X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=389da75fc527406441d524c4abdaf2a73d9c6ad3;hb=b7b29fb6c0b015ac4798ec4718ab0cfbdd79b20a;hp=38502445b7e45044f7d86a48be9ca640d886dbbf;hpb=161f6be325e2c5ee3aa9cc8158a9b5460bb472e7;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 3850244..3d8b8aa 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,416 +1,1365 @@ -package jalview.gui; - -import java.awt.*; -import javax.swing.*; -import java.util.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.analysis.*; - - -public class SeqCanvas extends JPanel -{ - 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; - boolean displaySearch = false; - int [] searchResults = null; - - int chunkHeight; - int chunkWidth; - - ColourSchemeI cs = new ZappoColourScheme(); - - public SeqCanvas(AlignViewport av) - { - this.av = av; - setLayout(new BorderLayout()); - } - - public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) { - int scalestartx = startx - startx%10 + 10; - - gg.setColor(Color.black); - - 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)); - } - } - - -/** - * Definitions of startx and endx (hopefully): - * SMJS This is what I'm working towards! - * startx is the first residue (starting at 0) to display. - * endx is the last residue to display (starting at 0). - * starty is the first sequence to display (starting at 0). - * endy is the last sequence to display (starting at 0). - * NOTE 1: The av limits are set in setFont in this class and - * in the adjustment listener in SeqPanel when the scrollbars move. - */ - - public void paintComponent(Graphics g) { - - AlignmentI da = av.getAlignment(); - - if (img == null || - imgWidth != getWidth() || - imgHeight != getHeight() - || paintFlag) - { - - imgWidth = (getWidth() > 0 ? getWidth() : 1); - imgHeight = (getHeight() > 0 ? getHeight() : 1); - - 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(); - - double charWidth = av.getCharWidth(); - int charHeight = av.getCharHeight(); - - chunkWidth = (int)(getWidth()/charWidth); - chunkHeight = (da.getHeight() + 2)*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()) { - 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,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); - } - - 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()))) { - System.out.println("LIMITS ERROR LIMITS ERROR"); - System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(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) { - -/* - 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(); - RendererI sr = av.getRenderer(); - - - /*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) - pid = AAFrequency.calculate(tmpseq,x1,x2); - - 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), - offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()), - (int)((x2-x1+1)*charWidth), - offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight())); - } - - SequenceI nextSeq; - SequenceGroup group; - for (int i = y1 ; i < y2 ;i++) - { - /* 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"); - } -*/ - nextSeq = av.getAlignment().getSequenceAt(i); - group = av.alignment.findGroup( nextSeq ); - if( group!=null ) - { - sr.drawSequence(g, group.cs, nextSeq, - x1, - x2, - (int) ( (x1 - startx) * charWidth), - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth, charHeight, - false, group.getDisplayBoxes(), group.getDisplayText(), group.getColourText(), - null, i); - } - else - { - sr.drawSequence(g, cs, nextSeq, - x1, - x2, - (int) ( (x1 - startx) * charWidth), - offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()), - charWidth,charHeight, - showScores, av.getShowBoxes(), av.getShowText(), av.getColourText(), - null, i); - - } - - - } - - - if(displaySearch) - { - for(int r=0; r= y1 && searchSeq <= y2) - { - SequenceRenderer ssr = (SequenceRenderer) sr; - ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (int) ( (searchStart - startx) * charWidth), - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - charHeight), - (int) charWidth, - charHeight); - - } - } - } - - - } - - // public int groupX, groupY, groupendX, groupendY; - - public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) { - g.setColor(c); - g.fillRect(x1,y1,width,height); - } - - public int getChunkWidth() { - 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(); - } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.renderer.ScaleRenderer; +import jalview.renderer.ScaleRenderer.ScaleMark; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + +import java.awt.AlphaComposite; +import java.awt.BasicStroke; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.RenderingHints; +import java.awt.Shape; +import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; +import java.util.List; + +import