-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
- Color resBoxColour;\r
- float transparency = 1.0f;\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
-\r
- // This is actually an Integer held in the hashtable,\r
- // Retrieved using the key feature type\r
- Object currentColour;\r
-\r
- String [] renderOrder;\r
-\r
-\r
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- initColours();\r
- }\r
-\r
-\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- lastSequence = seq;\r
- sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
-\r
- if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
- return Color.white;\r
-\r
- currentColour = null;\r
-\r
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
-\r
- if(currentColour==null)\r
- return initialCol;\r
-\r
- return new Color( ((Integer)currentColour).intValue() );\r
- }\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
-\r
- boolean overview = false;\r
-\r
- int white = Color.white.getRGB();\r
- public int findFeatureColour(int initialCol, int seqIndex, int column)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seqIndex!=lastSequenceIndex)\r
- {\r
- lastSequence = av.alignment.getSequenceAt(seqIndex);\r
- lastSequenceIndex = seqIndex;\r
- sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
- return Color.white.getRGB();\r
-\r
- currentColour = null;\r
-\r
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
-\r
- if(currentColour==null)\r
- return initialCol;\r
-\r
- return ((Integer)currentColour).intValue();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- // String type;\r
- // SequenceFeature sf;\r
- int lastSequenceIndex=-1;\r
- SequenceI lastSequence;\r
- SequenceFeature [] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
-\r
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1, int width, int height)\r
- {\r
- if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
- return;\r
-\r
-\r
- if(g!=null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- if (av.featuresDisplayed == null || renderOrder==null)\r
- {\r
- findAllFeatures();\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(lastSequence==null || seq!=lastSequence)\r
- {\r
- lastSequence = seq;\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if (transparency != 1 && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
- }\r
-\r
- if(!overview)\r
- {\r
- spos = lastSequence.findPosition(start);\r
- epos = lastSequence.findPosition(end);\r
- }\r
-\r
- String type;\r
- for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
-\r
- // loop through all features in sequence to find\r
- // current feature to render\r
- for (sfindex = 0; sfindex < sfSize; sfindex++)\r
- {\r
- if (!sequenceFeatures[sfindex].type.equals(type))\r
- continue;\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
-\r
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
-\r
- if (overview)\r
- {\r
-\r
- if (sequenceFeatures[sfindex].begin - 1 <= start &&\r
- sequenceFeatures[sfindex].end + 1 >= start)\r
- {\r
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
- type);\r
- }\r
-\r
- }\r
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1, width, height);\r
-\r
-\r
- }\r
-\r
- }\r
-\r
- if(transparency!=1.0f && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, 1.0f));\r
- }\r
- }\r
-\r
-\r
- char s;\r
- int i;\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height)\r
- {\r
-\r
- if (((fstart <= end) && (fend >= start)))\r
- {\r
- if (fstart < start)\r
- { // fix for if the feature we have starts before the sequence start,\r
- fstart = start; // but the feature end is still valid!!\r
- }\r
-\r
- if (fend >= end)\r
- {\r
- fend = end;\r
- }\r
-\r
- for (i = fstart; i <= fend; i++)\r
- {\r
- s = seq.getSequence().charAt(i);\r
-\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- g.setColor(featureColour);\r
-\r
- g.fillRect( (i - start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + (width * (i - start)),\r
- (y1 + height) - height / 5); //pady = height / 5;\r
-\r
- }\r
- }\r
- }\r
-\r
- void findAllFeatures()\r
- {\r
- av.featuresDisplayed = new Hashtable();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
- getSequenceFeatures();\r
-\r
- if (features == null)\r
- continue;\r
-\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
- {\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer( getColour(features[index].getType()).getRGB()) );\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- renderOrder = new String[av.featuresDisplayed.size()];\r
- Enumeration en = av.featuresDisplayed.keys();\r
- int i = 0;\r
- while(en.hasMoreElements())\r
- {\r
- renderOrder[i] = en.nextElement().toString();\r
- i++;\r
- }\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- return (Color)featureColours.get(featureType);\r
- }\r
-\r
- public void addNewFeature(String name, Color col)\r
- {\r
-\r
- setColour(name, col);\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
-\r
- av.featuresDisplayed.put(name, "NOGROUP");\r
- }\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\r
- }\r
-\r
- public void setTransparency(float value)\r
- {\r
- transparency = value;\r
- }\r
-\r
- public float getTransparency()\r
- {\r
- return transparency;\r
- }\r
-\r
- public void setFeaturePriority(Object [][] data)\r
- {\r
- // The feature table will display high priority\r
- // features at the top, but theses are the ones\r
- // we need to render last, so invert the data\r
- av.featuresDisplayed.clear();\r
-\r
- renderOrder = new String[data.length];\r
-\r
- if(data.length>0)\r
- for(int i=data.length-1; i>-1; i--)\r
- {\r
- String type = data[i][0].toString();\r
- setColour(type, (Color)data[i][1]);\r
- if( ((Boolean)data[i][2]).booleanValue() )\r
- {\r
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
- }\r
- renderOrder[i] = type;\r
- }\r
-\r
- }\r
-\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
- {\r
- featureColours.put("active site", new Color(255, 75, 0));\r
- featureColours.put("binding site", new Color(245, 85, 0));\r
- featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
- featureColours.put("chain", new Color(225, 105, 0));\r
- featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
- featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
- featureColours.put("cross-link", new Color(195, 135, 0));\r
- featureColours.put("disulfide bond", new Color(230,230,0));\r
- featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
- featureColours.put("domain", new Color(165, 165, 0));\r
- featureColours.put("glycosylation site", new Color(155, 175, 0));\r
- featureColours.put("helix", new Color(145, 185, 0));\r
- featureColours.put("initiator methionine", new Color(135, 195, 5));\r
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
- featureColours.put("modified residue", new Color(105, 225, 35));\r
- featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
- featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
- featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
- featureColours.put("peptide", new Color(55, 235, 85));\r
- featureColours.put("propeptide", new Color(45, 225, 95));\r
- featureColours.put("region of interest", new Color(35, 215, 105));\r
- featureColours.put("repeat", new Color(25, 205, 115));\r
- featureColours.put("selenocysteine", new Color(15, 195, 125));\r
- featureColours.put("sequence conflict", new Color(5, 185, 135));\r
- featureColours.put("sequence variant", new Color(0, 175, 145));\r
- featureColours.put("short sequence motif", new Color(0, 165, 155));\r
- featureColours.put("signal peptide", new Color(0, 155, 165));\r
- featureColours.put("site", new Color(0, 145, 175));\r
- featureColours.put("splice variant", new Color(0, 135, 185));\r
- featureColours.put("strand", new Color(0, 125, 195));\r
- featureColours.put("topological domain", new Color(0, 115, 205));\r
- featureColours.put("transit peptide", new Color(0, 105, 215));\r
- featureColours.put("transmembrane region", new Color(0, 95, 225));\r
- featureColours.put("turn", new Color(0, 85, 235));\r
- featureColours.put("unsure residue", new Color(0, 75, 245));\r
- featureColours.put("zinc finger region", new Color(0, 65, 255));\r
- }\r
-\r
-}\r