\r
import java.awt.*;\r
import javax.swing.*;\r
-import java.util.*;\r
+import java.awt.event.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
import jalview.analysis.*;\r
int imgHeight;\r
\r
AlignViewport av;\r
- int pady = 2;\r
- int oldstartx;\r
- int oldstarty;\r
- int oldendx;\r
- int oldendy;\r
\r
public boolean paintFlag = false;\r
+\r
boolean showScores = false;\r
+ boolean displaySearch = false;\r
+ int [] searchResults = null;\r
\r
int chunkHeight;\r
int chunkWidth;\r
\r
- Graphics debugG;\r
- FeatureRenderer fr = new FeatureRenderer();\r
- BlockRenderer br = new BlockRenderer();\r
- CpGRenderer cgr = new CpGRenderer();\r
-\r
- ColourSchemeI cs = new ZappoColourScheme();\r
\r
public SeqCanvas(AlignViewport av)\r
{\r
this.av = av;\r
setLayout(new BorderLayout());\r
+\r
}\r
\r
- public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) {\r
+ public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {\r
int scalestartx = startx - startx%10 + 10;\r
\r
gg.setColor(Color.black);\r
*/\r
\r
public void paintComponent(Graphics g) {\r
- debugG = g;\r
\r
AlignmentI da = av.getAlignment();\r
\r
if (img == null ||\r
imgWidth != getWidth() ||\r
- imgHeight != getHeight() ||\r
- paintFlag == true) {\r
+ imgHeight != getHeight()\r
+ || paintFlag)\r
+ {\r
\r
- imgWidth = (getWidth() > 0 ? getWidth() : 1);\r
- imgHeight = (getHeight() > 0 ? getHeight() : 1);\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
\r
img = createImage(imgWidth,imgHeight);\r
gg = img.getGraphics();\r
\r
- // SMJS I added this in to update the AV when the size changes\r
- // until I figure out how this should be done\r
- setFont(av.getFont());\r
-\r
gg.setFont(av.getFont());\r
\r
paintFlag = false;\r
-\r
- oldstartx = -1;\r
- oldendx = -1;\r
- oldstarty = -1;\r
- oldendy = -1;\r
}\r
\r
- int startx = av.getStartRes();\r
- int starty = av.getStartSeq();\r
-\r
- int endx = av.getEndRes();\r
- int endy = av.getEndSeq();\r
-\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
-\r
- chunkWidth = (int)(getWidth()/charWidth);\r
- chunkHeight = (da.getHeight() + 2)*charHeight;\r
+ chunkWidth = getWidth()/av.charWidth;\r
+ chunkHeight = (da.getHeight() + 2)*av.charHeight;\r
\r
av.setChunkHeight(chunkHeight);\r
av.setChunkWidth(chunkWidth);\r
\r
- int offy = av.getStartSeq();\r
\r
- if (oldendx == -1) {\r
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
\r
- /* if (av.getWrapAlignment() == true) {\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
}\r
\r
}\r
- } else*/ {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
- oldstarty = starty;\r
- oldendy = endy;\r
-\r
- }\r
- }\r
-\r
- else if (oldstartx < startx)\r
- {\r
- // This is dragging horizontal scrollbar to the right\r
-\r
- int delx = (int)((startx - oldstartx) * charWidth);\r
- int delx2 = (int)((oldendx - startx + 1) * charWidth);\r
-\r
- gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);\r
-\r
- if (startx > oldendx)\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- else\r
- drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0);\r
-\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
-\r
- } else if (oldstartx > startx)\r
- {\r
- // Horizontal scrollbar pulled to the left\r
-\r
- int delx = (int)((oldstartx - startx) * charWidth);\r
- int delx2 = (int)((endx - oldstartx +1) * charWidth);\r
-\r
- gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);\r
-\r
- if (oldstartx > endx) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0);\r
}\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
-\r
- } else if (oldstarty < starty) {\r
- // Vertical scrollbar down\r
- int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);\r
-\r
- gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely);\r
-\r
- if (starty > oldendy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0);\r
+ else*/\r
+ {\r
+ drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);\r
}\r
\r
- oldstarty = starty;\r
- oldendy = endy;\r
-\r
- } else if (oldstarty > starty) {\r
-\r
- // Vertical scrollbar up\r
- int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);\r
\r
- gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);\r
-\r
- if (oldstarty > endy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);\r
- }\r
-\r
- oldstarty = starty;\r
- oldendy = endy;\r
- }\r
-\r
- if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {\r
+ /* if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {\r
System.out.println("LIMITS ERROR LIMITS ERROR");\r
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
- }\r
-\r
+ System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
+ }*/\r
\r
g.drawImage(img,0,0,this);\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
