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
initColours();\r
}\r
\r
- //boolean highlightTransparent = true;\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.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.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(g!=null)\r
+ fm = g.getFontMetrics();\r
\r
- while (e.hasMoreElements())\r
+ if (av.featuresDisplayed == null || renderOrder==null)\r
+ {\r
+ findAllFeatures();\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
+ }\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
- 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
+ if (!sequenceFeatures[sfindex].type.equals(type))\r
+ continue;\r
\r
- if(sf==null)\r
- continue;\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(featureGroups!=null\r
- && sf.getFeatureGroup()!=null\r
- && featureGroups.containsKey(sf.getFeatureGroup())\r
- && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())\r
- {\r
- continue;\r
- }\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
+ continue;\r
\r
+ if (overview)\r
+ {\r
\r
- if (sf.getBegin() > seq.getEnd())\r
+ if (sequenceFeatures[sfindex].begin - 1 <= start &&\r
+ sequenceFeatures[sfindex].end + 1 >= 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(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
- 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
}\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
+ 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
+ }\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 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
+ av.featuresDisplayed.clear();\r
+\r
+ renderOrder = new String[data.length];\r
\r
- for(int i=data.length-1; i>-1; i--)\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
- featuresDisplayed.addElement(type);\r
+ {\r
+ av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
+ }\r
+\r
+ renderOrder[i] = type;\r
}\r
+\r
}\r
\r
Hashtable featureColours = new Hashtable();\r
final Frame frame;\r
Panel groupPanel;\r
Panel featurePanel = new Panel();\r
+ ScrollPane scrollPane;\r
\r
public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
{\r
setTableData();\r
\r
this.setLayout(new BorderLayout());\r
- ScrollPane sp = new ScrollPane();\r
- sp.add(featurePanel);\r
- add(sp, BorderLayout.CENTER);\r
+ scrollPane = new ScrollPane();\r
+ scrollPane.add(featurePanel);\r
+ add(scrollPane, BorderLayout.CENTER);\r
if(groupPanel!=null)\r
{\r
- sp = new ScrollPane();\r
- sp.add(groupPanel);\r
+ groupPanel.setLayout(\r
+ new GridLayout(groupPanel.getComponentCount() / 4, 4));\r
+ groupPanel.validate();\r
\r
- add(sp, BorderLayout.NORTH);\r
- sp.validate();\r
- sp.setSize( 100, 55);\r
+ add(groupPanel, BorderLayout.NORTH);\r
}\r
frame = new Frame();\r
frame.add(this);\r
if (height>400)\r
height = 400;\r
\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 200,\r
+ jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 250,\r
height);\r
}\r
\r
fr.featureGroups.clear();\r
\r
Vector allFeatures = new Vector();\r
- Enumeration tmpfeatures;\r
- SequenceFeature sf;\r
+ SequenceFeature[] tmpfeatures;\r
\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
continue;\r
\r
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures().elements();\r
- while (tmpfeatures.hasMoreElements())\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
{\r
- sf = (SequenceFeature) tmpfeatures.nextElement();\r
- if (!allFeatures.contains(sf.getType()))\r
+ if(tmpfeatures[index].getFeatureGroup()!=null\r
+ && tmpfeatures[index].getFeatureGroup().length()>0\r
+ && !fr.featureGroups.containsKey(tmpfeatures[index].getFeatureGroup()))\r
{\r
- allFeatures.addElement(sf.getType());\r
- Color col = fr.getColour(sf.getType());\r
- boolean displayed = true;\r
- if (fr.featuresDisplayed != null)\r
- displayed = fr.featuresDisplayed.contains(sf.getType());\r
-\r
- Checkbox check = new Checkbox(sf.getType(), displayed);\r
- check.addMouseListener(this);\r
- check.addMouseMotionListener(this);\r
- check.setBackground(col);\r
- check.addItemListener(this);\r
- featurePanel.add(check);\r
- }\r
- if(sf.getFeatureGroup()!=null\r
- && !fr.featureGroups.containsKey(sf.getFeatureGroup()))\r
- {\r
- fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));\r
+ fr.featureGroups.put(tmpfeatures[index].getFeatureGroup(), new Boolean(true));\r
if(groupPanel==null)\r
+ {\r
groupPanel = new Panel();\r
+ }\r
\r
- Checkbox check = new Checkbox(sf.getFeatureGroup(), true);\r
+ Checkbox check = new Checkbox(tmpfeatures[index].getFeatureGroup(), true);\r
check.setFont(new Font("Serif", Font.BOLD, 12));\r
check.addItemListener(this);\r
groupPanel.add(check);\r
}\r
+\r
+ if (!allFeatures.contains(tmpfeatures[index].getType()))\r
+ {\r
+ allFeatures.addElement(tmpfeatures[index].getType());\r
+ }\r
+\r
+\r
+ index ++;\r
}\r
}\r
\r
+ resetTable();\r
featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));\r
featurePanel.validate();\r
}\r
\r
+ void resetTable()\r
+ {\r
+ featurePanel.removeAll();\r
+ Enumeration groups = fr.featureGroups.keys();\r
+ SequenceFeature [] tmpfeatures;\r
+ String group, type;\r
+ Vector checksAdded = new Vector();\r
+\r
+ while(groups.hasMoreElements())\r
+ {\r
+ group = groups.nextElement().toString();\r
+ if ( !( (Boolean) fr.featureGroups.get(group)).booleanValue())\r
+ continue;\r
+\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
+ continue;\r
+\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ if (tmpfeatures[index].getFeatureGroup() != null &&\r
+ tmpfeatures[index].getFeatureGroup().equals(group))\r
+ {\r
+ type = tmpfeatures[index].getType();\r
+ if(!checksAdded.contains(type))\r
+ {\r
+ checksAdded.addElement(type);\r
+ Checkbox check = new Checkbox(type, true);\r
+ check.addMouseListener(this);\r
+ check.addMouseMotionListener(this);\r
+ check.setBackground(fr.getColour(type));\r
+ check.addItemListener(this);\r
+ featurePanel.add(check);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+ }\r
+ featurePanel.validate();\r
+ if(scrollPane!=null)\r
+ scrollPane.validate();\r
+ }\r
+\r
public void itemStateChanged(ItemEvent evt)\r
{\r
- if(evt!=null)\r
+ if (evt != null)\r
{\r
//Is the source a top level featureGroup?\r
Checkbox source = (Checkbox) evt.getSource();\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
\r
+ resetTable();\r
return;\r
}\r
}\r
Component[] comps = featurePanel.getComponents();\r
int cSize = comps.length;\r
\r
- Object[][] data = new Object[cSize][3];\r
-\r
+ Object[][] tmp = new Object[cSize][3];\r
+ int tmpSize = 0;\r
for (int i = 0; i < cSize; i++)\r
{\r
Checkbox check = (Checkbox) comps[i];\r
- data[i][0] = check.getLabel();\r
- data[i][1] = fr.getColour(check.getLabel());\r
- data[i][2] = new Boolean(check.getState());\r
+ if(!check.getState())\r
+ continue;\r
+\r
+ tmp[tmpSize][0] = check.getLabel();\r
+ tmp[tmpSize][1] = fr.getColour(check.getLabel());\r
+ tmp[tmpSize][2] = new Boolean(check.getState());\r
+ tmpSize++;\r
}\r
\r
+ Object[][]data = new Object[tmpSize][3];\r
+ System.arraycopy(tmp, 0, data,0, tmpSize);\r
+\r
fr.setFeaturePriority(data);\r
ap.seqPanel.seqCanvas.repaint();\r
if (ap.overviewPanel != null)\r
sr = new SequenceRenderer(av);\r
sr.graphics = nullFrame.getGraphics();\r
sr.renderGaps( false );\r
+ sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
fr.drawText = false;\r
+ fr.overview = true;\r
\r
\r
\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
- featuresDisplayed;\r
fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+ fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
}\r
\r
\r
float sampleCol = (float) alwidth / (float) width;\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
- int lastcol=-1, lastrow=-1;\r
+ int lastcol=-1, lastrow=0;\r
Color color = Color.yellow;\r
int row, col;\r
- for (col = 0; col < width; col++)\r
+ jalview.datamodel.SequenceI sequence;\r
+ for (row = 0; row < sequencesHeight; row++)\r
{\r
- for (row = 0; row < sequencesHeight; row++)\r
+ sequence = av.getAlignment().getSequenceAt(lastrow);\r
+ for (col = 0; col < width; col++)\r
{\r
if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
{\r
continue;\r
}\r
\r
- if (av.conservation != null)\r
- {\r
- mg.translate(col, sequencesHeight);\r
- ap.annotationPanel.drawGraph(mg, av.conservation,\r
- (int) (sampleCol) + 1,\r
- graphHeight,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol) + 1);\r
- mg.translate( -col, -sequencesHeight);\r
- }\r
-\r
lastrow = (int)(row*sampleRow);\r
lastcol = (int)(col*sampleCol);\r
\r
if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
{\r
- color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
\r
+ color = sr.findSequenceColour(sequence, lastcol);\r
\r
if (av.showSequenceFeatures)\r
color = fr.findFeatureColour(color,\r
- av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
+ sequence,\r
+ lastcol);\r
}\r
\r
mg.setColor(color);\r
}\r
}\r
\r
+ if (av.conservation != null)\r
+ {\r
+ for (col = 0; col < width; col++)\r
+ {\r
+ lastcol = (int) (col * sampleCol);\r
+ {\r
+ mg.translate(col, sequencesHeight);\r
+ ap.annotationPanel.drawGraph(mg, av.conservation,\r
+ (int) (sampleCol) + 1,\r
+ graphHeight,\r
+ (int) (col * sampleCol),\r
+ (int) (col * sampleCol) + 1);\r
+ mg.translate( -col, -sequencesHeight);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
\r
System.gc();\r
\r
git://source.jalview.org / jalview.git / commitdiff