X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=c1eeafa30277f1ebb8826fb026d5f1e0935f130e;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=bf8366547f6d93fb38e857de28994fd5c3b3b758;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bf83665..c1eeafa 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,267 +1,428 @@
-/*
-* 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 = AAFrequency.PID_GAPS;
-
- /** Consenus as a hashtable array */
- Hashtable [] consensus;
-
- /** Conservation string as a char array */
- char [] conservation;
-
- /** DOCUMENT ME!! */
- int inc = 30;
-
-
- /**
- * 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[ResidueProperties.aaIndex[aa.charAt(0)]];
- }
-
-
-
- public Color findColour(String s, int j)
- {
- Color currentColour;
- int index = ResidueProperties.aaIndex[s.charAt(0)];
-
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
- {
- currentColour = colors[index];
- }
- else
- {
- currentColour = Color.white;
- }
-
- if(conservationColouring)
- 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(String s, int j)
- {
- char c = s.charAt(0);
- if ('a' <= c && c <= 'z')
- {
- // TO UPPERCASE !!!
- //Faster than toUpperCase
- c -= ('a' - 'A');
- s = String.valueOf(c);
- }
-
- if (consensus == null || consensus[j] == null)
- return false;
-
- if ( ( ( (Integer) consensus[j].get(AAFrequency.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(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);
- }
-
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
-
- void applyConservation(Color currentColour, int i)
- {
-
- if ((conservation[i] != '*') && (conservation[i] != '+'))
- {
- if(jalview.util.Comparison.isGap(conservation[i]))
- {
- currentColour = Color.white;
- }
- else
- {
- float t = 11 - (conservation[i] - '0');
- if(t==0)
- {
- currentColour = Color.white;
- return;
- }
-
- 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);
- }
- }
- }
-
-
-}
+/*
+ * 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.analysis.Conservation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * Base class for residue-based colour schemes
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+ public static final String NONE = "None";
+
+ final int[] symbolIndex;
+
+ boolean conservationColouring = false;
+
+ Color[] colors = null;
+
+ int threshold = 0;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+ protected boolean ignoreGaps = false;
+
+ /*
+ * Consensus data indexed by column
+ */
+ ProfilesI consensus;
+
+ /*
+ * Conservation string as a char array
+ */
+ char[] conservation;
+
+ /*
+ * The conservation slider percentage setting
+ */
+ 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;
+ }
+
+ /**
+ * Returns the colour for symbol 'A'. Intended for use in a 'fixed colour'
+ * colour scheme (for example a feature colour).
+ */
+ @Override
+ public Color findColour()
+ {
+ 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]];
+ }
+
+ @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
+ */
+ @Override
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the percentage consensus threshold value, and whether gaps are ignored
+ * in percentage identity calculation
+ *
+ * @param consensusThreshold
+ * @param ignoreGaps
+ */
+ @Override
+ public void setThreshold(int consensusThreshold, boolean ignoreGaps)
+ {
+ threshold = consensusThreshold;
+ this.ignoreGaps = ignoreGaps;
+ }
+
+ /**
+ * Answers true if there is a consensus profile for the specified column, and
+ * the given residue matches the consensus (or joint consensus) residue for
+ * the column, and the percentage identity for the profile is equal to or
+ * greater than the current threshold; else answers false. The percentage
+ * calculation depends on whether or not we are ignoring gapped sequences.
+ *
+ * @param residue
+ * @param column
+ * (index into consensus profiles)
+ *
+ * @return
+ * @see #setThreshold(int, boolean)
+ */
+ public boolean aboveThreshold(char residue, int column)
+ {
+ if ('a' <= residue && residue <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ residue -= ('a' - 'A');
+ }
+
+ if (consensus == null)
+ {
+ return false;
+ }
+
+ ProfileI profile = consensus.get(column);
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ if (profile != null
+ && profile.getModalResidue().contains(String.valueOf(residue)))
+ {
+ if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ @Override
+ public boolean conservationApplied()
+ {
+ return conservationColouring;
+ }
+
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
+ @Override
+ public void setConservationInc(int i)
+ {
+ inc = i;
+ }
+
+ @Override
+ public int getConservationInc()
+ {
+ return inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param consensus
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setConsensus(ProfilesI consensus)
+ {
+ if (consensus == null)
+ {
+ return;
+ }
+
+ this.consensus = consensus;
+ }
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (cons == null)
+ {
+ conservationColouring = false;
+ conservation = null;
+ }
+ else
+ {
+ conservationColouring = true;
+ int iSize = cons.getConsSequence().getLength();
+ conservation = new char[iSize];
+ for (int i = 0; i < iSize; i++)
+ {
+ conservation[i] = cons.getConsSequence().getCharAt(i);
+ }
+ }
+
+ }
+
+ /**
+ * Applies a combination of column conservation score, and conservation
+ * percentage slider, to 'bleach' out the residue colours towards white.
+ *
+ * If a column is fully conserved (identical residues, conservation score 11,
+ * shown as *), or all 10 physico-chemical properties are conserved
+ * (conservation score 10, shown as +), then the colour is left unchanged.
+ *
+ * Otherwise a 'bleaching' factor is computed and applied to the colour. This
+ * is designed to fade colours for scores of 0-9 completely to white at slider
+ * positions ranging from 18% - 100% respectively.
+ *
+ * @param currentColour
+ * @param column
+ *
+ * @return bleached (or unmodified) colour
+ */
+ Color applyConservation(Color currentColour, int column)
+ {
+ if (conservation == null || conservation.length <= column)
+ {
+ return currentColour;
+ }
+ char conservationScore = conservation[column];
+
+ /*
+ * if residues are fully conserved (* or 11), or all properties
+ * are conserved (+ or 10), leave colour unchanged
+ */
+ if (conservationScore == '*' || conservationScore == '+'
+ || conservationScore == (char) 10
+ || conservationScore == (char) 11)
+ {
+ return currentColour;
+ }
+
+ if (Comparison.isGap(conservationScore))
+ {
+ return Color.white;
+ }
+
+ /*
+ * convert score 0-9 to a bleaching factor 1.1 - 0.2
+ */
+ float bleachFactor = (11 - (conservationScore - '0')) / 10f;
+
+ /*
+ * scale this up by 0-5 (percentage slider / 20)
+ * as a result, scores of: 0 1 2 3 4 5 6 7 8 9
+ * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
+ */
+ bleachFactor *= (inc / 20f);
+
+ return ColorUtils.bleachColour(currentColour, bleachFactor);
+ }
+
+ @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);
+ }
+ }
+
+ /**
+ * Answers false if the colour scheme is nucleotide or peptide specific, and
+ * the data does not match, else false. 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 dataset) for residue type
+ */
+ boolean nucleotide = false;
+ AnnotatedCollectionI context = ac.getContext();
+ if (context != null)
+ {
+ if (context instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) context).isNucleotide();
+ }
+ else
+ {
+ // not sure what's going on, play safe
+ return true;
+ }
+ }
+ else if (ac instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) ac).isNucleotide();
+ }
+ else
+ {
+ 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;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Residue";
+ }
+}