float scaleh = 1f;\r
int width;\r
int sequencesHeight;\r
- int graphHeight = 30;\r
+ int graphHeight = 20;\r
int boxX = -1;\r
int boxY = -1;\r
int boxWidth = -1;\r
int boxHeight = -1;\r
boolean resizing = false;\r
\r
+ // Can set different properties in this seqCanvas than\r
+ // main visible SeqCanvas\r
+ SequenceRenderer sr;\r
+ FeatureRenderer fr;\r
+\r
/**\r
* Creates a new OverviewPanel object.\r
*\r
this.ap = ap;\r
setLayout(null);\r
\r
+ sr = new SequenceRenderer(av);\r
+ sr.renderGaps( false );\r
+ fr = new FeatureRenderer(av);\r
+ fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+ fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\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
+ if(av.conservation==null)\r
+ graphHeight = 0;\r
+\r
+\r
if (av.alignment.getWidth() > av.alignment.getHeight())\r
{\r
// wider\r
width = 400;\r
sequencesHeight = (int) (400f / initialScale);\r
+ if(sequencesHeight<40)\r
+ sequencesHeight = 40;\r
}\r
else\r
{\r
{\r
public void mouseDragged(MouseEvent evt)\r
{\r
+ if(!av.wrapAlignment)\r
doMouseDragged(evt);\r
}\r
});\r
{\r
public void mousePressed(MouseEvent evt)\r
{\r
+ if(!av.wrapAlignment)\r
doMousePressed(evt);\r
}\r
\r
public void mouseReleased(MouseEvent evt)\r
{\r
+ if(!av.wrapAlignment)\r
doMouseReleased(evt);\r
}\r
});\r
boxY = evt.getY();\r
checkValid();\r
\r
- if (!resizing)\r
- {\r
- ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),\r
+ ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),\r
(int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
}\r
\r
/**\r
boxY = evt.getY();\r
checkValid();\r
\r
- if (!resizing)\r
- {\r
- ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
+ ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
+ (int) (boxY / scaleh / av.getCharHeight()));\r
+ repaint();\r
}\r
\r
/**\r
{\r
if (resizing)\r
{\r
+ resizeAgain = true;\r
return;\r
}\r
\r
resizing = true;\r
\r
+ if ( (getWidth() > 0) && (getHeight() > 0))\r
+ {\r
+ width = getWidth();\r
+ sequencesHeight = getHeight() - graphHeight;\r
+ }\r
+\r
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
+ setBoxPosition();\r
+\r
Thread thread = new Thread(this);\r
thread.start();\r
repaint();\r
}\r
\r
+ // This is set true if the user resizes whilst\r
+ // the overview is being calculated\r
+ boolean resizeAgain = false;\r
+\r
/**\r
* DOCUMENT ME!\r
*/\r
int alwidth = av.alignment.getWidth();\r
int alheight = av.alignment.getHeight();\r
\r
- if ((getWidth() > 0) && (getHeight() > 0))\r
- {\r
- width = getWidth();\r
- sequencesHeight = getHeight() - graphHeight;\r
- }\r
-\r
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
int fullsizeWidth = alwidth * av.getCharWidth();\r
miniMe = new BufferedImage(width, sequencesHeight + graphHeight,\r
BufferedImage.TYPE_INT_RGB);\r
\r
+\r
Graphics mg = miniMe.getGraphics();\r
- BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- Graphics g = consensus.getGraphics();\r
- ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
- mg.drawImage(consensus, 0, sequencesHeight, width,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
+ mg.setColor(Color.orange);\r
+ mg.fillRect(0,0,width, miniMe.getHeight());\r
\r
- boolean oldRenderGaps = av.renderGaps;\r
+ float sampleCol = (float) alwidth / (float) width;\r
+ float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
- try\r
+ int lastcol=-1, lastrow=-1;\r
+ Color color = Color.white;\r
+ for (int col = 0; col < width; col++)\r
{\r
- // We'll have to draw the full size alignment in chunks, as an image of the\r
- // whole alignment requires too much memory\r
