X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=a531df5233440dbc68af4d933fb94688aed0c058;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=62e46be31283376eb59c9f00e75e984904c3a25c;hpb=0ae0539d4fc9e78d94c33afe0ac07457464afd16;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 62e46be..a531df5 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,30 +1,39 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 java.util.*;
-import java.util.List;
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
 
-import java.awt.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 public class ResidueProperties
 {
-  public static Hashtable scoreMatrices = new Hashtable();
+  public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable();
 
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
@@ -692,19 +701,20 @@ public class ResidueProperties
   }
 
   /**
-   * Nucleotide Ambiguity Codes 
+   * Nucleotide Ambiguity Codes
    */
-  public static final Hashtable<String,String[]> ambiguityCodes=new Hashtable<String,String[]>();
+  public static final Hashtable<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+
   /**
-   * Codon triplets with additional symbols for unambiguous codons that include ambiguity codes
+   * Codon triplets with additional symbols for unambiguous codons that include
+   * ambiguity codes
    */
-  public static final Hashtable<String,String> codonHash2 = new Hashtable<String,String>();
-  
+  public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+
   /**
    * all ambiguity codes for a given base
    */
-  public final static Hashtable<String,List<String>> _ambiguityCodes = new Hashtable<String,List<String>>();
-
+  public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
 
   static
   {
@@ -813,13 +823,13 @@ public class ResidueProperties
     codonHash2.put("AAC", "N");
     codonHash2.put("AAT", "N");
 
-    codonHash2.put("CAA", "E");
-    codonHash2.put("CAG", "E");
+    codonHash2.put("CAA", "Q");
+    codonHash2.put("CAG", "Q");
     codonHash2.put("CAC", "H");
     codonHash2.put("CAT", "H");
 
-    codonHash2.put("GAA", "Q");
-    codonHash2.put("GAG", "Q");
+    codonHash2.put("GAA", "E");
+    codonHash2.put("GAG", "E");
     codonHash2.put("GAC", "D");
     codonHash2.put("GAT", "D");
 
@@ -827,9 +837,9 @@ public class ResidueProperties
     codonHash2.put("TAT", "Y");
 
     codonHash2.put("ACA", "T");
-    codonHash2.put("AAG", "T");
     codonHash2.put("ACC", "T");
     codonHash2.put("ACT", "T");
+    codonHash2.put("ACG", "T");
 
     codonHash2.put("CCA", "P");
     codonHash2.put("CCG", "P");
@@ -889,10 +899,10 @@ public class ResidueProperties
 
