X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=b8435260aed051b4a94b00080cf96c56da70ead1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=531b4d0dcbc5ad4a22e108cffe08daa895dd554d;hpb=b57fe83e78a9fb160a4765099880827b82222c53;p=jalview.git diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index 531b4d0..b843526 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,29 +1,36 @@ /* - * 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 2.9) + * Copyright (C) 2015 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.appletgui; -import java.awt.*; +import jalview.api.FeatureRenderer; +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.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; -public class SequenceRenderer +public class SequenceRenderer implements jalview.api.SequenceRenderer { AlignViewport av; @@ -50,7 +57,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -62,7 +69,7 @@ public class SequenceRenderer public Color getResidueBoxColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i)) { @@ -73,17 +80,42 @@ 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; + } + 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))) @@ -96,10 +128,10 @@ public class SequenceRenderer } } - + public Color findSequenceColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); drawBoxes(seq, i, i, 0); return resBoxColour; } @@ -128,7 +160,8 @@ public class SequenceRenderer int length = seq.getLength(); int curStart = -1; - int curWidth = av.charWidth; + int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av + .getCharHeight(); Color tempColour = null; while (i <= end) @@ -153,40 +186,41 @@ public class SequenceRenderer { if (tempColour != null) { - graphics.fillRect(av.charWidth * (curStart - start), y1, - curWidth, av.charHeight); + graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth, + avCharHeight); } graphics.setColor(resBoxColour); curStart = i; - curWidth = av.charWidth; + curWidth = avCharWidth; tempColour = resBoxColour; } else { - curWidth += av.charWidth; + curWidth += avCharWidth; } i++; } - graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, - av.charHeight); + graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth, + avCharHeight); } public void drawText(SequenceI seq, int start, int end, int y1) { + int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); Font boldFont = null; boolean bold = false; - if (av.upperCasebold) + if (av.isUpperCasebold()) { - boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight); + boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight); graphics.setFont(av.getFont()); } - y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady + y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady int charOffset = 0; @@ -197,7 +231,7 @@ public class SequenceRenderer } char s = ' '; - + boolean srep = av.isDisplayReferenceSeq(); for (int i = start; i <= end; i++) { graphics.setColor(Color.black); @@ -220,10 +254,9 @@ public class SequenceRenderer getBoxColour(currentSequenceGroup.cs, seq, i); graphics.setColor(resBoxColour.darker()); } - if (currentSequenceGroup.getShowunconserved()) + if (currentSequenceGroup.getShowNonconserved()) { - // cheat - use this if we have a consensus for each group: s = getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.'); - s = getDisplayChar(av.consensus, i, s, '.'); + s = getDisplayChar(srep, i, s, '.'); } } else @@ -245,14 +278,14 @@ public class SequenceRenderer graphics.setColor(resBoxColour); } } - if (av.getShowunconserved()) + if (av.getShowUnconserved()) { - s = getDisplayChar(av.consensus, i, s, '.'); - + s = getDisplayChar(srep, i, s, '.'); + } } - if (av.upperCasebold) + if (av.isUpperCasebold()) { fm = graphics.getFontMetrics(); if ('A' <= s && s <= 'Z') @@ -271,21 +304,26 @@ public class SequenceRenderer } } - - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + av.charWidth + + charOffset = (avCharWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + avCharWidth * (i - start), y1); } } - - private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c) + private char getDisplayChar(final boolean usesrep, int position, char s, + char c) { - char conschar = consensus.annotations[position].displayCharacter.charAt(0); - if (conschar!='-' && s==conschar) + // TODO - use currentSequenceGroup rather than alignment + // currentSequenceGroup.getConsensus() + char conschar = (usesrep) ? av.getAlignment().getSeqrep() + .getCharAt(position) + : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter + .charAt(0); + if (!jalview.util.Comparison.isGap(conschar) && s == conschar) { - s= c; + s = c; } return s; } @@ -313,11 +351,11 @@ public class SequenceRenderer public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1) { - int pady = av.charHeight / 5; + int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); + int pady = avCharHeight / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), - av.charHeight); + graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight); graphics.setColor(Color.white); char s = '~'; @@ -331,19 +369,19 @@ public class SequenceRenderer s = seq.getCharAt(i); } - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (avCharWidth - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1 - + av.charWidth * (i - start), y1 + av.charHeight - pady); + + avCharWidth * (i - start), y1 + avCharHeight - pady); } } } public void drawCursor(SequenceI seq, int res, int x1, int y1) { - int pady = av.charHeight / 5; + int pady = av.getCharHeight() / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); graphics.setColor(Color.white); graphics.setColor(Color.white); @@ -352,9 +390,9 @@ public class SequenceRenderer if (av.validCharWidth) { - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); + (y1 + av.getCharHeight()) - pady); } }