- // Max size depends on the font size, the following is a\r
- // guess at a size which works\r
- int maxSize = 2000 / av.getFont().getSize();\r
- BufferedImage block;\r
- int blockx = 0;\r
- int blocky = 0;\r
- int blockw = 0;\r
- int blockh = 0;\r
- int eRes = 0;\r
- int eSeq = 0;\r
-\r
- av.setRenderGaps(false);\r
-\r
- for (int sRes = 0, chunkx = 0; sRes < alwidth;\r
- sRes += maxSize, chunkx++)\r
+ for (int row = 0; row < sequencesHeight; row++)\r
+ {\r
+ if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
{\r
- eSeq = 0;\r
- eRes += maxSize;\r
-\r
- if (eRes > alwidth)\r
- {\r
- eRes = alwidth;\r
- }\r
-\r
- for (int sSeq = 0, chunky = 0; sSeq < alheight;\r
- sSeq += maxSize, chunky++)\r
- {\r
- eSeq += maxSize;\r
-\r
- if (eSeq > alheight)\r
- {\r
- eSeq = alheight;\r
- }\r
-\r
- blocky = 0;\r
- blockx = (int) ((float) sRes / (float) alwidth * width);\r
-\r
- block = new BufferedImage((eRes - sRes) * av.charWidth,\r
- (eSeq - sSeq) * av.charHeight,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- g = block.getGraphics();\r
+ miniMe.setRGB(col,row,color.getRGB());\r
+ continue;\r
+ }\r
\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,\r
- sRes, sSeq, 0);\r
+ lastrow = (int)(row*sampleRow);\r
+ lastcol = (int)(col*sampleCol);\r
\r
- blockh = (int) ((float) (eSeq - sSeq) / (float) alheight * sequencesHeight) +\r
- 1;\r
- blockw = (int) ((float) (eRes - sRes) / (float) alwidth * width) +\r
- 1;\r
+ if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+ {\r
+ color = sr.getResidueBoxColour(\r
+ av.alignment.getSequenceAt(lastrow), lastcol);\r
\r
- blocky += (int) ((float) sSeq / (float) alheight * sequencesHeight);\r
+ if(av.showSequenceFeatures)\r
+ color = fr.findFeatureColour(color, av.alignment.getSequenceAt(lastrow),\r
+ lastcol);\r
+ }\r
\r
- mg.drawImage(block, blockx, blocky, blockx + blockw,\r
- blocky + blockh, 0, 0, block.getWidth(),\r
- block.getHeight(), this);\r
+ miniMe.setRGB(col,row,color.getRGB());\r
\r
- block = null;\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
}\r
- catch (OutOfMemoryError error)\r
- {\r
- System.err.println(\r
- "Out of memory when trying to calculate the overview window image!");\r
- }\r
\r
- av.setRenderGaps(oldRenderGaps);\r
+ System.gc();\r
+\r
resizing = false;\r
\r
setBoxPosition();\r
+\r
+ if(resizeAgain)\r
+ {\r
+ resizeAgain = false;\r
+ updateOverviewImage();\r
+ }\r
}\r
\r
/**\r
*/\r
public void setBoxPosition()\r
{\r
+ int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
+ int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\r
+\r
+ scalew = (float) width / (float) fullsizeWidth;\r
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
+\r
boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew);\r
*/\r
public void paintComponent(Graphics g)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
- g.setColor(Color.black);\r
-\r
- if (resizing)\r
+ if (miniMe != null && !resizing)\r
{\r
- g.setFont(new Font("Verdana", Font.BOLD, 15));\r
- g.drawString("Recalculating", 5, sequencesHeight / 2);\r
- g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
+ g.drawImage(miniMe, 0, 0, this);\r
}\r
else\r
{\r
- if (miniMe != null)\r
- {\r
- g.drawImage(miniMe, 0, 0, this);\r
- }\r
-\r
- g.setColor(Color.red);\r
- g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 15));\r
+ g.drawString("Recalculating", 5, sequencesHeight / 2);\r
+ g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
}\r
+\r
+\r
+ g.setColor(Color.red);\r
+ g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
+\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff