int max; //used by mouseDragged to see if user\r
boolean mouseDragging = false;\r
\r
+ boolean MAC = false;\r
+\r
/**\r
* Creates a new AnnotationPanel object.\r
*\r
*/\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
+\r
+ if(System.getProperty("os.name").startsWith("Mac"))\r
+ MAC = true;\r
+\r
ToolTipManager.sharedInstance().registerComponent(this);\r
ToolTipManager.sharedInstance().setInitialDelay(0);\r
ToolTipManager.sharedInstance().setDismissDelay(10000);\r
*/\r
public void mousePressed(MouseEvent evt)\r
{\r
- int height = 0;\r
- activeRow = -1;\r
+\r
\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
if(aa==null)\r
return;\r
\r
+\r
+ int height = 0;\r
+ activeRow = 0;\r
+\r
+\r
for (int i = 0; i < aa.length; i++)\r
{\r
if (aa[i].visible)\r
}\r
}\r
\r
+\r
if (SwingUtilities.isRightMouseButton(evt))\r
{\r
if (av.getColumnSelection() == null)\r
*/\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
+\r
+\r
g.setFont(av.getFont());\r
\r
if (fm == null)\r
g.setColor(Color.white);\r
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
\r
- if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
(av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\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 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
lastSS = ' ';\r
lastSSX = 0;\r
\r
-\r
if (row.graph>0)\r
{\r
if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
iconOffset = 0;\r
}\r
\r
- int column = startRes;\r
- int yPos = startRes;\r
-\r
- while (yPos < endRes)\r
+ x = 0;\r
+ while (x < endRes-startRes)\r
{\r
if (av.hasHiddenColumns)\r
{\r
- column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
if (column > row.annotations.length-1)\r
{\r
break;\r
}\r
}\r
else\r
- column = yPos;\r
+ column = startRes+x;\r
+\r
\r
if ((row.annotations.length <= column) ||\r
(row.annotations[column] == null))\r
validRes = true;\r
}\r
\r
- x = (yPos - 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
\r
- if (validRes &&\r
+ if (av.validCharWidth && validRes &&\r
(row.annotations[column].displayCharacter.length() > 0))\r
{\r
\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 (((row.annotations[column - 1] == null)\r
- ||\r
- (!row.annotations[column].displayCharacter.equals(\r
- row.annotations[column - 1].displayCharacter))))\r
+ else if (\r
+ row.annotations[column - 1] == null\r
+ ||(!row.annotations[column].displayCharacter.equals(\r
+ row.annotations[column - 1].displayCharacter)\r
+ ||\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 + 3);\r
}\r
}\r
\r
{\r
case 'H':\r
g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX, 7, 8, 8);\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+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-av.charWidth,\r
+ y+4+iconOffset,\r
+ av.charWidth,\r
+ 7, 270,180);\r
+ x2 -= av.charWidth/2;\r
+ }\r
+\r
+ g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);\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 - 4, x - 4, x },\r
+ x*av.charWidth - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[] { x*av.charWidth - 5,\r
+ x*av.charWidth - 5,\r
+ x*av.charWidth },\r
new int[]\r
{\r
y + iconOffset, y + 14 + iconOffset,\r
- y + 8 + iconOffset\r
+ y + 7 + 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
- yPos++;\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
case 'H':\r
- g.setColor(HELIX_COLOUR);\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
+ 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
+ {\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
\r
break;\r
\r
case 'E':\r
g.setColor(SHEET_COLOUR);\r
\r
- if (row.annotations[endRes] !=null\r
- && row.annotations[endRes].secondaryStructure != 'E')\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
+ x*av.charWidth - lastSSX - 4, 7);\r
g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\r
+ {x*av.charWidth - 5,\r
+ x*av.charWidth - 5,\r
+ x*av.charWidth},\r
new int[]\r
{\r
y + iconOffset, y + 14 + iconOffset,\r
}\r
else\r
g.fillRect(lastSSX, y + 4 + iconOffset,\r
- x - lastSSX, 7);\r
+ x*av.charWidth - lastSSX, 7);\r
\r
break;\r
\r
\r
default:\r
g.setColor(Color.gray);\r
- g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);\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
if(sRes>aa.annotations.length)\r
return;\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
if(sRes==0)\r
{\r
- sRes++;\r
- x+=av.charWidth;\r
+ x++;\r
}\r
\r
int y1=y, y2=y;\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+1)*av.charWidth,y2);\r
\r
-\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- Graphics2D g2 = (Graphics2D)g;\r
- g2.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_SQUARE,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[] { 5f, 3f }, 0f));\r
-\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
- g2.setStroke(new BasicStroke());\r
- }\r
-\r
eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int column = sRes;\r
- int yPos = sRes;\r
+ int column;\r
int aaMax = aa.annotations.length-1;\r
\r
- while( yPos < eRes )\r
+ while( x < eRes - sRes )\r
{\r
+ column = sRes + x;\r
if(av.hasHiddenColumns)\r
{\r
- column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
- if(column > aaMax)\r
- {\r
- break;\r
- }\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
- else\r
- column = yPos;\r
\r
- yPos ++;\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
+ x++;\r
continue;\r
}\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
- g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
- x += av.charWidth;\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
+ Graphics2D g2 = (Graphics2D)g;\r
+ g2.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_SQUARE,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[] { 5f, 3f }, 0f));\r
+\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g2.setStroke(new BasicStroke());\r
+ }\r
}\r
\r
public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\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
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- Graphics2D g2 = (Graphics2D)g;\r
- g2.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_SQUARE,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[] { 5f, 3f }, 0f));\r
-\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
- g2.setStroke(new BasicStroke());\r
- }\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
-\r
- int column = sRes;\r
- int yPos = sRes;\r
+ int column;\r
int aaMax = aa.annotations.length-1;\r
\r
- while( yPos < eRes )\r
+ while( x < eRes-sRes )\r
{\r
+ column = sRes + x;\r
if(av.hasHiddenColumns)\r
{\r
- column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
- if(column > aaMax)\r
- {\r
- break;\r
- }\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
- else\r
- column = yPos;\r
\r
- yPos ++;\r
+ if(column > aaMax)\r
+ {\r
+ break;\r
+ }\r
\r
if (aa.annotations[column] == null)\r
{\r
- x += av.charWidth;\r
+ x ++;\r
continue;\r
}\r
\r
-\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
+ g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
+\r
+ x ++ ;\r
\r
- x += av.charWidth;\r
}\r
+ if(aa.threshold!=null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ Graphics2D g2 = (Graphics2D)g;\r
+ g2.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_SQUARE,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[] { 5f, 3f }, 0f));\r
\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g2.setStroke(new BasicStroke());\r
+ }\r
}\r
\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
git://source.jalview.org / jalview.git / blobdiff