X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=03ab5364b4d54f20362ca306c0706af6e3b5476f;hb=HEAD;hp=b905c452ba87dcce2683ded2f74c2ec0fdc5cd36;hpb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b905c45..03ab536 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,267 +1,227 @@
-/*
-* 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)
- 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(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!
- */
-
- Color 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)
- {
- 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;
- }
-
-
-}
+/*
+ * 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.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+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";
+
+ /*
+ * default display name for a user defined colour scheme
+ */
+ public static final String USER_DEFINED = "User Defined";
+
+ /*
+ * name for (new) "User Defined.." colour scheme menu item
+ */
+ public static final String USER_DEFINED_MENU = "*User Defined*";
+
+ /*
+ * the canonical name of the annotation colour scheme
+ * (may be used to identify it in menu items)
+ */
+ public static final String ANNOTATION_COLOUR = "Annotation";
+
+ /*
+ * 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;
+ }
+
+ /**
+ * Find a colour without an index in a sequence
+ */
+ public Color findColour(char c)
+ {
+ Color colour = Color.white;
+
+ if (colors != null && symbolIndex != null && c < symbolIndex.length
+ && symbolIndex[c] < colors.length)
+ {
+ colour = colors[symbolIndex[c]];
+ }
+
+ return colour;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Default implementation looks up the residue colour in a fixed scheme, or
+ * returns White if not found. Override this method for a colour scheme that
+ * depends on the column position or sequence.
+ *
+ * @param c
+ * @param j
+ * @param seq
+ * @return
+ */
+ protected Color findColour(char c, int j, SequenceI seq)
+ {
+ return findColour(c);
+ }
+
+ @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;
+ }
+ if (ac == null)
+ {
+ return true;
+ }
+ /*
+ * pop-up menu on selection group before group created
+ * (no alignment context)
+ */
+ // TODO: add nucleotide flag to SequenceGroup?
+ if (ac instanceof SequenceGroup && ac.getContext() == null)
+ {
+ return true;
+ }
+
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = ac.isNucleotide();
+
+ /*
+ * 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;
+ }
+
+ /**
+ * Default method returns false. Override this to return true in colour
+ * schemes that have a colour associated with gap residues.
+ */
+ @Override
+ public boolean hasGapColour()
+ {
+ return false;
+ }
+}