X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=fc8b1b13ca5d67207bf70c26a5f527758812418e;hb=09d9063e70931a6cb75d16b230f5cd0665f0f340;hp=90833c9c731d14a72cf4fa6a00789861b3d28fda;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 90833c9..fc8b1b1 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,285 +1,198 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- * 
+ * 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/>.
+ * 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.analysis.AAFrequency;
-import jalview.analysis.Conservation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Hashtable;
+import java.util.Map;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * Base class for residue-based colour schemes
  */
-public class ResidueColourScheme implements ColourSchemeI
+public abstract class ResidueColourScheme implements ColourSchemeI
 {
+  public static final String NONE = "None";
 
-  boolean conservationColouring = false;
+  public static final String USER_DEFINED = "User Defined";
 
-  Color[] colors = null;
+  /*
+   * 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;
 
-  int threshold = 0;
+  /*
+   * colour for residue characters as indexed by symbolIndex
+   */
+  Color[] colors = null;
 
   /* 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;
-
-  int conservationLength = 0;
-
-  /** DOCUMENT ME!! */
-  int inc = 30;
+  protected boolean ignoreGaps = false;
 
   /**
    * Creates a new ResidueColourScheme object.
    * 
+   * @param final int[] index table into colors (ResidueProperties.naIndex or
+   *        ResidueProperties.aaIndex)
    * @param colors
-   *          DOCUMENT ME!
-   * @param threshold
-   *          DOCUMENT ME!
+   *          colours for symbols in sequences
    */
-  public ResidueColourScheme(Color[] colours, int threshold)
+  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
   {
+    symbolIndex = aaOrnaIndex;
     this.colors = colours;
-    this.threshold = threshold;
   }
 
   /**
-   * Creates a new ResidueColourScheme object.
+   * 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
    */
+  @Override
   public Color findColour(char c)
   {
-    return colors == null ? Color.white
-            : colors[ResidueProperties.aaIndex[c]];
+    return colors == null ? Color.white : colors[symbolIndex[c]];
   }
 
+  /**
+   * 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)
+  public Color findColour(char c, int j, SequenceI seq,
+          String consensusResidue, float pid)
   {
-    Color currentColour;
+    return findColour(c, j, seq);
+  }
 
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      currentColour = colors[ResidueProperties.aaIndex[c]];
-    }
-    else
-    {
-      currentColour = Color.white;
-    }
+  protected Color findColour(char c, int j, SequenceI seq)
+  {
+    Color colour = Color.white;
 
-    if (conservationColouring)
+    if (colors != null && symbolIndex != null && c < symbolIndex.length
+            && symbolIndex[c] < colors.length)
     {
-      currentColour = applyConservation(currentColour, j);
+      colour = colors[symbolIndex[c]];
     }
+    // colour = adjustColour(c, j, colour);
 
-    return currentColour;
+    return colour;
   }
-  @Override public void alignmentChanged(AnnotatedCollectionI alignment) {};
 
-  /**
-   * Get the percentage threshold for this colour scheme
-   * 
-   * @return Returns the percentage threshold
-   */
-  public int getThreshold()
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    return threshold;
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param ct
-   *          DOCUMENT ME!
+   * 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.
    */
-  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(char c, int j)
+  @Override
+  public boolean isApplicableTo(AnnotatedCollectionI ac)
   {
-    if ('a' <= c && c <= 'z')
+    if (!isPeptideSpecific() && !isNucleotideSpecific())
     {
-      // TO UPPERCASE !!!
-      // Faster than toUpperCase
-      c -= ('a' - 'A');
+      return true;
     }
 
-    if (consensus == null || consensus.length < j || consensus[j] == null)
+    /*
+     * inspect the data context (alignment) for residue type
+     */
+    boolean nucleotide = false;
+    if (ac instanceof AlignmentI)
     {
-      return false;
+      nucleotide = ((AlignmentI) ac).isNucleotide();
     }
-
-    if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
-            && consensus[j].contains(String.valueOf(c)))
+    else
     {
-      if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      AnnotatedCollectionI context = ac.getContext();
+      if (context instanceof AlignmentI)
       {
+        nucleotide = ((AlignmentI) context).isNucleotide();
+      }
+      else
+      {
+        // not sure what's going on, play safe
         return true;
       }
     }
 
-    return false;
-  }
-
-  public boolean conservationApplied()
-  {
-    return conservationColouring;
-  }
-
-  public void setConservationInc(int i)
-  {
-    inc = i;
-  }
-
-  public int getConservationInc()
-  {
-    return inc;
+    /*
+     * does data type match colour scheme type?
+     */
+    return (nucleotide && isNucleotideSpecific())
+            || (!nucleotide && isPeptideSpecific());
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers true if the colour scheme is normally only for peptide data
    * 
-   * @param consensus
-   *          DOCUMENT ME!
+   * @return
    */
-  public void setConsensus(Hashtable[] consensus)
+  public boolean isPeptideSpecific()
   {
-    if (consensus == null)
-    {
-      return;
-    }
-
-    this.consensus = consensus;
+    return false;
   }
 
-  public void setConservation(Conservation cons)
+  /**
+   * Answers true if the colour scheme is normally only for nucleotide data
+   * 
+   * @return
+   */
+  public boolean isNucleotideSpecific()
   {
-    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);
-      }
-      conservationLength = conservation.length;
-    }
-
+    return false;
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * Default method returns true. Override this to return false in colour
+   * schemes that are not determined solely by the sequence symbol.
    */
-
-  Color applyConservation(Color currentColour, int i)
+  @Override
+  public boolean isSimple()
   {
-
-    if ((conservationLength > i) && (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;
+    return true;
   }
-
 }