X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=f9ab0156721ee9f892cb37be967ef5d761238b9b;hb=09b64bea954c283bde1d21c0a230f51f1ae89373;hp=bb65f105783db1181c73f4be9fc58e4c7c4aa535;hpb=23a895e23655fc6621388b3a4add05c47131c239;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index bb65f10..f9ab015 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -2,14 +2,13 @@ package jalview.gui; import java.awt.*; import javax.swing.*; -import java.awt.event.*; import jalview.datamodel.*; -import jalview.schemes.*; import jalview.analysis.*; public class SeqCanvas extends JPanel { + FeatureRenderer fr; Image img; Graphics gg; int imgWidth; @@ -30,20 +29,27 @@ 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)); } + } @@ -58,127 +64,68 @@ 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); @@ -197,7 +144,7 @@ public class SeqCanvas extends JPanel */ - if (y2 > starty && y1 < av.getEndSeq()) + /* if (y2 > starty && y1 < av.getEndSeq()) { fillBackground(g, Color.red, @@ -205,101 +152,100 @@ 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; - 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; + + /// First draw the sequences + ///////////////////////////// for (int i = y1 ; i < y2 ;i++) { nextSeq = av.getAlignment().getSequenceAt(i); - group = av.alignment.findGroup( nextSeq ); - - sr.drawSequence(g, nextSeq, group,x1,x2, - (x1 - startx) * charWidth, - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight,null, i); - + sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2, + (x1 - startx) * av.charWidth, + offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth,av.charHeight,null, i); - if( group!=null ) + if(av.showSequenceFeatures) { + fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2, + (x1 - startx) * av.charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), + av.charWidth, av.charHeight, null, i); + } + } + // + ///////////////////////////////////// - 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()); + // Now outline any areas if necessary + ///////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + java.util.Vector groups = av.alignment.getGroups(); + int sx = -1, sy = -1, ex = -1; + int groupIndex = -1; + if (group == null && groups.size() > 0) + { + group = (SequenceGroup) groups.elementAt(0); + groupIndex = 0; + } - if (!inGroup) + if (group != null) + do + { + int oldY = -1; + int i = 0; + boolean inGroup = false; + for (i = y1; i < y2; i++) { - g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box - inGroup=true; + sx = (group.getStartRes() - startx) * av.charWidth; + sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth; + + if (group.sequences.contains(av.alignment.getSequenceAt(i)) + && sx < getWidth() + && ex > 0) + { + if (!inGroup) + { + oldY = sy; + inGroup = true; + if (group == av.getSelectionGroup()) + g.setColor(Color.RED.brighter()); + else + g.setColor(group.getOutlineColour()); + } + } + else + { + if (inGroup) + { + g.drawRect(sx, oldY, ex, (sy - oldY)); + inGroup = false; + } + } + } + if (inGroup) + { + sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); + g.drawRect(sx, oldY, ex, (sy - oldY)); + inGroup = false; } - 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 - - oldStartX = sx; - oldEndX = ex; - oldY = ey; + groupIndex++; + if (groupIndex >= groups.size()) + break; - } - else if(inGroup) - { - g.setColor(Color.lightGray); - g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box - } - else - inGroup = false; + group = (SequenceGroup) groups.elementAt(groupIndex); - 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; + } + while (groupIndex < groups.size()); - } /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// if(displaySearch) { for(int r=0; r= 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); } } }