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
// A higher level for grouping features of a\r
// particular type\r
Hashtable featureGroups = null;\r
\r
- Color currentColour = null;\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
- boolean drawText = true;\r
FontMetrics fm;\r
int charOffset;\r
\r
initColours();\r
}\r
\r
- //boolean highlightTransparent = true;\r
+\r
+ public void transferSettings(FeatureRenderer fr)\r
+ {\r
+ renderOrder = fr.renderOrder;\r
+ featureGroups = fr.featureGroups;\r
+ featureColours = fr.featureColours;\r
+ }\r
+\r
+\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ overview = true;\r
+ if(!av.showSequenceFeatures)\r
+ return initialCol;\r
+\r
+ lastSequence = seq;\r
+ sequenceFeatures = lastSequence.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
+ /**\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
+ return initialCol;\r
+\r
+ if(seqIndex!=lastSequenceIndex)\r
+ {\r
+ lastSequence = av.alignment.getSequenceAt(seqIndex);\r
+ lastSequenceIndex = seqIndex;\r
+ sequenceFeatures = lastSequence.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 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 x1, int y1, int width, int height)\r
+ int start, int end, int y1, int width, int height)\r
{\r
- fm = g.getFontMetrics();\r
-\r
- if(seq.getSequenceFeatures()==null)\r
- return;\r
+ if ( seq.getSequenceFeatures() == null\r
+ || seq.getSequenceFeatures().length==0)\r
+ return;\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
\r
+ if (av.featuresDisplayed == null || renderOrder==null)\r
+ {\r
+ findAllFeatures();\r
+ if(av.featuresDisplayed.size()<1)\r
+ return;\r
\r
- while (e.hasMoreElements())\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
+ fm = g.getFontMetrics();\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
+ continue;\r
+\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\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
+ if (!sequenceFeatures[sfindex].type.equals(type))\r
+ continue;\r
\r
- if(featureGroups!=null\r
- && sf.getFeatureGroup()!=null\r
- && featureGroups.containsKey(sf.getFeatureGroup())\r
- && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())\r
- {\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 (sf.getBegin() > seq.getEnd())\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
- if (type.equals("disulfide bond"))\r
- {\r
+ }\r
+ else if (sequenceFeatures[sfindex].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
+ 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(sf.getBegin()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\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
+ char s;\r
+ int i;\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
+ int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height)\r
{\r
- if ( ( (fstart <= end) && (fend >= start)))\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
{\r
fend = end;\r
}\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
\r
- if (jalview.util.Comparison.isGap(s))\r
+ for (i = fstart; i <= fend; i++)\r
{\r
- continue;\r
- }\r
+ s = seq.getSequence().charAt(i);\r
\r
- currentColour = getColour(type);\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
- g.setColor(currentColour);\r
+ g.setColor(featureColour);\r
\r
- g.fillRect( (i - start) * width, y1, width, height);\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);\r
+ charOffset + (width * (i - start)),\r
+ (y1 + height) - height / 5); //pady = height / 5;\r
+\r
}\r
- }\r
}\r
}\r
\r
- Image offscreen;\r
- Frame nullframe;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ void findAllFeatures()\r
{\r
- currentColour = initialCol;\r
- if(offscreen == null)\r
+ av.featuresDisplayed = new Hashtable();\r
+ Vector allfeatures = new Vector();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- nullframe = new Frame();\r
- nullframe.addNotify();\r
- offscreen = nullframe.createImage(1, 1);\r
- }\r
+ SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
\r
- drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
- return currentColour;\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
+ 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
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 addNewFeature(String name, Color col)\r
{\r
+\r
setColour(name, col);\r
- if (featuresDisplayed == null)\r
- featuresDisplayed = new Vector();\r
- featuresDisplayed.insertElementAt(name, 0);\r
- }\r
+ if(av.featuresDisplayed==null)\r
+ av.featuresDisplayed = new Hashtable();\r
\r
\r
- /* public void setTransparency(float value)\r
- {\r
- transparency = value;\r
+ av.featuresDisplayed.put(name, "NOGROUP");\r
}\r
\r
- public float getTransparency()\r
+ public void setColour(String featureType, Color col)\r
{\r
- return transparency;\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(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
+ // 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
+ av.featuresDisplayed.clear();\r
+\r
+ renderOrder = new String[data.length];\r
+\r
+ if (data.length > 0)\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
Hashtable featureColours = new Hashtable();\r
git://source.jalview.org / jalview.git / blobdiff