X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=83badd0da33d0fa9ebbc71b6d8a4e6b00e32903b;hb=13a74c42398c4a2d3794242efec6e52b949b5e5d;hp=3f332b5fddfe0e32bd1bb09a8794938947d53bab;hpb=d03971168d7f0192862cf5b57602ecf3e341b457;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index 3f332b5..83badd0 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,315 +1,47 @@ -/* - * 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.gui; - -import jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - -import java.awt.image.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - Color resBoxColour; - float transparency = 1.0f; - FontMetrics fm; - int charOffset; - boolean drawText = true; - - // The following vector holds the features which are - // to be added, in the correct order or rendering - Vector featuresDisplayed = null; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - initColours(); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - BufferedImage bi; - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - if(!av.showSequenceFeatures) - return initialCol; - - if (bi == null) - bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB); - - bi.setRGB(0,0, initialCol.getRGB()); - - drawText = false; - - drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1); - drawText = true; - - return new Color(bi.getRGB(0, 0)); - } - - - /** - * 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) - { - -//System.out.println(start+" "+end+" "+x1+" "+y1); - if (seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().size()==0) - return; - - fm = g.getFontMetrics(); - - if (transparency != 1) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); - } - - String type; - SequenceFeature sf; - if (featuresDisplayed == null) - findAllFeatures(); - - Enumeration e = featuresDisplayed.elements(), e2; - - // Loop through each visible feature - while (e.hasMoreElements()) - { - - type = e.nextElement().toString(); - e2 = seq.getDatasetSequence().getSequenceFeatures().elements(); - // loop through all features in sequence to find - // current feature to render - while (e2.hasMoreElements()) - { - - sf = (SequenceFeature) e2.nextElement(); - if (!type.equals(sf.getType())) - 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); - } - } - - if(transparency!=1.0f) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); - } - } - - - 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; - } - - g.setColor(getColour(type)); - - 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); //pady = height / 5; - } - } - } - } - - void findAllFeatures() - { - Vector features = new Vector(); - SequenceFeature sf; - featuresDisplayed = new Vector(); - Enumeration e; - for (int i = 0; i < av.alignment.getHeight(); i++) - { - features = av.alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures(); - if (features == null) - continue; - - e = features.elements(); - while (e.hasMoreElements()) - { - sf = (SequenceFeature) e.nextElement(); - if (!featuresDisplayed.contains(sf.getType())) - { - featuresDisplayed.addElement(sf.getType()); - } - } - } - } - - 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 - featuresDisplayed.clear(); - 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(230,230,0)); - 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +/** + * A class that manages drawing of sequence features for the Swing gui + */ +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer +{ + AlignmentPanel ap; + + /** + * Creates a new FeatureRenderer object + * + * @param alignPanel + */ + public FeatureRenderer(AlignmentPanel alignPanel) + { + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) + { + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); + } + } +}