X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=3164748b4fccd0f373d81e94be3821b61ba1b7ab;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=785d22d36323b4766837f048420f26a65a5ae4d7;hpb=e8bf50102d1e937c715bf15046ae5076343313c0;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 785d22d..3164748 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,156 +1,332 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class ResidueColourScheme implements ColourSchemeI -{ - Color[] colors; - int threshold = 0; - - /* Set when threshold colouring to either pid_gaps or pid_nogaps*/ - protected String ignoreGaps = "pid_gaps"; - - /** DOCUMENT ME!! */ - public Hashtable [] consensus; - - /** - * Creates a new ResidueColourScheme object. - * - * @param colors DOCUMENT ME! - * @param threshold DOCUMENT ME! - */ - public ResidueColourScheme(Color[] colors, int threshold) - { - this.colors = colors; - this.threshold = threshold; - } - - /** - * Creates a new ResidueColourScheme object. - */ - public ResidueColourScheme() - { - } - - /** - * DOCUMENT ME! - * - * @param consensus DOCUMENT ME! - */ - public void setConsensus(Vector vconsensus) - { - int i, iSize=vconsensus.size(); - consensus = new Hashtable[iSize]; - for(i=0; i= threshold) - { - return true; - } - } - - return false; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.util.Hashtable; +import java.util.Map; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class ResidueColourScheme implements ColourSchemeI +{ + final int[] symbolIndex; + + boolean conservationColouring = false; + + Color[] colors = null; + + int threshold = 0; + + /* Set when threshold colouring to either pid_gaps or pid_nogaps */ + protected String ignoreGaps = AAFrequency.PID_GAPS; + + /** Consenus as a hashtable array */ + Hashtable[] consensus; + + /** Conservation string as a char array */ + char[] conservation; + + int conservationLength = 0; + + /** DOCUMENT ME!! */ + int inc = 30; + + /** + * Creates a new ResidueColourScheme object. + * + * @param final int[] index table into colors (ResidueProperties.naIndex or + * ResidueProperties.aaIndex) + * @param colors + * colours for symbols in sequences + * @param threshold + * threshold for conservation shading + */ + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, + int threshold) + { + symbolIndex = aaOrnaIndex; + this.colors = colours; + this.threshold = threshold; + } + + /** + * 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; + } + + /** + * Find a colour without an index in a sequence + */ + public Color findColour(char c) + { + return colors == null ? Color.white : colors[symbolIndex[c]]; + } + + @Override + public Color findColour(char c, int j, SequenceI seq) + { + Color currentColour; + + if (colors != null && symbolIndex != null && (threshold == 0) + || aboveThreshold(c, j)) + { + currentColour = colors[symbolIndex[c]]; + } + else + { + currentColour = Color.white; + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, 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 = AAFrequency.PID_NOGAPS; + } + else + { + this.ignoreGaps = AAFrequency.PID_GAPS; + } + } + + /** + * DOCUMENT ME! + * + * @param s + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean aboveThreshold(char c, int j) + { + if ('a' <= c && c <= 'z') + { + // TO UPPERCASE !!! + // Faster than toUpperCase + c -= ('a' - 'A'); + } + + if (consensus == null || consensus.length < j || consensus[j] == null) + { + return false; + } + + if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) + && consensus[j].contains(String.valueOf(c))) + { + if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold) + { + return true; + } + } + + return false; + } + + public boolean conservationApplied() + { + return conservationColouring; + } + + @Override + public void setConservationApplied(boolean conservationApplied) + { + conservationColouring = conservationApplied; + } + + public void setConservationInc(int i) + { + inc = i; + } + + public int getConservationInc() + { + return inc; + } + + /** + * DOCUMENT ME! + * + * @param consensus + * DOCUMENT ME! + */ + public void setConsensus(Hashtable[] consensus) + { + if (consensus == null) + { + return; + } + + this.consensus = consensus; + } + + public void setConservation(Conservation cons) + { + if (cons == null) + { + conservationColouring = false; + conservation = null; + } + else + { + conservationColouring = true; + int i, iSize = cons.getConsSequence().getLength(); + conservation = new char[iSize]; + for (i = 0; i < iSize; i++) + { + conservation[i] = cons.getConsSequence().getCharAt(i); + } + conservationLength = conservation.length; + } + + } + + /** + * DOCUMENT ME! + * + * @param s + * DOCUMENT ME! + * @param i + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + + Color applyConservation(Color currentColour, int i) + { + + if ((conservationLength > i) && (conservation[i] != '*') + && (conservation[i] != '+')) + { + if (jalview.util.Comparison.isGap(conservation[i])) + { + currentColour = Color.white; + } + else + { + float t = 11 - (conservation[i] - '0'); + if (t == 0) + { + return Color.white; + } + + int red = currentColour.getRed(); + int green = currentColour.getGreen(); + int blue = currentColour.getBlue(); + + int dr = 255 - red; + int dg = 255 - green; + int db = 255 - blue; + + dr *= t / 10f; + dg *= t / 10f; + db *= t / 10f; + + red += (inc / 20f) * dr; + green += (inc / 20f) * dg; + blue += (inc / 20f) * db; + + if (red > 255 || green > 255 || blue > 255) + { + currentColour = Color.white; + } + else + { + currentColour = new Color(red, green, blue); + } + } + } + return currentColour; + } + + @Override + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) + { + } + + @Override + public ColourSchemeI applyTo(AnnotatedCollectionI sg, + Map hiddenRepSequences) + { + try + { + return getClass().newInstance(); + } catch (Exception q) + { + throw new Error(MessageManager.formatMessage( + "error.implementation_error_cannot_duplicate_colour_scheme", + new String[] { getClass().getName() }), q); + } + } +}