceFeatures[sfindex].getEnd() < spos)) - continue; - - if (overview) - { - 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, width, height); - 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, width, height); - - } - else - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1, width, height); - - } - } - - if(transparencySetter!=null && g!=null) - { - transparencySetter.setTransparency(g, 1.0f); - } - } - - - char s; - int i; - void renderFeature(Graphics g, SequenceI seq, - int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height) - { - - 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; - } - - 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) * width, y1, width, height); - - if(!av.validCharWidth) - continue; - - g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (width * (i - start)), - (y1 + height) - height / 5); //pady = height / 5; - - } - } - } - - void findAllFeatures() - { - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures(); - - if (features == null) - continue; - - int index = 0; - while (index < features.length) - { - if (!av.featuresDisplayed.containsKey(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--; - } - } - - public Color getColour(String featureType) - { - return (Color)featureColours.get(featureType); - } - - public void addNewFeature(String name, Color col) - { - - setColour(name, col); - if(av.featuresDisplayed==null) - av.featuresDisplayed = new Hashtable(); - - - av.featuresDisplayed.put(name, "NOGROUP"); - } - - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - 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(); - - 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; - } - } -} - - class TransparencySetter - { - void setTransparency(Graphics g, float value) - { - // Graphics2D g2 = (Graphics2D) g; - // g2.setComposite( - // AlphaComposite.getInstance( - // AlphaComposite.SRC_OVER, value)); - } - } - - - - +/* + * 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.appletgui; + +import java.util.*; + +import java.awt.*; + +import java.awt.event.*; + +import jalview.appletgui.FeatureSettings.MyCheckbox; +import jalview.datamodel.*; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.GraduatedColor; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer implements jalview.api.FeatureRenderer +{ + AlignViewport av; + + Hashtable featureColours = new Hashtable(); + + // A higher level for grouping features of a + // particular type + Hashtable featureGroups = null; + + // Holds web links for feature groups and feature types + // in the form label|link + Hashtable featureLinks = null; + + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; + + String[] renderOrder; + + FontMetrics fm; + + int charOffset; + + float transparency = 1f; + + TransparencySetter transparencySetter = null; + + /** + * Creates a new FeatureRenderer object. + * + * @param av + * DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) + { + this.av = av; + + if (!System.getProperty("java.version").startsWith("1.1")) + { + transparencySetter = new TransparencySetter(); + } + } + + public void transferSettings(FeatureRenderer fr) + { + renderOrder = fr.renderOrder; + featureGroups = fr.featureGroups; + featureColours = fr.featureColours; + transparency = fr.transparency; + if (av!=null && fr.av!=null && fr.av!=av) + { + if (fr.av.featuresDisplayed!=null) + { + if (av.featuresDisplayed==null) + { + av.featuresDisplayed = new Hashtable(); + } else { + av.featuresDisplayed.clear(); + } + Enumeration en=fr.av.featuresDisplayed.keys(); + while (en.hasMoreElements()) + { + av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); + } + } + } + } + + static String lastFeatureAdded; + + static String lastFeatureGroupAdded; + + static String lastDescriptionAdded; + + int featureIndex = 0; + + boolean deleteFeature = false; + + FeatureColourPanel colourPanel; + + class FeatureColourPanel extends Panel + { + String label = ""; + + private Color maxCol; + + private boolean isColourByLabel, isGcol; + + /** + * render a feature style in the amend feature dialog box + */ + public void updateColor(Object newcol) + { + + Color bg, col = null; + GraduatedColor gcol = null; + String vlabel = ""; + if (newcol instanceof Color) + { + isGcol = false; + col = (Color) newcol; + gcol = null; + } + else if (newcol instanceof GraduatedColor) + { + isGcol = true; + gcol = (GraduatedColor) newcol; + col = null; + } + else + { + throw new Error("Invalid color for MyCheckBox"); + } + if (col != null) + { + setBackground(bg = col); + } + else + { + if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + { + vlabel += " " + + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" + : "(<)"); + } + if (isColourByLabel = gcol.isColourByLabel()) + { + setBackground(bg = Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(bg = gcol.getMinColor()); + maxCol = gcol.getMaxColor(); + } + } + label = vlabel; + setBackground(bg); + repaint(); + } + + FeatureColourPanel() + { + super(null); + } + + public void paint(Graphics g) + { + Dimension d = getSize(); + if (isGcol) + { + if (isColourByLabel) + { + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + g.setColor(Color.black); + Font f = new Font("Verdana", Font.PLAIN, 10); + g.setFont(f); + g.drawString("Label", 0, 0); + } + else + { + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + + } + } + } + + } + + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) + { + Panel bigPanel = new Panel(new BorderLayout()); + final TextField name = new TextField(16); + final TextField source = new TextField(16); + final TextArea description = new TextArea(3, 35); + final TextField start = new TextField(8); + final TextField end = new TextField(8); + final Choice overlaps; + Button deleteButton = new Button("Delete"); + deleteFeature = false; + + colourPanel = new FeatureColourPanel(); + colourPanel.setSize(110, 15); + final FeatureRenderer fr = this; + + Panel panel = new Panel(new GridLayout(3, 1)); + + featureIndex = 0; // feature to be amended. + Panel tmp; + + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) + { + panel = new Panel(new GridLayout(4, 1)); + tmp = new Panel(); + tmp.add(new Label("Select Feature: ")); + overlaps = new Choice(); + for (int i = 0; i < features.length; i++) + { + String item = features[i].getType() + "/" + features[i].getBegin() + + "-" + features[i].getEnd(); + + if (features[i].getFeatureGroup() != null) + item += " (" + features[i].getFeatureGroup() + ")"; + + overlaps.addItem(item); + } + + tmp.add(overlaps); + + overlaps.addItemListener(new java.awt.event.ItemListener() + { + public void itemStateChanged(java.awt.event.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.setText(features[index].getBegin() + ""); + end.setText(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()); + } + + colourPanel.updateColor(col); + } + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// + + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label("Name: ", Label.RIGHT)); + tmp.add(name); + + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label("Group: ", Label.RIGHT)); + tmp.add(source); + + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label("Colour: ", Label.RIGHT)); + tmp.add(colourPanel); + + bigPanel.add(panel, BorderLayout.NORTH); + + panel = new Panel(); + panel.add(new Label("Description: ", Label.RIGHT)); + panel.add(new ScrollPane().add(description)); + + if (!newFeatures) + { + bigPanel.add(panel, BorderLayout.SOUTH); + + panel = new Panel(); + panel.add(new Label(" Start:", Label.RIGHT)); + panel.add(start); + panel.add(new Label(" End:", Label.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"; + } + } + + String title = newFeatures ? "Create New Sequence Feature(s)" + : "Amend/Delete Features for " + sequences[0].getName(); + + final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, + 240); + + dialog.setMainPanel(bigPanel); + + if (newFeatures) + { + name.setText(lastFeatureAdded); + source.setText(lastFeatureGroupAdded); + } + else + { + dialog.ok.setLabel("Amend"); + dialog.buttonPanel.add(deleteButton, 1); + deleteButton.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + deleteFeature = true; + dialog.setVisible(false); + } + }); + name.setText(features[0].getType()); + source.setText(features[0].getFeatureGroup()); + } + + start.setText(features[0].getBegin() + ""); + end.setText(features[0].getEnd() + ""); + description.setText(features[0].getDescription()); + Color col = getColour(name.getText()); + if (col == null) + { + col = new jalview.schemes.UserColourScheme() + .createColourFromName(name.getText()); + } + Object fcol = getFeatureStyle(name.getText()); + // simply display the feature color in a box + colourPanel.updateColor(fcol); + dialog.setResizable(true); + // TODO: render the graduated color in the box. + colourPanel.addMouseListener(new java.awt.event.MouseAdapter() + { + public void mousePressed(java.awt.event.MouseEvent evt) + { + if (!colourPanel.isGcol) + { + new UserDefinedColours(fr, ap.alignFrame); + } + else + { + FeatureColourChooser fcc = new FeatureColourChooser( + ap.alignFrame, name.getText()); + dialog.transferFocus(); + } + } + }); + dialog.setVisible(true); + + jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + + if (dialog.accept) + { + // 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().replace('\n', ' '); + } + + if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) + lastFeatureGroupAdded = null; + + if (!newFeatures) + { + + SequenceFeature sf = features[featureIndex]; + if (dialog.accept) + { + sf.type = lastFeatureAdded; + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + if (!colourPanel.isGcol) + { + // update colour - otherwise its already done. + setColour(sf.type, colourPanel.getBackground()); + } + try + { + sf.begin = Integer.parseInt(start.getText()); + sf.end = Integer.parseInt(end.getText()); + } catch (NumberFormatException ex) + { + } + + ffile.parseDescriptionHTML(sf, false); + } + if (deleteFeature) + { + sequences[0].deleteFeature(sf); + } + + } + else + { + if (dialog.accept && name.getText().length() > 0) + { + 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(); + } + + col = colourPanel.getBackground(); + // setColour(lastFeatureAdded, fcol); + + if (lastFeatureGroupAdded != null) + { + featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + } + if (fcol instanceof Color) + { + setColour(lastFeatureAdded, fcol); + } + av.featuresDisplayed.put(lastFeatureAdded, + getFeatureStyle(lastFeatureAdded)); + + findAllFeatures(); + + String[] tro = new String[renderOrder.length]; + tro[0] = renderOrder[renderOrder.length - 1]; + System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1); + renderOrder = tro; + } + else + { + // no update to the alignment + return false; + } + } + // refresh the alignment and the feature settings dialog + if (av.featureSettings != null) + { + av.featureSettings.refreshTable(); + } + // findAllFeatures(); + + ap.paintAlignment(true); + + return true; + } + + public Color findFeatureColour(Color initialCol, SequenceI seq, int i) + { + overview = true; + if (!av.showSequenceFeatures) + { + return initialCol; + } + + lastSeq = seq; + sequenceFeatures = lastSeq.getSequenceFeatures(); + if (sequenceFeatures == null) + { + return initialCol; + } + + sfSize = sequenceFeatures.length; + + if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i))) + { + return Color.white; + } + + currentColour = null; + + drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1); + + if (currentColour == null) + { + return initialCol; + } + + return new Color(((Integer) currentColour).intValue()); + } + + /** + * This is used by the Molecule Viewer to get the accurate colour of the + * rendered sequence + */ + boolean overview = false; + + /** + * 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; + + synchronized public void drawSequence(Graphics g, SequenceI seq, + int start, int end, int y1) + { + if (seq.getSequenceFeatures() == null + || seq.getSequenceFeatures().length == 0) + { + return; + } + + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, transparency); + } + + if (lastSeq == null || seq != lastSeq + || sequenceFeatures != seq.getSequenceFeatures()) + { + lastSeq = seq; + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + + if (av.featuresDisplayed == null || renderOrder == null) + { + findAllFeatures(); + if (av.featuresDisplayed.size() < 1) + { + return; + } + + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + if (!overview) + { + spos = lastSeq.findPosition(start); + epos = lastSeq.findPosition(end); + if (g != null) + { + fm = g.getFontMetrics(); + } + } + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + if (!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 + && featureGroups + .containsKey(sequenceFeatures[sfindex].featureGroup) + && !