/*\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
fr = new FeatureRenderer(av);\r
sr = new SequenceRenderer(av);\r
setLayout(new BorderLayout());\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
setBackground(Color.white);\r
}\r
\r
ypos += av.charHeight;\r
\r
if(av.hasHiddenColumns)\r
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ {\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
\r
- // EAST SCALE\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+ // WEST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
SequenceI seq = av.alignment.getSequenceAt(i);\r
return;\r
}\r
\r
- img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) img.getGraphics();\r
- gg.setFont(av.getFont());\r
+ if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())\r
+ {\r
+ try{\r
+ img = new BufferedImage(imgWidth, imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }catch(OutOfMemoryError er)\r
+ {\r
+ System.gc();\r
+ System.out.println(er +" making image, SeqCanvas");\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.\r
+ desktop,\r
+ "Out of memory creating alignment image!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+\r
+ return;\r
+ }\r
+ }\r
\r
if (av.antiAlias)\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
String getMask()\r
{\r
String mask = "00";\r
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+ int maxWidth = 0;\r
+ int tmp;\r
+ for(int i=0; i<av.alignment.getHeight(); i++)\r
+ {\r
+ tmp = av.alignment.getSequenceAt(i).getEnd();\r
+ if(tmp>maxWidth)\r
+ maxWidth = tmp;\r
+ }\r
+\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
{\r
mask += "0";\r
}\r
public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
int startRes)\r
{\r
-\r
AlignmentI al = av.getAlignment();\r
\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- int LABEL_EAST = 0;\r
\r
if (av.scaleRightWrapped)\r
{\r
LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
- int LABEL_WEST = 0;\r
\r
if (av.scaleLeftWrapped)\r
{\r
\r
int endx;\r
int ypos = hgap;\r
+ int maxwidth = av.alignment.getWidth();\r
+\r
+ if(av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\r
\r
- while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
{\r
endx = startRes + cWidth -1;\r
\r
- if (endx > al.getWidth())\r
+ if (endx > maxwidth)\r
{\r
- endx = al.getWidth();\r
+ endx = maxwidth;\r
}\r
\r
g.setFont(av.getFont());\r
drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
+ if (av.hasHiddenColumns && av.showHiddenMarkers)\r
+ {\r
+ g.setColor(Color.blue);\r
+ int res;\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
+ i++)\r
+ {\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+ startRes;\r
+\r
+ if (res < 0 || res > endx - startRes)\r
+ continue;\r
+\r
+ gg.fillPolygon(new int[]\r
+ {res * av.charWidth - av.charHeight / 4,\r
+ res * av.charWidth + av.charHeight / 4,\r
+ res * av.charWidth},\r
+ new int[]\r
+ {\r
+ ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2) + 8\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+\r
+\r
// When printing we have an extra clipped region,\r
// the Printable page which we need to account for here\r
Shape clip = g.getClip();\r
annotations = new AnnotationPanel(av);\r
\r
annotations.drawComponent( (Graphics2D) g, startRes, endx+1);\r
- g.translate(0, -cHeight - ypos);\r
+ g.translate(0, -cHeight - ypos -3);\r
}\r
g.setClip(clip);\r
g.translate(-LABEL_WEST, 0);\r
\r
ypos += cHeight+getAnnotationHeight()+hgap;\r
- if(av.showAnnotation)\r
- ypos -= 3;\r
\r
startRes += cWidth;\r
}\r
\r
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
\r
- g1.setColor(Color.blue);\r
- g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
- startSeq + offset,\r
- (blockEnd - blockStart + 1) * av.charWidth - 1,\r
- startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
- g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,\r
- startSeq + offset,\r
- (blockEnd - blockStart + 1) * av.charWidth,\r
- startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+ if(av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\r
+\r
+ g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ 0 + offset,\r
+ (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ (endSeq - startSeq) * av.charHeight + offset);\r
+ }\r
\r
g1.translate( -screenY * av.charWidth, 0);\r
screenY += blockEnd - blockStart + 1;\r
blockEnd = blockStart + (endRes - startRes) - screenY;\r
g1.translate(screenY * av.charWidth, 0);\r
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
g1.translate( -screenY * av.charWidth, 0);\r
}\r
}\r
int sy = -1;\r
int ex = -1;\r
int groupIndex = -1;\r
+ int visWidth = (endRes - startRes +1) * av.charWidth;\r
\r
if ((group == null) && (av.alignment.getGroups().size() > 0))\r
{\r
groupIndex = 0;\r
}\r
\r
+\r
if (group != null)\r
{\r
do\r
ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
1;\r
\r
- if(sx+ex<0 || sx>imgWidth)\r
+ if(sx+ex<0 || sx>visWidth)\r
{\r
continue;\r
}\r
\r
if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
- group.sequences.contains(av.alignment.getSequenceAt(\r
- i)))\r
+ group.getSequences(false).\r
+ contains(av.alignment.getSequenceAt(i)))\r
{\r
if ((bottom == -1) &&\r
- !group.sequences.contains(\r
+ !group.getSequences(false).contains(\r
av.alignment.getSequenceAt(i + 1)))\r
{\r
bottom = sy + av.charHeight;\r
if (!inGroup)\r
{\r
if (((top == -1) && (i == 0)) ||\r
- !group.sequences.contains(\r
+ !group.getSequences(false).contains(\r
av.alignment.getSequenceAt(i - 1)))\r
{\r
top = sy;\r
{\r
if (inGroup)\r
{\r
- if (sx >= 0 && sx < imgWidth)\r
+ if (sx >= 0 && sx < visWidth)\r
g.drawLine(sx, oldY, sx, sy);\r
\r
- if (sx + ex < imgWidth)\r
+ if (sx + ex < visWidth)\r
g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
if (sx < 0)\r
sx = 0;\r
}\r
\r
- if (sx + ex > imgWidth)\r
- ex = imgWidth;\r
+ if (sx + ex > visWidth)\r
+ ex = visWidth;\r
\r
else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
ex = (endRes - startRes + 1) * av.charWidth;\r
if (inGroup)\r
{\r
sy = offset + ( (i - startSeq) * av.charHeight);\r
- if (sx >= 0 && sx < imgWidth)\r
+ if (sx >= 0 && sx < visWidth)\r
g.drawLine(sx, oldY, sx, sy);\r
\r
- if (sx + ex < imgWidth)\r
+ if (sx + ex < visWidth)\r
g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
if (sx < 0)\r
sx = 0;\r
}\r
\r
- if (sx + ex > imgWidth)\r
- ex = imgWidth;\r
+ if (sx + ex > visWidth)\r
+ ex = visWidth;\r
else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
ex = (endRes - startRes + 1) * av.charWidth;\r
\r
\r
groupIndex++;\r
\r
+ g.setStroke(new BasicStroke());\r
+\r
if (groupIndex >= av.alignment.getGroups().size())\r
{\r
break;\r
\r
group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
\r
- g.setStroke(new BasicStroke());\r
+\r
}\r
while (groupIndex < av.alignment.getGroups().size());\r
\r
git://source.jalview.org / jalview.git / blobdiff