X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=1dc48d286ec2ef6178074644255f9f1fda7fa25f;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=091a1270931aad62682f475639876521ec1a5942;hpb=d355ad106f73e0de0abc3fb3f375af4eaf352591;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java old mode 100755 new mode 100644 index 091a127..1dc48d2 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,290 +1,480 @@ -/* - * 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; - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; - Graphics graphics; - - // The following vector holds the features which are - // to be added, in the correct order or rendering - Vector featuresDisplayed; - - Color currentColour = null; - - boolean drawText = true; - FontMetrics fm; - int charOffset; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - initColours(); - } - - //boolean highlightTransparent = true; - /** - * 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! - */ - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int x1, int y1, int width, int height) - { - fm = g.getFontMetrics(); - - if(seq.getSequenceFeatures()==null) - return; - - Enumeration e = null, e2; - String type; - if(featuresDisplayed!=null) - e = featuresDisplayed.elements(); - else - e = seq.getSequenceFeatures().elements(); - - - while (e.hasMoreElements()) - { - SequenceFeature sf=null; - if(featuresDisplayed!=null) - { - e2 = seq.getSequenceFeatures().elements(); - type = e.nextElement().toString(); - while(e2.hasMoreElements()) - { - sf = (SequenceFeature) e2.nextElement(); - if(sf.getType().equals(type)) - break; - else - sf = null; - } - } - else - { - sf = (SequenceFeature) e.nextElement(); - type = sf.getType(); - } - - if(sf==null) - continue; - - - if (sf.getBegin() > seq.getEnd()) - { - continue; - } - - if (type.equals("disulfide bond")) - { - - renderFeature(g, seq, - seq.findIndex(sf.getBegin()) - 1, - seq.findIndex(sf.getBegin()) - 1, - type, start, end, x1, y1, width, height); - renderFeature(g, seq, - seq.findIndex(sf.getEnd()) - 1, - seq.findIndex(sf.getEnd()) - 1, - type, start, end, x1, y1, width, height); - - } - else - renderFeature(g, seq, - seq.findIndex(sf.getBegin()) - 1, - seq.findIndex(sf.getEnd()) - 1, - type, start, end, x1, y1, width, height); - - } - } - - void renderFeature(Graphics g, SequenceI seq, - int fstart, int fend, String type, int start, int end, - int x1, 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 (int i = fstart; i <= fend; i++) - { - char s = seq.getSequence().charAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } - - currentColour = getColour(type); - - g.setColor(currentColour); - - g.fillRect( (i - start) * width, y1, width, height); - - if (drawText) - { - g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + x1 + (width * (i - start)), - (y1 + height) - height / 5); - } - } - } - } - - Image offscreen; - Frame nullframe; - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - currentColour = initialCol; - if(offscreen == null) - { - nullframe = new Frame(); - nullframe.addNotify(); - offscreen = nullframe.createImage(1, 1); - } - - drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1); - return currentColour; - } - - - - public Color getColour(String featureType) - { - return (Color)featureColours.get(featureType); - } - - 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(featuresDisplayed!=null) - featuresDisplayed.removeAllElements(); - else - featuresDisplayed = new Vector(); - - for(int i=data.length-1; i>-1; i--) - { - String type = data[i][0].toString(); - setColour(type, (Color)data[i][1]); - if( ((Boolean)data[i][2]).booleanValue() ) - featuresDisplayed.addElement(type); - } - } - - Hashtable featureColours = new Hashtable(); - void initColours() - { - featureColours.put("active site", new Color(255, 75, 0)); - featureColours.put("binding site", new Color(245, 85, 0)); - featureColours.put("calcium-binding region", new Color(235, 95, 0)); - featureColours.put("chain", new Color(225, 105, 0)); - featureColours.put("coiled-coil region", new Color(215, 115, 0)); - featureColours.put("compositionally biased region", new Color(205, 125, 0)); - featureColours.put("cross-link", new Color(195, 135, 0)); - featureColours.put("disulfide bond", new Color(185, 145, 0)); - featureColours.put("DNA-binding region", new Color(175, 155, 0)); - featureColours.put("domain", new Color(165, 165, 0)); - featureColours.put("glycosylation site", new Color(155, 175, 0)); - featureColours.put("helix", new Color(145, 185, 0)); - featureColours.put("initiator methionine", new Color(135, 195, 5)); - featureColours.put("lipid moiety-binding region", new Color(125, 205, 15)); - featureColours.put("metal ion-binding site", new Color(115, 215, 25)); - featureColours.put("modified residue", new Color(105, 225, 35)); - featureColours.put("mutagenesis site", new Color(95, 235, 45)); - featureColours.put("non-consecutive residues", new Color(85, 245, 55)); - featureColours.put("non-terminal residue", new Color(75, 255, 65)); - featureColours.put("nucleotide phosphate-binding region", - new Color(65, 245, 75)); - featureColours.put("peptide", new Color(55, 235, 85)); - featureColours.put("propeptide", new Color(45, 225, 95)); - featureColours.put("region of interest", new Color(35, 215, 105)); - featureColours.put("repeat", new Color(25, 205, 115)); - featureColours.put("selenocysteine", new Color(15, 195, 125)); - featureColours.put("sequence conflict", new Color(5, 185, 135)); - featureColours.put("sequence variant", new Color(0, 175, 145)); - featureColours.put("short sequence motif", new Color(0, 165, 155)); - featureColours.put("signal peptide", new Color(0, 155, 165)); - featureColours.put("site", new Color(0, 145, 175)); - featureColours.put("splice variant", new Color(0, 135, 185)); - featureColours.put("strand", new Color(0, 125, 195)); - featureColours.put("topological domain", new Color(0, 115, 205)); - featureColours.put("transit peptide", new Color(0, 105, 215)); - featureColours.put("transmembrane region", new Color(0, 95, 225)); - featureColours.put("turn", new Color(0, 85, 235)); - featureColours.put("unsure residue", new Color(0, 75, 245)); - featureColours.put("zinc finger region", new Color(0, 65, 255)); - } - -} - - - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Label; +import java.awt.Panel; +import java.awt.ScrollPane; +import java.awt.TextArea; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Hashtable; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer +{ + + // Holds web links for feature groups and feature types + // in the form label|link + Hashtable featureLinks = null; + + /** + * Creates a new FeatureRenderer object. + * + * @param av + * DOCUMENT ME! + */ + public FeatureRenderer(AlignmentViewport av) + { + super(); + this.av = av; + + setTransparencyAvailable(!System.getProperty("java.version") + .startsWith("1.1")); + } + + 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( + MessageManager + .getString("error.invalid_colour_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(MessageManager.getString("label.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 ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { 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(MessageManager.getString("label.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); + setVisible(lastFeatureAdded); // if user edited name then make sure new + // type is visible + } + 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); + } + + Color newColour = colourPanel.getBackground(); + // setColour(lastFeatureAdded, fcol); + + if (lastFeatureGroupAdded != null) + { + setGroupVisibility(lastFeatureGroupAdded, true); + } + setColour(lastFeatureAdded, newColour); // was fcol + setVisible(lastFeatureAdded); + findAllFeatures(false); // different to original applet behaviour ? + // findAllFeatures(); + } + else + { + // no update to the alignment + return false; + } + } + // refresh the alignment and the feature settings dialog + if (((jalview.appletgui.AlignViewport) av).featureSettings != null) + { + ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable(); + } + // findAllFeatures(); + + ap.paintAlignment(true); + + return true; + } +}