X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=ad704c3004cfb46747a64952ae313f8db35e0b42;hb=ca2d191924169cd2fa37a9eafcb7d4de41b28c53;hp=98329b4920fef212710fe3c504bfdccfde4e0d95;hpb=5feda00b43b9156b7a86b232b63a5da0736113ee;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 98329b4..ad704c3 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 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, J Engelhardt, LM Lui, 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) { @@ -81,7 +80,7 @@ public class SequenceRenderer public Color getResidueBoxColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i)) { @@ -92,7 +91,7 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } return resBoxColour; @@ -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(); @@ -204,7 +205,7 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } } @@ -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.getAlignmentConsensusAnnotation(), i, s, '.'); + } } @@ -342,7 +343,7 @@ public class SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); if (av.getShowBoxes()) { @@ -358,7 +359,7 @@ public class SequenceRenderer { if (!getboxColour) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -367,10 +368,10 @@ public class SequenceRenderer graphics.setColor(av.textColour2); } } - if (av.showUnconserved) + if (av.getShowUnconserved()) { - s = getDisplayChar(av.consensus, i, s, '.'); - + s = getDisplayChar(av.getAlignmentConsensusAnnotation(), 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); } } }