\r
import java.awt.*;\r
\r
-import jalview.analysis.*;\r
import jalview.datamodel.*;\r
\r
public class SeqCanvas\r
\r
AlignViewport av;\r
\r
- boolean showScores = false;\r
boolean displaySearch = false;\r
int[] searchResults = null;\r
\r
\r
boolean fastPaint = false;\r
\r
+ boolean isOverview = false;\r
+\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
}\r
if (value != -1)\r
{\r
- int x = LABEL_WEST - fm.stringWidth(value + "");\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
g.drawString(value + "", x,\r
ypos + i * av.charHeight - av.charHeight / 5);\r
}\r
}\r
if (value != -1)\r
{\r
- g.drawString(value + "", 0,\r
+ g.drawString(value + "", av.charWidth/2,\r
ypos + i * av.charHeight - av.charHeight / 5);\r
}\r
}\r
\r
public void fastPaint(int horizontal, int vertical)\r
{\r
- if (horizontal == 0 && vertical == 0 || gg == null)\r
+ if (gg == null)\r
{\r
return;\r
}\r
\r
public void paint(Graphics g)\r
{\r
+ sr.renderGaps(av.renderGaps);\r
+\r
if (fastPaint)\r
{\r
g.drawImage(img, 0, 0, this);\r
\r
if (av.getWrapAlignment())\r
{\r
- drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);\r
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
}\r
else\r
{\r
int LABEL_WEST, LABEL_EAST;\r
public int getWrappedCanvasWidth(int cwidth)\r
{\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
- }\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+ }\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
- }\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
\r
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
\r
+\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * @return String\r
+ */\r
+ String getMask()\r
+ {\r
+ String mask = "0";\r
+ for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
+ }\r
+\r
public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
int startRes)\r
{\r
\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- int LABEL_EAST = 0;\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+ LABEL_EAST = fm.stringWidth(getMask()+"0");\r
}\r
+\r
int LABEL_WEST = 0;\r
+\r
if (av.scaleLeftWrapped)\r
{\r
- LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
\r
if (av.scaleRightWrapped)\r
{\r
- g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+ g.translate( - (canvasWidth - LABEL_EAST), 0);\r
}\r
\r
g.translate(LABEL_WEST, 0);\r
drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
- // When printing we have an extra clipped region,\r
- // the Printable page which we need to account for here\r
- Shape clip = g.getClip();\r
- if (clip == null)\r
- {\r
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
- }\r
- else\r
- {\r
- g.setClip(0,\r
- (int) clip.getBounds().y,\r
- cWidth * av.charWidth,\r
- (int) clip.getBounds().height\r
- );\r
- }\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
+ if(g.getClip()==null)\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+\r
+ if (av.alignment.getWidth() >= av.vconsensus.size())\r
+ {\r
+ endx = av.vconsensus.size() - 2;\r
+ }\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ g.setClip(null);\r
g.translate( -LABEL_WEST, 0);\r
\r
ypos += cHeight;\r
sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
(x1 - startx) * av.charWidth,\r
offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ (i-starty)*av.charHeight,\r
av.charWidth, av.charHeight);\r
\r
if (av.showSequenceFeatures)\r
fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
(x1 - startx) * av.charWidth,\r
offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ (i-starty)*av.charHeight,\r
av.charWidth, av.charHeight);\r
}\r
}\r
groupIndex = 0;\r
}\r
\r
- if (group != null)\r
+ if (group != null && !isOverview)\r
{\r
do\r
{\r
- int oldY = -1;\r
- int i = 0;\r
- boolean inGroup = false;\r
- int top = -1, bottom = -1;\r
- for (i = y1; i < y2; i++)\r
- {\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
\r
- if (sx < getSize().width\r
- && ex > 0\r
- && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
+ for (i = y1; i < y2; i++)\r
{\r
- if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||\r
- !group.sequences.contains(av.alignment.\r
- getSequenceAt(i + 1))))\r
- {\r
- bottom = sy + av.charHeight;\r
- }\r
+ sx = (group.getStartRes() - startx) * av.charWidth;\r
+ sy = offset + ((i - starty) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
+ 1;\r
\r
- if (!inGroup)\r
- {\r
- if (top == -1 && i == 0 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
+ if(sx+ex<0 || sx>imgWidth)\r
{\r
- top = sy;\r
+ continue;\r
}\r
\r
- oldY = sy;\r
- inGroup = true;\r
- if (group == av.getSelectionGroup())\r
+ if ( (sx <= (x2-x1)*av.charWidth) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
{\r
- g.setColor(new Color(255, 0, 0));\r
+ if ((bottom == -1) &&\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i + 1)))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (((top == -1) && (i == 0)) ||\r
+ !group.sequences.contains(\r
+ av.alignment.getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
}\r
else\r
{\r
- g.setColor(group.getOutlineColour());\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
}\r
- }\r
}\r
- else\r
+\r
+ if (inGroup)\r
{\r
- if (inGroup)\r
- {\r
+ sy = offset + ( (i - starty) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
\r
- inGroup = false;\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
}\r
- }\r
- }\r
\r
- if (inGroup)\r
- {\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
+ inGroup = false;\r
}\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
\r
- }\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
- inGroup = false;\r
- }\r
- groupIndex++;\r
- if (groupIndex >= groups.size())\r
- {\r
- break;\r
- }\r
+ groupIndex++;\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ if (groupIndex >= groups.size())\r
+ {\r
+ break;\r
+ }\r
\r
+ group = (SequenceGroup) groups.elementAt(groupIndex);\r
}\r
while (groupIndex < groups.size());\r
}\r
searchEnd,\r
(searchStart - startx) * av.charWidth,\r
offset +\r
- AlignmentUtil.getPixelHeight(starty,\r
- searchSeq,\r
- av.charHeight),\r
+ (searchSeq-starty)*av.charHeight,\r
av.charWidth,\r
av.charHeight);\r
}\r