update author list in license for (JAL-826)

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2488d77..4c8394f 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * This file is part of Jalview.
  * 
@@ -30,6 +30,8 @@ public class ResidueProperties
 
   public static final int[] nucleotideIndex;
 
+  public static final int[] purinepyrimidineIndex;
+
   public static final Hashtable aa3Hash = new Hashtable();
 
   public static final Hashtable aa2Triplet = new Hashtable();
@@ -144,6 +146,54 @@ public class ResidueProperties
     nucleotideName.put("y", "Unknown Pyrimidine");
     nucleotideName.put("N", "Unknown");
     nucleotideName.put("n", "Unknown");
+    nucleotideName.put("W", "Weak nucleotide (A or T)");
+    nucleotideName.put("w", "Weak nucleotide (A or T)");
+    nucleotideName.put("S", "Strong nucleotide (G or C)");
+    nucleotideName.put("s", "Strong nucleotide (G or C)");
+    nucleotideName.put("M", "Amino (A or C)");
+    nucleotideName.put("m", "Amino (A or C)");
+    nucleotideName.put("K", "Keto (G or T)");
+    nucleotideName.put("k", "Keto (G or T)");
+    nucleotideName.put("B", "Not A (G or C or T)");
+    nucleotideName.put("b", "Not A (G or C or T)");
+    nucleotideName.put("H", "Not G (A or C or T)");
+    nucleotideName.put("h", "Not G (A or C or T)");
+    nucleotideName.put("D", "Not C (A or G or T)");
+    nucleotideName.put("d", "Not C (A or G or T)");
+    nucleotideName.put("V", "Not T (A or G or C");
+    nucleotideName.put("v", "Not T (A or G or C");
+
+  }
+
+  static
+  {
+    purinepyrimidineIndex = new int[255];
+    for (int i = 0; i < 255; i++)
+    {
+      purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap
+      // gaps.
+    }
+
+    purinepyrimidineIndex['A'] = 0;
+    purinepyrimidineIndex['a'] = 0;
+    purinepyrimidineIndex['C'] = 1;
+    purinepyrimidineIndex['c'] = 1;
+    purinepyrimidineIndex['G'] = 0;
+    purinepyrimidineIndex['g'] = 0;
+    purinepyrimidineIndex['T'] = 1;
+    purinepyrimidineIndex['t'] = 1;
+    purinepyrimidineIndex['U'] = 1;
+    purinepyrimidineIndex['u'] = 1;
+    purinepyrimidineIndex['I'] = 2;
+    purinepyrimidineIndex['i'] = 2;
+    purinepyrimidineIndex['X'] = 2;
+    purinepyrimidineIndex['x'] = 2;
+    purinepyrimidineIndex['R'] = 0;
+    purinepyrimidineIndex['r'] = 0;
+    purinepyrimidineIndex['Y'] = 1;
+    purinepyrimidineIndex['y'] = 1;
+    purinepyrimidineIndex['N'] = 2;
+    purinepyrimidineIndex['n'] = 2;
   }
 
   static
@@ -280,14 +330,22 @@ public class ResidueProperties
       new Color(235, 65, 60), // G
       new Color(60, 136, 238), // T
       new Color(60, 136, 238), // U
-      Color.white, // I
-      Color.white, // X
+      Color.white, // I (inosine)
+      Color.white, // X (xanthine)
       Color.white, // R
       Color.white, // Y
       Color.white, // N
       Color.white, // Gap
   };
 
+  // Added for PurinePyrimidineColourScheme
+  public static final Color[] purinepyrimidine =
+  { new Color(255, 131, 250), // A, G, R purines purplish/orchid
+      new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
+      Color.white, // all other nucleotides
+      Color.white // Gap
+  };
+
   // Zappo
   public static final Color[] zappo =
   { Color.pink, // A
@@ -540,7 +598,7 @@ public class ResidueProperties
 
   public static final Color[] pidColours =
   { midBlue, new Color(153, 153, 255),
-  // Color.lightGray,
+      // Color.lightGray,
       new Color(204, 204, 255), };
 
   public static final float[] pidThresholds =
@@ -1258,6 +1316,46 @@ public class ResidueProperties
     return ss.toString();
   }
 
+  /**
+   * Used by getRNASecStrucState
+   * 
+   */
+  public static Hashtable toRNAssState;
+  static
+  {
+    toRNAssState = new Hashtable();
+    toRNAssState.put(")", "S");
+    toRNAssState.put("(", "S");
+  }
+
+  /**
+   * translate to RNA secondary structure representation
+   * 
+   * @param ssstring
+   * @return ssstring as a RNA-state secondary structure assignment.
+   */
+  public static String getRNASecStrucState(String ssstring)
+  {
+    if (ssstring == null)
+    {
+      return null;
+    }
+    StringBuffer ss = new StringBuffer();
+    for (int i = 0; i < ssstring.length(); i++)
+    {
+      String ssc = ssstring.substring(i, i + 1);
+      if (toRNAssState.containsKey(ssc))
+      {
+        ss.append((String) toRNAssState.get(ssc));
+      }
+      else
+      {
+        ss.append(" ");
+      }
+    }
+    return ss.toString();
+  }
+
   // main method generates perl representation of residue property hash
   // / cut here
   public static void main(String[] args)