- System.out.println("drawPanel called with g = " + g);\r
- System.out.println(" x1 = " + x1);\r
- System.out.println(" x2 = " + x2);\r
- System.out.println(" y1 = " + y1);\r
- System.out.println(" y2 = " + y2);\r
- System.out.println(" startx = " + startx);\r
- System.out.println(" starty = " + starty);\r
-*/\r
\r
g.setFont(av.getFont());\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
-\r
- // Vector pid = av.calcNewConsensus();\r
-\r
+ int charWidth = av.getCharWidth();\r
+ int charHeight = av.getCharHeight();\r
RendererI sr = av.getRenderer();\r
\r
-/* Vector tmpseq = new Vector();\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++) {\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
+ /*Vector pid = av.getConsensus(false);\r
+ Vector tmpseq = new Vector();\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
- }\r
- }\r
\r
- if (sr instanceof SequenceRenderer) {\r
+ if (sr instanceof SequenceRenderer)\r
pid = AAFrequency.calculate(tmpseq,x1,x2);\r
\r
- } else if (sr instanceof GraphRenderer) {\r
+ else if (sr instanceof GraphRenderer)\r
pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
av.getAlignment().getSequences(),\r
av.getPIDWindow(),x1,x2);\r
\r
- }*/\r
-\r
- if (y2 > starty && y1 < av.getEndSeq()) {\r
+*/\r
\r
- fillBackground(g,\r
- Color.white,\r
- (int)((x1-startx)*charWidth),\r
+ if (y2 > starty && y1 < av.getEndSeq())\r
+ {\r
+ fillBackground(g,\r
+ Color.red,\r
+ (x1-startx)*charWidth,\r
offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),\r
- (int)((x2-x1+1)*charWidth),\r
+ (x2-x1+1)*charWidth,\r
offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));\r
}\r
\r
- for (int i = y1 ; i < y2 ;i++) {\r
-\r
- RendererI r = sr;\r
-\r
- /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
- r = fr;\r
- System.out.println("use feature renderer");\r
- // } else if ( i == 0) {\r
- // r = br;\r
- } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
- r = cgr;\r
- System.out.println("cg renderer");\r
- }*/\r
-\r
- r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),\r
- x1,\r
- x2,\r
- (int)((x1-startx)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()),\r
- charWidth,\r
- charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av);\r
+ SequenceI nextSeq;\r
+ SequenceGroup group=null;\r
+ boolean newGroup=false;\r
+ int sx=-1, sy=-1, ex=-1, ey=-1;\r
+ int oldStartX=0,oldEndX=0,oldY=0;\r
+ for (int i = y1 ; i < y2 ;i++)\r
+ {\r
+ nextSeq = av.getAlignment().getSequenceAt(i);\r
+ if(group==null || group!=av.alignment.findGroup( nextSeq ))\r
+ newGroup = true;\r
+ else\r
+ newGroup = false;\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
+\r
+\r
+ if( group!=null )\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
+\r
+\r
+ if (newGroup)\r
+ {\r
+ g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box\r
+ g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\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
+ oldStartX = sx;\r
+ oldEndX = ex;\r
+ oldY = ey;\r
+\r
+ }\r
+ else if(sx>-1)\r
+ {\r
+ g.setColor(Color.lightGray);\r
+ g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box\r
+ }\r
+\r
+ group = av.getRubberbandGroup();\r
+ if( group !=null && group.sequences.contains(nextSeq) )\r
+ {\r
+ g.setColor(Color.red);\r
+\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 (newGroup)\r
+ {\r
+ g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box\r
+ g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\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
+ // oldStartX = sx;\r
+ // oldEndX = ex;\r
+ // oldY = ey;\r
+\r
+ }\r
\r
}\r
- }\r
\r
+ /// Highlight search Results once all sequences have been drawn\r
+ if(displaySearch)\r
+ {\r
+ for(int r=0; r<searchResults.length; r+=3)\r
+ {\r
+ int searchSeq = searchResults[r];\r
+ int searchStart = searchResults[r+1];\r
+ int searchEnd = searchResults[r+2];\r
+\r
+ if (searchSeq >= y1 && searchSeq <= y2)\r
+ {\r
+ SequenceRenderer ssr = (SequenceRenderer) sr;\r
+ ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),\r
+ searchStart,\r
+ searchEnd,\r
+ (searchStart - startx) * charWidth,\r
+ offset +\r
+ AlignmentUtil.getPixelHeight(starty, searchSeq,\r
+ charHeight),\r
+ charWidth,\r
+ 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
return chunkWidth;\r
}\r
\r
+ public void highlightSearchResults(int [] results)\r
+ {\r
+ // results are in the order sequence, startRes, endRes\r
+ if(results==null)\r
+ displaySearch = false;\r
+ else\r
+ displaySearch = true;\r
+\r
+ searchResults = results;\r
+\r
+ paintFlag = true;\r
+ repaint();\r
+ }\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff