/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
*/\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
\r
-import java.util.*;\r
+import jalview.datamodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class FeatureRenderer\r
{\r
- AlignViewport av;\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Graphics graphics;\r
-\r
- // The following vector holds the features which are\r
- // to be added, in the correct order or rendering\r
- Vector featuresDisplayed;\r
-\r
- Color currentColour = null;\r
-\r
- boolean drawText = true;\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\r
+ AlignViewport av;\r
+\r
+ Hashtable featureColours = new Hashtable();\r
+\r
+ // A higher level for grouping features of a\r
+ // particular type\r
+ Hashtable featureGroups = null;\r
+\r
+ // Holds web links for feature groups and feature types\r
+ // in the form label|link\r
+ Hashtable featureLinks = null;\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
+ FontMetrics fm;\r
+ int charOffset;\r
+\r
+ float transparency = 1f;\r
+\r
+ TransparencySetter transparencySetter = 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
+\r
+ if (!System.getProperty("java.version").startsWith("1.1"))\r
+ {\r
+ transparencySetter = new TransparencySetter();\r
+ }\r
+ }\r
+\r
+ public void transferSettings(FeatureRenderer fr)\r
+ {\r
+ renderOrder = fr.renderOrder;\r
+ featureGroups = fr.featureGroups;\r
+ featureColours = fr.featureColours;\r
+ transparency = fr.transparency;\r
+ }\r
+\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ overview = true;\r
+ if (!av.showSequenceFeatures)\r
{\r
- this.av = av;\r
- initColours();\r
+ return initialCol;\r
}\r
\r
- //boolean highlightTransparent = true;\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
+ lastSequence = seq;\r
+ sequenceFeatures = lastSequence.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
{\r
- fm = g.getFontMetrics();\r
+ return initialCol;\r
+ }\r
\r
- if(seq.getSequenceFeatures()==null)\r
- return;\r
+ sfSize = sequenceFeatures.length;\r
\r
- Enumeration e = null, e2;\r
- String type;\r
- if(featuresDisplayed!=null)\r
- e = featuresDisplayed.elements();\r
- else\r
- e = seq.getSequenceFeatures().elements();\r
+ if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
+ {\r
+ return Color.white;\r
+ }\r
\r
+ currentColour = null;\r
\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf=null;\r
- if(featuresDisplayed!=null)\r
- {\r
- e2 = seq.getSequenceFeatures().elements();\r
- type = e.nextElement().toString();\r
- while(e2.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e2.nextElement();\r
- if(sf.getType().equals(type))\r
- break;\r
- else\r
- sf = null;\r
- }\r
- }\r
- else\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- type = sf.getType();\r
- }\r
-\r
- if(sf==null)\r
- continue;\r
-\r
-\r
- if (sf.getBegin() > seq.getEnd())\r
- {\r
- continue;\r
- }\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
+ drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);\r
\r
+ if (currentColour == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ return new Color( ( (Integer) currentColour).intValue());\r
+ }\r
+\r
+ /**\r
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\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
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ if (seqIndex != lastSequenceIndex)\r
+ {\r
+ lastSequence = av.alignment.getSequenceAt(seqIndex);\r
+ lastSequenceIndex = seqIndex;\r
+ sequenceFeatures = lastSequence.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
+ {\r
+ return initialCol;\r
}\r
+\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
+ if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
+ {\r
+ return Color.white.getRGB();\r
}\r
\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, String type, int start, int end,\r
- int x1, int y1, int width, int height)\r
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);\r
+\r
+ if (currentColour == null)\r
{\r
- if ( ( (fstart <= end) && (fend >= start)))\r
+ return initialCol;\r
+ }\r
+\r
+ return ( (Integer) currentColour).intValue();\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)\r
+ {\r
+ if (seq.getSequenceFeatures() == null\r
+ || seq.getSequenceFeatures().length == 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (transparencySetter != null && g != null)\r
+ {\r
+ transparencySetter.setTransparency(g, transparency);\r
+ }\r
+\r
+ if (av.featuresDisplayed == null || renderOrder == null)\r
+ {\r
+ findAllFeatures();\r
+ if (av.featuresDisplayed.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if (lastSequence == null || seq != lastSequence)\r
+ {\r
+ lastSequence = seq;\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if (!overview)\r
+ {\r
+ spos = lastSequence.findPosition(start);\r
+ epos = lastSequence.findPosition(end);\r
+ if (g != null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
+ }\r
+ String type;\r
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
+ {\r
+ type = renderOrder[renderIndex];\r
+ if (!av.featuresDisplayed.containsKey(type))\r
+ {\r
+ continue;\r
+ }\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 (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
+ if (!sequenceFeatures[sfindex].type.equals(type))\r
+ {\r
+ continue;\r
}\r
\r
- if (fend >= end)\r
+ if (featureGroups != null\r
+ && sequenceFeatures[sfindex].featureGroup != null\r
+ &&\r
+ featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
+ &&\r
+ ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
+ featureGroup)).\r
+ booleanValue())\r
{\r
- fend = end;\r
+ continue;\r
}\r
- for (int i = fstart; i <= fend; i++)\r
+\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
{\r
- char s = seq.getSequence().charAt(i);\r
+ continue;\r
+ }\r
\r
- if (jalview.util.Comparison.isGap(s))\r
+ if (overview)\r
+ {\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r
{\r
- continue;\r
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
+ type);\r
}\r
\r
- currentColour = getColour(type);\r
-\r
- g.setColor(currentColour);\r
+ }\r
+ else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
+ {\r
\r
- g.fillRect( (i - start) * width, y1, width, height);\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);\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);\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);\r
- }\r
}\r
+ else\r
+ {\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);\r
+ }\r
+\r
}\r
}\r
\r
- Image offscreen;\r
- Frame nullframe;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ if (transparencySetter != null && g != null)\r
+ {\r
+ transparencySetter.setTransparency(g, 1.0f);\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,\r
+ int end, int y1)\r
+ {\r
+\r
+ if ( ( (fstart <= end) && (fend >= start)))\r
{\r
- currentColour = initialCol;\r
- if(offscreen == null)\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
- nullframe = new Frame();\r
- nullframe.addNotify();\r
- offscreen = nullframe.createImage(1, 1);\r
+ fend = end;\r
}\r
\r
- drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
- return currentColour;\r
- }\r
+ for (i = fstart; i <= fend; i++)\r
+ {\r
+ s = seq.getCharAt(i);\r
\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
+ g.setColor(featureColour);\r
\r
- public Color getColour(String featureType)\r
- {\r
- return (Color)featureColours.get(featureType);\r
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
+\r
+ if (!av.validCharWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(Color.white);\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + (av.charWidth * (i - start)),\r
+ (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
+\r
+ }\r
}\r
+ }\r
+\r
+ void findAllFeatures()\r
+ {\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
\r
- public void setColour(String featureType, Color col)\r
+ av.featuresDisplayed = new Hashtable();\r
+ Vector allfeatures = new Vector();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- featureColours.put(featureType, col);\r
+ SequenceFeature[] features = av.alignment.getSequenceAt(i).\r
+ getSequenceFeatures();\r
+\r
+ if (features == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ int index = 0;\r
+ while (index < features.length)\r
+ {\r
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
+ {\r
+ if (getColour(features[index].getType()) == null)\r
+ {\r
+ featureColours.put(features[index].getType(),\r
+ ucs.createColourFromName(features[index].\r
+ getType()));\r
+ }\r
+\r
+ av.featuresDisplayed.put(features[index].getType(),\r
+ new Integer(getColour(features[index].\r
+ getType()).getRGB()));\r
+ allfeatures.addElement(features[index].getType());\r
+ }\r
+ index++;\r
+ }\r
}\r
\r
- /* public void setTransparency(float value)\r
+ renderOrder = new String[allfeatures.size()];\r
+ Enumeration en = allfeatures.elements();\r
+ int i = allfeatures.size() - 1;\r
+ while (en.hasMoreElements())\r
{\r
- transparency = value;\r
+ renderOrder[i] = en.nextElement().toString();\r
+ i--;\r
}\r
+ }\r
\r
- public float getTransparency()\r
- {\r
- return transparency;\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
- public void setFeaturePriority(Object [][] data)\r
+ setColour(name, col);\r
+ if (av.featuresDisplayed == null)\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
- if(featuresDisplayed!=null)\r
- featuresDisplayed.removeAllElements();\r
- else\r
- featuresDisplayed = new Vector();\r
-\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
+ av.featuresDisplayed = new Hashtable();\r
}\r
\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\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 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
+ if (av.featuresDisplayed != null)\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(185, 145, 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",\r
- 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
+ av.featuresDisplayed.clear();\r
}\r
\r
-}\r
+ renderOrder = new String[data.length];\r
\r
+ if (data.length > 0)\r
+ {\r
+ for (int i = 0; i < data.length; 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
\r
+ renderOrder[data.length - i - 1] = type;\r
+ }\r
+ }\r
+ }\r
+}\r
\r
+class TransparencySetter\r
+{\r
+ void setTransparency(Graphics g, float value)\r
+ {\r
+ /* Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, value));*/\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff