\r
import java.util.*;\r
\r
-import java.awt.image.*;\r
-\r
\r
/**\r
* DOCUMENT ME!\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
// A higher level for grouping features of a\r
// particular type\r
Hashtable featureGroups = null;\r
\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
+\r
/**\r
* Creates a new FeatureRenderer object.\r
*\r
initColours();\r
}\r
\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.getDatasetSequence().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
- BufferedImage bi;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\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 (bi == null)\r
- bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);\r
+ if(seqIndex!=lastSequenceIndex)\r
+ {\r
+ lastSequence = av.alignment.getSequenceAt(seqIndex);\r
+ lastSequenceIndex = seqIndex;\r
+ sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
+ if(sequenceFeatures==null)\r
+ return initialCol;\r
\r
- bi.setRGB(0,0, initialCol.getRGB());\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
\r
- drawText = false;\r
\r
- drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
- drawText = true;\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 new Color(bi.getRGB(0, 0));\r
+ return ((Integer)currentColour).intValue();\r
}\r
\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
-\r
- //System.out.println(start+" "+end+" "+x1+" "+y1);\r
- if (seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().size()==0)\r
+ if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
+ || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
return;\r
\r
- fm = g.getFontMetrics();\r
\r
- if (transparency != 1)\r
+ if(g!=null)\r
+ fm = g.getFontMetrics();\r
+\r
+\r
+ if (av.featuresDisplayed == null || renderOrder==null)\r
+ {\r
+ findAllFeatures();\r
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
+ if(lastSequence==null || seq!=lastSequence)\r
+ {\r
+ lastSequence = seq;\r
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
+\r
+ if (transparency != 1 && g!=null)\r
{\r
Graphics2D g2 = (Graphics2D) g;\r
g2.setComposite(\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
+ if(!overview)\r
{\r
+ spos = lastSequence.findPosition(start);\r
+ epos = lastSequence.findPosition(end);\r
+ }\r
+\r
+ String type;\r
+ for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
+ {\r
+ type = renderOrder[renderIndex];\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
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\r
{\r
-\r
- sf = (SequenceFeature) e2.nextElement();\r
- if (!type.equals(sf.getType()))\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
+ 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 (sf.getBegin() > seq.getEnd())\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
continue;\r
\r
- if (type.equals("disulfide bond"))\r
+ if (overview)\r
+ {\r
+\r
+ if (sequenceFeatures[sfindex].begin - 1 <= start &&\r
+ sequenceFeatures[sfindex].end + 1 >= start)\r
+ {\r
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
+ type);\r
+ }\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
+ 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(sf.getEnd()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\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
+ 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
- if(transparency!=1.0f)\r
+ if(transparency!=1.0f && g!=null)\r
{\r
Graphics2D g2 = (Graphics2D) g;\r
g2.setComposite(\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, 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
\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
+ 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
- for (int i = fstart; i <= fend; i++)\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+\r
+ for (i = fstart; i <= fend; i++)\r
{\r
- char s = seq.getSequence().charAt(i);\r
+ s = seq.getSequence().charAt(i);\r
\r
if (jalview.util.Comparison.isGap(s))\r
{\r
continue;\r
}\r
\r
- g.setColor(getColour(type));\r
+ g.setColor(featureColour);\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
+ g.setColor(Color.white);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + (width * (i - start)),\r
+ (y1 + height) - height / 5); //pady = height / 5;\r
+\r
}\r
- }\r
+ }\r
}\r
\r
void findAllFeatures()\r
{\r
- Vector features = new Vector();\r
- SequenceFeature sf;\r
- featuresDisplayed = new Vector();\r
- Enumeration e;\r
+ av.featuresDisplayed = new Hashtable();\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
+ SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
getSequenceFeatures();\r
+\r
if (features == null)\r
continue;\r
\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
+ int index = 0;\r
+ while (index < features.length)\r
{\r
- sf = (SequenceFeature) e.nextElement();\r
- if (!featuresDisplayed.contains(sf.getType()))\r
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
{\r
- featuresDisplayed.addElement(sf.getType());\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
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
+ if(av.featuresDisplayed==null)\r
+ av.featuresDisplayed = new Hashtable();\r
+\r
+\r
+ av.featuresDisplayed.put(name, "NOGROUP");\r
}\r
\r
public void setColour(String featureType, Color col)\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
+ av.featuresDisplayed.clear();\r
+\r
+ renderOrder = new String[data.length];\r
+\r
+ if(data.length>0)\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.put(type, new Integer(getColour(type).getRGB()));\r
+ }\r
+ renderOrder[i] = type;\r
}\r
+\r
}\r
\r
Hashtable featureColours = new Hashtable();\r
final FeatureRenderer fr;\r
final AlignmentPanel ap;\r
final AlignViewport av;\r
+ Hashtable allFeatures;\r
Object [][] originalData;\r
final JInternalFrame frame;\r
JScrollPane scrollPane = new JScrollPane();\r
bigPanel.add(transPanel, BorderLayout.SOUTH);\r
bigPanel.add(scrollPane, BorderLayout.CENTER);\r
if(groupPanel!=null)\r
+ {\r
+ groupPanel.setLayout(\r
+ new GridLayout(groupPanel.getComponentCount()/3, 4));\r
+ groupPanel.validate();\r
bigPanel.add(groupPanel, BorderLayout.NORTH);\r
-\r
+ }\r
add(bigPanel, BorderLayout.CENTER);\r
add(buttonPanel, BorderLayout.SOUTH);\r
\r
else\r
fr.featureGroups.clear();\r
\r
- Vector allFeatures = new Vector();\r
- Vector features;\r
- Enumeration e;\r
- SequenceFeature sf;\r
+ allFeatures = new Hashtable();\r
+ SequenceFeature[] features;\r
\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
getSequenceFeatures();\r
+\r
if (features == null)\r
continue;\r
\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
+ int index = 0;\r
+ while (index < features.length)\r
{\r
- sf = (SequenceFeature) e.nextElement();\r
- if(sf.getFeatureGroup()!=null\r
- && !fr.featureGroups.containsKey(sf.getFeatureGroup()))\r
+ if(features[index].getFeatureGroup()!=null\r
+ && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))\r
{\r
- fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));\r
+ fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));\r
if(groupPanel==null)\r
groupPanel = new JPanel();\r
\r
- final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true);\r
+ final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);\r
check.setFont(new Font("Serif", Font.BOLD, 12));\r
check.addItemListener(new ItemListener()\r
{\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
}\r
-\r
+ resetTable();\r
}\r
});\r
groupPanel.add(check);\r
}\r
- if (!allFeatures.contains(sf.getType()))\r
+ if (!allFeatures.contains(features[index].getType()))\r
{\r
- allFeatures.addElement(sf.getType());\r
+ if(features[index].featureGroup!=null)\r
+ allFeatures.put(features[index].getType(), features[index].featureGroup);\r
+ else\r
+ allFeatures.put(features[index].getType(), "NOGROUP");\r
}\r
+ index++;\r
}\r
}\r
if(allFeatures.size()<1)\r
return;\r
}\r
\r
+ resetTable();\r
+ }\r
+\r
+ void resetTable()\r
+ {\r
int fSize = allFeatures.size();\r
\r
String type;\r
boolean originalExists = false;\r
- if(originalData!=null)\r
+ if (originalData != null)\r
originalExists = true;\r
else\r
originalData = new Object[fSize][3];\r
\r
- Object [][] data = new Object[fSize][3];\r
- for(int i=0; i<fSize; i++)\r
+ Object[][] tmp = new Object[fSize][3];\r
+ int tmpIndex = 0;\r
+\r
+ Enumeration en = allFeatures.keys();\r
+ int i=0;\r
+ while(en.hasMoreElements())\r
{\r
- type = allFeatures.elementAt(i).toString();\r
+ type = en.nextElement().toString();\r
Color col = fr.getColour(type);\r
- data[i][0]=type;\r
- data[i][1]=col;\r
- if(fr.featuresDisplayed!=null)\r
- data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
- else\r
- data[i][2] = new Boolean(true);\r
-\r
- if(!originalExists)\r
+\r
+\r
+ //This will ignore any features which are in groups not shown\r
+ if(fr.featureGroups==null\r
+ || ((Boolean)fr.featureGroups.get(allFeatures.get(type))).booleanValue())\r
+ {\r
+ tmp[tmpIndex][0] = type;\r
+ tmp[tmpIndex][1] = col;\r
+ if (av.featuresDisplayed != null)\r
+ tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
+ else\r
+ tmp[tmpIndex][2] = new Boolean(true);\r
+\r
+ tmpIndex++;\r
+ }\r
+\r
+\r
+ if (!originalExists)\r
{\r
originalData[i][0] = type;\r
originalData[i][1] = col;\r
- if (fr.featuresDisplayed != null)\r
- originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
+ if (av.featuresDisplayed != null)\r
+ originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));\r
else\r
originalData[i][2] = new Boolean(true);\r
}\r
+ i++;\r
}\r
- ////////////////////////////////////\r
- //Now build the table\r
- table = new JTable(new FeatureTableModel(data));\r
- scrollPane.setViewportView(table);\r
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setDefaultRenderer(Color.class,\r
- new ColorRenderer());\r
\r
- table.setDefaultEditor(Color.class,\r
- new ColorEditor());\r
+ Object [][]data = new Object[tmpIndex][3];\r
+ System.arraycopy(tmp, 0, data,0, tmpIndex);\r
\r
- table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+ table = new JTable(new FeatureTableModel(data));\r
+ scrollPane.setViewportView(table);\r
+ table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setDefaultRenderer(Color.class,\r
+ new ColorRenderer());\r
\r
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\r
\r
- table.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = table.rowAtPoint(evt.getPoint());\r
- }\r
- });\r
+ table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
\r
- table.addMouseMotionListener(new MouseMotionAdapter()\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
+ });\r
+\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if(newRow!=selectedRow\r
+ && selectedRow!=-1\r
+ && newRow!=-1)\r
{\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- int newRow = table.rowAtPoint(evt.getPoint());\r
- if(newRow!=selectedRow\r
- && selectedRow!=-1\r
- && newRow!=-1)\r
- {\r
- Object[] temp = new Object[3];\r
- temp[0] = table.getValueAt(selectedRow, 0);\r
- temp[1] = table.getValueAt(selectedRow, 1);\r
- temp[2] = table.getValueAt(selectedRow, 2);\r
+ Object[] temp = new Object[3];\r
+ temp[0] = table.getValueAt(selectedRow, 0);\r
+ temp[1] = table.getValueAt(selectedRow, 1);\r
+ temp[2] = table.getValueAt(selectedRow, 2);\r
\r
- table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
- table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
- table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
+ table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
+ table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
+ table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
\r
- table.setValueAt(temp[0], newRow, 0);\r
- table.setValueAt(temp[1], newRow, 1);\r
- table.setValueAt(temp[2], newRow, 2);\r
+ table.setValueAt(temp[0], newRow, 0);\r
+ table.setValueAt(temp[1], newRow, 1);\r
+ table.setValueAt(temp[2], newRow, 2);\r
\r
- selectedRow = newRow;\r
- }\r
- }\r
- });\r
+ selectedRow = newRow;\r
+ }\r
+ }\r
+ });\r
+\r
+ updateFeatureRenderer(data);\r
\r
}\r
\r
\r
sr = new SequenceRenderer(av);\r
sr.renderGaps( false );\r
+ sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
+ fr.overview = true;\r
\r
\r
// scale the initial size of overviewpanel to shape of alignment\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.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+ fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
}\r
\r
int alwidth = av.alignment.getWidth();\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
int lastcol=-1, lastrow=-1;\r
- Color color = Color.white;\r
- for (int col = 0; col < width; col++)\r
+ int color = Color.white.getRGB();\r
+ int row, col;\r
+ for (row = 0; row < sequencesHeight; row++)\r
{\r
- for (int row = 0; row < sequencesHeight; row++)\r
- {\r
+ for (col = 0; col < width; col++)\r
+ {\r
if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
{\r
- miniMe.setRGB(col,row,color.getRGB());\r
+ miniMe.setRGB(col,row,color);\r
continue;\r
}\r
\r
if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
{\r
color = sr.getResidueBoxColour(\r
- av.alignment.getSequenceAt(lastrow), lastcol);\r
+ av.alignment.getSequenceAt(lastrow), lastcol).getRGB();\r
\r
if(av.showSequenceFeatures)\r
- color = fr.findFeatureColour(color, av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
+ color = fr.findFeatureColour(color, lastrow, lastcol);\r
\r
}\r
\r
- miniMe.setRGB(col,row,color.getRGB());\r
+ miniMe.setRGB(col,row,color);\r
+\r
\r
- if (av.conservation != null)\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
graphHeight,\r
(int) (col * sampleCol),\r
(int) (col * sampleCol) + 1);\r
- mg.translate(-col, -sequencesHeight);\r
+ mg.translate( -col, -sequencesHeight);\r
}\r
}\r
}\r
-\r
System.gc();\r
\r
resizing = false;\r
git://source.jalview.org / jalview.git / commitdiff