X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7f30c2489ada6adc0b43fc1ea0cb955e9877c0b3;hb=f5700411d71ab46a54d9e7dd46223b59fd1565b8;hp=c697d1e5fe5b0eb579e3887a8c6a129d1def9c76;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index c697d1e..7f30c24 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -2,7 +2,7 @@ package jalview.gui; import java.awt.*; import javax.swing.*; -import java.util.*; +import java.awt.event.*; import jalview.datamodel.*; import jalview.schemes.*; import jalview.analysis.*; @@ -16,32 +16,26 @@ public class SeqCanvas extends JPanel int imgHeight; AlignViewport av; - int pady = 2; - int oldstartx; - int oldstarty; - int oldendx; - int oldendy; public boolean paintFlag = false; + boolean showScores = false; + boolean displaySearch = false; + int [] searchResults = null; int chunkHeight; int chunkWidth; - Graphics debugG; - FeatureRenderer fr = new FeatureRenderer(); - BlockRenderer br = new BlockRenderer(); - CpGRenderer cgr = new CpGRenderer(); - - ColourSchemeI cs = new ZappoColourScheme(); public SeqCanvas(AlignViewport av) { this.av = av; setLayout(new BorderLayout()); + PaintRefresher.Register(this); + } - public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) { + public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) { int scalestartx = startx - startx%10 + 10; gg.setColor(Color.black); @@ -65,56 +59,38 @@ public class SeqCanvas extends JPanel */ public void paintComponent(Graphics g) { - debugG = g; AlignmentI da = av.getAlignment(); if (img == null || imgWidth != getWidth() || - imgHeight != getHeight() || - paintFlag == true) { + imgHeight != getHeight() + || paintFlag) + { - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); + imgWidth = getWidth(); + imgHeight = getHeight(); img = createImage(imgWidth,imgHeight); gg = img.getGraphics(); - // SMJS I added this in to update the AV when the size changes - // until I figure out how this should be done - setFont(av.getFont()); - gg.setFont(av.getFont()); paintFlag = false; - - oldstartx = -1; - oldendx = -1; - oldstarty = -1; - oldendy = -1; } - int startx = av.getStartRes(); - int starty = av.getStartSeq(); - - int endx = av.getEndRes(); - int endy = av.getEndSeq(); - - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - chunkWidth = (int)(getWidth()/charWidth); - chunkHeight = (da.getHeight() + 2)*charHeight; + chunkWidth = getWidth()/av.charWidth; + chunkHeight = (da.getHeight() + 2)*av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); - int offy = av.getStartSeq(); - if (oldendx == -1) { - fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight); - /* if (av.getWrapAlignment() == true) { + 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; @@ -178,92 +154,17 @@ public class SeqCanvas extends JPanel } } - } else*/ { - 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 = (int)((startx - oldstartx) * charWidth); - int delx2 = (int)((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 = (int)((oldstartx - startx) * charWidth); - int delx2 = (int)((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); + else*/ + { + drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,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,(int)((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); - - gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely); - if (oldstarty > endy) { - drawPanel(gg,startx,endx,starty,endy,startx,starty,0); - } else { - drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0); - } - - oldstarty = starty; - oldendy = endy; - } - - if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) { + /* if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) { System.out.println("LIMITS ERROR LIMITS ERROR"); - System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth()); - } - + System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth()); + }*/ g.drawImage(img,0,0,this); @@ -274,78 +175,158 @@ public class SeqCanvas extends JPanel public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { -/* - 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()); - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - // Vector pid = av.calcNewConsensus(); - + int charWidth = av.getCharWidth(); + int charHeight = av.getCharHeight(); RendererI sr = av.getRenderer(); -/* Vector tmpseq = new Vector(); - - for (int i = 0; i < av.getAlignment().getHeight(); i++) { - if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { + /*Vector pid = av.getConsensus(false); + Vector tmpseq = new Vector(); + for (int i = 0; i < av.getAlignment().getHeight(); i++) + if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) tmpseq.addElement(av.getAlignment().getSequenceAt(i)); - } - } - if (sr instanceof SequenceRenderer) { + if (sr instanceof SequenceRenderer) pid = AAFrequency.calculate(tmpseq,x1,x2); - } else if (sr instanceof GraphRenderer) { + else if (sr instanceof GraphRenderer) pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0), av.getAlignment().getSequences(), av.getPIDWindow(),x1,x2); - }*/ - - if (y2 > starty && y1 < av.getEndSeq()) { +*/ - fillBackground(g, - Color.white, - (int)((x1-startx)*charWidth), + /* if (y2 > starty && y1 < av.getEndSeq()) + { + fillBackground(g, + Color.red, + (x1-startx)*charWidth, offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), - (int)((x2-x1+1)*charWidth), + (x2-x1+1)*charWidth, offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); - } - - for (int i = y1 ; i < y2 ;i++) { - - RendererI r = sr; - - /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { - r = fr; - System.out.println("use feature renderer"); - // } else if ( i == 0) { - // r = br; - } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) { - r = cgr; - System.out.println("cg renderer"); - }*/ + }*/ - r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i), - x1, - x2, - (int)((x1-startx)*charWidth), - offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()), - charWidth, - charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av); + 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; + 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); + + group = av.alignment.findGroup( nextSeq ); + groups = av.alignment.findAllGroups( nextSeq ); + + sr.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.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()); + + + if (!inGroup) + { + g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box + inGroup=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 + + oldStartX = sx; + oldEndX = ex; + 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; } - } + /// Highlight search Results once all sequences have been drawn + if(displaySearch) + { + for(int r=0; r= y1 && searchSeq <= y2) + { + SequenceRenderer ssr = (SequenceRenderer) sr; + ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), + searchStart, + searchEnd, + (searchStart - startx) * charWidth, + offset + + AlignmentUtil.getPixelHeight(starty, searchSeq, + charHeight), + charWidth, + charHeight); + } + } + } + } public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { g.setColor(c); @@ -356,4 +337,19 @@ public class SeqCanvas extends JPanel return chunkWidth; } + public void highlightSearchResults(int [] results) + { + // results are in the order sequence, startRes, endRes + if(results==null) + displaySearch = false; + else + displaySearch = true; + + searchResults = results; + + paintFlag = true; + repaint(); + } + + }