X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=56e70acffb17f92dbdba210db100dfd0cc1f6d1e;hb=012fc200ee0d124003524855ac7cd50be4b7456c;hp=c4de7cda92564873ff47b3e4206d39d36599d9cf;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index c4de7cd..56e70ac 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -62,7 +62,7 @@ public class SeqCanvas extends JComponent fr = new FeatureRenderer(av); sr = new SequenceRenderer(av); setLayout(new BorderLayout()); - PaintRefresher.Register(this, av.alignment); + PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); } @@ -328,9 +328,34 @@ public class SeqCanvas extends JComponent return; } - img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); + if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight()) + { + try{ + img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + }catch(OutOfMemoryError er) + { + System.gc(); + System.out.println(er +" making image, SeqCanvas"); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop. + desktop, + "Out of memory creating alignment image!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); + + return; + } + } if (av.antiAlias) gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, @@ -477,6 +502,35 @@ public class SeqCanvas extends JComponent drawNorthScale(g, startRes, endx, ypos); } + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); + i++) + { + res = av.getColumnSelection().findHiddenRegionPosition(i) - + startRes; + + if (res < 0 || res > endx - startRes) + continue; + + gg.fillPolygon(new int[] + {res * av.charWidth - av.charHeight / 4, + res * av.charWidth + av.charHeight / 4, + res * av.charWidth}, + new int[] + { + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2) + 8 + }, 3); + + } + } + + + // When printing we have an extra clipped region, // the Printable page which we need to account for here Shape clip = g.getClip(); @@ -568,15 +622,15 @@ public class SeqCanvas extends JComponent draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - g1.setColor(Color.blue); - g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, - startSeq + offset, - (blockEnd - blockStart + 1) * av.charWidth - 1, - startSeq + (endSeq - startSeq) * av.charHeight + offset); - g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth, - startSeq + offset, - (blockEnd - blockStart + 1) * av.charWidth, - startSeq + (endSeq - startSeq) * av.charHeight + offset); + if(av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + (endSeq - startSeq) * av.charHeight + offset); + } g1.translate( -screenY * av.charWidth, 0); screenY += blockEnd - blockStart + 1; @@ -588,6 +642,7 @@ public class SeqCanvas extends JComponent blockEnd = blockStart + (endRes - startRes) - screenY; g1.translate(screenY * av.charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + g1.translate( -screenY * av.charWidth, 0); } } @@ -669,6 +724,7 @@ public class SeqCanvas extends JComponent int sy = -1; int ex = -1; int groupIndex = -1; + int visWidth = (endRes - startRes +1) * av.charWidth; if ((group == null) && (av.alignment.getGroups().size() > 0)) { @@ -676,6 +732,7 @@ public class SeqCanvas extends JComponent groupIndex = 0; } + if (group != null) { do @@ -693,7 +750,7 @@ public class SeqCanvas extends JComponent ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; - if(sx+ex<0 || sx>imgWidth) + if(sx+ex<0 || sx>visWidth) { continue; } @@ -740,10 +797,10 @@ public class SeqCanvas extends JComponent { if (inGroup) { - if (sx >= 0 && sx < imgWidth) + if (sx >= 0 && sx < visWidth) g.drawLine(sx, oldY, sx, sy); - if (sx + ex < imgWidth) + if (sx + ex < visWidth) g.drawLine(sx + ex, oldY, sx + ex, sy); if (sx < 0) @@ -752,8 +809,8 @@ public class SeqCanvas extends JComponent sx = 0; } - if (sx + ex > imgWidth) - ex = imgWidth; + if (sx + ex > visWidth) + ex = visWidth; else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) ex = (endRes - startRes + 1) * av.charWidth; @@ -778,10 +835,10 @@ public class SeqCanvas extends JComponent if (inGroup) { sy = offset + ( (i - startSeq) * av.charHeight); - if (sx >= 0 && sx < imgWidth) + if (sx >= 0 && sx < visWidth) g.drawLine(sx, oldY, sx, sy); - if (sx + ex < imgWidth) + if (sx + ex < visWidth) g.drawLine(sx + ex, oldY, sx + ex, sy); if (sx < 0) @@ -790,8 +847,8 @@ public class SeqCanvas extends JComponent sx = 0; } - if (sx + ex > imgWidth) - ex = imgWidth; + if (sx + ex > visWidth) + ex = visWidth; else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) ex = (endRes - startRes + 1) * av.charWidth; @@ -812,6 +869,8 @@ public class SeqCanvas extends JComponent groupIndex++; + g.setStroke(new BasicStroke()); + if (groupIndex >= av.alignment.getGroups().size()) { break; @@ -819,7 +878,7 @@ public class SeqCanvas extends JComponent group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); - g.setStroke(new BasicStroke()); + } while (groupIndex < av.alignment.getGroups().size());