X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=d5dd927e48d83acdab329e4319a6bc7042afad9f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=cd7c23179992b82e5f30ea7bc6acedd71f9566b0;hpb=39e39119e514275f48786e592cc24c251d212c66;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index cd7c231..d5dd927 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,57 +1,81 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * 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 - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.*; -import java.awt.image.*; -import javax.swing.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; +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 javax.swing.JComponent; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class SeqCanvas - extends JComponent +public class SeqCanvas extends JComponent { 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! + * + * @param av + * DOCUMENT ME! */ public SeqCanvas(AlignmentPanel ap) { @@ -73,14 +97,17 @@ public class SeqCanvas return fr; } - /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param startx DOCUMENT ME! - * @param endx DOCUMENT ME! - * @param ypos 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) { @@ -92,50 +119,54 @@ public class SeqCanvas for (int i = scalestartx; i < endx; i += 10) { int value = i; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { value = av.getColumnSelection().adjustForHiddenColumns(value); } g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth, - ypos - (av.charHeight / 2)); + 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); + 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! + * + * @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) + if (av.hasHiddenColumns()) { startx = av.getColumnSelection().adjustForHiddenColumns(startx); endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } // WEST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - SequenceI seq = av.alignment.getSequenceAt(i); + SequenceI seq = av.getAlignment().getSequenceAt(i); int index = startx; int value = -1; @@ -148,43 +179,47 @@ public class SeqCanvas continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = av.getAlignment().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)); + 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! + * + * @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) + if (av.hasHiddenColumns()) { endx = av.getColumnSelection().adjustForHiddenColumns(endx); } SequenceI seq; // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - seq = av.alignment.getSequenceAt(i); + seq = av.getAlignment().getSequenceAt(i); int index = endx; int value = -1; @@ -204,38 +239,35 @@ public class SeqCanvas if (value != -1) { - g.drawString(String.valueOf(value), 0, - (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) + - (av.charHeight / 5)); } } } - boolean fastpainting=false; + + 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 + * 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) + if (fastpainting || gg == null) { return; } - fastpainting=true; - if (gg == null) - { - return; - } - + fastpainting = true; fastPaint = true; - gg.copyArea(horizontal * av.charWidth, - vertical * av.charHeight, - imgWidth, - imgHeight, - -horizontal * av.charWidth, - -vertical * av.charHeight); + gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight, + imgWidth, imgHeight, -horizontal * av.charWidth, -vertical + * av.charHeight); int sr = av.startRes; int er = av.endRes; @@ -279,32 +311,32 @@ public class SeqCanvas gg.translate(transX, transY); drawPanel(gg, sr, er, ss, es, 0); - gg.translate( -transX, -transY); + gg.translate(-transX, -transY); repaint(); - fastpainting=false; + 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. + * 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) { - BufferedImage lcimg = img; // take reference since other threads may null img and call later. + 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))) + if (lcimg != null + && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g + .getClipBounds().height))) { g.drawImage(lcimg, 0, 0, this); fastPaint = false; @@ -318,37 +350,25 @@ public class SeqCanvas imgWidth -= (imgWidth % av.charWidth); imgHeight -= (imgHeight % av.charHeight); - if ( (imgWidth < 1) || (imgHeight < 1)) + if ((imgWidth < 1) || (imgHeight < 1)) { return; } - if (lcimg == null || imgWidth != lcimg.getWidth() || imgHeight != lcimg.getHeight()) + if (lcimg == null || imgWidth != lcimg.getWidth() + || imgHeight != lcimg.getHeight()) { try { lcimg = img = new BufferedImage(imgWidth, imgHeight, - BufferedImage.TYPE_INT_RGB); + BufferedImage.TYPE_INT_RGB); gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); - } - catch (OutOfMemoryError er) + } 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); - } - }); + System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); return; } @@ -357,7 +377,7 @@ public class SeqCanvas if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + RenderingHints.VALUE_ANTIALIAS_ON); } gg.setColor(Color.white); @@ -374,14 +394,14 @@ public class SeqCanvas g.drawImage(lcimg, 0, 0, this); - } /** * DOCUMENT ME! - * - * @param cwidth DOCUMENT ME! - * + * + * @param cwidth + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public int getWrappedCanvasWidth(int cwidth) @@ -406,6 +426,7 @@ public class SeqCanvas /** * Generates a string of zeroes. + * * @return String */ String getMask() @@ -413,9 +434,9 @@ public class SeqCanvas String mask = "00"; int maxWidth = 0; int tmp; - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - tmp = av.alignment.getSequenceAt(i).getEnd(); + tmp = av.getAlignment().getSequenceAt(i).getEnd(); if (tmp > maxWidth) { maxWidth = tmp; @@ -431,14 +452,18 @@ public class SeqCanvas /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param canvasWidth DOCUMENT ME! - * @param canvasHeight DOCUMENT ME! - * @param startRes 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) + public void drawWrappedPanel(Graphics g, int canvasWidth, + int canvasHeight, int startRes) { AlignmentI al = av.getAlignment(); @@ -469,14 +494,14 @@ public class SeqCanvas int endx; int ypos = hgap; - int maxwidth = av.alignment.getWidth() - 1; + int maxwidth = av.getAlignment().getWidth() - 1; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } - while ( (ypos <= canvasHeight) && (startRes < maxwidth)) + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { endx = startRes + cWidth - 1; @@ -497,7 +522,7 @@ public class SeqCanvas { g.translate(canvasWidth - LABEL_EAST, 0); drawEastScale(g, startRes, endx, ypos); - g.translate( - (canvasWidth - LABEL_EAST), 0); + g.translate(-(canvasWidth - LABEL_EAST), 0); } g.translate(LABEL_WEST, 0); @@ -507,15 +532,15 @@ public class SeqCanvas drawNorthScale(g, startRes, endx, ypos); } - if (av.hasHiddenColumns && av.showHiddenMarkers) + if (av.hasHiddenColumns() && av.showHiddenMarkers) { g.setColor(Color.blue); int res; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); - i++) + for (int i = 0; i < av.getColumnSelection().getHiddenColumns() + .size(); i++) { - res = av.getColumnSelection().findHiddenRegionPosition(i) - - startRes; + res = av.getColumnSelection().findHiddenRegionPosition(i) + - startRes; if (res < 0 || res > endx - startRes) { @@ -523,15 +548,11 @@ public class SeqCanvas } 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); + { 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); } } @@ -546,8 +567,8 @@ public class SeqCanvas } else { - g.setClip(0, (int) clip.getBounds().getY(), - cWidth * av.charWidth, (int) clip.getBounds().getHeight()); + g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth, + (int) clip.getBounds().getHeight()); } drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); @@ -560,11 +581,12 @@ public class SeqCanvas annotations = new AnnotationPanel(av); } - annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, g, + -1, startRes, endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); - g.translate( -LABEL_WEST, 0); + g.translate(-LABEL_WEST, 0); ypos += cHeight + getAnnotationHeight() + hgap; @@ -573,6 +595,7 @@ public class SeqCanvas } AnnotationPanel annotations; + int getAnnotationHeight() { if (!av.showAnnotation) @@ -590,18 +613,24 @@ public class SeqCanvas /** * 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! + * + * @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) + void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, + int endSeq, int offset) { - if (!av.hasHiddenColumns) + if (!av.hasHiddenColumns()) { draw(g1, startRes, endRes, startSeq, endSeq, offset); } @@ -613,7 +642,7 @@ public class SeqCanvas int blockStart = startRes; int blockEnd = endRes; - for (int i = 0; i < regions.size(); i++) + for (int i = 0; regions != null && i < regions.size(); i++) { int[] region = (int[]) regions.elementAt(i); int hideStart = region[0]; @@ -635,13 +664,12 @@ public class SeqCanvas { 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); + g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) * av.charWidth + - 1, (endSeq - startSeq) * av.charHeight + offset); } - g1.translate( -screenY * av.charWidth, 0); + g1.translate(-screenY * av.charWidth, 0); screenY += blockEnd - blockStart + 1; blockStart = hideEnd + 1; } @@ -652,84 +680,85 @@ public class SeqCanvas g1.translate(screenY * av.charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - g1.translate( -screenY * av.charWidth, 0); + g1.translate(-screenY * av.charWidth, 0); } } } - //int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // 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) + 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 - ///////////////////////////// + // / First draw the sequences + // /////////////////////////// for (int i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); - - sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), - startRes, endRes, - offset + ( (i - startSeq) * av.charHeight)); + 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) * av.charHeight)); if (av.showSequenceFeatures) { - fr.drawSequence(g, nextSeq, startRes, endRes, - offset + ( (i - startSeq) * av.charHeight)); + fr.drawSequence(g, nextSeq, startRes, endRes, offset + + ((i - startSeq) * av.charHeight)); } - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// + // / Highlight search Results once all sequences have been drawn + // //////////////////////////////////////////////////////// if (searchResults != null) { int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); + 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)); + visibleResults[r + 1], (visibleResults[r] - startRes) + * av.charWidth, offset + + ((i - startSeq) * av.charHeight)); } } } - if (av.cursorMode && cursorY == i - && cursorX >= startRes && cursorX <= endRes) + if (av.cursorMode && cursorY == i && cursorX >= startRes + && cursorX <= endRes) { - sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, - offset + ( (i - startSeq) * av.charHeight)); + sr.drawCursor(nextSeq, cursorX, + (cursorX - startRes) * av.charWidth, offset + + ((i - startSeq) * av.charHeight)); } } - if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0) + 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) + 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; @@ -738,9 +767,9 @@ public class SeqCanvas int groupIndex = -1; int visWidth = (endRes - startRes + 1) * av.charWidth; - if ( (group == null) && (av.alignment.getGroups().size() > 0)) + if ((group == null) && (av.getAlignment().getGroups().size() > 0)) { - group = (SequenceGroup) av.alignment.getGroups().elementAt(0); + group = av.getAlignment().getGroups().get(0); groupIndex = 0; } @@ -757,32 +786,30 @@ public class SeqCanvas 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; + 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 ((sx <= (endRes - startRes) * av.charWidth) + && group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i))) { - if ( (bottom == -1) && - !group.getSequences(null).contains( - av.alignment.getSequenceAt(i + 1))) + if ((bottom == -1) + && !group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i + 1))) { bottom = sy + av.charHeight; } if (!inGroup) { - if ( ( (top == -1) && (i == 0)) || - !group.getSequences(null).contains( - av.alignment.getSequenceAt(i - 1))) + if (((top == -1) && (i == 0)) + || !group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i - 1))) { top = sy; } @@ -792,11 +819,9 @@ public class SeqCanvas if (group == av.getSelectionGroup()) { - g.setStroke(new BasicStroke(1, - BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, - new float[] - {5f, 3f}, 0f)); + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); g.setColor(Color.RED); } else @@ -855,7 +880,7 @@ public class SeqCanvas if (inGroup) { - sy = offset + ( (i - startSeq) * av.charHeight); + sy = offset + ((i - startSeq) * av.charHeight); if (sx >= 0 && sx < visWidth) { g.drawLine(sx, oldY, sx, sy); @@ -900,15 +925,15 @@ public class SeqCanvas g.setStroke(new BasicStroke()); - if (groupIndex >= av.alignment.getGroups().size()) + if (groupIndex >= av.getAlignment().getGroups().size()) { break; } - group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + group = av.getAlignment().getGroups() + .get(groupIndex); - } - while (groupIndex < av.alignment.getGroups().size()); + } while (groupIndex < av.getAlignment().getGroups().size()); } @@ -916,8 +941,9 @@ public class SeqCanvas /** * DOCUMENT ME! - * - * @param results DOCUMENT ME! + * + * @param results + * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) {