     codonHash2.put("TTC", "F");
     codonHash2.put("TTT", "F");
-    
+
     buildAmbiguityCodonSet();
   }
-  
+
   /**
    * programmatic generation of codons including ambiguity codes
    */
@@ -928,7 +938,8 @@ public class ResidueProperties
     }
     // and programmatically add in the ambiguity codes that yield the same amino
     // acid
-    String[] unambcodons = codonHash2.keySet().toArray(new String[codonHash2.size()]);
+    String[] unambcodons = codonHash2.keySet().toArray(
+            new String[codonHash2.size()]);
     for (String codon : unambcodons)
     {
       String residue = codonHash2.get(codon);
@@ -963,7 +974,7 @@ public class ResidueProperties
         char _anuc;
         for (ipos = 0; ipos < tpos.length; ipos++)
         {
-          if (acodon[ipos].length==0 || tpos[ipos] < 0)
+          if (acodon[ipos].length == 0 || tpos[ipos] < 0)
           {
             _acodon += codon.charAt(ipos);
             allres[ipos] = new char[]
@@ -995,7 +1006,7 @@ public class ResidueProperties
             _codon += allres[j][cpos[j]];
           }
           String tr = codonHash2.get(_codon);
-          if (valid = (tr!=null && tr.equals(residue)))
+          if (valid = (tr != null && tr.equals(residue)))
           {
             // advance to next combination
             ipos = acodon.length - 1;
@@ -1009,14 +1020,14 @@ public class ResidueProperties
         if (valid)
         {
           // Add this to the set of codons we will translate
-//          System.out.println("Adding ambiguity codon: " + _acodon + " for "
-//                  + residue);
+          // System.out.println("Adding ambiguity codon: " + _acodon + " for "
+          // + residue);
           codonHash2.put(_acodon, residue);
         }
         else
         {
-//          System.err.println("Rejecting ambiguity codon: " + _acodon
-//                  + " for " + residue);
+          // System.err.println("Rejecting ambiguity codon: " + _acodon
+          // + " for " + residue);
         }
         // next combination
         ipos = acodon.length - 1;
@@ -1415,6 +1426,79 @@ public class ResidueProperties
     propHash.put("proline", proline);
     propHash.put("polar", polar);
   }
+  static
+  {
+    int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
+    for (int i = 0; i < maxProteinIndex; i++)
+    {
+      int maxF = 0, maxP = 0, maxEP = 0;
+      String ic = "";
+      if (aa.length > i)
+      {
+        ic += aa[i];
+      }
+      else
+      {
+        ic = "-";
+      }
+      for (int j = i + 1; j < maxProteinIndex; j++)
+      {
+        String jc = "";
+        if (aa.length > j)
+        {
+          jc += aa[j];
+        }
+        else
+        {
+          jc = "-";
+        }
+        propMatrixF[i][j] = 0;
+        propMatrixPos[i][j] = 0;
+        propMatrixEpos[i][j] = 0;
+        for (Enumeration<String> en = propHash.keys(); en
+                .hasMoreElements();)
+        {
+          String ph = en.nextElement();
+          Map<String, Integer> pph = (Map<String, Integer>) propHash
+                  .get(ph);
+          if (pph.get(ic) != null && pph.get(jc) != null)
+          {
+            int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
+            // Still working on these definitions.
+            propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
+            propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
+            propMatrixF[i][j] += icp == jcp ? 2 : 0;
+            propMatrixF[j][i] += icp == jcp ? 2 : 0;
+            propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
+            propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
+          }
+        }
+        if (maxF < propMatrixF[i][j])
+        {
+          maxF = propMatrixF[i][j];
+        }
+        if (maxP < propMatrixPos[i][j])
+        {
+          maxP = propMatrixPos[i][j];
+        }
+        if (maxEP < propMatrixEpos[i][j])
+        {
+          maxEP = propMatrixEpos[i][j];
+        }
+      }
+      propMatrixF[i][i] = maxF;
+      propMatrixPos[i][i] = maxP;
+      propMatrixEpos[i][i] = maxEP;
+    }
+    // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
+    // scoreMatrices.put("Conservation Pos", new
+    // ScoreMatrix("Conservation Pos",propMatrixPos,0));
+    // scoreMatrices.put("Conservation Both", new
+    // ScoreMatrix("Conservation Both",propMatrixF,0));
+    // scoreMatrices.put("Conservation EnhPos", new
+    // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
+    scoreMatrices.put("PID", new PIDScoreModel());
+  }
 
   private ResidueProperties()
   {
@@ -1490,12 +1574,13 @@ public class ResidueProperties
       return _codonTranslate(lccodon);
     }
     String cdn = codonHash2.get(lccodon.toUpperCase());
-    if (cdn!=null && cdn.equals("*"))
+    if (cdn != null && cdn.equals("*"))
     {
       return "STOP";
     }
     return cdn;
   }
+
   public static String _codonTranslate(String lccodon)
   {
     String codon = lccodon.toUpperCase();
@@ -1539,13 +1624,24 @@ public class ResidueProperties
   public static ScoreMatrix getScoreMatrix(String pwtype)
   {
     Object val = scoreMatrices.get(pwtype);
-    if (val != null)
+    if (val != null && val instanceof ScoreMatrix)
     {
       return (ScoreMatrix) val;
     }
     return null;
   }
 
