\r
AlignViewport av;\r
\r
- boolean displaySearch = false;\r
- int[] searchResults = null;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
+ SearchResults searchResults = null;\r
\r
boolean fastPaint = false;\r
\r
\r
+ int cursorX = 0;\r
+ int cursorY = 0;\r
+\r
+\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
\r
}\r
\r
- public void fastPaint(int horizontal, int vertical)\r
+ int lastsr=0;\r
+ void fastPaint(int horizontal, int vertical)\r
{\r
- if (gg == null)\r
+ if ( fastPaint || gg == null)\r
{\r
return;\r
}\r
\r
+\r
+ // Its possible on certain browsers that the call to fastpaint\r
+ // is faster than it can paint, so this check here catches\r
+ // this possibility\r
+ if(lastsr + horizontal != av.startRes)\r
+ {\r
+ horizontal = av.startRes - lastsr;\r
+ }\r
+\r
+ lastsr = av.startRes;\r
+\r
+ fastPaint = true;\r
gg.copyArea(horizontal * av.charWidth,\r
vertical * av.charHeight,\r
- imgWidth,\r
- imgHeight,\r
+ imgWidth - horizontal * av.charWidth,\r
+ imgHeight - vertical * av.charHeight,\r
-horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ -vertical * av.charHeight);\r
+\r
+\r
\r
int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
transX = 0, transY = 0;\r
+\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
transX = (er - sr - horizontal) * av.charWidth;\r
\r
gg.translate(transX, transY);\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);\r
- drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
gg.translate( -transX, -transY);\r
\r
- fastPaint = true;\r
repaint();\r
\r
}\r
\r
public void paint(Graphics g)\r
{\r
- sr.renderGaps(av.renderGaps);\r
\r
if (fastPaint)\r
{\r
}\r
else\r
{\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,\r
- av.startSeq, 0);\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
if (av.scaleLeftWrapped)\r
*/\r
String getMask()\r
{\r
- String mask = "0";\r
+ String mask = "00";\r
for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
{\r
mask += "0";\r
\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(getMask()+"0");\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
int LABEL_WEST = 0;\r
av.endRes = av.startRes + cWidth;\r
\r
\r
- int endx = (startRes + cWidth) - 1;\r
+ int endx;\r
int ypos = hgap;\r
\r
\r
while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
{\r
+ endx = startRes + cWidth;\r
+\r
+ if (endx > al.getWidth())\r
+ {\r
+ endx = al.getWidth();\r
+ }\r
+\r
g.setColor(Color.black);\r
\r
if (av.scaleLeftWrapped)\r
drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
-\r
- if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
- {\r
- endx = av.vconsensus.size() - 2;\r
- }\r
-\r
-\r
if(g.getClip()==null)\r
g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
g.setClip(null);\r
\r
\r
if(annotations==null)\r
annotations = new AnnotationPanel(av);\r
\r
- annotations.drawComponent( g, startRes, endx + 1);\r
+ annotations.drawComponent( g, startRes, endx );\r
g.translate(0, -cHeight - ypos-4);\r
}\r
g.translate(-LABEL_WEST, 0);\r
\r
\r
startRes += cWidth;\r
- endx = (startRes + cWidth) - 1;\r
-\r
- if (endx > al.getWidth())\r
- {\r
- endx = al.getWidth();\r
- }\r
}\r
\r
}\r
return annotations.adjustPanelHeight();\r
}\r
\r
- synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,\r
- int startx, int starty, int offset)\r
+ void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)\r
{\r
\r
g.setFont(av.getFont());\r
SequenceI nextSeq;\r
/// First draw the sequences\r
/////////////////////////////\r
- for (int i = y1; i < y2; i++)\r
+ for (int i = startSeq; i < endSeq; i++)\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- (i - starty) * av.charHeight,\r
- av.charWidth, av.charHeight);\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- (i - starty) * av.charHeight,\r
+ fr.drawSequence(g, nextSeq, startRes, endRes,\r
+ offset + ((i - startSeq) * av.charHeight),\r
av.charWidth, av.charHeight);\r
}\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);\r
+ if (visibleResults != null)\r
+ for (int r = 0; r < visibleResults.length; r += 2)\r
+ {\r
+ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
+ visibleResults[r + 1],\r
+ (visibleResults[r] - startRes) * av.charWidth,\r
+ offset + ( (i - startSeq) * av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
+ }\r
+\r
+ if (av.cursorMode && cursorY == i\r
+ && cursorX >= startRes && cursorX <= endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
+ }\r
+\r
}\r
\r
- /////////////////////////////////////\r
+ //\r
+ /////////////////////////////////////\r
+ // Now outline any areas if necessary\r
+ /////////////////////////////////////\r
+ SequenceGroup group = av.getSelectionGroup();\r
\r
- // Now outline any areas if necessary\r
- /////////////////////////////////////\r
- SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
+ int groupIndex = -1;\r
\r
- int sx = -1, sy = -1, ex = -1;\r
- int groupIndex = -1;\r
- if (group == null && groups.size() > 0)\r
- {\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ if ((group == null) && (av.alignment.getGroups().size() > 0))\r
+ {\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
groupIndex = 0;\r
- }\r
- if (group != null)\r
- {\r
- do\r
- {\r
- int oldY = -1;\r
- int i = 0;\r
- boolean inGroup = false;\r
- int top = -1;\r
- int bottom = -1;\r
+ }\r
\r
- for (i = y1; i < y2; i++)\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
+ if ( group != null)\r
+ {\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
\r
- if(sx+ex<0 || sx>imgWidth)\r
- {\r
- continue;\r
- }\r
+ for (i = startSeq; i < endSeq; i++)\r
+ {\r
+ sx = (group.getStartRes() - startRes) * av.charWidth;\r
+ sy = offset + ((i - startSeq) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
+ 1;\r
\r
- if ( (sx <= (x2-x1)*av.charWidth) &&\r
- group.sequences.contains(av.alignment.getSequenceAt(\r
- i)))\r
+ if(sx+ex<0 || sx>imgWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
+ {\r
+ if (bottom == -1)\r
{\r
+ if(i == endSeq-1 || // Dont check for i+1 if on the bottom row\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
\r
- if (bottom == -1)\r
- {\r
- if(i == y2-1 || // Dont check for i+1 if on the bottom row\r
- !group.sequences.contains(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
-\r
- g.setColor(Color.red);\r
- }\r
- else\r
- {\r
- g.setColor(group.getOutlineColour());\r
- }\r
- }\r
+ bottom = sy + av.charHeight;\r
}\r
- else\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
+ if (inGroup)\r
{\r
- if (inGroup)\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
- 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
+ ex += sx;\r
+ sx = 0;\r
+ }\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
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
\r
- if (sx + ex < imgWidth)\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
\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
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\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
}\r
+ }\r
\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
- }\r
+ if (inGroup)\r
+ {\r
+ sy = offset + ( (i - startSeq) * 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
- inGroup = false;\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
}\r
\r
- groupIndex++;\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
\r
- if (groupIndex >= groups.size())\r
+ if (top != -1)\r
{\r
- break;\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
}\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
- }\r
- while (groupIndex < groups.size());\r
- }\r
-\r
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if (displaySearch)\r
- {\r
- for (int r = 0; r < searchResults.length; r += 3)\r
- {\r
- int searchSeq = searchResults[r];\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
\r
- if (searchSeq >= y1 && searchSeq < y2)\r
- {\r
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
+ inGroup = false;\r
+ }\r
\r
- int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
- int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
+ groupIndex++;\r
\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if (searchStart < x1)\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
{\r
- searchStart = x1;\r
- }\r
- if (searchEnd > x2)\r
- {\r
- searchEnd = x2;\r
+ break;\r
}\r
\r
- ssr.drawHighlightedText(seq,\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- (searchSeq-starty)*av.charHeight,\r
- av.charWidth,\r
- av.charHeight);\r
- }\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
}\r
+ while (groupIndex < av.alignment.getGroups().size());\r
}\r
-\r
}\r
\r
- public void highlightSearchResults(int[] results)\r
+ public void highlightSearchResults(SearchResults results)\r
{\r
- // results are in the order sequence, startRes, endRes\r
- if (results == null)\r
- {\r
- displaySearch = false;\r
- }\r
- else\r
- {\r
- displaySearch = true;\r
- }\r
-\r
searchResults = results;\r
\r
repaint();\r
git://source.jalview.org / jalview.git / blobdiff