X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=358417b81b6c5d58fa12568a5b35caeb0bf26f25;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=f16bccac39f58c3c8f22b7afa8594fd29f10c03c;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f16bcca..358417b 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,90 +1,208 @@
-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 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 <http://www.gnu.org/licenses/>.
+ * 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 jalview.util.Comparison;
+
+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;
+  }
+
+  /**
+   * Find a colour without an index in a sequence
+   */
+  public Color findColour(char c)
+  {
+    Color colour = Color.white;
+
+    if (!Comparison.isGap(c) && 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<SequenceI, SequenceCollectionI> 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;
+  }
+}