/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
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
+ sr.forOverview = true;\r
+ fr = new FeatureRenderer(av);\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
- doMouseDragged(evt);\r
+ if (!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
{\r
public void mousePressed(MouseEvent evt)\r
{\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- doMouseReleased(evt);\r
+ if(!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
updateOverviewImage();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
-\r
- checkValid();\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\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
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\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
- }\r
\r
/**\r
* DOCUMENT ME!\r
\r
if (boxX > (width - boxWidth))\r
{\r
- boxX = width - boxWidth;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ //Try smallest possible box\r
+ boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
+ av.getCharWidth() * scalew);\r
+ }\r
+ boxX = width - boxWidth;\r
+ }\r
+\r
+ int col = (int) (boxX / scalew / av.getCharWidth());\r
+ int row = (int) (boxY / scaleh / av.getCharHeight());\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ if (!av.getColumnSelection().isVisible(col))\r
+ {\r
+ return;\r
+ }\r
+\r
+ col = av.getColumnSelection().findColumnPosition(col);\r
}\r
+\r
+ if( av.hasHiddenRows )\r
+ {\r
+ row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
+ }\r
+\r
+ ap.setScrollValues( col, row );\r
+\r
}\r
\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
+\r
Thread thread = new Thread(this);\r
thread.start();\r
repaint();\r
{\r
miniMe = null;\r
\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );\r
+ }\r
\r
- if ((getWidth() > 0) && (getHeight() > 0))\r
- {\r
- width = getWidth();\r
- sequencesHeight = getHeight() - graphHeight;\r
- }\r
+ int alwidth = av.alignment.getWidth();\r
+ int alheight = av.alignment.getHeight()\r
+ +av.alignment.getHiddenSequences().getSize();\r
\r
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\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
+ float sampleCol = (float) alwidth / (float) width;\r
+ float sampleRow = (float) alheight / (float) sequencesHeight;\r
+\r
+ int lastcol=-1, lastrow=-1;\r
+ int color = Color.white.getRGB();\r
+ int row, col;\r
+ jalview.datamodel.SequenceI seq;\r
+ boolean hiddenRow = false;\r
+ for (row = 0; row < sequencesHeight; row++)\r
+ {\r
+ if((int)(row*sampleRow)==lastrow)\r
+ {\r
+ //No need to recalculate the colours,\r
+ //Just copy from the row above\r
+ for (col = 0; col < width; col++)\r
+ {\r
+ miniMe.setRGB(col, row, miniMe.getRGB(col, row-1));\r
+ }\r
+ continue;\r
+ }\r
\r
- boolean oldRenderGaps = av.renderGaps;\r
+ lastrow = (int)(row*sampleRow);\r
\r
- try\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
+ hiddenRow = false;\r
+ if (av.hasHiddenRows)\r
+ {\r
+ seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
+ if (seq == null)\r
{\r
- if(resizeAgain)\r
- break;\r
+ int index =\r
+ av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);\r
\r
- eSeq = 0;\r
- eRes += maxSize;\r
+ seq = av.alignment.getSequenceAt(index);\r
+ }\r
+ else\r
+ {\r
+ hiddenRow = true;\r
+ }\r
+ }\r
+ else\r
+ seq = av.alignment.getSequenceAt(lastrow);\r
\r
- if (eRes > alwidth)\r
- {\r
- eRes = alwidth;\r
- }\r
+ if(seq==null)\r
+ {\r
+ System.out.println(lastrow+" null");\r
+ continue;\r
+ }\r
\r
- for (int sSeq = 0, chunky = 0; sSeq < alheight;\r
- sSeq += maxSize, chunky++)\r
- {\r
- eSeq += maxSize;\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);\r
+ continue;\r
+ }\r
\r
- if (eSeq > alheight)\r
- {\r
- eSeq = alheight;\r
- }\r
\r
- blocky = 0;\r
- blockx = (int) ((float) sRes / (float) alwidth * width);\r
+ lastcol = (int)(col*sampleCol);\r
\r
- block = new BufferedImage((eRes - sRes) * av.charWidth,\r
- (eSeq - sSeq) * av.charHeight,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- g = block.getGraphics();\r
+ if (seq.getLength() > lastcol)\r
+ {\r
+ color = sr.getResidueBoxColour(\r
+ seq, lastcol).getRGB();\r
\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,\r
- sRes, sSeq, 0);\r
+ if (av.showSequenceFeatures)\r
+ color = fr.findFeatureColour(color, seq, lastcol);\r
+ }\r
+ else\r
+ {\r
+ color = -1; //White\r
+ }\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(hiddenRow ||\r
+ (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
+ {\r
+ color = new Color(color).darker().darker().getRGB();\r
+ }\r
\r
- blocky += (int) ((float) sSeq / (float) alheight * sequencesHeight);\r
\r
- mg.drawImage(block, blockx, blocky, blockx + blockw,\r
- blocky + blockh, 0, 0, block.getWidth(),\r
- block.getHeight(), null);\r
+ miniMe.setRGB(col,row,color);\r
\r
- block = null;\r
- }\r
- }\r
+\r
+ }\r
}\r
- catch (OutOfMemoryError error)\r
+\r
+ if (av.conservation != null)\r
{\r
- System.err.println(\r
- "Out of memory when trying to calculate the overview window image!");\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
System.gc();\r
\r
- av.setRenderGaps(oldRenderGaps);\r
resizing = false;\r
\r
setBoxPosition();\r
public void setBoxPosition()\r
{\r
int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
- int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\r
+ int fullsizeHeight = (av.alignment.getHeight()\r
+ +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();\r
+\r
+ int startRes = av.getStartRes();\r
+ int endRes = av.getEndRes();\r
+\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);\r
+ endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
+ }\r
+\r
+ int startSeq = av.startSeq;\r
+ int endSeq = av.endSeq;\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ startSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
+\r
+ endSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
+\r
+ }\r
+\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
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
- boxY;\r
+ boxX = (int) (startRes * av.getCharWidth() * scalew);\r
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+\r
+\r
+ if(av.hasHiddenColumns)\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+ else\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+\r
+\r
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
+\r
repaint();\r
}\r
\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