X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=6a2a479244c4c9d52ea709fb2dedc34796a69cea;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=0d2db232b6f5724aadfbb50c62a1c78cd73c906a;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 0d2db23..6a2a479 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,263 +1,209 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* 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 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. -* -* 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 -*/ -package jalview.schemes; - -import jalview.analysis.*; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class ResidueColourScheme implements ColourSchemeI -{ - - boolean conservationColouring = false; - boolean consensusColouring = false; - - Color[] colors; - int threshold = 0; - - /* Set when threshold colouring to either pid_gaps or pid_nogaps*/ - protected String ignoreGaps = "pid_gaps"; - - /** Consenus as a hashtable array */ - Hashtable [] consensus; - - /** Conservation string as a char array */ - char [] conservation; - - /** DOCUMENT ME!! */ - int inc = 30; - - /** - * The colour to be calculated, manipulated and returned - */ - Color currentColour = null; - - - - /** - * Creates a new ResidueColourScheme object. - * - * @param colors DOCUMENT ME! - * @param threshold DOCUMENT ME! - */ - public ResidueColourScheme(Color[] colours, int threshold) - { - this.colors = colours; - this.threshold = threshold; - } - - /** - * Creates a new ResidueColourScheme object. - */ - public ResidueColourScheme() - { - } - - /** - * Find a colour without an index in a sequence - */ - public Color findColour(String aa) - { - return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()]; - } - - - - public Color findColour(String s, int j) - { - - int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue(); - - if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j)) - { - currentColour = colors[index]; - } - else - { - currentColour = Color.white; - } - - if(conservationColouring) - applyConservation(j); - - - return currentColour; - } - - - /** - * Get the percentage threshold for this colour scheme - * - * @return Returns the percentage threshold - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param ct DOCUMENT ME! - */ - public void setThreshold(int ct, boolean ignoreGaps) - { - threshold = ct; - if(ignoreGaps) - this.ignoreGaps = "pid_nogaps"; - else - this.ignoreGaps = "pid_gaps"; - } - - /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param j DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean aboveThreshold(String s, int j) - { - if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) && - consensus[j].contains(s)) - { - if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold) - { - return true; - } - } - - return false; - } - - - public boolean conservationApplied() - { - return conservationColouring; - } - - public void setConservationInc(int i) - { - inc = i; - } - - public int getConservationInc() - { - return inc; - } - - /** - * DOCUMENT ME! - * - * @param consensus DOCUMENT ME! - */ - public void setConsensus(Vector vconsensus) - { - if(vconsensus==null) - return; - - int i, iSize=vconsensus.size(); - consensus = new Hashtable[iSize]; - for(i=0; i 255 || green > 255 || blue > 255) - currentColour = Color.white; - else - currentColour = new Color(red, green, blue); - } - } - } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.schemes; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceI; + +import java.awt.Color; +import java.util.Map; + +/** + * Base class for residue-based colour schemes + */ +public abstract class ResidueColourScheme implements ColourSchemeI +{ + public static final String NONE = "None"; + + public static final String USER_DEFINED = "User Defined"; + + /* + * lookup up by character value e.g. 'G' to the colors array index + * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K + */ + final int[] symbolIndex; + + /* + * colour for residue characters as indexed by symbolIndex + */ + Color[] colors = null; + + /* Set when threshold colouring to either pid_gaps or pid_nogaps */ + protected boolean ignoreGaps = false; + + /** + * Creates a new ResidueColourScheme object. + * + * @param final int[] index table into colors (ResidueProperties.naIndex or + * ResidueProperties.aaIndex) + * @param colors + * colours for symbols in sequences + */ + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours) + { + symbolIndex = aaOrnaIndex; + this.colors = colours; + } + + /** + * Creates a new ResidueColourScheme object with a lookup table for indexing + * the colour map + */ + public ResidueColourScheme(int[] aaOrNaIndex) + { + symbolIndex = aaOrNaIndex; + } + + /** + * Creates a new ResidueColourScheme object - default constructor for + * non-sequence dependent colourschemes + */ + public ResidueColourScheme() + { + symbolIndex = null; + } + + /** + * Returns the colour for symbol 'A'. Intended for use in a 'fixed colour' + * colour scheme (for example a feature colour). + */ + @Override + public Color findColour() + { + // TODO delete this method in favour of ColorUtils.parseColourString()? + return findColour('A'); + } + + /** + * Find a colour without an index in a sequence + */ + @Override + public Color findColour(char c) + { + return colors == null ? Color.white : colors[symbolIndex[c]]; + } + + /** + * Default is to call the overloaded method that ignores consensus. A colour + * scheme that depends on consensus (for example, Blosum62), should override + * this method instead. + */ + @Override + public Color findColour(char c, int j, SequenceI seq, + String consensusResidue, float pid) + { + return findColour(c, j, seq); + } + + protected Color findColour(char c, int j, SequenceI seq) + { + Color colour = Color.white; + + if (colors != null && symbolIndex != null && c < symbolIndex.length + && symbolIndex[c] < colors.length) + { + colour = colors[symbolIndex[c]]; + } + // colour = adjustColour(c, j, colour); + + return colour; + } + + @Override + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) + { + } + + /** + * Answers false if the colour scheme is nucleotide or peptide specific, and + * the data does not match, else true. Override to modify or extend this test + * as required. + */ + @Override + public boolean isApplicableTo(AnnotatedCollectionI ac) + { + if (!isPeptideSpecific() && !isNucleotideSpecific()) + { + return true; + } + + /* + * inspect the data context (alignment) for residue type + */ + boolean nucleotide = false; + if (ac instanceof AlignmentI) + { + nucleotide = ((AlignmentI) ac).isNucleotide(); + } + else + { + AnnotatedCollectionI context = ac.getContext(); + if (context instanceof AlignmentI) + { + nucleotide = ((AlignmentI) context).isNucleotide(); + } + else + { + // not sure what's going on, play safe + return true; + } + } + + /* + * does data type match colour scheme type? + */ + return (nucleotide && isNucleotideSpecific()) + || (!nucleotide && isPeptideSpecific()); + } + + /** + * Answers true if the colour scheme is normally only for peptide data + * + * @return + */ + public boolean isPeptideSpecific() + { + return false; + } + + /** + * Answers true if the colour scheme is normally only for nucleotide data + * + * @return + */ + public boolean isNucleotideSpecific() + { + return false; + } + + /** + * Default method returns true. Override this to return false in colour + * schemes that are not determined solely by the sequence symbol. + */ + @Override + public boolean isSimple() + { + return true; + } +}