javax.swing.JComponent; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent implements ViewportListenerI +{ + final FeatureRenderer fr; + + final SequenceRenderer seqRdr; + + BufferedImage img; + + Graphics2D gg; + + AlignViewport av; + + boolean fastPaint = false; + + int LABEL_WEST; + + int LABEL_EAST; + + int cursorX = 0; + + int cursorY = 0; + + int charHeight = 0; + + int charWidth = 0; + + boolean fastpainting = false; + + AnnotationPanel annotations; + + /** + * Creates a new SeqCanvas object. + * + * @param av + * DOCUMENT ME! + */ + public SeqCanvas(AlignmentPanel ap) + { + this.av = ap.av; + updateViewport(); + fr = new FeatureRenderer(ap); + seqRdr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); + + av.getRanges().addPropertyChangeListener(this); + } + + public SequenceRenderer getSequenceRenderer() + { + return seqRdr; + } + + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + private void updateViewport() + { + charHeight = av.getCharHeight(); + charWidth = av.getCharWidth(); + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param startx + * DOCUMENT ME! + * @param endx + * DOCUMENT ME! + * @param ypos + * DOCUMENT ME! + */ + private void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { + updateViewport(); + for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, + endx)) + { + int mpos = mark.column; // (i - startx - 1) + if (mpos < 0) + { + continue; + } + String mstring = mark.text; + + if (mark.major) + { + if (mstring != null) + { + g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2)); + } + g.drawLine((mpos * charWidth) + (charWidth / 2), + (ypos + 2) - (charHeight / 2), + (mpos * charWidth) + (charWidth / 2), ypos - 2); + } + } + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param startx + * DOCUMENT ME! + * @param endx + * DOCUMENT ME! + * @param ypos + * DOCUMENT ME! + */ + void drawWestScale(Graphics g, int startx, int endx, int ypos) + { + FontMetrics fm = getFontMetrics(av.getFont()); + ypos += charHeight; + + if (av.hasHiddenColumns()) + { + startx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(startx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); + } + + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; + } + + // WEST SCALE + for (int i = 0; i < av.getAlignment().getHeight(); i++) + { + SequenceI seq = av.getAlignment().getSequenceAt(i); + int index = startx; + int value = -1; + + while (index < endx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index++; + + continue; + } + + value = av.getAlignment().getSequenceAt(i).findPosition(index); + + break; + } + + if (value != -1) + { + int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) + - charWidth / 2; + g.drawString(value + "", x, + (ypos + (i * charHeight)) - (charHeight / 5)); + } + } + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param startx + * DOCUMENT ME! + * @param endx + * DOCUMENT ME! + * @param ypos + * DOCUMENT ME! + */ + void drawEastScale(Graphics g, int startx, int endx, int ypos) + { + ypos += charHeight; + + if (av.hasHiddenColumns()) + { + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); + } + + SequenceI seq; + // EAST SCALE + for (int i = 0; i < av.getAlignment().getHeight(); i++) + { + seq = av.getAlignment().getSequenceAt(i); + int index = endx; + int value = -1; + + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; + + continue; + } + + value = seq.findPosition(index); + + break; + } + + if (value != -1) + { + g.drawString(String.valueOf(value), 0, + (ypos + (i * charHeight)) - (charHeight / 5)); + } + } + } + + + /** + * need to make this thread safe move alignment rendering in response to + * slider adjustment + * + * @param horizontal + * shift along + * @param vertical + * shift up or down in repaint + */ + public void fastPaint(int horizontal, int vertical) + { + if (fastpainting || gg == null) + { + return; + } + fastpainting = true; + fastPaint = true; + updateViewport(); + + ViewportRanges ranges = av.getRanges(); + int sr = ranges.getStartRes(); + int er = ranges.getEndRes(); + int ss = ranges.getStartSeq(); + int es = ranges.getEndSeq(); + int transX = 0; + int transY = 0; + + gg.copyArea(horizontal * charWidth, vertical * charHeight, + img.getWidth(), img.getHeight(), -horizontal * charWidth, + -vertical * charHeight); + + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal; + } + else if (vertical > 0) // scroll down + { + ss = es - vertical; + + if (ss < ranges.getStartSeq()) + { // ie scrolling too fast, more than a page at a time + ss = ranges.getStartSeq(); + } + else + { + transY = img.getHeight() - ((vertical + 1) * charHeight); + } + } + else if (vertical < 0) + { + es = ss - vertical; + + if (es > ranges.getEndSeq()) + { + es = ranges.getEndSeq(); + } + } + + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, 