X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c33f3ed371da55393dac4948cb9c8679fd06c619;hb=9ee6d0820f9b6b253900b00da9b1531f9b40e057;hp=00b4e954f52b9a614f6eec87a7ae011260ca57a3;hpb=a11e13d8fffacf8115a4d83e4254bf94a87d6600;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 00b4e95..c33f3ed 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -10,18 +10,14 @@ import jalview.analysis.*; public class SeqCanvas extends JPanel { - ColourSchemeI globalColorScheme = null; + FeatureRenderer fr; Image img; Graphics gg; int imgWidth; int imgHeight; AlignViewport av; - int pady = 2; - int oldstartx; - int oldstarty; - int oldendx; - int oldendy; + public boolean paintFlag = false; boolean showScores = false; @@ -35,19 +31,27 @@ public class SeqCanvas extends JPanel public SeqCanvas(AlignViewport av) { this.av = av; + fr = new FeatureRenderer(av); setLayout(new BorderLayout()); + PaintRefresher.Register(this); } - public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) { + public void drawScale(Graphics g, int startx, int endx,int ypos) { int scalestartx = startx - startx%10 + 10; - gg.setColor(Color.black); + g.setColor(Color.black); + + for (int i=scalestartx;i < endx;i+= 10) + { + String string = String.valueOf(i); + g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2); + + g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2, + (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 ); - for (int i=scalestartx;i < endx;i+= 10) { - String string = String.valueOf(i); - gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2)); } + } @@ -62,244 +66,72 @@ public class SeqCanvas extends JPanel * in the adjustment listener in SeqPanel when the scrollbars move. */ - public void paintComponent(Graphics g) { - - AlignmentI da = av.getAlignment(); + public void paintComponent(Graphics g) + { - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() - || paintFlag) + if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag) { - - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); - + imgWidth = getWidth(); + imgHeight = getHeight(); img = createImage(imgWidth,imgHeight); gg = img.getGraphics(); - gg.setFont(av.getFont()); - - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; paintFlag = false; } - int startx = av.getStartRes(); - int starty = av.getStartSeq(); - - int endx = av.getEndRes(); - int endy = av.getEndSeq(); - - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - chunkWidth = getWidth()/charWidth; - chunkHeight = (da.getHeight() + 2)*charHeight; + chunkWidth = getWidth()/av.charWidth; + chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); - int offy = av.getStartSeq(); + fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - - if (av.getWrapAlignment()) { - startx = (int)(offy/chunkWidth)*chunkWidth; - endx = startx + chunkWidth; - starty = offy%chunkHeight; - endy = starty + da.getHeight(); - - int ypos = 0; - int rowstart = starty; - - if (starty == 0) { - ypos = 2*charHeight; - } else if (starty == 1) { - starty = 0; - ypos = charHeight; - } - - if (endy > da.getHeight()) { - endy = da.getHeight(); - } - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - - if (rowstart < 2) { - drawScale(startx,endx,charWidth,charHeight,ypos); - } - - drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos); - - if (rowstart == 0) { - ypos = ypos + chunkHeight; - } else if (rowstart == 1) { - ypos = ypos + chunkHeight; - } else { - ypos = ypos + chunkHeight - rowstart*charHeight; - } + if (av.getWrapAlignment()) + drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + else + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0); - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels + g.drawImage(img,0,0,this); - while (ypos <= getHeight()) { - drawScale(startx,endx,charWidth,charHeight,ypos); - drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos); + } - ypos += chunkHeight; - startx += chunkWidth; - endx = startx + chunkWidth; + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) + { + AlignmentI da = av.getAlignment(); - if (endy > da.getHeight()) { - endy = da.getHeight(); - } + int cWidth = canvasWidth/av.charWidth; + int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - if (endx > da.getWidth()) { - endx = da.getWidth(); - } + int endx = startRes+cWidth-1; + int ypos = 2*av.charHeight; - } - } - else + while (ypos <= canvasHeight) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - - oldstartx = startx; - oldendx = endx; - oldstarty = starty; - oldendy = endy; - - } - } - - else if (oldstartx < startx) - { - // This is dragging horizontal scrollbar to the right - - int delx = (startx - oldstartx) * charWidth; - int delx2 = (oldendx - startx + 1) * charWidth; - - gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0); - - if (startx > oldendx) - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - else - drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0); - - - oldstartx = startx; - oldendx = endx; - - } else if (oldstartx > startx) - { - // Horizontal scrollbar pulled to the left - - int delx = (oldstartx - startx) * charWidth; - int delx2 = (endx - oldstartx +1) * charWidth; - - gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0); - - if (oldstartx > endx) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0); - } - - oldstartx = startx; - oldendx = endx; - - } else if (oldstarty < starty) { - // Vertical scrollbar down - int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight); - int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight); - - gg.copyArea(0,dely,(endx-startx+1)*charWidth,dely2,0,-dely); - - if (starty > oldendy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0); - } - - oldstarty = starty; - oldendy = endy; - - } else if (oldstarty > starty) { - - // Vertical scrollbar up - int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight); - int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight); + drawScale(g, startRes, endx, ypos); + drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos); - gg.copyArea(0,0,(endx-startx+1)*charWidth,dely2,0,dely); + ypos += cHeight; + startRes += cWidth; + endx = startRes + cWidth - 1; - if (oldstarty > endy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0); + if (endx > da.getWidth()) + endx = da.getWidth(); } - oldstarty = starty; - oldendy = endy; - } - - if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) { - System.out.println("LIMITS ERROR LIMITS ERROR"); - System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth()); - } - - - // gg.setColor(Color.red); - // gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY ); - // gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 ); - - - g.drawImage(img,0,0,this); - } - - public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { -/* - Startx and starty appear to be the same as x1, y1, unless you find different - x1 x2 - y1************************************************** - * * - * * - * * - * * - **************************************************y2 - -/* - System.out.println("drawPanel called with g = " + g); - System.out.println(" x1 = " + x1); - System.out.println(" x2 = " + x2); - System.out.println(" y1 = " + y1); - System.out.println(" y2 = " + y2); - System.out.println(" startx = " + startx); - System.out.println(" starty = " + starty); -*/ g.setFont(av.getFont()); int charWidth = av.getCharWidth(); int charHeight = av.getCharHeight(); RendererI sr = av.getRenderer(); - /*Vector pid = av.getConsensus(false); Vector tmpseq = new Vector(); for (int i = 0; i < av.getAlignment().getHeight(); i++) @@ -316,41 +148,52 @@ public class SeqCanvas extends JPanel */ - if (y2 > starty && y1 < av.getEndSeq()) + /* if (y2 > starty && y1 < av.getEndSeq()) { fillBackground(g, - Color.WHITE, + Color.red, (x1-startx)*charWidth, offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), (x2-x1+1)*charWidth, offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); - } + }*/ SequenceI nextSeq; SequenceGroup group=null; - boolean newGroup=false; - int sx, sy, ex, ey; + SequenceGroup [] groups=null; + boolean inGroup=false; // are we in a defined group? + boolean inRB=false; //Are we in a rubberband group? + int sx=-1, sy=-1, ex=-1, ey=-1; int oldStartX=0,oldEndX=0,oldY=0; + int oldRStartX=0,oldREndX=0,oldRY=0; for (int i = y1 ; i < y2 ;i++) { nextSeq = av.getAlignment().getSequenceAt(i); - if(group==null || group!=av.alignment.findGroup( nextSeq )) - newGroup = true; - else - newGroup = false; - group = av.alignment.findGroup( nextSeq ); + group = av.alignment.findGroup( nextSeq ); + groups = av.alignment.findAllGroups( nextSeq ); - sr.drawSequence(g, nextSeq, group,x1,x2, + sr.drawSequence(g, nextSeq, groups,x1,x2, (x1 - startx) * charWidth, offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), charWidth,charHeight,null, i); + if(av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, groups, x1, x2, + (x1 - startx) * charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), + charWidth, charHeight, null, i); + } + + + if( group!=null ) { - g.setColor(Color.GREEN); + g.setColor(Color.lightGray); sx = (group.getStartRes()-startx)*charWidth; sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()); @@ -358,10 +201,10 @@ public class SeqCanvas extends JPanel ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight()); - if (newGroup) + if (!inGroup) { - g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box + inGroup=true; } g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side @@ -374,6 +217,49 @@ public class SeqCanvas extends JPanel oldY = ey; } + else if(inGroup) + { + g.setColor(Color.lightGray); + g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box + } + else + inGroup = false; + + group = av.getRubberbandGroup(); + if( group != null && group.sequences.contains(nextSeq) ) + { + g.setColor(Color.RED.brighter()); + sx = (group.getStartRes() - startx) * charWidth; + sy = offset + + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()); + ex = (group.getEndRes() + 1 - startx) * charWidth; + ey = offset + + AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight()); + + if (!inRB) + { + + g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box + inRB = true; + } + + g.drawLine(sx, sy, sx, ey); // vertical line, left hand side + g.drawLine(ex, sy, ex, ey); // vertical line, right hand side + if (i == y2 - 1) // last line of alignment, seal the box + g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box + + oldRStartX = sx; + oldREndX = ex; + oldRY = ey; + } + else if(inRB) + { + g.setColor(Color.RED.brighter()); + g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box + inRB = false; + } + else + inRB = false; } @@ -386,10 +272,10 @@ public class SeqCanvas extends JPanel int searchStart = searchResults[r+1]; int searchEnd = searchResults[r+2]; - if (searchSeq >= y1 && searchSeq <= y2) + if (searchSeq >= y1 && searchSeq < y2) { SequenceRenderer ssr = (SequenceRenderer) sr; - ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq), + ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), searchStart, searchEnd, (searchStart - startx) * charWidth, @@ -402,55 +288,8 @@ public class SeqCanvas extends JPanel } } - - - - /*bg.drawImage(image,0,0,null); - int size=width*height; - int pixel, b, x,y; - if(value!=0 ) - { - if(painted!=null) - { - for(int i=0; i