X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=954a95ed2951a9694281031280c7fa1bb986aedf;hb=49606a763a26d7e130b06078558f079603ea8bae;hp=21c401a447ee1d0cbf52a97dd56deedb57b65cc8;hpb=011c92dbea927aa8ae693ae75bf1b42a1c564aef;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 21c401a..954a95e 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,6 +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 @@ -34,21 +35,30 @@ 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; - boolean drawText = true; FontMetrics fm; int charOffset; + float transparency = 1f; + + TransparencySetter transparencySetter = null; + /** * Creates a new FeatureRenderer object. * @@ -57,12 +67,24 @@ public class FeatureRenderer public FeatureRenderer(AlignViewport av) { this.av = av; - initColours(); + + 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; } public Color findFeatureColour(Color initialCol, SequenceI seq, int i) { + overview = true; if(!av.showSequenceFeatures) return initialCol; @@ -78,18 +100,18 @@ 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; 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(); @@ -115,7 +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; @@ -145,19 +167,23 @@ 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) return; - - if(g!=null) - fm = g.getFontMetrics(); + 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; } @@ -171,11 +197,15 @@ public class FeatureRenderer { spos = lastSequence.findPosition(start); epos = lastSequence.findPosition(end); + if(g!=null) + fm = g.getFontMetrics(); } String type; for(int renderIndex=0; renderIndex= start) + if (sequenceFeatures[sfindex].begin <= start && + sequenceFeatures[sfindex].end >= start) { currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. type); @@ -218,13 +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 @@ -232,11 +261,14 @@ 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); } + } + if(transparencySetter!=null && g!=null) + { + transparencySetter.setTransparency(g, 1.0f); } } @@ -244,7 +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))) @@ -270,13 +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; } } @@ -284,7 +319,11 @@ 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++) { SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures(); @@ -297,20 +336,29 @@ 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()); } index++; } } - renderOrder = new String[av.featuresDisplayed.size()]; - Enumeration en = av.featuresDisplayed.keys(); - int i = 0; + renderOrder = new String[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + int i = allfeatures.size()-1; while(en.hasMoreElements()) { renderOrder[i] = en.nextElement().toString(); - i++; + i--; } } @@ -337,73 +385,40 @@ public class FeatureRenderer 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 - av.featuresDisplayed.clear(); + // 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 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; + } } +} - Hashtable featureColours = new Hashtable(); - void initColours() + class TransparencySetter + { + void setTransparency(Graphics g, float value) { - 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)); + //Graphics2D g2 = (Graphics2D) g; + // g2.setComposite( + // AlphaComposite.getInstance( + // AlphaComposite.SRC_OVER, value)); } + } -}