X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=2f7a5e0220a366291ca00030c016e83c5897d90d;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=95946f92c26d8f15522d232ce4728256f96ba226;hpb=bcfc2937c9284fb9611008dbcfa712f14447dd1f;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 95946f9..2f7a5e0 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,111 +1,221 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import java.util.*;
-import java.awt.*;
-
-public class ResidueColourScheme implements ColourSchemeI {
- Color [] colors;
- int threshold = 90;
-
- public ResidueColourScheme(Color[] colors, int threshold) {
- this.colors = colors;
- this.threshold = threshold;
- }
-
- public ResidueColourScheme() {
- }
-
- public Color findColour(String aa)
- {
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
- }
-
- public Color findColour(SequenceI seq,String s, int j, Vector aa) {
- try {
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
- } catch (Exception e) {
- return Color.white;
- }
- }
-
- // aa should maybe be a class
- public Color getColour(SequenceI seq, int j,Vector aa) {
-
- Color c = Color.white;
- String s = seq.getSequence(j,j+1);
-
- if (threshold > 0 && aa != null)
- {
- if (aboveThreshold(aa,seq,j,threshold))
- c = findColour(seq,s,j,aa);
- }
- else
- c = findColour(seq,s,j,aa);
-
-
- return c;
- }
- public int getThreshold() {
- return threshold;
- }
-
- public void setThreshold(int ct) {
- threshold = ct;
- }
-
- public Vector getColours(SequenceI s, Vector aa) {
- Vector colours = new Vector();
-
- for (int j = 0; j < s.getLength(); j++)
- colours.addElement(getColour(s,j,aa));
-
- return colours;
- }
-
- public Vector getColours(SequenceGroup sg, Vector aa) {
- Vector colours = new Vector();
-
- for (int j = 0; j < sg.getSize(); j++) {
- SequenceI s = sg.getSequenceAt(j);
-
- for (int i = 0; i < s.getLength();i++) {
- colours.addElement(getColour(s,i,aa));
- }
- }
- return colours;
- }
-
- public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
- String s = seq.getSequence(j,j+1);
- Hashtable hash = (Hashtable)aa.elementAt(j);
-
- if (j < aa.size()) {
- String maxRes = (String)hash.get("maxResidue");
-
- double sc = 0;
-
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
- int maxCount = ((Integer)hash.get("maxCount")).intValue();
- int resCount = ((Integer)hash.get(s)).intValue();
-
- sc = resCount * 100.0 / resCount;
-
- // This should be isGap somewhere
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
- if (sc >= (double)threshold) {
- return true;
- }
- }
- }
- }
- return false;
- }
-
- public boolean canThreshold() {
- return true;
- }
- public boolean isUserDefinable() {
- return false;
- }
-}
+/*
+ * 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*";
+
+ /*
+ * 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;
+ }
+}