X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=eab6e39fa8fefada05dd9fc932570331faad988b;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=c41c35fa9f02c3a2a29e6c3c60dbb5c88077d688;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index c41c35f..eab6e39 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -1,56 +1,64 @@ /* - * 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.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.renderer.ResidueColourFinder; +import jalview.renderer.seqfeatures.FeatureColourFinder; -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; boolean renderGaps = true; - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; Color resBoxColour; Graphics graphics; - boolean forOverview = false; + ResidueColourFinder resColourFinder; public SequenceRenderer(AlignViewport av) { this.av = av; + resColourFinder = new ResidueColourFinder(); } /** * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void prepare(Graphics g, boolean renderGaps) { @@ -60,46 +68,29 @@ public class SequenceRenderer this.renderGaps = renderGaps; } - public Color getResidueBoxColour(SequenceI seq, int i) - { - allGroups = av.alignment.findAllGroups(seq); - - if (inCurrentSequenceGroup(i)) - { - if (currentSequenceGroup.getDisplayBoxes()) - { - getBoxColour(currentSequenceGroup.cs, seq, i); - } - } - else if (av.getShowBoxes()) - { - getBoxColour(av.globalColourScheme, seq, i); - } - - return resBoxColour; - } - - void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) + /** + * 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 finder + * @return + */ + @Override + public Color getResidueColour(final SequenceI seq, int position, + FeatureColourFinder finder) { - if (cs != null) - { - resBoxColour = cs.findColour(seq.getCharAt(i), i); - } - else if (forOverview - && !jalview.util.Comparison.isGap(seq.getCharAt(i))) - { - resBoxColour = Color.lightGray; - } - else - { - resBoxColour = Color.white; - } - + // TODO replace 8 or so code duplications with calls to this method + // (refactored as needed) + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), allGroups, seq, position, finder); } public Color findSequenceColour(SequenceI seq, int i) { - allGroups = av.alignment.findAllGroups(seq); + allGroups = av.getAlignment().findAllGroups(seq); drawBoxes(seq, i, i, 0); return resBoxColour; } @@ -128,24 +119,30 @@ 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 resBoxColour = Color.white; Color tempColour = null; while (i <= end) { resBoxColour = Color.white; if (i < length) { - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } } @@ -153,40 +150,41 @@ 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 +195,7 @@ public class SequenceRenderer } char s = ' '; - + boolean srep = av.isDisplayReferenceSeq(); for (int i = start; i <= end; i++) { graphics.setColor(Color.black); @@ -208,7 +206,9 @@ public class SequenceRenderer continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -217,9 +217,14 @@ public class SequenceRenderer if (currentSequenceGroup.getColourText()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); graphics.setColor(resBoxColour.darker()); } + if (currentSequenceGroup.getShowNonconserved()) + { + s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); + } } else { @@ -230,7 +235,8 @@ public class SequenceRenderer if (av.getColourText()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { graphics.setColor(resBoxColour.darker()); @@ -240,9 +246,14 @@ 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') @@ -262,41 +273,65 @@ public class SequenceRenderer } - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + av.charWidth - * (i - start), y1); + charOffset = (avCharWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), + charOffset + avCharWidth * (i - start), y1); } } - boolean inCurrentSequenceGroup(int res) + /** + * 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) { - if (allGroups == null) - { - return false; - } - - for (int i = 0; i < allGroups.length; i++) + // 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)) { - if (allGroups[i].getStartRes() <= res - && allGroups[i].getEndRes() >= res) - { - currentSequenceGroup = allGroups[i]; - return true; - } + sequenceChar = conservedChar; } - - return false; + return sequenceChar; } - public void drawHighlightedText(SequenceI seq, int start, int end, - int x1, int y1) + 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 +345,20 @@ public class SequenceRenderer s = seq.getCharAt(i); } - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1 - + av.charWidth * (i - start), y1 + av.charHeight - pady); + charOffset = (avCharWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), + charOffset + x1 + 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 +367,9 @@ 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); } }