X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7d953989280b719458107acbddd20ed0802e899d;hb=refs%2Fheads%2Ffeatures%2FJAL-653_JAL-1766_htslib_refseqsupport;hp=4b0a1a65c9926fcd5158365117d08a77c365ea60;hpb=a5966c42d9ed98731eb186b31e4a52895d4e24b5;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 4b0a1a6..7d95398 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,489 +1,979 @@ -package jalview.gui; - -import java.awt.*; -import java.awt.image.*; -import javax.swing.*; -import jalview.datamodel.*; -import jalview.analysis.*; - - -public class SeqCanvas extends JComponent -{ - FeatureRenderer fr; - BufferedImage img; - Graphics2D gg; - int imgWidth; - int imgHeight; - - AlignViewport av; - - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; - - int chunkHeight; - int chunkWidth; - - boolean fastPaint = false; - - - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - setLayout(new BorderLayout()); - PaintRefresher.Register(this); - - } - - void drawNorthScale(Graphics g, int startx, int endx,int ypos) { - int scalestartx = startx - startx % 10 + 10; - - g.setColor(Color.black); - - // NORTH SCALE - 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); - - } - } - - void drawWestScale(Graphics g, int startx, int endx, int ypos) - { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos+= av.charHeight; - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = startx; - int value = -1; - while (index < endx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) - { - index++; - continue; - } - - value = av.alignment.getSequenceAt(i).findPosition(index); - break; - } - if(value!=-1) - { - int x = LABEL_WEST - fm.stringWidth(value+""); - g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5); - } - } - } - - void drawEastScale(Graphics g, int startx, int endx, int ypos) -{ - ypos+= av.charHeight; - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = endx; - int value = -1; - while (index > startx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) - { - index--; - continue; - } - - value = av.alignment.getSequenceAt(i).findPosition(index); - break; - } - if(value!=-1) - g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); - } - -} - - - - - -public void fastPaint(int horizontal, int vertical) -{ - if (horizontal == 0 && vertical == 0 || gg==null) - return; - - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, - -vertical * av.charHeight); - - int sr = av.startRes, er = av.endRes + 1, ss = av.startSeq, es = av.endSeq, - transX = 0, transY = 0; - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.charWidth; - sr = er - horizontal; - } - else if (horizontal < 0) - er = sr - horizontal; - - else if (vertical > 0) // scroll down - { - ss = es - vertical; - if(ss av.endSeq) - es = av.endSeq; - } - - - gg.translate(transX, transY); - - gg.setColor(Color.white); - gg.fillRect(0,0, (er-sr)*av.charWidth, (es-ss)*av.charHeight); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); - gg.translate( -transX, -transY); - - fastPaint = true; - repaint(); - -} - -/** - * 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) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - - if (fastPaint) - { - g.drawImage(img, 0, 0, this); - fastPaint = false; - return; - } - - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); - if(imgWidth==0 || imgHeight==0) - return; - - imgWidth -= imgWidth%av.charWidth; - imgHeight-= imgHeight%av.charHeight; - - img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D)img.getGraphics(); - gg.setFont(av.getFont()); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); - - gg.setColor(Color.white); - gg.fillRect(0,0,imgWidth,imgHeight); - - chunkWidth = getWrappedCanvasWidth( getWidth() ); - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); - - - 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); - - g.drawImage(img, 0, 0, this); - - } - - int LABEL_WEST, LABEL_EAST; - public int getWrappedCanvasWidth(int cwidth) - { - FontMetrics fm = getFontMetrics(av.getFont()); - - LABEL_EAST = 0; - LABEL_WEST = 0; - - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); - - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); - - return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - } - - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) - { - AlignmentI al = av.getAlignment(); - - FontMetrics fm = getFontMetrics(av.getFont()); - - int LABEL_EAST = 0; - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( al.getWidth()+"000" ); - int LABEL_WEST = 0; - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth(al.getWidth()+"0"); - - - int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; - - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; - - while (ypos <= canvasHeight && startRes al.getWidth()) - endx = al.getWidth(); - } - - } - - - public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { - - Graphics2D g = (Graphics2D)g1; - g.setFont(av.getFont()); - RendererI sr = av.getRenderer(); - - SequenceI nextSeq; - - /// First draw the sequences - ///////////////////////////// - for (int i = y1 ; i < y2 ;i++) - { - nextSeq = av.alignment.getSequenceAt(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(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); - } - } - // - ///////////////////////////////////// - - // 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 (group != null) - do - { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top=-1, bottom =-1; - for (i = y1; i < y2; i++) - { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1; - - if (sx < getWidth() - && ex > 0 - && group.sequences.contains(av.alignment.getSequenceAt(i))) - { - if (bottom == -1 && - !group.sequences.contains(av.alignment.getSequenceAt(i + 1))) - bottom = sy + av.charHeight ; - - if (!inGroup) - { - if (top == -1 && i==0 || - !group.sequences.contains(av.alignment.getSequenceAt(i - 1))) - top = sy; - - - oldY = sy; - inGroup = true; - if (group == av.getSelectionGroup()) - { - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f )); - g.setColor(Color.RED); - } - else - { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } - } - else - { - if (inGroup) - { - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top =-1; - } - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - - inGroup = false; - } - } - } - - if (inGroup) - { - - if(top!=-1) - { - g.drawLine(sx, top, sx + ex, top); - top =-1; - } - if(bottom!=-1) - { - g.drawLine(sx, bottom-1, sx + ex, bottom-1); - bottom = -1; - - } - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); - inGroup = false; - } - groupIndex++; - if (groupIndex >= groups.size()) - break; - - group = (SequenceGroup) groups.elementAt(groupIndex); - - } - while (groupIndex < groups.size()); - - - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if(displaySearch) - { - for(int r=0; r= y1 && searchSeq < y2) - { - SequenceRenderer ssr = (SequenceRenderer) sr; - if(searchStart x2) - searchEnd = x2; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); - } - } - } - - } - - - - public void highlightSearchResults(int [] results) - { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; - - searchResults = results; - - 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.SearchResultsI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.renderer.ScaleRenderer; +import jalview.renderer.ScaleRenderer.ScaleMark; +import jalview.viewmodel.ViewportRanges; + +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.util.List; + +import javax.swing.JComponent; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent +{ + final FeatureRenderer fr; + + final SequenceRenderer sr; + + BufferedImage img; + + Graphics2D gg; + + int imgWidth; + + int imgHeight; + + AlignViewport av; + + boolean fastPaint = false; + + int LABEL_WEST; + + int LABEL_EAST; + + int cursorX = 0; + + int cursorY = 0; + + /** + * Creates a new SeqCanvas object. + * + * @param av + * DOCUMENT ME! + */ + public SeqCanvas(AlignmentPanel ap) + { + this.av = ap.av; + updateViewport(); + fr = new FeatureRenderer(ap); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); + } + + public SequenceRenderer getSequenceRenderer() + { + return sr; + } + + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + int charHeight = 0, charWidth = 0; + + 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.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().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.getColumnSelection().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)); + } + } + } + + boolean fastpainting = false; + + /** + * 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(); + gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, + imgHeight, -horizontal * charWidth, -vertical * charHeight); + + 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; + + if (horizontal > 0) // scrollbar pulled right, image to the left + { + er++; + transX = (er - sr - horizontal) * charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal - 1; + } + 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 = imgHeight - ((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) + { + updateViewport(); + BufferedImage lcimg = img; // take reference since other threads may null + // img and call later. + super.paintComponent(g); + + if (lcimg != null + && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g + .getClipBounds().height))) + { + g.drawImage(lcimg, 0, 0, this); + fastPaint = false; + return; + } + + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); + + imgWidth -= (imgWidth % charWidth); + imgHeight -= (imgHeight % charHeight); + + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } + + if (lcimg == null || imgWidth != lcimg.getWidth() + || imgHeight != lcimg.getHeight()) + { + try + { + lcimg = img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); + + return; + } + } + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); + + ViewportRanges ranges = av.getRanges(); + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + } + else + { + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); + } + + g.drawImage(lcimg, 0, 0, this); + + } + + /** + * 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! + */ + public void drawWrappedPanel(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + updateViewport(); + AlignmentI al = av.getAlignment(); + + FontMetrics fm = getFontMetrics(av.getFont()); + + 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().setEndRes(av.getRanges().getStartRes() + cWidth); + + int endx; + int ypos = hgap; + int maxwidth = av.getAlignment().getWidth() - 1; + + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + 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; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns() + .size(); i++) + { + res = av.getColumnSelection().findHiddenRegionPosition(i) + - 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(), 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; + } + } + + AnnotationPanel annotations; + + int getAnnotationHeight() + { + if (!av.isShowAnnotation()) + { + return 0; + } + + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + return annotations.adjustPanelHeight(); + } + + /** + * DOCUMENT ME! + * + * @param g1 + * DOCUMENT ME! + * @param startRes + * DOCUMENT ME! + * @param endRes + * DOCUMENT ME! + * @param startSeq + * DOCUMENT ME! + * @param endSeq + * DOCUMENT ME! + * @param offset + * DOCUMENT ME! + */ + public 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 + { + List regions = av.getColumnSelection().getHiddenColumns(); + + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int[] region : regions) + { + 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) * 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); + } + } + + } + + // int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // int x1, int x2, int y1, int y2, int startx, int starty, + private void draw(Graphics g, int startRes, int endRes, int startSeq, + int endSeq, int offset) + { + g.setFont(av.getFont()); + sr.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; + } + sr.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)); + } + + // / 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) + { + sr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], (visibleResults[r] - startRes) + * charWidth, offset + + ((i - startSeq) * charHeight)); + } + } + } + + if (av.cursorMode && cursorY == i && cursorX >= startRes + && cursorX <= endRes) + { + sr.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 = av.getSelectionGroup(); + + int sx = -1; + int sy = -1; + int ex = -1; + int groupIndex = -1; + int visWidth = (endRes - startRes + 1) * charWidth; + + if ((group == null) && (av.getAlignment().getGroups().size() > 0)) + { + group = av.getAlignment().getGroups().get(0); + groupIndex = 0; + } + + if (group != null) + { + do + { + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + + for (i = startSeq; i <= endSeq; i++) + { + sx = (group.getStartRes() - startRes) * charWidth; + sy = offset + ((i - startSeq) * charHeight); + ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1; + + if (sx + ex < 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; + + if (group == av.getSelectionGroup()) + { + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, + 0f)); + g.setColor(Color.RED); + } + else + { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + } + } + } + else + { + if (inGroup) + { + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + { + ex = visWidth; + } + + else if (sx + ex >= (endRes - startRes + 1) * charWidth) + { + ex = (endRes - startRes + 1) * charWidth; + } + + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top = -1; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + ex, bottom); + bottom = -1; + } + + inGroup = false; + } + } + } + + if (inGroup) + { + sy = offset + ((i - startSeq) * charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + { + ex = visWidth; + } + else if (sx + ex >= (endRes - startRes + 1) * charWidth) + { + ex = (endRes - startRes + 1) * charWidth; + } + + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top = -1; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + bottom = -1; + } + + inGroup = false; + } + + groupIndex++; + + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.getAlignment().getGroups().size()) + { + break; + } + + group = av.getAlignment().getGroups().get(groupIndex); + + } while (groupIndex < av.getAlignment().getGroups().size()); + + } + + } + + /** + * DOCUMENT ME! + * + * @param results + * DOCUMENT ME! + */ + public void highlightSearchResults(SearchResultsI results) + { + img = null; + + av.setSearchResults(results); + + repaint(); + } +}