sr = new SequenceRenderer(av);\r
sr.graphics = nullFrame.getGraphics();\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
\r
// scale the initial size of overviewpanel to shape of alignment\r
return;\r
}\r
\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+ fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+ }\r
+\r
resizing = true;\r
\r
if ( (getSize().width > 0) && (getSize().height > 0))\r
int alwidth = av.alignment.getWidth();\r
int alheight = av.alignment.getHeight();\r
\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\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
if (getSize().width > 0 && getSize().height > 0)\r
{\r
width = getSize().width;\r
float sampleCol = (float) alwidth / (float) width;\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 lastcol=0, lastseq=0;\r
+ int xstart=0, ystart=0;\r
+ Color color = Color.yellow;\r
+ int col, sameRow = 0, sameCol = 0;\r
+ jalview.datamodel.SequenceI sequence;\r
+\r
+ for (int row = 0; row <= sequencesHeight; row++)\r
{\r
- for (int row = 0; row < sequencesHeight; row++)\r
+ if((int)(row*sampleRow)==lastseq)\r
+ {\r
+ sameRow ++;\r
+ continue;\r
+ }\r
+\r
+ sequence = av.getAlignment().getSequenceAt(lastseq);\r
+\r
+ for (col = 0; col < width; col++)\r
{\r
- if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+ if((int)(col*sampleCol) == lastcol)\r
{\r
- mg.setColor(color);\r
- mg.fillRect(col,row,1,1);\r
+ sameCol ++;\r
continue;\r
}\r
\r
- lastrow = (int)(row*sampleRow);\r
lastcol = (int)(col*sampleCol);\r
\r
- if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+ if(sequence.getLength()>lastcol)\r
{\r
- color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\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
+ else\r
+ color = color.white;\r
\r
mg.setColor(color);\r
- mg.fillRect(col,row,1,1);\r
+ if (sameCol == 1 && sameRow == 1)\r
+ mg.drawLine(xstart, ystart, xstart, ystart);\r
+ else\r
+ mg.fillRect(xstart, ystart, sameCol, sameRow);\r
+\r
+ xstart = col;\r
+ sameCol = 1;\r
+ }\r
+\r
+\r
+ lastseq = (int)(row*sampleRow);\r
+ ystart = row;\r
+ sameRow = 1;\r
+ }\r
\r
- if (av.conservation != null)\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
+\r
+\r
System.gc();\r
\r
resizing = false;\r