X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=03fc129a2e99b8747c35a3709ad5fae405b7c37f;hb=a45b4529c64901e9e4b53b6c74ee804370c91002;hp=3181cf4fa9c027878d3969660289c699eb1bb1a5;hpb=96786b7b949dc261a9556e13a17870166915d0e9;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 3181cf4..03fc129 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,156 +1,204 @@
-/*
-* 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<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String aa)
-    {
-        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String s, int j)
-    {
-        if ((threshold == 0) || aboveThreshold(s, j))
-        {
-            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
-        }
-        else
-        {
-            return Color.white;
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ct DOCUMENT ME!
-     */
-    public void setThreshold(int ct, boolean ignoreGaps)
-    {
-        threshold = ct;
-        if(ignoreGaps)
-          this.ignoreGaps = "pid_nogaps";
-        else
-          this.ignoreGaps = "pid_gaps";
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean aboveThreshold(String s, int j)
-    {
-      if(consensus==null)
-        System.out.println("its null");
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
-                consensus[j].contains(s))
-        {
-            float ratio =  ((Float)consensus[j].get(ignoreGaps)).floatValue();
-
-            if (ratio >= threshold)
-            {
-                return true;
-            }
-        }
-
-        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.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+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;
+    }
+    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;
+  }
+}