0); + gg.translate(-transX, -transY); + + repaint(); + fastpainting = false; + } + + /** + * Definitions of startx and endx (hopefully): SMJS This is what I'm working + * towards! startx is the first residue (starting at 0) to display. endx is + * the last residue to display (starting at 0). starty is the first sequence + * to display (starting at 0). endy is the last sequence to display (starting + * at 0). NOTE 1: The av limits are set in setFont in this class and in the + * adjustment listener in SeqPanel when the scrollbars move. + */ + + // Set this to false to force a full panel paint + @Override + public void paintComponent(Graphics g) + { + super.paintComponent(g); + + updateViewport(); + + ViewportRanges ranges = av.getRanges(); + + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + // selectImage is the selection group outline image + BufferedImage selectImage = drawSelectionGroup( + ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq()); + + if ((img != null) && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + BufferedImage lcimg = buildLocalImage(selectImage); + g.drawImage(lcimg, 0, 0, this); + fastPaint = false; + } + else if ((width > 0) && (height > 0)) + { + // img is a cached version of the last view we drew, if any + // if we have no img or the size has changed, make a new one + if (img == null || width != img.getWidth() + || height != img.getHeight()) + { + img = setupImage(); + if (img == null) + { + return; + } + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); + + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + } + else + { + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); + } + + // lcimg is a local *copy* of img which we'll draw selectImage on top of + BufferedImage lcimg = buildLocalImage(selectImage); + g.drawImage(lcimg, 0, 0, this); + } + } + + /** + * Draw an alignment panel for printing + * + * @param g1 + * Graphics object to draw with + * @param startRes + * start residue of print area + * @param endRes + * end residue of print area + * @param startSeq + * start sequence of print area + * @param endSeq + * end sequence of print area + */ + public void drawPanelForPrinting(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq) + { + BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + startSeq, endSeq); + drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); + ((Graphics2D) g1).setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g1.drawImage(selectImage, 0, 0, this); + } + + /** + * Draw a wrapped alignment panel for printing + * + * @param g + * Graphics object to draw with + * @param canvasWidth + * width of drawing area + * @param canvasHeight + * height of drawing area + * @param startRes + * start residue of print area + */ + public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + SequenceGroup group = av.getSelectionGroup(); + + drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + + if (group != null) + { + BufferedImage selectImage = null; + try + { + selectImage = new BufferedImage(canvasWidth, canvasHeight, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println("Print image OutOfMemory Error.\n" + er); + new OOMWarning("Creating wrapped alignment image for printing", er); + } + if (selectImage != null) + { + Graphics2D g2 = selectImage.createGraphics(); + setupSelectionGroup(g2, selectImage); + drawWrappedSelection(g2, group, canvasWidth, canvasHeight, + startRes); + + g2.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g.drawImage(selectImage, 0, 0, this); + g2.dispose(); + } + } + } + + /* + * Make a local image by combining the cached image img + * with any selection + */ + private BufferedImage buildLocalImage(BufferedImage selectImage) + { + // clone the cached image + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + Graphics2D g2d = lcimg.createGraphics(); + g2d.drawImage(img, 0, 0, null); + + // overlay selection group on lcimg + if (selectImage != null) + { + g2d.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g2d.drawImage(selectImage, 0, 0, this); + } + g2d.dispose(); + + return lcimg; + } + + /* + * Set up a buffered image of the correct height and size for the sequence canvas + */ + private BufferedImage setupImage() + { + BufferedImage lcimg = null; + + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + if ((width < 1) || (height < 1)) + { + return null; + } + + try + { + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println( + "Group image OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); + + return null; + } + + return lcimg; + } + + /** + * DOCUMENT ME! + * + * @param cwidth + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); + + LABEL_EAST = 0; + LABEL_WEST = 0; + + if (av.getScaleRightWrapped()) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + if (av.getScaleLeftWrapped()) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth; + } + + /** + * Generates a string of zeroes. + * + * @return String + */ + String getMask() + { + String mask = "00"; + int maxWidth = 0; + int tmp; + for (int i = 0; i < av.getAlignment().getHeight(); i++) + { + tmp = av.getAlignment().getSequenceAt(i).getEnd(); + if (tmp > maxWidth) + { + maxWidth = tmp; + } + } + + for (int i = maxWidth; i > 0; i /= 10) + { + mask += "0"; + } + return mask; + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param canvasWidth + * DOCUMENT ME! + * @param canvasHeight + * DOCUMENT ME! + * @param startRes + * DOCUMENT ME! + */ + private void drawWrappedPanel(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + updateViewport(); + AlignmentI al = av.getAlignment(); + + FontMetrics fm = getFontMetrics(av.getFont()); + + LABEL_EAST = 0; + LABEL_WEST = 0; + + if (av.getScaleRightWrapped()) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + if (av.getScaleLeftWrapped()) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + av.setWrappedWidth(cWidth); + + av.getRanges().setViewportStartAndWidth(startRes, cWidth); + + int endx; + int ypos = hgap; + int maxwidth = av.getAlignment().getWidth(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); + } + + while ((ypos <= canvasHeight) && (startRes < maxwidth)) + { + endx = startRes + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.setFont(av.getFont()); + g.setColor(Color.black); + + if (av.getScaleLeftWrapped()) + { + drawWestScale(g, startRes, endx, ypos); + } + + if (av.getScaleRightWrapped()) + { + g.translate(canvasWidth - LABEL_EAST, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate(-(canvasWidth - LABEL_EAST), 0); + } + + g.translate(LABEL_WEST, 0); + + if (av.getScaleAboveWrapped()) + { + drawNorthScale(g, startRes, endx, ypos); + } + + if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) + { + g.setColor(Color.blue); + int res; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + List positions = hidden.findHiddenRegionPositions(); + for (int pos : positions) + { + res = pos - startRes; + + if (res < 0 || res > endx - startRes) + { + continue; + } + + gg.fillPolygon( + new int[] + { res * charWidth - charHeight / 4, + res * charWidth + charHeight / 4, res * charWidth }, + new int[] + { ypos - (charHeight / 2), ypos - (charHeight / 2), + ypos - (charHeight / 2) + 8 }, + 3); + + } + } + + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); + + if (clip == null) + { + g.setClip(0, 0, cWidth * charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, + (int) clip.getBounds().getHeight()); + } + + drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); + + if (av.isShowAnnotation()) + { + g.translate(0, cHeight + ypos + 3); + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + annotations.renderer.drawComponent(annotations, av, g, -1, startRes, + endx + 1); + g.translate(0, -cHeight - ypos - 3); + } + g.setClip(clip); + g.translate(-LABEL_WEST, 0); + + ypos += cHeight + getAnnotationHeight() + hgap; + + startRes += cWidth; + } + } + + /* + * Draw a selection group over a wrapped alignment + */ + private void drawWrappedSelection(Graphics2D g, SequenceGroup group, + int canvasWidth, + int canvasHeight, int startRes) + { + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + int startx = startRes; + int endx; + int ypos = hgap; // vertical offset + int maxwidth = av.getAlignment().getWidth(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); + } + + // chop the wrapped alignment extent up into panel-sized blocks and treat + // each block as if it were a block from an unwrapped alignment + while ((ypos <= canvasHeight) && (startx < maxwidth)) + { + // set end value to be start + width, or maxwidth, whichever is smaller + endx = startx + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.translate(LABEL_WEST, 0); + + drawUnwrappedSelection(g, group, startx, endx, 0, + av.getAlignment().getHeight() - 1, + ypos); + + g.translate(-LABEL_WEST, 0); + + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; + + // update horizontal offset + startx += cWidth; + } + } + + int getAnnotationHeight() + { + if (!av.isShowAnnotation()) + { + return 0; + } + + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + return annotations.adjustPanelHeight(); + } + + /* + * Draw an alignment panel for printing + * + * @param g1 + * Graphics object to draw with + * @param startRes + * start residue of print area + * @param endRes + * end residue of print area + * @param startSeq + * start sequence of print area + * @param endSeq + * end sequence of print area + * @param offset + * vertical offset + */ + private void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + updateViewport(); + if (!av.hasHiddenColumns()) + { + draw(g1, startRes, endRes, startSeq, endSeq, offset); + } + else + { + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int[] region : av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy()) + { + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } + + blockEnd = hideStart - 1; + + g1.translate(screenY * charWidth, 0); + + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + if (av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + + g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1, + (endSeq - startSeq + 1) * charHeight + offset); + } + + g1.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + + if (screenY > (endRes - startRes)) + { + // already rendered last block + return; + } + } + + if (screenY <= (endRes - startRes)) + { + // remaining visible region to render + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + g1.translate(-screenY * charWidth, 0); + } + } + + } + + private void draw(Graphics g, int startRes, int endRes, int startSeq, + int endSeq, int offset) + { + g.setFont(av.getFont()); + seqRdr.prepare(g, av.isRenderGaps()); + + SequenceI nextSeq; + + // / First draw the sequences + // /////////////////////////// + for (int i = startSeq; i <= endSeq; i++) + { + nextSeq = av.getAlignment().getSequenceAt(i); + if (nextSeq == null) + { + // occasionally, a race condition occurs such that the alignment row is + // empty + continue; + } + seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + startRes, endRes, offset + ((i - startSeq) * charHeight)); + + if (av.isShowSequenceFeatures()) + { + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * charHeight), false); + } + + // / Highlight search Results once all sequences have been drawn + // //////////////////////////////////////////////////////// + if (av.hasSearchResults()) + { + int[] visibleResults = av.getSearchResults().getResults(nextSeq, + startRes, endRes); + if (visibleResults != null) + { + for (int r = 0; r < visibleResults.length; r += 2) + { + seqRdr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], (visibleResults[r] - startRes) + * charWidth, offset + + ((i - startSeq) * charHeight)); + } + } + } + + if (av.cursorMode && cursorY == i && cursorX >= startRes + && cursorX <= endRes) + { + seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); + } + } + + if (av.getSelectionGroup() != null + || av.getAlignment().getGroups().size() > 0) + { + drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); + } + + } + + void drawGroupsBoundaries(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + Graphics2D g = (Graphics2D) g1; + // + // /////////////////////////////////// + // Now outline any areas if necessary + // /////////////////////////////////// + + SequenceGroup group = null; + int groupIndex = -1; + + if (av.getAlignment().getGroups().size() > 0) + { + group = av.getAlignment().getGroups().get(0); + groupIndex = 0; + } + + if (group != null) + { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + + do + { + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, + endSeq, offset); + + groupIndex++; + + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.getAlignment().getGroups().size()) + { + break; + } + + group = av.getAlignment().getGroups().get(groupIndex); + + } while (groupIndex < av.getAlignment().getGroups().size()); + + } + + } + + + /* + * Draw the selection group as a separate image and overlay + */ + private BufferedImage drawSelectionGroup(int startRes, int endRes, + int startSeq, int endSeq) + { + // get a new image of the correct size + BufferedImage selectionImage = setupImage(); + + if (selectionImage == null) + { + return null; + } + + SequenceGroup group = av.getSelectionGroup(); + if (group == null) + { + // nothing to draw + return null; + } + + // set up drawing colour + Graphics2D g = (Graphics2D) selectionImage.getGraphics(); + + setupSelectionGroup(g, selectionImage); + + if (!av.getWrapAlignment()) + { + drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, + 0); + } + else + { + drawWrappedSelection(g, group, getWidth(), getHeight(), + av.getRanges().getStartRes()); + } + + g.dispose(); + return selectionImage; + } + + /* + * Set up graphics for selection group + */ + private void setupSelectionGroup(Graphics2D g, + BufferedImage selectionImage) + { + // set background to transparent + g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); + g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + + // set up foreground to draw red dashed line + g.setComposite(AlphaComposite.Src); + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + } + + /* + * Draw a selection group over an unwrapped alignment + * @param g graphics object to draw with + * @param group selection