/*\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
AlignmentPanel ap;\r
int activeRow = -1;\r
BufferedImage image;\r
+ BufferedImage fadedImage;\r
Graphics2D gg;\r
FontMetrics fm;\r
int imgWidth = 0;\r
\r
\r
int height = 0;\r
- activeRow = 0;\r
+ activeRow = -1;\r
\r
\r
for (int i = 0; i < aa.length; i++)\r
}\r
\r
\r
- if (SwingUtilities.isRightMouseButton(evt))\r
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
{\r
if (av.getColumnSelection() == null)\r
{\r
if(graphStretch>-1)\r
{\r
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
- if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
+ if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
graphStretchY = evt.getY();\r
adjustPanelHeight();\r
ap.repaint();\r
\r
gg.setFont(av.getFont());\r
fm = gg.getFontMetrics();\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, image.getHeight());\r
}\r
\r
\r
*/\r
public void fastPaint(int horizontal)\r
{\r
- if ((horizontal == 0) || gg==null ||\r
- (av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
+ if ((horizontal == 0)\r
+ || gg==null\r
+ || av.alignment.getAlignmentAnnotation()==null\r
+ || av.alignment.getAlignmentAnnotation().length < 1\r
+ || av.updatingConsensus\r
+ || av.updatingConservation)\r
{\r
repaint();\r
return;\r
*/\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
+ if(av.updatingConsensus || av.updatingConservation)\r
+ {\r
+ //We'll keep a record of the old image,\r
+ //and draw a faded image until the calculation\r
+ //has completed\r
+ if(fadedImage==null\r
+ || fadedImage.getWidth()!=imgWidth\r
+ || fadedImage.getHeight()!=image.getHeight())\r
+ {\r
+ fadedImage = new BufferedImage(\r
+ imgWidth, image.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
\r
+ Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
\r
- g.setFont(av.getFont());\r
+ fadedG.setColor(Color.white);\r
+ fadedG.fillRect(0, 0, imgWidth, image.getHeight());\r
+\r
+ fadedG.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, .3f));\r
+ fadedG.drawImage(image, 0, 0, this);\r
+\r
+ }\r
+\r
+ }\r
+ else\r
+ fadedImage = null;\r
+\r
+\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
\r
+ g.setFont(av.getFont());\r
if (fm == null)\r
fm = g.getFontMetrics();\r
\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
+\r
\r
if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
(av.alignment.getAlignmentAnnotation().length < 1))\r
return;\r
}\r
\r
+\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int x = 0;\r
- int y = 0;\r
+ int x = 0, y = 0;\r
+ int column=0;\r
char lastSS;\r
int lastSSX;\r
int iconOffset = av.charHeight / 2;\r
continue;\r
}\r
\r
+\r
lastSS = ' ';\r
lastSSX = 0;\r
\r
-\r
if (row.graph>0)\r
{\r
if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
}\r
}\r
\r
+ if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
+ {\r
+ y += av.charHeight;\r
+\r
+ g.drawImage(fadedImage,\r
+ 0,y-row.height,imgWidth, y,\r
+ 0,y-row.height,imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+\r
+\r
if (row.hasText)\r
{\r
- iconOffset = av.charHeight / 2;\r
+ iconOffset = av.charHeight / 2 + 4;\r
}\r
else\r
{\r
iconOffset = 0;\r
}\r
\r
- int column = startRes;\r
-\r
- while (column < endRes)\r
+ x = 0;\r
+ while (x < endRes-startRes)\r
{\r
if (av.hasHiddenColumns)\r
{\r
- column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
if (column > row.annotations.length-1)\r
{\r
break;\r
}\r
}\r
+ else\r
+ column = startRes+x;\r
+\r
\r
if ((row.annotations.length <= column) ||\r
(row.annotations[column] == null))\r
validRes = true;\r
}\r
\r
- x = (column - startRes) * av.charWidth;\r
\r
if (activeRow == i)\r
{\r
\r
if (v == column)\r
{\r
- g.fillRect((column - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
+ g.fillRect(x * av.charWidth, y,\r
+ av.charWidth, av.charHeight);\r
}\r
}\r
}\r
\r
if (column == 0 || row.graph>0)\r
{\r
- g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x*av.charWidth)+charOffset,\r
+ y + iconOffset );\r
}\r
else if (\r
row.annotations[column - 1] == null\r
(row.annotations[column].displayCharacter.length() <2 &&\r
