\r
sr = new SequenceRenderer(av);\r
sr.renderGaps( false );\r
+ sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
- fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
- fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+ fr.overview = true;\r
+\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
{\r
miniMe = null;\r
\r
+ if (av.showSequenceFeatures)\r
+ {\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
int alheight = av.alignment.getHeight();\r
\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
lastrow = (int)(row*sampleRow);\r
lastcol = (int)(col*sampleCol);\r
\r
- color = sr.getResidueBoxColour(\r
- av.alignment.getSequenceAt(lastrow), lastcol);\r
-\r
- if(av.showSequenceFeatures)\r
+ if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
{\r
- color = fr.findFeatureColour(color,\r
- av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
- }\r
+ color = sr.getResidueBoxColour(\r
+ av.alignment.getSequenceAt(lastrow), lastcol).getRGB();\r
+\r
+ if(av.showSequenceFeatures)\r
+ color = fr.findFeatureColour(color, lastrow, lastcol);\r
+\r
+ }\r
+ else\r
+ {\r
+ color = -1; //White\r
+ }\r
\r
- miniMe.setRGB(col,row,color.getRGB());\r
+ miniMe.setRGB(col,row,color);\r
\r
- if (av.conservation != null)\r
+\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