X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=5b89ca1e486a608245614ae9d7dc06603a04677f;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=1194d08afceca7ad43f51caf76d68317ffdd3b40;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 1194d08..5b89ca1 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -18,571 +18,892 @@ */ package jalview.gui; +import jalview.datamodel.*; + import java.awt.*; import java.awt.image.*; + import javax.swing.*; -import jalview.analysis.*; -import jalview.datamodel.*; -public class SeqCanvas - extends JComponent +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas extends JComponent { - FeatureRenderer fr; - SequenceRenderer sr; - 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; - int LABEL_WEST; - int LABEL_EAST; - - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(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) + final FeatureRenderer fr; + final SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; + int imgWidth; + int imgHeight; + AlignViewport av; + SearchResults searchResults = null; + 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(AlignViewport av) { - 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); + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); } - } - void drawWestScale(Graphics g, int startx, int endx, int ypos) - { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos += av.charHeight; + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; + } - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + public FeatureRenderer getFeatureRenderer() { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = startx; - int value = -1; + return fr; + } - while (index < endx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) - { - index++; + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } - continue; - } + public AlignViewport getViewport() + { + return av; + } - value = av.alignment.getSequenceAt(i).findPosition(index); - break; - } + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param endx DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ + void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { + int scalestartx = startx - (startx % 10) + 10; - if (value != -1) - { - int x = LABEL_WEST - fm.stringWidth(value + ""); - g.drawString(value + "", x, - (ypos + (i * av.charHeight)) - (av.charHeight / 5)); - } - } - } + g.setColor(Color.black); + + // NORTH SCALE + for (int i = scalestartx; i < endx; i += 10) + { + int value = i; + if(av.hasHiddenColumns) + value = av.getColumnSelection().adjustForHiddenColumns(value); - void drawEastScale(Graphics g, int startx, int endx, int ypos) - { - ypos += av.charHeight; + g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth, + ypos - (av.charHeight / 2)); - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + 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); + } + } + + /** + * 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) { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = endx; - int value = -1; + FontMetrics fm = getFontMetrics(av.getFont()); + ypos += av.charHeight; - while (index > startx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + if(av.hasHiddenColumns) { - index--; - - continue; + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - value = av.alignment.getSequenceAt(i).findPosition(index); + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - break; - } + // WEST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI seq = av.alignment.getSequenceAt(i); + int index = startx; + int value = -1; - if (value != -1) - { - g.drawString(value + "", 0, - (ypos + (i * av.charHeight)) - (av.charHeight / 5)); - } - } - } + while (index < endx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index++; - public void fastPaint(int horizontal, int vertical) - { - if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null)) - { - return; - } + continue; + } - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, - -vertical * av.charHeight); + value = av.alignment.getSequenceAt(i).findPosition(index); - int sr = av.startRes; - int er = av.endRes; - int ss = av.startSeq; - int es = av.endSeq; - int transX = 0; - int transY = 0; + break; + } - 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; + if (value != -1) + { + int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2; + g.drawString(value + "", x, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } } - else if (vertical > 0) // scroll down - { - ss = es - vertical; - if (ss < av.startSeq) - { // ie scrolling too fast, more than a page at a time - ss = av.startSeq; - } - else - { - transY = imgHeight - (vertical * av.charHeight); - } - } - else if (vertical < 0) + /** + * 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) { - es = ss - vertical; + ypos += av.charHeight; - if (es > av.endSeq) - { - es = av.endSeq; - } + if(av.hasHiddenColumns) + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + + SequenceI seq; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + 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 = seq.findPosition(index); + + break; + } + + if (value != -1) + { + g.drawString(String.valueOf(value), 0, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } } - gg.translate(transX, transY); - - gg.setColor(Color.white); - gg.fillRect(0, 0, (er - sr + 1) * 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) + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) { - g.drawImage(img, 0, 0, this); - fastPaint = false; + if (gg == null) + { + return; + } - return; - } - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); + fastPaint = true; - imgWidth -= (imgWidth % av.charWidth); - imgHeight -= (imgHeight % av.charHeight); + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, + -vertical * av.charHeight); - if ( (imgWidth < 1) || (imgHeight < 1)) - { - return; - } + int sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int transY = 0; - 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); + if (horizontal > 0) // scrollbar pulled right, image to the left + { + er ++; + transX = (er - sr - horizontal) * av.charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal-1; + } + else if (vertical > 0) // scroll down + { + ss = es - vertical; - chunkWidth = getWrappedCanvasWidth(getWidth()); - chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; + if (ss < av.startSeq) + { // ie scrolling too fast, more than a page at a time + ss = av.startSeq; + } + else + { + transY = imgHeight - (vertical * av.charHeight); + } + } + else if (vertical < 0) + { + es = ss - vertical; + + if (es > av.endSeq) + { + es = av.endSeq; + } + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, 0); + gg.translate(-transX, -transY); - if (av.getWrapAlignment()) - { - drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + repaint(); } - else + + /** + * 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 + public void paintComponent(Graphics g) { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, - av.startRes, av.startSeq, 0); - } + super.paintComponent(g); - g.drawImage(img, 0, 0, this); - } - public int getWrappedCanvasWidth(int cwidth) - { - FontMetrics fm = getFontMetrics(av.getFont()); - LABEL_EAST = 0; - LABEL_WEST = 0; + if ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - if (av.scaleRightWrapped) - { - LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000"); - } - if (av.scaleLeftWrapped) - { - LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + ""); - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - } + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, - int startRes) - { - AlignmentI al = av.getAlignment(); + if ((imgWidth < 1) || (imgHeight < 1)) + { + return; + } - FontMetrics fm = getFontMetrics(av.getFont()); + if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight()) + { + try{ + img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + }catch(OutOfMemoryError er) + { + System.gc(); + System.out.println(er +" making image, SeqCanvas"); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop. + desktop, + "Out of memory creating alignment image!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); - int LABEL_EAST = 0; + return; + } + } - if (av.scaleRightWrapped) - { - LABEL_EAST = fm.stringWidth(al.getWidth() + "000"); - } + if (av.antiAlias) + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); - int LABEL_WEST = 0; + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - 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; + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + } + else + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } + + g.drawImage(img, 0, 0, this); - av.endRes = av.startRes + cWidth; + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } - int endx = (startRes + cWidth) - 1; - int ypos = 2 * av.charHeight; + } - while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) { - g.setColor(Color.black); + FontMetrics fm = getFontMetrics(av.getFont()); - if (av.scaleLeftWrapped) - { - drawWestScale(g, startRes, endx, ypos); - } + LABEL_EAST = 0; + LABEL_WEST = 0; - if (av.scaleRightWrapped) - { - g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0); - } + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - g.translate(LABEL_WEST, 0); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - if (av.scaleAboveWrapped) - { - drawNorthScale(g, startRes, endx, ypos); - } + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } - // 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) + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() + { + String mask = "00"; + int maxWidth = 0; + int tmp; + for(int i=0; imaxWidth) + maxWidth = tmp; } - else + + for (int i = maxWidth; i > 0; i /= 10) { - g.setClip(0, (int) clip.getBounds().getY(), - cWidth * av.charWidth, (int) clip.getBounds().getHeight()); + mask += "0"; } + return mask; + } - drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); - g.setClip(clip); - g.translate( -LABEL_WEST, 0); + /** + * 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) + { + AlignmentI al = av.getAlignment(); - ypos += cHeight; - startRes += cWidth; - endx = (startRes + cWidth) - 1; + FontMetrics fm = getFontMetrics(av.getFont()); - if (endx > al.getWidth()) - { - endx = al.getWidth(); - } - } - } - synchronized 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()); - sr.renderGaps(av.renderGaps); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - SequenceI nextSeq; - /// First draw the sequences - ///////////////////////////// - for (int i = y1; i < y2; i++) - { - nextSeq = av.alignment.getSequenceAt(i); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - 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); + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; - 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); - } - } + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - // - ///////////////////////////////////// - // Now outline any areas if necessary - ///////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - java.util.Vector groups = av.alignment.getGroups(); + av.setWrappedWidth(cWidth); - int sx = -1; - int sy = -1; - int ex = -1; - int groupIndex = -1; + av.endRes = av.startRes + cWidth; - 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; - int bottom = -1; + int endx; + int ypos = hgap; + int maxwidth = av.alignment.getWidth(); - for (i = y1; i < y2; i++) + if(av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1; + + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { - 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))) + endx = startRes + cWidth -1; + + if (endx > maxwidth) { - if ( (bottom == -1) && - !group.sequences.contains( - av.alignment.getSequenceAt(i + 1))) + endx = maxwidth; + } + + g.setFont(av.getFont()); + g.setColor(Color.black); + + if (av.scaleLeftWrapped) { - bottom = sy + av.charHeight; + drawWestScale(g, startRes, endx, ypos); } - if (!inGroup) + if (av.scaleRightWrapped) { - if ( ( (top == -1) && (i == 0)) || - !group.sequences.contains( - av.alignment.getSequenceAt(i - 1))) - { - top = sy; - } + g.translate(canvasWidth - LABEL_EAST, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate(-(canvasWidth - LABEL_EAST), 0); + } - oldY = sy; - inGroup = true; + g.translate(LABEL_WEST, 0); - 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 + if (av.scaleAboveWrapped) + { + drawNorthScale(g, startRes, endx, ypos); + } + + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); + i++) { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); + res = av.getColumnSelection().findHiddenRegionPosition(i) - + startRes; + + if (res < 0 || res > endx - startRes) + continue; + + gg.fillPolygon(new int[] + {res * av.charWidth - av.charHeight / 4, + res * av.charWidth + av.charHeight / 4, + res * av.charWidth}, + new int[] + { + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2) + 8 + }, 3); + } } - } - else - { - if (inGroup) + + + + // 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.drawLine(sx, oldY, sx, sy); - g.drawLine(sx + ex, oldY, sx + ex, sy); + g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), + cWidth * av.charWidth, (int) clip.getBounds().getHeight()); + } - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + if(av.showAnnotation) + { + g.translate(0, cHeight + ypos + 3); + if(annotations==null) + annotations = new AnnotationPanel(av); - inGroup = false; + annotations.drawComponent( (Graphics2D) g, 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.showAnnotation) + return 0; - if (inGroup) + 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! + */ + void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + if(!av.hasHiddenColumns) + { + draw(g1, startRes, endRes, startSeq, endSeq, offset); + } + else + { + java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); + + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int i = 0; i < regions.size(); i++) { - if (top != -1) + int[] region = (int[]) regions.elementAt(i); + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) { - g.drawLine(sx, top, sx + ex, top); - top = -1; + blockStart += (hideEnd - hideStart) + 1; + continue; } - if (bottom != -1) + blockEnd = hideStart - 1; + + g1.translate(screenY * av.charWidth, 0); + + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + if(av.getShowHiddenMarkers()) { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; + g1.setColor(Color.blue); + + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + (endSeq - startSeq) * av.charHeight + offset); } - sy = offset + - AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - g.drawLine(sx, oldY, sx, sy); - g.drawLine(sx + ex, oldY, sx + ex, sy); - inGroup = false; + g1.translate( -screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; } - groupIndex++; - - if (groupIndex >= groups.size()) + if (screenY <= (endRes - startRes)) { - break; - } + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * av.charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - group = (SequenceGroup) groups.elementAt(groupIndex); + g1.translate( -screenY * av.charWidth, 0); + } } - while (groupIndex < groups.size()); + } - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if (displaySearch) - { - for (int r = 0; r < searchResults.length; r += 3) - { - int searchSeq = searchResults[r]; - if ( (searchSeq >= y1) && (searchSeq < y2)) + + + //int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // int x1, int x2, int y1, int y2, int startx, int starty, + void draw(Graphics g, + int startRes, int endRes, + int startSeq, int endSeq, + int offset) + { + g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); + + SequenceI nextSeq; + + /// First draw the sequences + ///////////////////////////// + for (int i = startSeq; i < endSeq; i++) { - SequenceI seq = av.getAlignment().getSequenceAt(searchSeq); + nextSeq = av.alignment.getSequenceAt(i); - int searchStart = seq.findIndex(searchResults[r + 1]) - 1; - int searchEnd = seq.findIndex(searchResults[r + 2]) - 1; + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); - SequenceRenderer ssr = (SequenceRenderer) sr; + if (av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * av.charHeight)); + } - if (searchStart < x1) - { - searchStart = x1; - } + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if (searchResults != null) + { + int[] visibleResults = searchResults.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) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } + } - if (searchEnd > x2) - { - searchEnd = x2; + if(av.cursorMode && cursorY==i + && cursorX>=startRes && cursorX<=endRes) + { + sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } } - ssr.drawHighlightedText(seq, searchStart, searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, - searchSeq, - av.charHeight), av.charWidth, av.charHeight); + if(av.getSelectionGroup()!=null || av.alignment.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) * av.charWidth; + + if ((group == null) && (av.alignment.getGroups().size() > 0)) + { + group = (SequenceGroup) av.alignment.getGroups().elementAt(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) * av.charWidth; + sy = offset + ((i - startSeq) * av.charHeight); + ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - + 1; + + if(sx+ex<0 || sx>visWidth) + { + continue; + } + + if ( (sx <= (endRes-startRes)*av.charWidth) && + group.getSequences(null). + contains(av.alignment.getSequenceAt(i))) + { + if ((bottom == -1) && + !group.getSequences(null).contains( + av.alignment.getSequenceAt(i + 1))) + { + bottom = sy + av.charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) || + !group.getSequences(null).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) + { + 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) * av.charWidth) + ex = (endRes - startRes + 1) * av.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) * av.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) * av.charWidth) + ex = (endRes - startRes + 1) * av.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.alignment.getGroups().size()) + { + break; + } + + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + + + } + while (groupIndex < av.alignment.getGroups().size()); + } - } - } - } - public void highlightSearchResults(int[] results) - { - // results are in the order sequence, startRes, endRes - if (results == null) - { - displaySearch = false; } - else + + /** + * DOCUMENT ME! + * + * @param results DOCUMENT ME! + */ + public void highlightSearchResults(SearchResults results) { - displaySearch = true; - } + img = null; - searchResults = results; + searchResults = results; - repaint(); - } + repaint(); + } }