((Boolean) featureGroups + .get(sequenceFeatures[sfindex].featureGroup)) + .booleanValue()) + { + continue; + } + + if (!overview + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) + { + continue; + } + + if (overview) + { + if (sequenceFeatures[sfindex].begin <= start + && sequenceFeatures[sfindex].end >= start) + { + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB());// 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])) + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1); + } + } + + } + } + + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, 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; + } + + 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 (!av.validCharWidth) + { + continue; + } + + g.setColor(Color.white); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av.charWidth * (i - start)), (y1 + av.charHeight) + - av.charHeight / 5); // pady = height / 5; + + } + } + } + + Hashtable minmax = null; + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } + + /** + * find all features on the alignment + */ + void findAllFeatures() + { + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); + + av.featuresDisplayed = new Hashtable(); + Vector allfeatures = new Vector(); + minmax = new Hashtable(); + + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceFeature[] features = av.alignment.getSequenceAt(i) + .getSequenceFeatures(); + + if (features == null) + { + continue; + } + + int index = 0; + while (index < features.length) + { + if (features[index].begin == 0 && features[index].end == 0) + { + index++; + continue; + } + if (!av.featuresDisplayed.containsKey(features[index].getType())) + { + 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()); + } + 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++; + } + } + + renderOrder = new String[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + int i = allfeatures.size() - 1; + while (en.hasMoreElements()) + { + renderOrder[i] = en.nextElement().toString(); + i--; + } + } + + /** + * 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; + } + + 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); + } + + /** + * + * @param sequenceFeature + * @return true if feature is visible. + */ + private boolean showFeature(SequenceFeature sequenceFeature) + { + Object fc = getFeatureStyle(sequenceFeature.type); + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).isColored(sequenceFeature); + } + else + { + return true; + } + } + + /** + * implement graduated colouring for features with scores + * + * @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()); + } + + 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 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(); + } + + /* + * if (visibleNew) { if (av.featuresDisplayed != null) { + * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new + * Hashtable(); } } if (data == null) { return; } + */ + + 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]); + if (((Boolean) data[i][2]).booleanValue()) + { + av.featuresDisplayed.put(type, new Integer(getColour(type) + .getRGB())); + } + + renderOrder[data.length - i - 1] = type; + } + } + } + + /** + * @return a simple list of feature group names or null + */ + public String[] getGroups() + { + buildGroupHash(); + if (featureGroups != null) + { + String[] gps = new String[featureGroups.size()]; + Enumeration gn = featureGroups.keys(); + int i = 0; + while (gn.hasMoreElements()) + { + gps[i++] = (String) gn.nextElement(); + } + return gps; + } + return null; + } + + /** + * get visible or invisible groups + * + * @param visible + * true to return visible groups, false to return hidden ones. + * @return list of groups + */ + public String[] getGroups(boolean visible) + { + buildGroupHash(); + if (featureGroups != null) + { + Vector gp = new Vector(); + + Enumeration gn = featureGroups.keys(); + while (gn.hasMoreElements()) + { + String nm = (String) gn.nextElement(); + Boolean state = (Boolean) featureGroups.get(nm); + if (state.booleanValue() == visible) + { + gp.addElement(nm); + } + } + String[] gps = new String[gp.size()]; + gp.copyInto(gps); + + int i = 0; + while (gn.hasMoreElements()) + { + gps[i++] = (String) gn.nextElement(); + } + return gps; + } + return null; + } + + /** + * set all feature groups in toset to be visible or invisible + * + * @param toset + * group names + * @param visible + * the state of the named groups to set + */ + public void setGroupState(String[] toset, boolean visible) + { + buildGroupHash(); + if (toset != null && toset.length > 0 && featureGroups != null) + { + boolean rdrw = false; + for (int i = 0; i < toset.length; i++) + { + Object st = featureGroups.get(toset[i]); + if (st != null) + { + featureGroups.put(toset[i], new Boolean(visible)); + rdrw = rdrw || (visible != ((Boolean) st).booleanValue()); + } + } + if (rdrw) + { + if (this.av != null) + if (this.av.featureSettings != null) + { + av.featureSettings.rebuildGroups(); + this.av.featureSettings.resetTable(true); + } + else + { + buildFeatureHash(); + } + if (av != null) + { + av.alignmentChanged(null); + } + } + } + } + + /** + * analyse alignment for groups and hash tables (used to be embedded in + * FeatureSettings.setTableData) + * + * @return true if features are on the alignment + */ + public boolean buildGroupHash() + { + boolean alignmentHasFeatures = false; + if (featureGroups == null) + { + featureGroups = new Hashtable(); + } + Vector allFeatures = new Vector(); + Vector allGroups = new Vector(); + SequenceFeature[] tmpfeatures; + String group; + for (int i = 0; i < av.alignment.getHeight(); i++) + { + if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + { + continue; + } + + alignmentHasFeatures = true; + + tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + int index = 0; + while (index < tmpfeatures.length) + { + if (tmpfeatures[index].getFeatureGroup() != null) + { + group = tmpfeatures[index].featureGroup; + if (!allGroups.contains(group)) + { + allGroups.addElement(group); + + boolean visible = true; + if (featureGroups.containsKey(group)) + { + visible = ((Boolean) featureGroups.get(group)).booleanValue(); + } + else + { + featureGroups.put(group, new Boolean(visible)); + } + } + } + + if (!allFeatures.contains(tmpfeatures[index].getType())) + { + allFeatures.addElement(tmpfeatures[index].getType()); + } + index++; + } + } + + return alignmentHasFeatures; + } + + /** + * rebuild the featuresDisplayed and renderorder list based on the + * featureGroups hash and any existing display state and force a repaint if + * necessary + * + * @return true if alignment has visible features + */ + public boolean buildFeatureHash() + { + boolean alignmentHasFeatures = false; + if (featureGroups == null) + { + alignmentHasFeatures = buildGroupHash(); + } + if (!alignmentHasFeatures) + return false; + Hashtable fdisp = av.featuresDisplayed; + Vector allFeatures = new Vector(); + SequenceFeature[] tmpfeatures; + String group; + for (int i = 0; i < av.alignment.getHeight(); i++) + { + if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + { + continue; + } + + alignmentHasFeatures = true; + + tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + int index = 0; + while (index < tmpfeatures.length) + { + boolean visible = true; + if (tmpfeatures[index].getFeatureGroup() != null) + { + group = tmpfeatures[index].featureGroup; + if (featureGroups.containsKey(group)) + { + visible = ((Boolean) featureGroups.get(group)).booleanValue(); + } + } + + if (visible && !allFeatures.contains(tmpfeatures[index].getType())) + { + allFeatures.addElement(tmpfeatures[index].getType()); + } + index++; + } + } + if (allFeatures.size() > 0) + { + String[] neworder = new String[allFeatures.size()]; + int p = neworder.length - 1; + for (int i = renderOrder.length - 1; i >= 0; i--) + { + if (allFeatures.contains(renderOrder[i])) + { + neworder[p--] = renderOrder[i]; + allFeatures.removeElement(renderOrder[i]); + } + else + { + av.featuresDisplayed.remove(renderOrder[i]); + } + } + for (int i = allFeatures.size() - 1; i > 0; i++) + { + Object e = allFeatures.elementAt(i); + if (e != null) + { + neworder[p--] = (String) e; + av.featuresDisplayed.put(e, getColour((String) e)); + } + } + renderOrder = neworder; + return true; + } + + return alignmentHasFeatures; + } + + /** + * + * @return the displayed feature type as an array of strings + */ + protected String[] getDisplayedFeatureTypes() + { + String[] typ = null; + synchronized (renderOrder) + { + typ = new String[renderOrder.length]; + System.arraycopy(renderOrder, 0, typ, 0, typ.length); + for (int i = 0; i < typ.length; i++) + { + if (av.featuresDisplayed.get(typ[i]) == null) + { + typ[i] = null; + } + } + } + return typ; + } +} + +class TransparencySetter +{ + void setTransparency(Graphics g, float value) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + value)); + } +}