\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
public void paint(Graphics g)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\r
+\r
+\r
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
if (image == null || imgWidth != image.getWidth(this))\r
}\r
\r
drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.drawImage(image, 0, 0, this);\r
}\r
\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
- char[] lastSS = new char[aa.length];\r
- int[] lastSSX = new int[aa.length];\r
+ char lastSS;\r
+ int lastSSX;\r
int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
\r
continue;\r
}\r
\r
-\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
if (row.graph>0)\r
{\r
iconOffset = 0;\r
}\r
\r
- for (j = startRes; j < endRes; j++)\r
+ int column = startRes;\r
+ while(column < endRes)\r
{\r
- if ((row.annotations.length <= j) ||\r
- (row.annotations[j] == null))\r
+ if ((row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
{\r
validRes = false;\r
}\r
validRes = true;\r
}\r
\r
- x = (j - startRes) * av.charWidth;\r
+ x = (column - startRes) * av.charWidth;\r
\r
- if (activeRow == i)\r
- {\r
- g.setColor(Color.red);\r
\r
- if (activeRes != null)\r
- {\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
-\r
- if (v == j)\r
- {\r
- g.fillRect((j - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (validRes &&\r
- (row.annotations[j].displayCharacter.length() > 0))\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
{\r
-\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
- 0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
-\r
- if (j == 0 || row.graph>0)\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
- }\r
- else if (((row.annotations[j - 1] == null) ||\r
- (row.annotations[j].displayCharacter != row.annotations[j -\r
- 1].displayCharacter)))\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
- }\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[column].colour);\r
+\r
+ if (column == 0 || row.graph>0)\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\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
+ }\r
}\r
\r
if (row.hasIcons)\r
{\r
if (!validRes ||\r
- (row.annotations[j].secondaryStructure != lastSS[i]))\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
{\r
- switch (lastSS[i])\r
+ switch (lastSS)\r
{\r
case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\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, 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, 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[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX - 4, 7);\r
g.fillPolygon(new int[] { x - 4, x - 4, x },\r
new int[]\r
{\r
\r
default:\r
g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
- x - lastSSX[i], 2);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ x - lastSSX, 2);\r
\r
break;\r
}\r
\r
if (validRes)\r
{\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
+ lastSS = row.annotations[column].secondaryStructure;\r
}\r
else\r
{\r
- lastSS[i] = ' ';\r
+ lastSS = ' ';\r
}\r
\r
- lastSSX[i] = x;\r
+ lastSSX = x;\r
}\r
}\r
+\r
+\r
+ column++;\r
}\r
\r
+ if(column>=row.annotations.length)\r
+ column = row.annotations.length-1;\r
+\r
x += av.charWidth;\r
\r
if (row.hasIcons)\r
{\r
- switch (lastSS[i])\r
+ switch (lastSS)\r
{\r
case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\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
+\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, 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, 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
+\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
+ if (row.annotations[endRes] ==null\r
+ || row.annotations[endRes].secondaryStructure != 'E')\r
{\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\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
}, 3);\r
}\r
else\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX, 7);\r
\r
break;\r
\r
- case 'C':\r
- break;\r
\r
default:\r
g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);\r
\r
break;\r
}\r
if(sRes>aa.annotations.length)\r
return;\r
\r
+\r
+\r
int x = 0;\r
\r
//Adjustment for fastpaint to left\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+1)*av.charWidth,y2);\r
+ g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
- }\r
-\r
- eRes = Math.min(eRes, aa.annotations.length);\r
for (int j = sRes; j < eRes; j++)\r
{\r
if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
x += av.charWidth;\r
}\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
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
\r
float range = max - min;\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(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\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+1)*av.charWidth,y2);\r
-\r
- eRes = Math.min(eRes, aa.annotations.length-1);\r
-\r
+ g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
for (int j = sRes; j < eRes; j++)\r
{\r
x += av.charWidth;\r
}\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
// used by overview window\r
\r
for (int j = sRes; j < eRes; j++)\r
{\r
- g.setColor(new Color(0, 0, 180));\r
+ g.setColor(aa.annotations[j].colour);\r
\r
height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
if(height>y)\r
git://source.jalview.org / jalview.git / blobdiff