+/*\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
-import jalview.schemes.*;\r
+\r
import java.awt.*;\r
+\r
import java.util.*;\r
\r
-public class FeatureRenderer implements RendererI {\r
+import java.awt.image.*;\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
+ boolean drawText = true;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed = null;\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
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\r
+ */\r
+ BufferedImage bi;\r
+ public synchronized Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ if(!av.showSequenceFeatures)\r
+ return initialCol;\r
+\r
+ if (bi == null)\r
+ bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);\r
+\r
+ bi.setRGB(0,0, initialCol.getRGB());\r
+\r
+ drawText = false;\r
\r
+ drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
+ drawText = true;\r
\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
- Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
- return c;\r
+ return new Color(bi.getRGB(0, 0));\r
}\r
\r
- public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) {\r
\r
- int i = start;\r
- int length = seq.getLength();\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
+ public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int x1, int y1, int width, int height)\r
+ {\r
\r
- Color currentColor = Color.black;\r
+//System.out.println(start+" "+end+" "+x1+" "+y1);\r
+ if (seq.getDatasetSequence().getSequenceFeatures() == null\r
+ || seq.getDatasetSequence().getSequenceFeatures().size()==0)\r
+ return;\r
\r
+ fm = g.getFontMetrics();\r
+\r
+ if (transparency != 1)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, transparency));\r
+ }\r
+\r
+ String type;\r
+ SequenceFeature sf;\r
+ if (featuresDisplayed == null)\r
+ findAllFeatures();\r
+\r
+ Enumeration e = featuresDisplayed.elements(), e2;\r
+\r
+ // Loop through each visible feature\r
+ while (e.hasMoreElements())\r
+ {\r
+\r
+ type = e.nextElement().toString();\r
+ e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ while (e2.hasMoreElements())\r
+ {\r
+\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if (!type.equals(sf.getType()))\r
+ continue;\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
+ continue;\r
+\r
+ if (type.equals("disulfide bond"))\r
+ {\r
+\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+\r
+ }\r
+ else\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+ }\r
+ }\r
\r
- int prev = -1;\r
- int fstart = 0;\r
- char prevc = '-';\r
+ if(transparency!=1.0f)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, 1.0f));\r
+ }\r
+ }\r
\r
- g.setColor(Color.magenta);\r
\r
- while (i <= end && i < length) {\r
- char c = seq.getCharAt(i);\r
- if (c != '-') {\r
+ void renderFeature(Graphics g, SequenceI seq,\r
+ int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
+ {\r
\r
- if (prevc != c) {\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 (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
- }\r
- g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
\r
- prevc = c;\r
- fstart = i;\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
}\r
- } else if (prevc != '-') {\r
- if (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
- }\r
- g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);\r
-\r
- prevc = c;\r
- } else {\r
- fstart = -1;\r
+\r
+ g.setColor(getColour(type));\r
+\r
+ g.fillRect( (i - start) * width, y1, width, height);\r
+\r
+ if(drawText)\r
+ {\r
+ g.setColor(Color.white);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - height / 5); //pady = height / 5;\r
+ }\r
}\r
- i++;\r
- }\r
-\r
- if (fstart != -1) {\r
- if (prevc == 'F') {\r
- g.setColor(Color.green);\r
- } else if (prevc == 'R') {\r
- g.setColor(Color.cyan);\r
- } else if (prevc == 'M') {\r
- g.setColor(Color.magenta);\r
- } else if (prevc == 'P') {\r
- g.setColor(Color.yellow);\r
}\r
+ }\r
\r
- //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);\r
+ void findAllFeatures()\r
+ {\r
+ Vector features = new Vector();\r
+ SequenceFeature sf;\r
+ featuresDisplayed = new Vector();\r
+ Enumeration e;\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
+ getSequenceFeatures();\r
+ if (features == null)\r
+ continue;\r
\r
+ e = features.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e.nextElement();\r
+ if (!featuresDisplayed.contains(sf.getType()))\r
+ {\r
+ featuresDisplayed.addElement(sf.getType());\r
+ }\r
}\r
+ }\r
+ }\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\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
+ featuresDisplayed.clear();\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
+ featuresDisplayed.addElement(type);\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
git://source.jalview.org / jalview.git / blobdiff