+  /**
+   * get a ScoreModel based on its string name
+   * 
+   * @param pwtype
+   * @return scoremodel of type pwtype or null
+   */
+  public static ScoreModelI getScoreModel(String pwtype)
+  {
+    return scoreMatrices.get(pwtype);
+  }
+
   public static int getPAM250(char c, char d)
   {
     int a = aaIndex[c];
@@ -1603,12 +1699,81 @@ public class ResidueProperties
    * Used by getRNASecStrucState
    * 
    */
-  public static Hashtable toRNAssState;
+  public static Hashtable<String, String> toRNAssState;
+
+  public static boolean RNAcloseParen[] = new boolean[255];
   static
   {
-    toRNAssState = new Hashtable();
-    toRNAssState.put(")", "S");
-    toRNAssState.put("(", "S");
+    toRNAssState = new Hashtable<String, String>();
+    toRNAssState.put(")", "(");
+    toRNAssState.put("(", "(");
+    toRNAssState.put("]", "[");
+    toRNAssState.put("[", "[");
+    toRNAssState.put("{", "{");
+    toRNAssState.put("}", "{");
+    toRNAssState.put(">", ">");
+    toRNAssState.put("<", ">");
+    toRNAssState.put("A", "A");
+    toRNAssState.put("a", "A");
+    toRNAssState.put("B", "B");
+    toRNAssState.put("b", "B");
+    toRNAssState.put("C", "C");
+    toRNAssState.put("c", "C");
+    toRNAssState.put("D", "D");
+    toRNAssState.put("d", "D");
+    toRNAssState.put("E", "E");
+    toRNAssState.put("e", "E");
+    toRNAssState.put("F", "F");
+    toRNAssState.put("f", "F");
+    toRNAssState.put("G", "G");
+    toRNAssState.put("g", "G");
+    toRNAssState.put("H", "H");
+    toRNAssState.put("h", "H");
+    toRNAssState.put("I", "I");
+    toRNAssState.put("i", "I");
+    toRNAssState.put("J", "J");
+    toRNAssState.put("j", "J");
+    toRNAssState.put("K", "K");
+    toRNAssState.put("k", "K");
+    toRNAssState.put("L", "L");
+    toRNAssState.put("l", "L");
+    toRNAssState.put("M", "M");
+    toRNAssState.put("m", "M");
+    toRNAssState.put("N", "N");
+    toRNAssState.put("n", "N");
+    toRNAssState.put("O", "O");
+    toRNAssState.put("o", "O");
+    toRNAssState.put("P", "P");
+    toRNAssState.put("p", "P");
+    toRNAssState.put("Q", "Q");
+    toRNAssState.put("q", "Q");
+    toRNAssState.put("R", "R");
+    toRNAssState.put("r", "R");
+    toRNAssState.put("S", "S");
+    toRNAssState.put("s", "S");
+    toRNAssState.put("T", "T");
+    toRNAssState.put("t", "T");
+    toRNAssState.put("U", "U");
+    toRNAssState.put("u", "U");
+    toRNAssState.put("V", "V");
+    toRNAssState.put("v", "V");
+    toRNAssState.put("W", "W");
+    toRNAssState.put("w", "W");
+    toRNAssState.put("X", "X");
+    toRNAssState.put("x", "X");
+    toRNAssState.put("Y", "Y");
+    toRNAssState.put("y", "Y");
+    toRNAssState.put("Z", "Z");
+    toRNAssState.put("z", "Z");
+    for (int p = 0; p < RNAcloseParen.length; p++)
+    {
+      RNAcloseParen[p] = false;
+    }
+    for (String k : toRNAssState.keySet())
+    {
+      RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+              .charAt(0);
+    }
   }
 
   /**
@@ -1629,7 +1794,8 @@ public class ResidueProperties
       String ssc = ssstring.substring(i, i + 1);
       if (toRNAssState.containsKey(ssc))
       {
-        ss.append((String) toRNAssState.get(ssc));
+        // valid ss character - so return it
+        ss.append(ssc); // (String) toRNAssState.get(ssc));
       }
       else
       {
@@ -1639,6 +1805,11 @@ public class ResidueProperties
     return ss.toString();
   }
 
+  public static boolean isCloseParenRNA(char dc)
+  {
+    return RNAcloseParen[dc];
+  }
+
   // main method generates perl representation of residue property hash
   // / cut here
   public static void main(String[] args)
@@ -1688,4 +1859,5 @@ public class ResidueProperties
     System.out.println("};");
   }
   // to here
+
 }