group + * @param startRes start residue of area to draw + * @param endRes end residue of area to draw + * @param startSeq start sequence of area to draw + * @param endSeq end sequence of area to draw + * @param offset vertical offset (used when called from wrapped alignment code) + */ + private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, int offset) + { + if (!av.hasHiddenColumns()) + { + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, + offset); + } + else + { + // package into blocks of visible columns + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int[] region : av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy()) + { + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } + + blockEnd = hideStart - 1; + + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + + if (screenY > (endRes - startRes)) + { + // already rendered last block + break; + } + } + + if (screenY <= (endRes - startRes)) + { + // remaining visible region to render + blockEnd = blockStart + (endRes - startRes) - screenY; + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + } + } + } + + /* + * Draw the selection group as a separate image and overlay + */ + private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, + int verticalOffset) + { + int visWidth = (endRes - startRes + 1) * charWidth; + + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + + int sx = -1; + int sy = -1; + int xwidth = -1; + + for (i = startSeq; i <= endSeq; i++) + { + // position of start residue of group relative to startRes, in pixels + sx = (group.getStartRes() - startRes) * charWidth; + + // width of group in pixels + xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) + - 1; + + sy = verticalOffset + (i - startSeq) * charHeight; + + if (sx + xwidth < 0 || sx > visWidth) + { + continue; + } + + if ((sx <= (endRes - startRes) * charWidth) + && group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i))) + { + if ((bottom == -1) && !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i + 1))) + { + bottom = sy + charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) || !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i - 1))) + { + top = sy; + } + + oldY = sy; + inGroup = true; + } + } + else + { + if (inGroup) + { + // if start position is visible, draw vertical line to left of + // group + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + // if end position is visible, draw vertical line to right of + // group + if (sx + xwidth < visWidth) + { + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); + } + + if (sx < 0) + { + xwidth += sx; + sx = 0; + } + + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (sx + xwidth >= (endRes - startRes + 1) * charWidth) + { + xwidth = (endRes - startRes + 1) * charWidth - sx; + } + + // draw horizontal line at top of group + if (top != -1) + { + g.drawLine(sx, top, sx + xwidth, top); + top = -1; + } + + // draw horizontal line at bottom of group + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + xwidth, bottom); + bottom = -1; + } + + inGroup = false; + } + } + } + + if (inGroup) + { + sy = verticalOffset + ((i - startSeq) * charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + xwidth < visWidth) + { + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); + } + + if (sx < 0) + { + xwidth += sx; + sx = 0; + } + + if (sx + xwidth > visWidth) + { + xwidth = visWidth; + } + else if (sx + xwidth >= (endRes - startRes + 1) * charWidth) + { + xwidth = (endRes - startRes + 1) * charWidth; + } + + if (top != -1) + { + g.drawLine(sx, top, sx + xwidth, top); + top = -1; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1); + bottom = -1; + } + + inGroup = false; + } + } + + /** + * DOCUMENT ME! + * + * @param results + * DOCUMENT ME! + */ + public void highlightSearchResults(SearchResultsI results) + { + img = null; + + av.setSearchResults(results); + + repaint(); + } + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + String eventName = evt.getPropertyName(); + + if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + { + fastPaint = true; + repaint(); + } + else if (av.getWrapAlignment()) + { + if (eventName.equals(ViewportRanges.STARTRES)) + { + repaint(); + } + } + else + { + int scrollX = 0; + if (eventName.equals(ViewportRanges.STARTRES)) + { + // Make sure we're not trying to draw a panel + // larger than the visible window + ViewportRanges vpRanges = av.getRanges(); + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes(); + if (scrollX > range) + { + scrollX = range; + } + else if (scrollX < -range) + { + scrollX = -range; + } + } + + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + // scroll - startres and endres both change + fastPaint(scrollX, 0); + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + } + } +}