/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
public AnnotationPanel(AlignmentPanel ap)\r
{\r
if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
MAC = true;\r
+ }\r
\r
this.ap = ap;\r
av = ap.av;\r
// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
}\r
\r
-\r
public AnnotationPanel(AlignViewport av)\r
{\r
this.av = av;\r
}\r
\r
-\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
ap.alabels.setScrollOffset( -evt.getValue());\r
// setHeight of panels\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
-\r
int height = 0;\r
if (aa != null)\r
{\r
aa[i].height += 16;\r
}\r
\r
- if (aa[i].graph>0)\r
+ if (aa[i].graph > 0)\r
{\r
aa[i].height += GRAPH_HEIGHT;\r
}\r
if (activeRow == -1)\r
{\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa ==null)\r
+ if (aa == null)\r
+ {\r
return;\r
+ }\r
\r
for (int j = 0; j < aa.length; j++)\r
{\r
\r
int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\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
+ 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
+ {\r
+ text.append(" " + aa[row].annotations[res].description);\r
+ }\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
}\r
\r
public void update(Graphics g)\r
{\r
\r
imgWidth = getSize().width;\r
- //(av.endRes - av.startRes + 1) * av.charWidth;\r
+ //(av.endRes - av.startRes + 1) * av.charWidth;\r
\r
if (image == null || imgWidth != image.getWidth(this))\r
{\r
fastPaint = false;\r
}\r
\r
-\r
if (fastPaint)\r
{\r
g.drawImage(image, 0, 0, this);\r
gg.fillRect(0, 0, getSize().width, getSize().height);\r
drawComponent(gg, av.startRes, av.endRes + 1);\r
\r
-\r
g.drawImage(image, 0, 0, this);\r
}\r
\r
{\r
g.setFont(av.getFont());\r
\r
-\r
g.setColor(Color.white);\r
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
\r
-\r
if (fm == null)\r
+ {\r
fm = g.getFontMetrics();\r
+ }\r
\r
-\r
- if ((av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.black);\r
+ if (av.validCharWidth)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\r
- if(av.validCharWidth)\r
- g.drawString("Alignment has no annotations", 20, 15);\r
-\r
- return;\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
}\r
\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ return;\r
+ }\r
\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
- boolean validRes = false;\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- boolean [] graphGroupDrawn = new boolean[aa.length];\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
+ boolean validRes = false;\r
\r
+ boolean[] graphGroupDrawn = new boolean[aa.length];\r
\r
- //\u03B2 \u03B1\r
- for (int i = 0; i < aa.length; i++)\r
+ //\u03B2 \u03B1\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ AlignmentAnnotation row = aa[i];\r
+\r
+ if (!row.visible)\r
{\r
- AlignmentAnnotation row = aa[i];\r
+ continue;\r
+ }\r
\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
- lastSS = ' ';\r
- lastSSX = 0;\r
+ if (row.graph > 0)\r
+ {\r
+ if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])\r
+ {\r
+ continue;\r
+ }\r
\r
- if (row.graph>0)\r
- {\r
- if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
- continue;\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
\r
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
+ if (row.hasText)\r
+ {\r
+ y -= av.charHeight;\r
+ }\r
+ }\r
\r
- if (row.hasText)\r
- {\r
- y -= av.charHeight;\r
- }\r
- }\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2;\r
+ }\r
+ else\r
+ {\r
+ iconOffset = 0;\r
+ }\r
\r
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2;\r
- }\r
- else\r
+ x = 0;\r
+ while (x < endRes - startRes)\r
+ {\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);\r
+ if (column > row.annotations.length - 1)\r
{\r
- iconOffset = 0;\r
+ break;\r
}\r
+ }\r
+ else\r
+ {\r
+ column = startRes + x;\r
+ }\r
\r
- x = 0;\r
- while(x < endRes-startRes)\r
- {\r
- if (av.hasHiddenColumns)\r
- {\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
- if ( (row.annotations.length <= column) ||\r
- (row.annotations[column] == null))\r
- {\r
- validRes = false;\r
- }\r
- else\r
- {\r
- validRes = true;\r
- }\r
-\r
-\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
- 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,\r
- (x*av.charWidth)+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,\r
- (x*av.charWidth)+charOffset,\r
- y + iconOffset + 3);\r
- }\r
- }\r
-\r
- if (row.hasIcons)\r
- {\r
- if (!validRes ||\r
- (row.annotations[column].secondaryStructure != 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*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*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 + 8 + iconOffset\r
- }, 3);\r
-\r
- break;\r
-\r
-\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX, y + 6 + iconOffset,\r
- (x*av.charWidth) - lastSSX, 2);\r
-\r
- break;\r
- }\r
-\r
- if (validRes)\r
- {\r
- lastSS = row.annotations[column].secondaryStructure;\r
- }\r
- else\r
- {\r
- lastSS = ' ';\r
- }\r
-\r
- lastSSX = (x*av.charWidth);\r
- }\r
- }\r
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].\r
+ displayCharacter.charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[column].colour);\r
\r
- column++;\r
- x++;\r
+ if (column == 0 || row.graph > 0)\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x * av.charWidth) + 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,\r
+ (x * av.charWidth) + charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ }\r
\r
- if(column>=row.annotations.length)\r
- column = row.annotations.length-1;\r
-\r
- // x ++;\r
-\r
- if (row.hasIcons)\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
{\r
switch (lastSS)\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
+ (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
+ 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
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,\r
+ 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,\r
- 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
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
-\r
break;\r
\r
case 'E':\r
g.setColor(SHEET_COLOUR);\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 + 8 + iconOffset\r
+ }, 3);\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
- if(!av.wrapAlignment || endRes==av.endRes)\r
g.fillRect(lastSSX, y + 6 + iconOffset,\r
- (x*av.charWidth) - lastSSX, 2);\r
+ (x * av.charWidth) - lastSSX, 2);\r
\r
break;\r
}\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS = row.annotations[column].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS = ' ';\r
+ }\r
+\r
+ lastSSX = (x * av.charWidth);\r
}\r
+ }\r
+\r
+ column++;\r
+ x++;\r
+ }\r
+\r
+ if (column >= row.annotations.length)\r
+ {\r
+ column = row.annotations.length - 1;\r
+ }\r
+\r
+ // x ++;\r
+\r
+ if (row.hasIcons)\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 * 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.graph>0)\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
+ 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[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
+ if (!av.wrapAlignment || endRes == av.endRes)\r
+ {\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (row.graph > 0)\r
+ {\r
+ if (row.graph == AlignmentAnnotation.LINE_GRAPH)\r
+ {\r
+ if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])\r
{\r
- if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
+ float groupmax = -999999, groupmin = 9999999;\r
+ for (int gg = 0; gg < aa.length; gg++)\r
+ {\r
+ if (aa[gg].graphGroup != row.graphGroup)\r
{\r
- if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
- {\r
- float groupmax=-999999, groupmin=9999999;\r
- for(int gg=0; gg<aa.length; gg++)\r
- {\r
- if(aa[gg].graphGroup!=row.graphGroup)\r
- continue;\r
-\r
- if(aa[gg]!=row)\r
- aa[gg].visible = false;\r
-\r
- if(aa[gg].graphMax>groupmax)\r
- groupmax = aa[gg].graphMax;\r
- if(aa[gg].graphMin<groupmin)\r
- groupmin = aa[gg].graphMin;\r
- }\r
-\r
- for (int gg = 0; gg < aa.length; gg++)\r
- {\r
- if (aa[gg].graphGroup == row.graphGroup)\r
- {\r
- drawLineGraph(g, aa[gg], startRes, endRes, y,\r
- groupmin, groupmax,\r
- row.graphHeight);\r
- }\r
- }\r
-\r
- graphGroupDrawn[ row.graphGroup ] = true;\r
- }\r
- else\r
- drawLineGraph(g, row, startRes, endRes,\r
- y, row.graphMin, row.graphMax, row.graphHeight );\r
+ continue;\r
}\r
- else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
- drawBarGraph(g, row, startRes, endRes,\r
- row.graphMin, row.graphMax, y);\r
- }\r
\r
- if (row.graph>0 && row.hasText)\r
- {\r
- y += av.charHeight;\r
- }\r
+ if (aa[gg] != row)\r
+ {\r
+ aa[gg].visible = false;\r
+ }\r
\r
- if (row.graph==0)\r
+ if (aa[gg].graphMax > groupmax)\r
+ {\r
+ groupmax = aa[gg].graphMax;\r
+ }\r
+ if (aa[gg].graphMin < groupmin)\r
+ {\r
+ groupmin = aa[gg].graphMin;\r
+ }\r
+ }\r
+\r
+ for (int gg = 0; gg < aa.length; gg++)\r
+ {\r
+ if (aa[gg].graphGroup == row.graphGroup)\r
+ {\r
+ drawLineGraph(g, aa[gg], startRes, endRes, y,\r
+ groupmin, groupmax,\r
+ row.graphHeight);\r
+ }\r
+ }\r
+\r
+ graphGroupDrawn[row.graphGroup] = true;\r
+ }\r
+ else\r
{\r
- y += aa[i].height;\r
+ drawLineGraph(g, row, startRes, endRes,\r
+ y, row.graphMin, row.graphMax, row.graphHeight);\r
}\r
+ }\r
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
+ {\r
+ drawBarGraph(g, row, startRes, endRes,\r
+ row.graphMin, row.graphMax, y);\r
+ }\r
+ }\r
+\r
+ if (row.graph > 0 && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
+ }\r
+\r
+ if (row.graph == 0)\r
+ {\r
+ y += aa[i].height;\r
}\r
+ }\r
}\r
\r
public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
float min, float max,\r
int graphHeight)\r
{\r
- if(sRes>aa.annotations.length)\r
+ if (sRes > aa.annotations.length)\r
+ {\r
return;\r
-\r
-\r
+ }\r
\r
int x = 0;\r
\r
//Adjustment for fastpaint to left\r
- if(eRes<av.endRes)\r
+ if (eRes < av.endRes)\r
+ {\r
eRes++;\r
+ }\r
\r
eRes = Math.min(eRes, aa.annotations.length);\r
\r
-\r
- if(sRes==0)\r
+ if (sRes == 0)\r
{\r
sRes++;\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
}\r
\r
- int y1=y, y2=y;\r
+ int y1 = y, y2 = y;\r
float range = max - min;\r
\r
////Draw origin\r
- if(min<0)\r
- y2 = y - (int)((0-min / range)*graphHeight);\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / range) * graphHeight);\r
+ }\r
\r
g.setColor(Color.gray);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\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
+ int aaMax = aa.annotations.length - 1;\r
\r
- while( x < eRes - sRes )\r
+ while (x < eRes - sRes)\r
{\r
column = sRes + x;\r
- if(av.hasHiddenColumns)\r
+ if (av.hasHiddenColumns)\r
{\r
column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
break;\r
}\r
\r
- if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
+ if (aa.annotations[column] == null || aa.annotations[column - 1] == null)\r
{\r
x++;\r
continue;\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.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);\r
+ y2 = y -\r
+ (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
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1,\r
+ x * av.charWidth + av.charWidth / 2, y2);\r
+ x++;\r
+ }\r
\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
+ if (aa.threshold != null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
- g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);\r
+ g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);\r
}\r
}\r
\r
float min, float max,\r
int y)\r
{\r
- if(sRes>aa.annotations.length)\r
+ if (sRes > aa.annotations.length)\r
+ {\r
return;\r
+ }\r
\r
eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int x=0, y1=y, y2=y;\r
+ int x = 0, y1 = y, y2 = y;\r
\r
float range = max - min;\r
\r
- if(min<0)\r
- y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);\r
+ }\r
\r
g.setColor(Color.gray);\r
\r
- g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);\r
\r
int column;\r
- int aaMax = aa.annotations.length-1;\r
+ int aaMax = aa.annotations.length - 1;\r
\r
- while( x < eRes-sRes )\r
+ while (x < eRes - sRes)\r
{\r
column = sRes + x;\r
- if(av.hasHiddenColumns)\r
+ if (av.hasHiddenColumns)\r
{\r
column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
\r
- if(column > aaMax)\r
+ if (column > aaMax)\r
{\r
- break;\r
+ break;\r
}\r
\r
if (aa.annotations[column] == null)\r
{\r
- x ++;\r
+ x++;\r
continue;\r
}\r
\r
- g.setColor(aa.annotations[column].colour);\r
- y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
+ g.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);\r
\r
- if(y1-y2>0)\r
- g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
- else\r
- g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
+ if (y1 - y2 > 0)\r
+ {\r
+ g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);\r
+ }\r
\r
- x ++ ;\r
+ x++;\r
\r
}\r
- if(aa.threshold!=null)\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
+ 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
// used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,\r
+ int sRes, int eRes)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, width, y);\r
- g.setColor(new Color(0, 0, 180));\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
\r
- int x = 0, height;\r
+ int x = 0, height;\r
\r
- for (int j = sRes; j < eRes; j++)\r
- {\r
- g.setColor(aa.annotations[j].colour);\r
+ for (int j = sRes; j < eRes; j++)\r
+ {\r
+ g.setColor(aa.annotations[j].colour);\r
\r
- height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
- if(height>y)\r
- height = y;\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- x += av.charWidth;\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+ if (height > y)\r
+ {\r
+ height = y;\r
}\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ x += av.charWidth;\r
}\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff