\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 displaySearch = false;\r
- int[] searchResults = null;\r
+ SearchResults searchResults = null;\r
\r
int chunkHeight;\r
int chunkWidth;\r
\r
boolean fastPaint = false;\r
\r
+\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
fr = new FeatureRenderer(av);\r
sr = new SequenceRenderer(av);\r
PaintRefresher.Register(this, av.alignment);\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
}\r
\r
+ MCview.AppletPDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.AppletPDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
+\r
void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
{\r
int scalestartx = startx - startx % 10 + 10;\r
\r
public void fastPaint(int horizontal, int vertical)\r
{\r
- if (horizontal == 0 && vertical == 0 || gg == null)\r
+ if (fastPaint || gg == null)\r
{\r
+ repaint();\r
return;\r
}\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ fastPaint = true;\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth,\r
+ imgHeight,\r
+ -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\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
gg.translate( -transX, -transY);\r
\r
- fastPaint = true;\r
repaint();\r
\r
}\r
\r
public void paint(Graphics g)\r
{\r
+\r
if (fastPaint)\r
{\r
g.drawImage(img, 0, 0, this);\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- chunkWidth = getWrappedCanvasWidth(getSize().width);\r
- chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\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
\r
g.drawImage(img, 0, 0, this);\r
\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
}\r
\r
int LABEL_WEST, LABEL_EAST;\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
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
+ int LABEL_EAST = 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
LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
+ int hgap = av.charHeight;\r
+ if(av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+\r
+ av.setWrappedWidth(cWidth);\r
\r
av.endRes = av.startRes + cWidth;\r
\r
- int endx = startRes + cWidth - 1;\r
- int ypos = 2 * av.charHeight;\r
\r
- while (ypos <= canvasHeight && startRes < av.alignment.getWidth())\r
+ int endx = (startRes + cWidth) - 1;\r
+ int ypos = hgap;\r
+\r
+\r
+ while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
{\r
- g.setColor(Color.black);\r
+ g.setColor(Color.black);\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- drawWestScale(g, startRes, endx, ypos);\r
- }\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST), 0);\r
- }\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
+ }\r
\r
- g.translate(LABEL_WEST, 0);\r
- if (av.scaleAboveWrapped)\r
- {\r
- drawNorthScale(g, startRes, endx, ypos);\r
- }\r
+ g.translate(LABEL_WEST, 0);\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
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
- g.translate( -LABEL_WEST, 0);\r
\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = startRes + cWidth - 1;\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
+ g.setClip(null);\r
+\r
+\r
+ if(av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos+4);\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
+\r
+ annotations.drawComponent( g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos-4);\r
+ }\r
+ g.translate(-LABEL_WEST, 0);\r
+\r
+ ypos += cHeight+getAnnotationHeight()+hgap;\r
\r
- if (endx > al.getWidth())\r
- {\r
- endx = al.getWidth();\r
- }\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
\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if(!av.showAnnotation)\r
+ return 0;\r
+\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\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
{\r
sr.renderGaps(av.renderGaps);\r
\r
SequenceI nextSeq;\r
-\r
/// First draw the sequences\r
- /////////////////////////////\r
- for (int i = y1; i < y2; i++)\r
- {\r
- nextSeq = av.alignment.getSequenceAt(i);\r
+ /////////////////////////////\r
+ for (int i = y1; i < y2; 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
\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.drawSequence(g, nextSeq, x1, x2,\r
(x1 - startx) * av.charWidth,\r
offset +\r
- (i-starty)*av.charHeight,\r
+ (i - starty) * av.charHeight,\r
av.charWidth, 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
- av.charWidth, av.charHeight);\r
- }\r
}\r
- //\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, x1, x2);\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] - startx) * av.charWidth,\r
+ offset + ( (i - starty) * av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
+ }\r
+ }\r
+\r
/////////////////////////////////////\r
\r
// Now outline any areas if necessary\r
group = (SequenceGroup) groups.elementAt(0);\r
groupIndex = 0;\r
}\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, bottom = -1;\r
- for (i = y1; i < y2; i++)\r
+ do\r
{\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + (i-starty)*av.charHeight;\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;\r
-\r
- if (sx < getSize().width\r
- && ex > 0\r
- && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||\r
- !group.sequences.contains(av.alignment.\r
- getSequenceAt(i + 1))))\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
+\r
+ for (i = y1; i < y2; i++)\r
{\r
- bottom = sy + av.charHeight;\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(sx+ex<0 || sx>imgWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ( (sx <= (x2-x1)*av.charWidth) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
+ {\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
+ }\r
+ else\r
+ {\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
- if (!inGroup)\r
+ if (inGroup)\r
{\r
- if (top == -1 && i == 0 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
- {\r
- top = sy;\r
- }\r
+ sy = offset + ( (i - starty) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
\r
- oldY = sy;\r
- inGroup = true;\r
- if (group == av.getSelectionGroup())\r
- {\r
- g.setColor(new Color(255, 0, 0));\r
- }\r
- else\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
{\r
- g.setColor(group.getOutlineColour());\r
+ ex += sx;\r
+ sx = 0;\r
}\r
- }\r
- }\r
- else\r
- {\r
- if (inGroup)\r
- {\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\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
\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
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
bottom = -1;\r
}\r
\r
- inGroup = false;\r
+ inGroup = false;\r
}\r
- }\r
- }\r
-\r
- if (inGroup)\r
- {\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 - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
-\r
- }\r
- sy = offset + (i-starty)*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
-\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
-\r
- }\r
- while (groupIndex < groups.size());\r
- }\r
+ groupIndex++;\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 (groupIndex >= groups.size())\r
+ {\r
+ break;\r
+ }\r
\r
- if (searchSeq >= y1 && searchSeq < y2)\r
- {\r
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
-\r
- int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
- int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
-\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if (searchStart < x1)\r
- {\r
- searchStart = x1;\r
- }\r
- if (searchEnd > x2)\r
- {\r
- searchEnd = x2;\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
+ group = (SequenceGroup) groups.elementAt(groupIndex);\r
}\r
- }\r
+ while (groupIndex < groups.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