X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=b3dfc97a9da19f5d0a1861b3e0e9f1017145de4a;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=c390041f565bfafe4b58211c92e7a3ca45f4f80f;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index c390041..b3dfc97 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. * - * 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 + * 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 . */ package jalview.gui; @@ -29,7 +28,7 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SequenceRenderer +public class SequenceRenderer implements jalview.api.SequenceRenderer { AlignViewport av; @@ -53,7 +52,7 @@ public class SequenceRenderer * Creates a new SequenceRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public SequenceRenderer(AlignViewport av) { @@ -64,7 +63,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -102,11 +101,11 @@ public class SequenceRenderer * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param i - * DOCUMENT ME! + * DOCUMENT ME! */ void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) { @@ -129,23 +128,23 @@ public class SequenceRenderer * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param sg - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start, int end, int y1) @@ -164,23 +163,25 @@ public class SequenceRenderer * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1) { + if (seq == null) + return; // fix for racecondition int i = start; int length = seq.getLength(); @@ -240,19 +241,19 @@ public class SequenceRenderer * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawText(SequenceI seq, int start, int end, int y1) { @@ -324,11 +325,11 @@ public class SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } - if (currentSequenceGroup.getShowunconserved()) // todo optimize + if (currentSequenceGroup.getShowNonconserved()) // todo optimize { // todo - use sequence group consensus - s = getDisplayChar(av.consensus, i, s, '.'); - + s = getDisplayChar(av.consensus, i, s, '.'); + } } @@ -369,8 +370,8 @@ public class SequenceRenderer } if (av.showUnconserved) { - s = getDisplayChar(av.consensus, i, s, '.'); - + s = getDisplayChar(av.consensus, i, s, '.'); + } } @@ -382,12 +383,15 @@ public class SequenceRenderer } } } - private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c) + + private char getDisplayChar(AlignmentAnnotation consensus, int position, + char s, char c) { - char conschar = consensus.annotations[position].displayCharacter.charAt(0); - if (conschar!='-' && s==conschar) + char conschar = consensus.annotations[position].displayCharacter + .charAt(0); + if (conschar != '-' && s == conschar) { - s= c; + s = c; } return s; } @@ -396,7 +400,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -425,19 +429,19 @@ public class SequenceRenderer * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1) @@ -462,10 +466,8 @@ public class SequenceRenderer } charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics - .drawString(String.valueOf(s), charOffset + x1 - + (av.charWidth * (i - start)), - (y1 + av.charHeight) - pady); + graphics.drawString(String.valueOf(s), charOffset + x1 + + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady); } } }