X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=507b7b04b94c391f789434ce4e589c70f5294a8c;hb=00386d5511d779b555e93dbf71f33675937e1570;hp=398aad9b70212e08bd65ee5713ad1d32b5759c85;hpb=6b9e5c5745220083e275a2d5e1d8c73d0dffe077;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 398aad9..507b7b0 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -10,6 +10,7 @@ import jalview.analysis.*; public class SeqCanvas extends JPanel { + FeatureRenderer fr; Image img; Graphics gg; int imgWidth; @@ -30,19 +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)); } + } @@ -57,127 +66,68 @@ 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(); imgHeight = getHeight(); - img = createImage(imgWidth,imgHeight); gg = img.getGraphics(); - gg.setFont(av.getFont()); - paintFlag = false; } + chunkWidth = getWidth()/av.charWidth; - chunkHeight = (da.getHeight() + 2)*av.charHeight; + chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); - - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - /* if (av.getWrapAlignment()) { - int offy = av.getStartSeq(); - 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; - } - - startx += chunkWidth; - endx = startx + chunkWidth; - starty = 0; - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - // Draw the rest of the panels - - 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; - - if (endy > da.getHeight()) { - endy = da.getHeight(); - } - - if (endx > da.getWidth()) { - endx = da.getWidth(); - } - - } - } - else*/ - { - drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0); - } + 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); - /* 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()); - }*/ - g.drawImage(img,0,0,this); } + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) + { + AlignmentI da = av.getAlignment(); + + int cWidth = canvasWidth/av.charWidth; + int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + int endx = startRes+cWidth-1; + int ypos = 2*av.charHeight; + + while (ypos <= canvasHeight) + { + drawScale(g, startRes, endx, ypos); + drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos); + + ypos += cHeight; + startRes += cWidth; + endx = startRes + cWidth - 1; + + if (endx > da.getWidth()) + endx = da.getWidth(); + } + + } public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { g.setFont(av.getFont()); - int charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); RendererI sr = av.getRenderer(); /*Vector pid = av.getConsensus(false); @@ -196,7 +146,7 @@ public class SeqCanvas extends JPanel */ - if (y2 > starty && y1 < av.getEndSeq()) + /* if (y2 > starty && y1 < av.getEndSeq()) { fillBackground(g, Color.red, @@ -204,10 +154,11 @@ public class SeqCanvas extends JPanel offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), (x2-x1+1)*charWidth, offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); - } + }*/ SequenceI nextSeq; SequenceGroup group=null; + 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; @@ -218,11 +169,23 @@ public class SeqCanvas extends JPanel nextSeq = av.getAlignment().getSequenceAt(i); group = av.alignment.findGroup( nextSeq ); + groups = av.alignment.findAllGroups( nextSeq ); + + sr.drawSequence(g, nextSeq, groups,x1,x2, + (x1 - startx) * av.charWidth, + offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth,av.charHeight,null, i); + + if(av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, groups, x1, x2, + (x1 - startx) * av.charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth, av.charHeight, null, i); + } + - sr.drawSequence(g, nextSeq, group,x1,x2, - (x1 - startx) * charWidth, - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight,null, i); if( group!=null ) @@ -230,10 +193,10 @@ public class SeqCanvas extends JPanel g.setColor(Color.lightGray); - 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()); + sx = (group.getStartRes()-startx)*av.charWidth; + sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + ex = (group.getEndRes()+1-startx)*av.charWidth; + ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.charHeight); if (!inGroup) @@ -264,12 +227,12 @@ public class SeqCanvas extends JPanel if( group != null && group.sequences.contains(nextSeq) ) { g.setColor(Color.RED.brighter()); - sx = (group.getStartRes() - startx) * charWidth; + sx = (group.getStartRes() - startx) * av.charWidth; sy = offset + - AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()); - ex = (group.getEndRes() + 1 - startx) * charWidth; + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + ex = (group.getEndRes() + 1 - startx) * av.charWidth; ey = offset + - AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight()); + AlignmentUtil.getPixelHeight(starty, i + 1, av.charHeight); if (!inRB) { @@ -307,18 +270,18 @@ 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, + (searchStart - startx) * av.charWidth, offset + AlignmentUtil.getPixelHeight(starty, searchSeq, - charHeight), - charWidth, - charHeight); + av.charHeight), + av.charWidth, + av.charHeight); } } }