X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=9023c4e8d2498bc9e67d26ef5c7b8ff27dfa7861;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=1d49da812594e27798d338b90e4e73892efb3a1e;hpb=63de5cd788f3ea4a30eb1e5037228d7abadc2871;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 1d49da8..9023c4e 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,27 +1,31 @@ /* - * 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 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * 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. + * + * 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 + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeI; -import jalview.datamodel.*; -import jalview.schemes.*; +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; /** * DOCUMENT ME! @@ -29,7 +33,7 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SequenceRenderer +public class SequenceRenderer implements jalview.api.SequenceRenderer { AlignViewport av; @@ -53,7 +57,7 @@ public class SequenceRenderer * Creates a new SequenceRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public SequenceRenderer(AlignViewport av) { @@ -64,7 +68,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -81,7 +85,7 @@ 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 +96,7 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } return resBoxColour; @@ -102,17 +106,17 @@ 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) { if (cs != null) { - resBoxColour = cs.findColour(seq.getCharAt(i), i); + resBoxColour = cs.findColour(seq.getCharAt(i), i, seq); } else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i))) @@ -129,23 +133,23 @@ 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) @@ -164,24 +168,25 @@ 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 + if (seq == null) + return; // fix for racecondition int i = start; int length = seq.getLength(); @@ -205,7 +210,7 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } } @@ -241,19 +246,19 @@ 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) { @@ -325,11 +330,12 @@ 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, + '.'); + } } @@ -343,7 +349,7 @@ public class SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); if (av.getShowBoxes()) { @@ -359,7 +365,7 @@ public class SequenceRenderer { if (!getboxColour) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -368,10 +374,11 @@ 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, + '.'); + } } @@ -383,12 +390,15 @@ 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; } @@ -397,7 +407,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -426,19 +436,19 @@ 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) @@ -463,10 +473,8 @@ 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); } } }