+ int x = 0, 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
+\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
+ continue;\r
+ }\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
+ y -= av.charHeight;\r
+ }\r
+ }\r
+\r
+ if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
+ {\r
+ y += av.charHeight;\r
+\r
+ g.drawImage(fadedImage,\r
+ 0,y-row.height,imgWidth, y,\r
+ 0,y-row.height,imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+\r
+\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2 + 4;\r
+ }\r
+ else\r
+ {\r
+ iconOffset = 0;\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
+\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 (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\r
+\r
+ if (av.getColumnSelection() != null)\r
+ {\r
+ for (int n = 0; n < av.getColumnSelection().size(); n++)\r
+ {\r
+ int v = av.getColumnSelection().columnAt(n);\r
+\r
+ if (v == column)\r
+ {\r
+ g.fillRect(x * av.charWidth, y,\r
+ av.charWidth, av.charHeight);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\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 );\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 );\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
+ 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
+ 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
+\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+1) * 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
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (row.graph>0 && row.graphHeight>0)\r
+ {\r
+ if(row.graph == AlignmentAnnotation.LINE_GRAPH )\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
+ }\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
+\r
+ if (row.graph==0)\r
+ {\r
+ y += aa[i].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