row.annotations[column].secondaryStructure==' ')))\r
{\r
- g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ x*av.charWidth+charOffset,\r
+ y + iconOffset );\r
}\r
}\r
\r
switch (lastSS)\r
{\r
case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- if(MAC)\r
- {\r
- //Off by 1 offset when drawing rects and ovals\r
- //to offscreen image on the MAC\r
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX, 7, 8, 8);\r
- break;\r
- }\r
-\r
- int sCol = (lastSSX / av.charWidth) + startRes;\r
- int x1 = lastSSX;\r
- int x2 = x;\r
-\r
- if(sCol==0 ||\r
- row.annotations[sCol-1]==null ||\r
- row.annotations[sCol-1].secondaryStructure!='H')\r
- {\r
- g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;\r
- x1 += av.charWidth/2;\r
- }\r
-\r
- if(row.annotations[column]==null ||\r
- row.annotations[column].secondaryStructure!='H')\r
- {\r
- g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);\r
- x2 -= av.charWidth/2;\r
- }\r
-\r
- g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);\r
+ g.setColor(HELIX_COLOUR);\r
+ if (MAC)\r
+ {\r
+ //Off by 1 offset when drawing rects and ovals\r
+ //to offscreen image on the MAC\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ (x*av.charWidth) - lastSSX, 7, 8, 8);\r
break;\r
+ }\r
+\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x*av.charWidth);\r
+\r
+ if(sCol==0 ||\r
+ row.annotations[sCol-1]==null ||\r
+ row.annotations[sCol-1].secondaryStructure!='H')\r
+ {\r
+ g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;\r
+ x1 += av.charWidth/2;\r
+ }\r
+\r
+ if(row.annotations[column]==null ||\r
+ row.annotations[column].secondaryStructure!='H')\r
+ {\r
+ g.fillArc((x*av.charWidth)-av.charWidth,\r
+ y+4+iconOffset, av.charWidth, 8, 270,180);\r
+ x2 -= av.charWidth/2;\r
+ }\r
+\r
+ g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
+ break;\r
\r
case 'E':\r
g.setColor(SHEET_COLOUR);\r
g.fillRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX - 4, 7);\r
- g.fillPolygon(new int[] { x - 5, x - 5, x },\r
+ (x*av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[] { (x*av.charWidth) - 4,\r
+ (x*av.charWidth) - 4,\r
+ (x*av.charWidth) },\r
new int[]\r
{\r
y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset\r
+ y + 8 + iconOffset\r
}, 3);\r
\r
break;\r
default:\r
g.setColor(Color.gray);\r
g.fillRect(lastSSX, y + 6 + iconOffset,\r
- x - lastSSX, 2);\r
+ (x*av.charWidth) - lastSSX, 2);\r
\r
break;\r
}\r
lastSS = ' ';\r
}\r
\r
- lastSSX = x;\r
+ lastSSX = (x*av.charWidth);\r
}\r
}\r
\r
- column++;\r
+\r
+ column++;\r
+ x++;\r
}\r
\r
if(column>=row.annotations.length)\r
- column = row.annotations.length-1;\r
+ column = row.annotations.length-1;\r
\r
- x += av.charWidth;\r
+ // x ++;\r
\r
if (row.hasIcons)\r
{\r
- switch (lastSS)\r
- {\r
+ switch (lastSS)\r
+ {\r
case 'H':\r
g.setColor(HELIX_COLOUR);\r
if (MAC)\r
//Off by 1 offset when drawing rects and ovals\r
//to offscreen image on the MAC\r
g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX, 7, 8, 8);\r
+ (x*av.charWidth) - lastSSX, 7, 8, 8);\r
break;\r
}\r
\r
-\r
int sCol = (lastSSX / av.charWidth) + startRes;\r
int x1 = lastSSX;\r
- int x2 = x;\r
-\r
- if(sCol==0 ||\r
- row.annotations[sCol-1]==null ||\r
- row.annotations[sCol-1].secondaryStructure!='H')\r
- {\r
- g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;\r
- x1 += av.charWidth/2;\r
- }\r
-\r
- if(row.annotations[column]==null ||\r
- row.annotations[column].secondaryStructure!='H')\r
+ int x2 = (x*av.charWidth);\r
+\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\r
{\r
- g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);\r
- x2 -= av.charWidth/2;\r
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
+ x1 += av.charWidth / 2;\r
}\r
\r
- g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);\r
-\r
- break;\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc((x*av.charWidth) - av.charWidth,\r
+ y + 4 + iconOffset, av.charWidth, 8, 270,\r
+ 180);\r
+ x2 -= av.charWidth / 2;\r
+ }\r
\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
\r
- if (row.annotations[endRes] ==null\r
- || row.annotations[endRes].secondaryStructure != 'E')\r
- {\r
- g.fillRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 5, x - 5, x},\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset\r
- }, 3);\r
- }\r
- else\r
- g.fillRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX, 7);\r
+ break;\r
\r
- break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
\r
+ if (row.annotations[endRes] == null\r
+ || row.annotations[endRes].secondaryStructure != 'E')\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x*av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {(x*av.charWidth) - 4,\r
+ (x*av.charWidth) - 4,\r
+ (x*av.charWidth)},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x+1) * av.charWidth - lastSSX, 7);\r
+ }\r
+ break;\r
\r
default:\r
- g.setColor(Color.gray);\r
- if(!av.wrapAlignment || endRes==av.endRes)\r
- g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);\r
+ g.setColor(Color.gray);\r
+ if(!av.wrapAlignment || endRes==av.endRes)\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x*av.charWidth) - lastSSX, 2);\r
\r
- break;\r
- }\r
- }\r
+ break;\r
+ }\r
+ }\r
\r
- if (row.graph>0)\r
+ if (row.graph>0 && row.graphHeight>0)\r
{\r
if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
{\r
\r
if(sRes==0)\r
{\r
- sRes++;\r
- x+=av.charWidth;\r
+ x++;\r
}\r
\r
int y1=y, y2=y;\r
\r
eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int column = sRes;\r
+ int column;\r
int aaMax = aa.annotations.length-1;\r
\r
- while( column < eRes )\r
+ while( x < eRes - sRes )\r
{\r
+ column = sRes + x;\r
if(av.hasHiddenColumns)\r
{\r
column = av.getColumnSelection().adjustForHiddenColumns(column);\r
- if(column > aaMax)\r
- {\r
- break;\r
- }\r
+ }\r
+\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
}\r
\r
if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
{\r
- x+=av.charWidth;\r
- column ++;\r
+ x++;\r
continue;\r
}\r
\r
y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
\r
- g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
- x += av.charWidth;\r
-\r
- column++;\r
-\r
+ g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
+ x ++;\r
}\r
+\r
if(aa.threshold!=null)\r
{\r
g.setColor(aa.threshold.colour);\r
\r
eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int x=0, y1, y2;\r
+ int x=0, y1=y, y2=y;\r
\r
float range = max - min;\r
\r
- y1 = y2 = y;\r
-\r
if(min<0)\r
y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
\r
\r
g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
-\r
- int column = sRes;\r
+ int column;\r
int aaMax = aa.annotations.length-1;\r
\r
- while( column < eRes )\r
+ while( x < eRes-sRes )\r
{\r
+ column = sRes + x;\r
if(av.hasHiddenColumns)\r
{\r
column = av.getColumnSelection().adjustForHiddenColumns(column);\r
- if(column > aaMax)\r
- {\r
+ }\r
+\r
+ if(column > aaMax)\r
+ {\r
break;\r
- }\r
}\r
\r
if (aa.annotations[column] == null)\r
{\r
- x += av.charWidth;\r
- column ++;\r
+ x ++;\r
continue;\r
}\r
\r
y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
\r
if(y1-y2>0)\r
- g.fillRect(x, y2, av.charWidth, y1-y2 );\r
+ g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
else\r
- g.fillRect(x, y1, av.charWidth, y2-y1 );\r
+ g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
\r
- x += av.charWidth;\r
- column ++;\r
+ x ++ ;\r
\r
}\r
if(aa.threshold!=null)\r
// used by overview window\r
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
{\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
g.setColor(Color.white);\r
g.fillRect(0, 0, width, y);\r
g.setColor(new Color(0, 0, 180));\r
\r
for (int j = sRes; j < eRes; j++)\r
{\r
+ if (aa.annotations[j] != null)\r
+ {\r
g.setColor(aa.annotations[j].colour);\r
\r
- height = (int) ((aa.annotations[j].value / aa.graphMax) * y);\r
- if(height>y)\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
+ if (height > y)\r
height = y;\r
\r
g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
x += av.charWidth;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff