X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=970d20e751ebc98b32e4c93d16c686519fd3bf20;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=c41c35fa9f02c3a2a29e6c3c60dbb5c88077d688;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index c41c35f..970d20e 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,30 +1,39 @@ /* - * 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.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 { + final static int CHAR_TO_UPPER = 'A' - 'a'; + AlignViewport av; FontMetrics fm; @@ -50,7 +59,7 @@ public class SequenceRenderer * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -60,9 +69,10 @@ public class SequenceRenderer this.renderGaps = renderGaps; } + @Override public Color getResidueBoxColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i)) { @@ -73,17 +83,42 @@ 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))) @@ -99,7 +134,7 @@ 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 +163,8 @@ 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 +189,41 @@ 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 +234,7 @@ public class SequenceRenderer } char s = ' '; - + boolean srep = av.isDisplayReferenceSeq(); for (int i = start; i <= end; i++) { graphics.setColor(Color.black); @@ -220,6 +257,10 @@ public class SequenceRenderer getBoxColour(currentSequenceGroup.cs, seq, i); graphics.setColor(resBoxColour.darker()); } + if (currentSequenceGroup.getShowNonconserved()) + { + s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); + } } else { @@ -240,9 +281,14 @@ public class SequenceRenderer graphics.setColor(resBoxColour); } } + if (av.getShowUnconserved()) + { + s = getDisplayChar(srep, i, s, '.', null); + + } } - if (av.upperCasebold) + if (av.isUpperCasebold()) { fm = graphics.getFontMetrics(); if ('A' <= s && s <= 'Z') @@ -262,13 +308,52 @@ 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); } } + /** + * Returns 'conservedChar' to represent the given position if the sequence + * character at that position is equal to the consensus (ignoring case), else + * returns the sequence character + * + * @param usesrep + * @param position + * @param sequenceChar + * @param conservedChar + * @return + */ + private char getDisplayChar(final boolean usesrep, int position, + char sequenceChar, char conservedChar, SequenceGroup currentGroup) + { + // TODO - use currentSequenceGroup rather than alignment + // currentSequenceGroup.getConsensus() + char conschar = (usesrep) ? (currentGroup == null + || position < currentGroup.getStartRes() + || position > currentGroup.getEndRes() ? av.getAlignment() + .getSeqrep().getCharAt(position) + : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep() + .getCharAt(position) : av.getAlignment().getSeqrep() + .getCharAt(position))) + : (currentGroup != null && currentGroup.getConsensus() != null + && position >= currentGroup.getStartRes() + && position <= currentGroup.getEndRes() && currentGroup + .getConsensus().annotations.length > position) ? currentGroup + .getConsensus().annotations[position].displayCharacter + .charAt(0) + : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter + .charAt(0); + if (!jalview.util.Comparison.isGap(conschar) + && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar)) + { + sequenceChar = conservedChar; + } + return sequenceChar; + } + boolean inCurrentSequenceGroup(int res) { if (allGroups == null) @@ -292,11 +377,11 @@ 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 = '~'; @@ -310,19 +395,19 @@ 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); @@ -331,9 +416,9 @@ 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); } }