/*\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
*/\r
public class SeqCanvas extends JComponent\r
{\r
- FeatureRenderer fr;\r
- SequenceRenderer sr;\r
+ final FeatureRenderer fr;\r
+ final SequenceRenderer sr;\r
BufferedImage img;\r
Graphics2D gg;\r
int imgWidth;\r
int LABEL_WEST;\r
int LABEL_EAST;\r
\r
+\r
+ int cursorX = 0;\r
+ int cursorY = 0;\r
+\r
+\r
/**\r
* Creates a new SeqCanvas object.\r
*\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
// NORTH SCALE\r
for (int i = scalestartx; i < endx; i += 10)\r
{\r
- String string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));\r
- g.drawString(string, (i - startx - 1) * av.charWidth,\r
+ int value = i;\r
+ if(av.hasHiddenColumns)\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+\r
+ g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,\r
ypos - (av.charHeight / 2));\r
\r
g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
FontMetrics fm = getFontMetrics(av.getFont());\r
ypos += av.charHeight;\r
\r
- // EAST SCALE\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\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
{\r
ypos += av.charHeight;\r
\r
+ if(av.hasHiddenColumns)\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+\r
+ SequenceI seq;\r
// EAST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
+ seq = av.alignment.getSequenceAt(i);\r
int index = endx;\r
int value = -1;\r
\r
continue;\r
}\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ value = seq.findPosition(index);\r
\r
break;\r
}\r
return;\r
}\r
\r
+\r
fastPaint = true;\r
\r
gg.copyArea(horizontal * av.charWidth,\r
int transX = 0;\r
int transY = 0;\r
\r
+\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
er ++;\r
{\r
super.paintComponent(g);\r
\r
- sr.renderGaps(av.renderGaps);\r
+\r
\r
if ( img != null && (fastPaint\r
|| (getVisibleRect().width != g.getClipBounds().width)\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
\r
if (pdbCanvas != null)\r
{\r
- pdbCanvas.updateSeqColours();\r
+ pdbCanvas.updateSeqColours();\r
}\r
\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
av.endRes = av.startRes + cWidth;\r
\r
\r
- int endx = (startRes + cWidth) - 1;\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 > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
+\r
g.setFont(av.getFont());\r
g.setColor(Color.black);\r
\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
cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
}\r
\r
- if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
- {\r
- endx = av.vconsensus.size() - 2;\r
- }\r
-\r
-\r
drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
\r
if(av.showAnnotation)\r
if(annotations==null)\r
annotations = new AnnotationPanel(av);\r
\r
- annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);\r
+ annotations.drawComponent( (Graphics2D) g, startRes, endx+1);\r
g.translate(0, -cHeight - ypos);\r
}\r
g.setClip(clip);\r
ypos -= 3;\r
\r
startRes += cWidth;\r
- endx = (startRes + cWidth) - 1;\r
-\r
- if (endx > al.getWidth())\r
- {\r
- endx = al.getWidth();\r
- }\r
}\r
}\r
\r
* DOCUMENT ME!\r
*\r
* @param g1 DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param x2 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param y2 DOCUMENT ME!\r
- * @param startx DOCUMENT ME!\r
- * @param starty DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ * @param endRes DOCUMENT ME!\r
+ * @param startSeq DOCUMENT ME!\r
+ * @param endSeq DOCUMENT ME!\r
* @param offset DOCUMENT ME!\r
*/\r
-\r
- float aaRatio = 2f/3f;\r
- public void increaseAARatio()\r
- {\r
- aaRatio += .025;\r
- if(aaRatio>1)\r
- aaRatio = 1;\r
-\r
- repaint();\r
- }\r
-\r
- public void decreaseAARation()\r
- {\r
- aaRatio -= .025;\r
- if(aaRatio<0)\r
- aaRatio = 0;\r
-\r
- repaint();\r
- }\r
-\r
-\r
void drawPanel(Graphics g1, int startRes, int endRes,\r
int startSeq, int endSeq, int offset)\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
\r
//int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
// int x1, int x2, int y1, int y2, int startx, int starty,\r
- void draw(Graphics g1,\r
+ void draw(Graphics g,\r
int startRes, int endRes,\r
int startSeq, int endSeq,\r
int offset)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
g.setFont(av.getFont());\r
+ sr.prepare(g, av.renderGaps);\r
\r
SequenceI nextSeq;\r
\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),\r
startRes, endRes,\r
offset + ( (i - startSeq) * av.charHeight));\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.drawSequence(g1, nextSeq, startRes, endRes,\r
- offset + ((i - startSeq) * av.charHeight), av.charWidth,\r
- av.charHeight);\r
+ fr.drawSequence(g, nextSeq, startRes, endRes,\r
+ offset + ((i - startSeq) * av.charHeight));\r
}\r
\r
/// Highlight search Results once all sequences have been drawn\r
sr.drawHighlightedText(nextSeq, visibleResults[r],\r
visibleResults[r + 1],\r
(visibleResults[r] - startRes) * av.charWidth,\r
- offset + ( (i - startSeq) * av.charHeight),\r
- av.charWidth, av.charHeight);\r
+ offset + ( (i - startSeq) * av.charHeight));\r
}\r
}\r
+\r
+ if(av.cursorMode && cursorY==i\r
+ && cursorX>=startRes && cursorX<=endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
+ }\r
}\r
\r
+ if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+\r
+ }\r
+\r
+ void drawGroupsBoundaries(Graphics g1,\r
+ int startRes, int endRes,\r
+ int startSeq, int endSeq,\r
+ int offset)\r
+ {\r
+ Graphics2D g = (Graphics2D)g1;\r
//\r
/////////////////////////////////////\r
// Now outline any areas if necessary\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
\r
group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+\r
+\r
}\r
while (groupIndex < av.alignment.getGroups().size());\r
+\r
}\r
+\r
}\r
\r
/**\r
git://source.jalview.org / jalview.git / blobdiff