\r
import java.awt.*;\r
import javax.swing.*;\r
-import java.awt.event.*;\r
import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
import jalview.analysis.*;\r
\r
\r
public class SeqCanvas extends JPanel\r
{\r
+ FeatureRenderer fr;\r
Image img;\r
- Graphics gg;\r
+ Graphics2D gg;\r
int imgWidth;\r
int imgHeight;\r
\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
+ fr = new FeatureRenderer(av);\r
setLayout(new BorderLayout());\r
PaintRefresher.Register(this);\r
\r
}\r
\r
- public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {\r
+ public void drawScale(Graphics g, int startx, int endx,int ypos) {\r
int scalestartx = startx - startx%10 + 10;\r
\r
- gg.setColor(Color.black);\r
+ g.setColor(Color.black);\r
+\r
+ for (int i=scalestartx;i < endx;i+= 10)\r
+ {\r
+ String string = String.valueOf(i);\r
+ g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);\r
+\r
+ g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,\r
+ (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );\r
\r
- for (int i=scalestartx;i < endx;i+= 10) {\r
- String string = String.valueOf(i);\r
- gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));\r
}\r
+\r
}\r
\r
\r
* in the adjustment listener in SeqPanel when the scrollbars move.\r
*/\r
\r
- public void paintComponent(Graphics g) {\r
-\r
- AlignmentI da = av.getAlignment();\r
+ public void paintComponent(Graphics g)\r
+ {\r
\r
- if (img == null ||\r
- imgWidth != getWidth() ||\r
- imgHeight != getHeight()\r
- || paintFlag)\r
+ if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)\r
{\r
-\r
imgWidth = getWidth();\r
imgHeight = getHeight();\r
-\r
img = createImage(imgWidth,imgHeight);\r
- gg = img.getGraphics();\r
-\r
+ gg = (Graphics2D)img.getGraphics();\r
gg.setFont(av.getFont());\r
-\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
paintFlag = false;\r
}\r
\r
+\r
chunkWidth = getWidth()/av.charWidth;\r
- chunkHeight = (da.getHeight() + 2)*av.charHeight;\r
+ chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
\r
av.setChunkHeight(chunkHeight);\r
av.setChunkWidth(chunkWidth);\r
\r
+ gg.setColor(Color.WHITE);\r
+ gg.fillRect(0,0,imgWidth,imgHeight);\r
\r
+ if (av.getWrapAlignment())\r
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+ else\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
\r
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
-\r
- /* if (av.getWrapAlignment()) {\r
- int offy = av.getStartSeq();\r
- startx = (int)(offy/chunkWidth)*chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = offy%chunkHeight;\r
- endy = starty + da.getHeight();\r
-\r
- int ypos = 0;\r
- int rowstart = starty;\r
-\r
- if (starty == 0) {\r
- ypos = 2*charHeight;\r
- } else if (starty == 1) {\r
- starty = 0;\r
- ypos = charHeight;\r
- }\r
-\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
-\r
- if (rowstart < 2) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- }\r
-\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);\r
-\r
- if (rowstart == 0) {\r
- ypos = ypos + chunkHeight;\r
- } else if (rowstart == 1) {\r
- ypos = ypos + chunkHeight;\r
- } else {\r
- ypos = ypos + chunkHeight - rowstart*charHeight;\r
- }\r
-\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = 0;\r
\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
- // Draw the rest of the panels\r
+ g.drawImage(img,0,0,this);\r
\r
- while (ypos <= getHeight()) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);\r
+ }\r
\r
- ypos += chunkHeight;\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+ {\r
+ AlignmentI da = av.getAlignment();\r
\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
+ int cWidth = canvasWidth/av.charWidth;\r
+ int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
+ int endx = startRes+cWidth-1;\r
+ int ypos = 2*av.charHeight;\r
\r
- }\r
- }\r
- else*/\r
+ while (ypos <= canvasHeight)\r
{\r
- drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);\r
- }\r
-\r
+ drawScale(g, startRes, endx, ypos);\r
+ drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);\r
\r
- /* if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {\r
- System.out.println("LIMITS ERROR LIMITS ERROR");\r
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
- }*/\r
+ ypos += cHeight;\r
+ startRes += cWidth;\r
+ endx = startRes + cWidth - 1;\r
\r
- g.drawImage(img,0,0,this);\r
+ if (endx > da.getWidth())\r
+ endx = da.getWidth();\r
+ }\r
\r
}\r
\r
\r
+ public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
\r
\r
- public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
-\r
-\r
+ Graphics2D g = (Graphics2D)g1;\r
g.setFont(av.getFont());\r
- int charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
RendererI sr = av.getRenderer();\r
\r
/*Vector pid = av.getConsensus(false);\r
}*/\r
\r
SequenceI nextSeq;\r
- SequenceGroup group=null;\r
- boolean inGroup=false; // are we in a defined group?\r
- boolean inRB=false; //Are we in a rubberband group?\r
- int sx=-1, sy=-1, ex=-1, ey=-1;\r
- int oldStartX=0,oldEndX=0,oldY=0;\r
- int oldRStartX=0,oldREndX=0,oldRY=0;\r
+\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
for (int i = y1 ; i < y2 ;i++)\r
{\r
nextSeq = av.getAlignment().getSequenceAt(i);\r
\r
- group = av.alignment.findGroup( nextSeq );\r
-\r
- sr.drawSequence(g, nextSeq, group,x1,x2,\r
- (x1 - startx) * charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth,charHeight,null, i);\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth,av.charHeight,null, i);\r
\r
-\r
- if( group!=null )\r
+ if(av.showSequenceFeatures)\r
{\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
+ av.charWidth, av.charHeight, null, i);\r
+ }\r
+ }\r
+ //\r
+ /////////////////////////////////////\r
\r
- g.setColor(Color.lightGray);\r
-\r
- sx = (group.getStartRes()-startx)*charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());\r
- ex = (group.getEndRes()+1-startx)*charWidth;\r
- ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());\r
+ // Now outline any areas if necessary\r
+ /////////////////////////////////////\r
+ SequenceGroup group = av.getSelectionGroup();\r
+ java.util.Vector groups = av.alignment.getGroups();\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
+ groupIndex = 0;\r
+ }\r
\r
- if (!inGroup)\r
+ if (group != null)\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ for (i = y1; i < y2; i++)\r
{\r
- g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\r
- inGroup=true;\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;\r
+\r
+ if (group.sequences.contains(av.alignment.getSequenceAt(i))\r
+ && sx < getWidth()\r
+ && ex > 0)\r
+ {\r
+ if (!inGroup)\r
+ {\r
+ oldY = sy;\r
+ inGroup = true;\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(2, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,2f,2f}, 0f ));\r
+ g.setColor(Color.RED);\r
+ }\r
+ else\r
+ {\r
+ g.setStroke(new BasicStroke());\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ g.drawRect(sx, oldY, ex, (sy - oldY));\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
+ if (inGroup)\r
+ {\r
+ sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ g.drawRect(sx, oldY, ex, (sy - oldY));\r
+ inGroup = false;\r
}\r
\r
- g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side\r
- g.drawLine( ex,sy,ex,ey); // vertical line, right hand side\r
- if (i == y2 - 1)// last line of alignment, seal the box\r
- g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box\r
+ groupIndex++;\r
+ if (groupIndex >= groups.size())\r
+ break;\r
\r
- oldStartX = sx;\r
- oldEndX = ex;\r
- oldY = ey;\r
+ group = (SequenceGroup) groups.elementAt(groupIndex);\r
\r
- }\r
- else if(inGroup)\r
- {\r
- g.setColor(Color.lightGray);\r
- g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box\r
- }\r
- else\r
- inGroup = false;\r
-\r
- group = av.getRubberbandGroup();\r
- if( group != null && group.sequences.contains(nextSeq) )\r
- {\r
- g.setColor(Color.RED.brighter());\r
- sx = (group.getStartRes() - startx) * charWidth;\r
- sy = offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());\r
- ex = (group.getEndRes() + 1 - startx) * charWidth;\r
- ey = offset +\r
- AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());\r
-\r
- if (!inRB)\r
- {\r
-\r
- g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\r
- inRB = true;\r
- }\r
-\r
- g.drawLine(sx, sy, sx, ey); // vertical line, left hand side\r
- g.drawLine(ex, sy, ex, ey); // vertical line, right hand side\r
- if (i == y2 - 1) // last line of alignment, seal the box\r
- g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box\r
-\r
- oldRStartX = sx;\r
- oldREndX = ex;\r
- oldRY = ey;\r
- }\r
- else if(inRB)\r
- {\r
- g.setColor(Color.RED.brighter());\r
- g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box\r
- inRB = false;\r
- }\r
- else\r
- inRB = false;\r
+ }\r
+ while (groupIndex < groups.size());\r
\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
int searchStart = searchResults[r+1];\r
int searchEnd = searchResults[r+2];\r
\r
- if (searchSeq >= y1 && searchSeq <= y2)\r
+ if (searchSeq >= y1 && searchSeq < y2)\r
{\r
SequenceRenderer ssr = (SequenceRenderer) sr;\r
- ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),\r
+ ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
searchStart,\r
searchEnd,\r
- (searchStart - startx) * charWidth,\r
+ (searchStart - startx) * av.charWidth,\r
offset +\r
AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- charHeight),\r
- charWidth,\r
- charHeight);\r
+ av.charHeight),\r
+ av.charWidth,\r
+ av.charHeight);\r
}\r
}\r
}\r
\r
}\r
\r
- public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {\r
- g.setColor(c);\r
- g.fillRect(x1,y1,width,height);\r
- }\r
\r
public int getChunkWidth() {\r
return chunkWidth;\r
git://source.jalview.org / jalview.git / blobdiff