+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * 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.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
import java.util.*;\r
\r
+import java.awt.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class FeatureRenderer\r
{\r
AlignViewport av;\r
\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\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 void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
{\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
+ overview = true;\r
+ if (!av.showSequenceFeatures)\r
{\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- if(sf.getStart()>seq.getEnd())\r
- continue;\r
+ return initialCol;\r
+ }\r
+\r
+ lastSequence = seq;\r
+ sequenceFeatures = lastSequence.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ sfSize = sequenceFeatures.length;\r
+\r
+ if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
+ {\r
+ return Color.white;\r
+ }\r
+\r
+ currentColour = null;\r
+\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
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);\r
+\r
+ if (currentColour == null)\r
+ {\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
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
+ if (av.featuresDisplayed == null || renderOrder == null)\r
+ {\r
+ findAllFeatures();\r
+ if (av.featuresDisplayed.size() < 1)\r
+ {\r
+ return;\r
+ }\r
\r
- if( (fstart<=end && fend>=start) )\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
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
+ continue;\r
+ }\r
\r
- if(fstart==fend)\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
{\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
- g.setColor(Color.white);\r
+ continue;\r
+ }\r
\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\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
+ continue;\r
+ }\r
\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
+ {\r
+ continue;\r
}\r
- else\r
+\r
+ if (overview)\r
{\r
- for (int i = fstart; i <= fend; i++)\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r
{\r
- char s = seq.getSequence().charAt(i);\r
- if( jalview.util.Comparison.isGap(s) )\r
- continue;\r
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
+ type);\r
+ }\r
\r
- g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\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);\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
+ }\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
+ 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
+ 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.getCharAt(i);\r
\r
- g.setColor(Color.white);\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(featureColour);\r
+\r
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
+\r
+ if (!av.validCharWidth)\r
+ {\r
+ continue;\r
+ }\r
\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\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
+ av.featuresDisplayed = new Hashtable();\r
+ Vector allfeatures = new Vector();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\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
+ renderOrder = new String[allfeatures.size()];\r
+ Enumeration en = allfeatures.elements();\r
+ int i = allfeatures.size() - 1;\r
+ while (en.hasMoreElements())\r
+ {\r
+ renderOrder[i] = en.nextElement().toString();\r
+ i--;\r
}\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
+ {\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 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
+ av.featuresDisplayed.clear();\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