X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=eedb3eb87d92785c2c77487d4891c4d0ac19d718;hb=ec8b46fcbc994a7c3c0bb6e07235cdb564c3991d;hp=0fe3b869e9ac2d5335da9d08c17050aa92d083de;hpb=5099540b9d747283036a752baa5ea246e8a5e855;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 0fe3b86..eedb3eb 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) 2007 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 @@ -18,14 +18,11 @@ */ package jalview.gui; -import jalview.datamodel.*; - import java.awt.*; import java.awt.image.*; - import javax.swing.*; -import jalview.schemes.*; +import jalview.datamodel.*; /** * DOCUMENT ME! @@ -33,812 +30,894 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SeqCanvas extends JComponent +public class SeqCanvas + extends JComponent { - FeatureRenderer fr; - SequenceRenderer sr; - BufferedImage img; - Graphics2D gg; - int imgWidth; - int imgHeight; - AlignViewport av; - boolean displaySearch = false; - int[] searchResults = null; - boolean fastPaint = false; - int LABEL_WEST; - int LABEL_EAST; - - /** - * Creates a new SeqCanvas object. - * - * @param av DOCUMENT ME! - */ - public SeqCanvas(AlignViewport av) + 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(AlignmentPanel ap) + { + this.av = ap.av; + 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; + } + + + /** + * 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; + + g.setColor(Color.black); + + // NORTH SCALE + for (int i = scalestartx; i < endx; i += 10) { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(av); - setLayout(new BorderLayout()); - PaintRefresher.Register(this, av.alignment); - setBackground(Color.white); - } + int value = i; + if (av.hasHiddenColumns) + { + value = av.getColumnSelection().adjustForHiddenColumns(value); + } - MCview.PDBCanvas pdbCanvas; - public SequenceRenderer getSequenceRenderer() - { - return sr; - } + g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth, + ypos - (av.charHeight / 2)); - public FeatureRenderer getFeatureRenderer() - { - return fr; + 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); } - - public void setPDBCanvas(MCview.PDBCanvas pc) + } + + /** + * 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 += av.charHeight; + + if (av.hasHiddenColumns) { - pdbCanvas = pc; + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - public AlignViewport getViewport() + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) { - return av; + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } - - /** - * 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) + // WEST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) { - int scalestartx = startx - (startx % 10) + 10; - - g.setColor(Color.black); + SequenceI seq = av.alignment.getSequenceAt(i); + int index = startx; + int value = -1; - // NORTH SCALE - for (int i = scalestartx; i < endx; i += 10) + while (index < endx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) { - 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); + index++; + + continue; } + + value = av.alignment.getSequenceAt(i).findPosition(index); + + break; + } + + 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)); + } + } + } + + /** + * 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 += av.charHeight; + + if (av.hasHiddenColumns) + { + endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - /** - * 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; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos += av.charHeight; + seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + while (index > startx) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = startx; - int value = -1; - - while (index < endx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) - { - index++; + index--; - continue; - } + continue; + } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = seq.findPosition(index); - break; - } + break; + } - 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)); - } - } + if (value != -1) + { + g.drawString(String.valueOf(value), 0, + (ypos + (i * av.charHeight)) - (av.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) + } + + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) { - 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--; + return; + } - continue; - } + fastPaint = true; - value = av.alignment.getSequenceAt(i).findPosition(index); + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, + -vertical * av.charHeight); - break; - } + int sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int transY = 0; - if (value != -1) - { - g.drawString(String.valueOf(value), 0, - (ypos + (i * av.charHeight)) - (av.charHeight / 5)); - } - } + 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; - /** - * DOCUMENT ME! - * - * @param horizontal DOCUMENT ME! - * @param vertical DOCUMENT ME! - */ - public void fastPaint(int horizontal, int 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) { - if (gg == null) - { - return; - } + es = ss - vertical; - gg.copyArea(horizontal * av.charWidth, - vertical * av.charHeight, - imgWidth, - imgHeight, - -horizontal * av.charWidth, - -vertical * av.charHeight); - - int sr = av.startRes; - int er = av.endRes; - int ss = av.startSeq; - int es = av.endSeq; - int transX = 0; - int transY = 0; - - 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; + if (es > av.endSeq) + { + es = av.endSeq; + } + } - 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; + gg.translate(transX, transY); + drawPanel(gg, sr, er, ss, es, 0); + gg.translate( -transX, -transY); + + 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. + */ + + // Set this to false to force a full panel paint + public void paintComponent(Graphics g) + { + super.paintComponent(g); + + if (img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } - if (es > av.endSeq) - { - es = av.endSeq; - } - } + // this draws the whole of the alignment + imgWidth = getWidth(); + imgHeight = getHeight(); - gg.translate(transX, transY); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); - gg.translate(-transX, -transY); + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - fastPaint = true; - repaint(); + if ( (imgWidth < 1) || (imgHeight < 1)) + { + return; } - /** - * 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. - */ + 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); + } + }); + + return; + } + } - // Set this to false to force a full panel paint - public void paintComponent(Graphics g) + if (av.antiAlias) { - super.paintComponent(g); + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - sr.renderGaps(av.renderGaps); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - 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.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); - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); - imgWidth -= (imgWidth % av.charWidth); - imgHeight -= (imgHeight % av.charHeight); + } - if ((imgWidth < 1) || (imgHeight < 1)) - { - return; - } + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedCanvasWidth(int cwidth) + { + FontMetrics fm = getFontMetrics(av.getFont()); - 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); + LABEL_EAST = 0; + LABEL_WEST = 0; + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - if (av.getWrapAlignment()) - { - drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); - } - else - { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, - av.startRes, av.startSeq, 0); - } + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - g.drawImage(img, 0, 0, this); + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } + + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() + { + String mask = "00"; + int maxWidth = 0; + int tmp; + for (int i = 0; i < av.alignment.getHeight(); i++) + { + tmp = av.alignment.getSequenceAt(i).getEnd(); + if (tmp > maxWidth) + { + maxWidth = tmp; + } + } - if (pdbCanvas != null) - { - pdbCanvas.updateSeqColours(); - } + 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) + { + AlignmentI al = av.getAlignment(); + + FontMetrics fm = getFontMetrics(av.getFont()); + + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); } - /** - * DOCUMENT ME! - * - * @param cwidth DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedCanvasWidth(int cwidth) + int hgap = av.charHeight; + if (av.scaleAboveWrapped) { - FontMetrics fm = getFontMetrics(av.getFont()); + hgap += av.charHeight; + } - LABEL_EAST = 0; - LABEL_WEST = 0; + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - if (av.scaleRightWrapped) - { - LABEL_EAST = fm.stringWidth(getMask()); - } + av.setWrappedWidth(cWidth); - if (av.scaleLeftWrapped) - { - LABEL_WEST = fm.stringWidth(getMask()); - } + av.endRes = av.startRes + cWidth; - return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - } + int endx; + int ypos = hgap; + int maxwidth = av.alignment.getWidth() - 1; + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } - /** - * Generates a string of zeroes. - * @return String - */ - String getMask() + while ( (ypos <= canvasHeight) && (startRes < maxwidth)) { - String mask = "00"; - for (int i = av.alignment.getWidth(); i > 0; i /= 10) + endx = startRes + cWidth - 1; + + if (endx > maxwidth) { - mask += "0"; + endx = maxwidth; } - 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) - { + g.setFont(av.getFont()); + g.setColor(Color.black); + + if (av.scaleLeftWrapped) + { + drawWestScale(g, startRes, endx, ypos); + } - AlignmentI al = av.getAlignment(); + if (av.scaleRightWrapped) + { + g.translate(canvasWidth - LABEL_EAST, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate( - (canvasWidth - LABEL_EAST), 0); + } - FontMetrics fm = getFontMetrics(av.getFont()); + g.translate(LABEL_WEST, 0); - int LABEL_EAST = 0; + if (av.scaleAboveWrapped) + { + drawNorthScale(g, startRes, endx, ypos); + } - if (av.scaleRightWrapped) + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); + i++) { - LABEL_EAST = fm.stringWidth(getMask()); + 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); + } + } - int LABEL_WEST = 0; + // When printing we have an extra clipped region, + // the Printable page which we need to account for here + Shape clip = g.getClip(); - if (av.scaleLeftWrapped) + if (clip == null) + { + g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), + cWidth * av.charWidth, (int) clip.getBounds().getHeight()); + } + + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + + if (av.showAnnotation) + { + g.translate(0, cHeight + ypos + 3); + if (annotations == null) { - LABEL_WEST = fm.stringWidth(getMask()); + annotations = new AnnotationPanel(av); } - int hgap = av.charHeight; - if(av.scaleAboveWrapped) - hgap += av.charHeight; + annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); + g.translate(0, -cHeight - ypos - 3); + } + g.setClip(clip); + g.translate( -LABEL_WEST, 0); - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - int cHeight = av.getAlignment().getHeight() * av.charHeight; + ypos += cHeight + getAnnotationHeight() + hgap; - av.setWrappedWidth(cWidth); + startRes += cWidth; + } + } - av.endRes = av.startRes + cWidth; + AnnotationPanel annotations; + int getAnnotationHeight() + { + if (!av.showAnnotation) + { + return 0; + } + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } - int endx = (startRes + cWidth) - 1; - int ypos = hgap; + 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; - while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) - { - g.setFont(av.getFont()); - g.setColor(Color.black); + for (int i = 0; i < regions.size(); i++) + { + int[] region = (int[]) regions.elementAt(i); + int hideStart = region[0]; + int hideEnd = region[1]; - if (av.scaleLeftWrapped) - { - drawWestScale(g, startRes, endx, ypos); - } + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } - if (av.scaleRightWrapped) - { - g.translate(canvasWidth - LABEL_EAST, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate(-(canvasWidth - LABEL_EAST), 0); - } + blockEnd = hideStart - 1; - g.translate(LABEL_WEST, 0); + g1.translate(screenY * av.charWidth, 0); - if (av.scaleAboveWrapped) - { - drawNorthScale(g, startRes, endx, ypos); - } + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - // When printing we have an extra clipped region, - // the Printable page which we need to account for here - Shape clip = g.getClip(); + if (av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); - if (clip == null) - { - g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); - } - else - { - g.setClip(0, (int) clip.getBounds().getY(), - cWidth * av.charWidth, (int) clip.getBounds().getHeight()); - } + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + (endSeq - startSeq) * av.charHeight + offset); + } - if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size()) - { - endx = av.vconsensus.size() - 2; - } + g1.translate( -screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + } + if (screenY <= (endRes - startRes)) + { + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * av.charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); + g1.translate( -screenY * av.charWidth, 0); + } + } - if(av.showAnnotation) - { - g.translate(0, cHeight + ypos + 3); - if(annotations==null) - annotations = new AnnotationPanel(av); + } - annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); - g.translate(0, -cHeight - ypos); - } - g.setClip(clip); - g.translate(-LABEL_WEST, 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, + void draw(Graphics g, + int startRes, int endRes, + int startSeq, int endSeq, + int offset) + { + g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); - ypos += cHeight+getAnnotationHeight()+hgap; - if(av.showAnnotation) - ypos -= 3; + SequenceI nextSeq; - startRes += cWidth; - endx = (startRes + cWidth) - 1; + /// First draw the sequences + ///////////////////////////// + for (int i = startSeq; i < endSeq; i++) + { + nextSeq = av.alignment.getSequenceAt(i); - if (endx > al.getWidth()) - { - endx = al.getWidth(); - } - } - } + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); - AnnotationPanel annotations; - int getAnnotationHeight() - { - if(!av.showAnnotation) - return 0; + if (av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); + } - if(annotations==null) - annotations = new AnnotationPanel(av); + /// 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)); + } + } + } - return annotations.adjustPanelHeight(); + if (av.cursorMode && cursorY == i + && cursorX >= startRes && cursorX <= endRes) + { + sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } } - /** - * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - * @param x1 DOCUMENT ME! - * @param x2 DOCUMENT ME! - * @param y1 DOCUMENT ME! - * @param y2 DOCUMENT ME! - * @param startx DOCUMENT ME! - * @param starty DOCUMENT ME! - * @param offset DOCUMENT ME! - */ - - float aaRatio = 2f/3f; - public void increaseAARatio() + if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0) { - aaRatio += .025; - if(aaRatio>1) - aaRatio = 1; - - repaint(); + drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); } - public void decreaseAARation() + } + + 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)) { - aaRatio -= .025; - if(aaRatio<0) - aaRatio = 0; - - repaint(); + group = (SequenceGroup) av.alignment.getGroups().elementAt(0); + groupIndex = 0; } - - synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1, - int y2, int startx, int starty, int offset) + if (group != null) { - Graphics2D g = (Graphics2D) g1; - g.setFont(av.getFont()); - - SequenceI nextSeq, dna = null; - int aaHeight = av.charHeight, dnaHeight = av.charHeight; - Font dnafont = null, aafont = av.getFont(); - - /* if (av.getShowTranslation()) + do { - aaHeight = (int) (av.getCharHeight() * aaRatio); - dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio)); - java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform(); - transform.scale(1f / 3f, 1); - dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(), - dnaHeight); - dnafont = dnafont.deriveFont(transform); - - aafont = new Font(av.getFont().getName(), av.getFont().getStyle(), - aaHeight); - transform = new java.awt.geom.AffineTransform(); - transform.scale(1 / aaRatio, 1); - aafont = aafont.deriveFont(transform); - } -*/ + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; - ColourSchemeI cs = av.getGlobalColourScheme(); - - /// First draw the sequences - ///////////////////////////// - for (int i = y1; i < y2; i++) + for (i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); - g.setFont(aafont); - /* if(av.getShowTranslation()) + 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))) { - dna = nextSeq; - StringBuffer sb = new StringBuffer(); - for(int r = 0; r 0)) - { - group = (SequenceGroup) av.alignment.getGroups().elementAt(0); - groupIndex = 0; - } - - if (group != null) - { - do + } + else + { + if (inGroup) { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; - - for (i = y1; i < y2; i++) - { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + ((i - starty) * av.charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - - 1; - - if(sx+ex<0 || sx>imgWidth) - { - continue; - } - - if ( (sx <= (x2-x1)*av.charWidth) && - 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) - { - if (sx >= 0 && sx < imgWidth) - g.drawLine(sx, oldY, sx, sy); - - if (sx + ex < imgWidth) - g.drawLine(sx + ex, oldY, sx + ex, sy); - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - ex = imgWidth; - - else if (sx + ex >= (x2 - x1 + 1) * av.charWidth) - ex = (x2 - x1 + 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 - starty) * av.charHeight); - if (sx >= 0 && sx < imgWidth) - g.drawLine(sx, oldY, sx, sy); - - if (sx + ex < imgWidth) - g.drawLine(sx + ex, oldY, sx + ex, sy); - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - ex = imgWidth; - else if (sx + ex >= (x2 - x1 + 1) * av.charWidth) - ex = (x2 - x1 + 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++; - - if (groupIndex >= av.alignment.getGroups().size()) - { - break; - } - - group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); - } - while (groupIndex < av.alignment.getGroups().size()); - } + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } - /// 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 (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } - if ((searchSeq >= y1) && (searchSeq < y2)) - { - SequenceI seq = av.getAlignment().getSequenceAt(searchSeq); + if (sx < 0) + { + ex += sx; + sx = 0; + } - int searchStart = seq.findIndex(searchResults[r + 1]) - 1; - int searchEnd = seq.findIndex(searchResults[r + 2]) - 1; + if (sx + ex > visWidth) + { + ex = visWidth; + } - SequenceRenderer ssr = (SequenceRenderer) sr; + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + { + ex = (endRes - startRes + 1) * av.charWidth; + } - if (searchStart < x1) - { - searchStart = x1; - } + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top = -1; + } - if (searchEnd > x2) - { - searchEnd = x2; - } + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + ex, bottom); + bottom = -1; + } - ssr.drawHighlightedText(seq, searchStart, searchEnd, - (searchStart - startx) * av.charWidth, - offset + ((searchSeq - starty) * av.charHeight), - av.charWidth, av.charHeight); - } + inGroup = false; } + } } - } - /** - * DOCUMENT ME! - * - * @param results DOCUMENT ME! - */ - public void highlightSearchResults(int[] results) - { - // results are in the order sequence, startRes, endRes - if (results == null) + if (inGroup) { - displaySearch = false; + 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; } - else + + groupIndex++; + + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.alignment.getGroups().size()) { - displaySearch = true; + break; } - searchResults = results; + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + + } + while (groupIndex < av.alignment.getGroups().size()); - repaint(); } + + } + + /** + * DOCUMENT ME! + * + * @param results DOCUMENT ME! + */ + public void highlightSearchResults(SearchResults results) + { + img = null; + + searchResults = results; + + repaint(); + } }