/*\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
// 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
}\r
\r
- public void adjustPanelHeight()\r
+ public int adjustPanelHeight()\r
{\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].isGraph)\r
+ if (aa[i].graph>0)\r
{\r
aa[i].height += GRAPH_HEIGHT;\r
}\r
}\r
\r
this.setSize(getSize().width, height);\r
- ap.annotationScroller.setSize(getSize().width, height);\r
-\r
-// ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
\r
repaint();\r
\r
+ return height;\r
+\r
}\r
\r
public void addEditableColumn(int i)\r
if (activeRow == -1)\r
{\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa ==null)\r
+ return;\r
+\r
for (int j = 0; j < aa.length; j++)\r
{\r
if (aa[j].editable)\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
- g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\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
drawComponent(gg, av.startRes, av.endRes + 1);\r
g.drawImage(image, 0, 0, this);\r
-\r
}\r
\r
public void fastPaint(int horizontal)\r
repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ * @param endRes DOCUMENT ME!\r
+ */\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\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
- g.drawString("Alignment has no annotations", 20, 15);\r
- return;\r
- }\r
+ g.setFont(av.getFont());\r
\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (fm == null)\r
+ fm = g.getFontMetrics();\r
\r
- int j, x = 0, y = 0;\r
- char[] lastSS = new char[aa.length];\r
- int[] lastSSX = new int[aa.length];\r
- int iconOffset = av.charHeight / 2;\r
- boolean validRes = false;\r
- //\u03B2 \u03B1\r
\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- AlignmentAnnotation row = aa[i];\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
\r
- if (row.isGraph)\r
+ if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\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
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2;\r
- }\r
- else\r
- {\r
- iconOffset = 0;\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
}\r
\r
- for (j = startRes; j < endRes; j++)\r
- {\r
- if (row.annotations.length <= j || row.annotations[j] == null)\r
- {\r
- validRes = false;\r
- }\r
- else\r
- {\r
- validRes = true;\r
- }\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- x = (j - startRes) * av.charWidth;\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
- if (activeRow == i)\r
- {\r
+ boolean [] graphGroupDrawn = new boolean[aa.length];\r
\r
- g.setColor(Color.red);\r
\r
- if (activeRes != null)\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
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
- if (v == j)\r
+ continue;\r
+ }\r
+\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
+\r
+ if (row.graph>0)\r
+ {\r
+ if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
+ continue;\r
+\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
+\r
+ if (row.hasText)\r
{\r
- g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,\r
- row.height);\r
+ y -= av.charHeight;\r
}\r
- }\r
}\r
- }\r
\r
- if (validRes && row.annotations[j].displayCharacter.length() > 0)\r
- {\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
- if (j == 0 || row.isGraph)\r
+ if (row.hasText)\r
{\r
- if (row.annotations[0].secondaryStructure == 'H'\r
- || row.annotations[0].secondaryStructure == 'E')\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 3);\r
- }\r
+ iconOffset = av.charHeight / 2;\r
}\r
- else if ( (row.annotations[j].secondaryStructure == 'H'\r
- || row.annotations[j].secondaryStructure == 'E') &&\r
- (row.annotations[j - 1] == null ||\r
- row.annotations[j].secondaryStructure !=\r
- row.annotations[j - 1].secondaryStructure))\r
+ else\r
{\r
-\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 3);\r
+ iconOffset = 0;\r
}\r
\r
- if (!row.hasIcons)\r
+ x = 0;\r
+ while(x < endRes-startRes)\r
{\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 3);\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
+\r
+\r
+ column++;\r
+ x++;\r
}\r
- }\r
\r
- if (row.hasIcons)\r
- {\r
- if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])\r
+ if(column>=row.annotations.length)\r
+ column = row.annotations.length-1;\r
+\r
+ // x ++;\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, x - lastSSX[i],\r
- 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, 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,\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
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4,\r
- 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14 + iconOffset,\r
- y + 8 + iconOffset}, 3);\r
- break;\r
- case 'C':\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[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
- break;\r
- }\r
+ if(!av.wrapAlignment || endRes==av.endRes)\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x*av.charWidth) - lastSSX, 2);\r
\r
- if (validRes)\r
- {\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- }\r
- else\r
- {\r
- lastSS[i] = ' ';\r
+ break;\r
}\r
- lastSSX[i] = x;\r
}\r
- }\r
\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (row.annotations[j].value / row.graphMax) *\r
- GRAPH_HEIGHT);\r
-\r
- if (row.windowLength > 1)\r
+ if (row.graph>0)\r
{\r
- int total = 0;\r
- for (int i2 = j - (row.windowLength / 2);\r
- i2 < j + (row.windowLength / 2); i2++)\r
- {\r
- if (i2 < 0 || i2 >= av.alignment.getWidth())\r
+ if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
{\r
- continue;\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
}\r
+ else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
+ drawBarGraph(g, row, startRes, endRes,\r
+ row.graphMin, row.graphMax, y);\r
+ }\r
\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total /= row.windowLength;\r
- height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\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
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- }\r
+ }\r
+ }\r
+\r
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+ int sRes, int eRes,\r
+ int y,\r
+ float min, float max,\r
+ int graphHeight)\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
+ x+=av.charWidth;\r
+ }\r
\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
+\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
+ while( x < eRes - sRes )\r
+ {\r
+ column = sRes + x;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
}\r
\r
- x += av.charWidth;\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\r
\r
- if (row.hasIcons)\r
+ if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
{\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7,\r
- 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset}\r
- , 3);\r
- break;\r
- case 'C':\r
- break;\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
- break;\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
+\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
+ 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
+ int sRes, int eRes,\r
+ float min, float max,\r
+ int y)\r
+ {\r
+ if(sRes>aa.annotations.length)\r
+ return;\r
+\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\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
+\r
+ g.setColor(Color.gray);\r
+\r
+ g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
+\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 (row.isGraph && row.hasText)\r
+ if(column > aaMax)\r
{\r
- y += av.charHeight;\r
+ break;\r
}\r
- if (!row.isGraph)\r
+\r
+ if (aa.annotations[column] == null)\r
{\r
- y += aa[i].height;\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
+\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
+\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
// 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