X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=a24525ee5e2662a9708e85b559efd001efae1201;hb=df9b5e19bad989699ed5313ea7283754f522ed5d;hp=aa3f8306edf5f8e5ce6f351f85ca094092511b7a;hpb=f441357783f32298b738d32d5c87000ac0e33768;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index aa3f830..a24525e 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,7 +1,7 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -35,6 +35,7 @@ public class FeatureRenderer { AlignViewport av; + Hashtable featureColours = new Hashtable(); // A higher level for grouping features of a // particular type @@ -66,26 +67,18 @@ public class FeatureRenderer public FeatureRenderer(AlignViewport av) { this.av = av; - initColours(); if(!System.getProperty("java.version").startsWith("1.1")) transparencySetter = new TransparencySetter(); } - public void addFeatureLink(String feature, String link) - { - if(featureLinks == null) - featureLinks = new Hashtable(); - - featureLinks.put(feature, link); - } - public void transferSettings(FeatureRenderer fr) { renderOrder = fr.renderOrder; featureGroups = fr.featureGroups; featureColours = fr.featureColours; + transparency = fr.transparency; } @@ -107,7 +100,7 @@ public class FeatureRenderer currentColour = null; - drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1); + drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1); if(currentColour==null) return initialCol; @@ -144,7 +137,7 @@ public class FeatureRenderer currentColour = null; - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); + drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1); if(currentColour==null) return initialCol; @@ -174,7 +167,7 @@ public class FeatureRenderer int sfSize, sfindex, spos, epos; public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1, int width, int height) + int start, int end, int y1) { if ( seq.getSequenceFeatures() == null || seq.getSequenceFeatures().length==0) @@ -254,13 +247,13 @@ public class FeatureRenderer seq.findIndex(sequenceFeatures[sfindex].begin) - 1, new Color( ( (Integer) av.featuresDisplayed.get( sequenceFeatures[sfindex].type)).intValue()), - start, end, y1, width, height); + 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, width, height); + start, end, y1); } else @@ -268,7 +261,7 @@ public class FeatureRenderer seq.findIndex(sequenceFeatures[sfindex].begin) - 1, seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex].type), - start, end, y1, width, height); + start, end, y1); } } @@ -283,7 +276,7 @@ public class FeatureRenderer 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) + int fstart, int fend, Color featureColour, int start, int end, int y1) { if (((fstart <= end) && (fend >= start))) @@ -309,16 +302,16 @@ public class FeatureRenderer g.setColor(featureColour); - g.fillRect( (i - start) * width, y1, width, height); + g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); if(!av.validCharWidth) continue; g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; + charOffset = (av.charWidth - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), - charOffset + (width * (i - start)), - (y1 + height) - height / 5); //pady = height / 5; + charOffset + (av.charWidth * (i - start)), + (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5; } } @@ -326,6 +319,9 @@ public class FeatureRenderer void findAllFeatures() { + jalview.schemes.UserColourScheme ucs = new + jalview.schemes.UserColourScheme(); + av.featuresDisplayed = new Hashtable(); Vector allfeatures = new Vector(); for (int i = 0; i < av.alignment.getHeight(); i++) @@ -340,6 +336,14 @@ public class FeatureRenderer { 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()); @@ -402,60 +406,16 @@ public class FeatureRenderer renderOrder[data.length - i - 1] = 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)); - } } class TransparencySetter { void setTransparency(Graphics g, float value) { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, value)); + Graphics2D g2 = (Graphics2D) g; + g2.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, value)); } }