X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=c6a3df26bff6ca69a6d9af2ed304cc650789ee7a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a3dd5a6d10249d88e8684b83cdd3371841f68823;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index a3dd5a6..c6a3df2 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,27 +1,34 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.*; +import jalview.api.FeatureRenderer; +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 +36,7 @@ import jalview.schemes.*; * @author $author$ * @version $Revision$ */ -public class SequenceRenderer +public class SequenceRenderer implements jalview.api.SequenceRenderer { AlignViewport av; @@ -53,7 +60,7 @@ public class SequenceRenderer * Creates a new SequenceRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public SequenceRenderer(AlignViewport av) { @@ -64,7 +71,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -74,14 +81,15 @@ public class SequenceRenderer // If EPS graphics, stringWidth will be a double, not an int double dwidth = fm.getStringBounds("M", g).getWidth(); - monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth); + monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av.charWidth == dwidth); this.renderGaps = renderGaps; } + @Override public Color getResidueBoxColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i)) { @@ -92,27 +100,52 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } return resBoxColour; } /** + * Get the residue colour at the given sequence position - as determined by + * the sequence group colour (if any), else the colour scheme, possibly + * overridden by a feature colour. + * + * @param seq + * @param position + * @param fr + * @return + */ + @Override + public Color getResidueColour(final SequenceI seq, int position, + FeatureRenderer fr) + { + // TODO replace 8 or so code duplications with calls to this method + // (refactored as needed) + Color col = getResidueBoxColour(seq, position); + + if (fr != null) + { + col = fr.findFeatureColour(col, seq, position); + } + return col; + } + + /** * 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 +162,23 @@ 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 +197,27 @@ 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 +241,7 @@ public class SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } } @@ -240,19 +277,19 @@ 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) { @@ -282,6 +319,7 @@ public class SequenceRenderer } else { + boolean srep = av.isDisplayReferenceSeq(); boolean getboxColour = false; for (int i = start; i <= end; i++) { @@ -324,6 +362,13 @@ public class SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } + if (currentSequenceGroup.getShowNonconserved()) // todo optimize + { + // todo - use sequence group consensus + s = getDisplayChar(srep, i, s, + '.'); + + } } else @@ -336,7 +381,7 @@ public class SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); if (av.getShowBoxes()) { @@ -352,7 +397,7 @@ public class SequenceRenderer { if (!getboxColour) { - getBoxColour(av.globalColourScheme, seq, i); + getBoxColour(av.getGlobalColourScheme(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -361,6 +406,12 @@ public class SequenceRenderer graphics.setColor(av.textColour2); } } + if (av.getShowUnconserved()) + { + s = getDisplayChar(srep, i, s, + '.'); + + } } @@ -372,11 +423,25 @@ public class SequenceRenderer } } + private char getDisplayChar(final boolean usesrep, int position, + char s, char c) + { + // TODO - use currentSequenceGroup rather than alignemnt + // currentSequenceGroup.getConsensus() + char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter + .charAt(0); + if (conschar != '-' && s == conschar) + { + s = c; + } + return s; + } + /** * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -405,19 +470,19 @@ 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) @@ -442,10 +507,8 @@ 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); } } }