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
+ else\r
+ color = color.white;\r
\r
mg.setColor(color);\r
mg.drawLine(col,row,col,row);\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