/*\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 static int GRAPH_HEIGHT = 40;\r
\r
+ boolean MAC = false;\r
+\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ MAC = true;\r
+\r
this.ap = ap;\r
av = ap.av;\r
- this.setLayout(null);\r
+ setLayout(null);\r
adjustPanelHeight();\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
}\r
\r
this.setSize(getSize().width, height);\r
- if(ap!=null)\r
- ap.annotationScroller.setSize(getSize().width, height);\r
-\r
\r
repaint();\r
\r
}\r
\r
int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)\r
- {\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
+\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+\r
+ if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence position " + (res + 1));\r
+ if (aa[row].annotations[res].description != null)\r
+ text.append(" " + aa[row].annotations[res].description);\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
}\r
\r
public void update(Graphics g)\r
\r
public void paint(Graphics g)\r
{\r
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
+\r
+ imgWidth = getSize().width;\r
+ //(av.endRes - av.startRes + 1) * av.charWidth;\r
\r
if (image == null || imgWidth != image.getWidth(this))\r
{\r
\r
\r
g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
\r
if ((av.alignment.getAlignmentAnnotation() == null) ||\r
(av.alignment.getAlignmentAnnotation().length < 1))\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations", 20, 15);\r
+ if(av.validCharWidth)\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
\r
return;\r
}\r
\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int j;\r
int x = 0;\r
int y = 0;\r
+ int column=0;\r
char lastSS;\r
int lastSSX;\r
int iconOffset = av.charHeight / 2;\r
iconOffset = 0;\r
}\r
\r
- int column = startRes;\r
- while(column < endRes)\r
+ x = 0;\r
+ while(x < endRes-startRes)\r
{\r
- if ((row.annotations.length <= column) ||\r
- (row.annotations[column] == null))\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
+ if (column > row.annotations.length-1)\r
{\r
- validRes = false;\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ column = startRes+x;\r
+\r
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
}\r
else\r
{\r
- validRes = true;\r
+ validRes = true;\r
}\r
\r
- x = (column - startRes) * av.charWidth;\r
\r
-\r
- if (validRes &&\r
- (row.annotations[column].displayCharacter.length() > 0))\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
{\r
int charOffset = (av.charWidth -\r
fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
\r
if (column == 0 || row.graph>0)\r
{\r
- g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x*av.charWidth)+charOffset,\r
y + iconOffset + 3);\r
}\r
else if (\r
(row.annotations[column].displayCharacter.length() <2 &&\r
row.annotations[column].secondaryStructure==' ')))\r
{\r
- g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x*av.charWidth)+charOffset,\r
y + iconOffset + 3);\r
}\r
}\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*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;\r
+ int x2 = (x*av.charWidth);\r
\r
- if(row.annotations[sCol-1]==null ||\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
if(row.annotations[column]==null ||\r
row.annotations[column].secondaryStructure!='H')\r
{\r
- g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);\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
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 - 4, x - 4, 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
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
\r
column++;\r
+ x++;\r
}\r
\r
- x += av.charWidth;\r
+ if(column>=row.annotations.length)\r
+ column = row.annotations.length-1;\r
+\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
+ {\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;\r
+ int x2 = (x*av.charWidth);\r
\r
- if(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
+ 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
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
{\r
- g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);\r
- x2 -= av.charWidth/2;\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
- g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
\r
- break;\r
+ break;\r
\r
case 'E':\r
- g.setColor(SHEET_COLOUR);\r
-\r
- if (row.annotations.length > endRes\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 - 4, x - 4, 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
-\r
- break;\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 * av.charWidth - lastSSX, 7);\r
+ }\r
+ break;\r
\r
default:\r
- g.setColor(Color.gray);\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
+ break;\r
+ }\r
}\r
\r
if (row.graph>0)\r
return;\r
\r
\r
- eRes = Math.min(eRes, aa.annotations.length);\r
\r
int x = 0;\r
\r
if(eRes<av.endRes)\r
eRes++;\r
\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+\r
if(sRes==0)\r
{\r
sRes++;\r
\r
////Draw origin\r
if(min<0)\r
- y2 = (int)(y - (0-min / range)*graphHeight);\r
+ y2 = y - (int)((0-min / range)*graphHeight);\r
\r
g.setColor(Color.gray);\r
g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+ int column;\r
+ int aaMax = aa.annotations.length-1;\r
\r
- for (int j = sRes; j < eRes; j++)\r
+ while( x < eRes - sRes )\r
{\r
- if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+ column = sRes + x;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
+\r
+ if (column > aaMax)\r
{\r
- x+=av.charWidth;\r
+ break;\r
+ }\r
+\r
+ if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
+ {\r
+ x++;\r
continue;\r
}\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
- y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
- g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
- x += av.charWidth;\r
- }\r
\r
+ g.setColor(aa.annotations[column].colour);\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-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
- y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
- g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
- }\r
\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ }\r
}\r
\r
public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
if(sRes>aa.annotations.length)\r
return;\r
\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 = (int)(y - (0-min / (range))*aa.graphHeight);\r
+ y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
\r
g.setColor(Color.gray);\r
\r
g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
- for (int j = sRes; j < eRes; j++)\r
+ int column;\r
+ int aaMax = aa.annotations.length-1;\r
+\r
+ while( x < eRes-sRes )\r
{\r
+ column = sRes + x;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
+\r
+ if(column > aaMax)\r
+ {\r
+ break;\r
+ }\r
\r
- if (aa.annotations[j] == null)\r
+ if (aa.annotations[column] == null)\r
{\r
- x += av.charWidth;\r
+ x ++;\r
continue;\r
}\r
\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
+ g.setColor(aa.annotations[column].colour);\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
-\r
- x += av.charWidth;\r
- }\r
+ g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
\r
+ x ++ ;\r
\r
+ }\r
if(aa.threshold!=null)\r
{\r
g.setColor(aa.threshold.colour);\r
y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
- }\r
-\r
-\r
+ }\r
}\r
\r
// used by overview window\r
git://source.jalview.org / jalview.git / blobdiff