/*\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) 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
this.av = av;\r
}\r
\r
- public void renderGaps(boolean b)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void prepare(Graphics g, boolean renderGaps)\r
{\r
- renderGaps = b;\r
+ graphics = g;\r
+ fm = g.getFontMetrics();\r
+\r
+ this.renderGaps = renderGaps;\r
}\r
\r
public Color getResidueBoxColour(SequenceI seq, int i)\r
}\r
else if (av.getShowBoxes())\r
{\r
- getBoxColour(av.globalColourScheme, seq, i);\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
}\r
\r
return resBoxColour;\r
- }\r
+ }\r
\r
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
if (cs != null)\r
{\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);\r
}\r
- else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
+ else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
{\r
- resBoxColour = Color.lightGray;\r
+ resBoxColour = Color.lightGray;\r
}\r
else\r
{\r
public Color findSequenceColour(SequenceI seq, int i)\r
{\r
allGroups = av.alignment.findAllGroups(seq);\r
- drawBoxes(seq, i,i, 0);\r
+ drawBoxes(seq, i, i, 0);\r
return resBoxColour;\r
}\r
\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int y1)\r
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int y1)\r
{\r
- allGroups = sg;\r
-\r
- graphics = g;\r
+ if (seq == null)\r
+ {\r
+ return;\r
+ }\r
\r
- drawBoxes(seq, start, end, y1);\r
+ allGroups = sg;\r
\r
- fm = g.getFontMetrics();\r
- drawText(seq, start, end, y1);\r
+ drawBoxes(seq, start, end, y1);\r
\r
+ if (av.validCharWidth)\r
+ {\r
+ drawText(seq, start, end, y1);\r
+ }\r
}\r
\r
- public void drawBoxes(SequenceI seq, int start, int end, int y1)\r
+ public void drawBoxes(SequenceI seq, int start, int end, int y1)\r
{\r
int i = start;\r
int length = seq.getLength();\r
while (i <= end)\r
{\r
resBoxColour = Color.white;\r
- if(i < length)\r
+ if (i < length)\r
{\r
if (inCurrentSequenceGroup(i))\r
{\r
}\r
}\r
\r
-\r
if (resBoxColour != tempColour)\r
{\r
if (tempColour != null)\r
i++;\r
}\r
\r
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);\r
+ graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,\r
+ av.charHeight);\r
}\r
\r
public void drawText(SequenceI seq, int start, int end, int y1)\r
{\r
+ Font boldFont = null;\r
+ boolean bold = false;\r
+ if (av.upperCasebold)\r
+ {\r
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);\r
+\r
+ graphics.setFont(av.getFont());\r
+ }\r
\r
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady\r
+ y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady\r
\r
int charOffset = 0;\r
\r
// Need to find the sequence position here.\r
- if(end+1>=seq.getLength())\r
- end = seq.getLength()-1;\r
+ if (end + 1 >= seq.getLength())\r
+ {\r
+ end = seq.getLength() - 1;\r
+ }\r
\r
char s = ' ';\r
\r
}\r
}\r
\r
+ if (av.upperCasebold)\r
+ {\r
+ fm = graphics.getFontMetrics();\r
+ if ('A' <= s && s <= 'Z')\r
+ {\r
+ if (!bold)\r
+ {\r
+\r
+ graphics.setFont(boldFont);\r
+ }\r
+ bold = true;\r
+ }\r
+ else if (bold)\r
+ {\r
+ graphics.setFont(av.font);\r
+ bold = false;\r
+ }\r
+\r
+ }\r
+\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
graphics.drawString(String.valueOf(s),\r
- charOffset + av.charWidth * (i - start),\r
- y1 );\r
+ charOffset + av.charWidth * (i - start),\r
+ y1);\r
}\r
\r
}\r
}\r
\r
public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
- int y1, int width, int height)\r
+ int y1)\r
{\r
- int pady = height / 5;\r
+ int pady = av.charHeight / 5;\r
int charOffset = 0;\r
graphics.setColor(Color.black);\r
- graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
+ graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);\r
graphics.setColor(Color.white);\r
\r
char s = '~';\r
// Need to find the sequence position here.\r
- for (int i = start; i <= end; i++)\r
+ if (av.validCharWidth)\r
{\r
- if (i < seq.getLength())\r
+ for (int i = start; i <= end; i++)\r
{\r
- s = seq.getSequence().charAt(i);\r
+ if (i < seq.getLength())\r
+ {\r
+ s = seq.getCharAt(i);\r
+ }\r
+\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + av.charWidth * (i - start),\r
+ y1 + av.charHeight - pady);\r
}\r
+ }\r
+ }\r
+\r
+ public void drawCursor(SequenceI seq, int res, int x1, int y1)\r
+ {\r
+ int pady = av.charHeight / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.black);\r
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);\r
+ graphics.setColor(Color.white);\r
\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.setColor(Color.white);\r
+\r
+ char s = seq.getCharAt(res);\r
+ if (av.validCharWidth)\r
+ {\r
+\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ charOffset + x1,\r
+ (y1 + av.charHeight) - pady);\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff