JAL-2416 removed DNA and PAM250 matrices from ResidueProperties

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f623a96..61ff012 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
@@ -117,7 +118,10 @@ public class AlignSeq
 
   int gapExtend = 20;
 
-  float[][] lookup = ResidueProperties.getBLOSUM62();
+  float[][] lookup = ((ScoreMatrix) ScoreModels.getInstance().forName(
+          ScoreModels.BLOSUM62)).getMatrix();
+
+  // ResidueProperties.getBLOSUM62();
 
   String[] intToStr = pep;
 
@@ -600,6 +604,9 @@ public class AlignSeq
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
 
+    PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
+            .getInstance().forName(ScoreModels.PAM250);
+
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
@@ -616,25 +623,27 @@ public class AlignSeq
       output.append(NEWLINE);
       output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
 
-      // Print out the matching chars
+      /*
+       * Print out the match symbols:
+       * | for exact match (ignoring case)
+       * . if PAM250 score is positive
+       * else a space
+       */
       for (int i = 0; i < len; i++)
       {
         if ((i + (j * len)) < astr1.length())
         {
-          boolean sameChar = Comparison.isSameResidue(
-                  astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
-                  false);
-          if (sameChar
-                  && !jalview.util.Comparison.isGap(astr1.charAt(i
-                          + (j * len))))
+          char c1 = astr1.charAt(i + (j * len));
+          char c2 = astr2.charAt(i + (j * len));
+          boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+          if (sameChar && !Comparison.isGap(c1))
           {
             pid++;
             output.append("|");
           }
           else if (type.equals("pep"))
           {
-            if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
-                    astr2.charAt(i + (j * len))) > 0)
+            if (pam250.getPairwiseScore(c1, c2) > 0)
             {
               output.append(".");
             }

diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java
index c795f3f..367a0de 100644 (file)
--- a/src/jalview/api/SiftsClientI.java
+++ b/src/jalview/api/SiftsClientI.java
@@ -100,7 +100,7 @@ public interface SiftsClientI
    * @return Sequence<->Structure mapping as int[][]
    * @throws SiftsException
    */
-  public StringBuffer getMappingOutput(MappingOutputPojo mop)
+  public StringBuilder getMappingOutput(MappingOutputPojo mop)
           throws SiftsException;
 
   /**

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 0b1b7cc..77fa9e8 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -521,56 +521,6 @@ public class ResidueProperties
       { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
           -4, -4, -4, -4, -4, -4, 1 }, };
 
-  public static final float[][] PAM250 = {
-      { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
-          0, 0, 0, 0, -8 },
-      { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
-          -2, -1, 0, -1, -8 },
-      { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
-          2, 1, 0, -8 },
-      { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4,
-          -2, 3, 3, -1, -8 },
-      { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
-          -8, 0, -2, -4, -5, -3, -8 },
-      { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
-          -2, 1, 3, -1, -8 },
-      { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4,
-          -2, 3, 3, -1, -8 },
-      { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
-          -1, 0, 0, -1, -8 },
-      { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
-          -2, 1, 2, -1, -8 },
-      { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
-          -1, 4, -2, -2, -1, -8 },
-      { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
-          -1, 2, -3, -3, -1, -8 },
-      { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4,
-          -2, 1, 0, -1, -8 },
-      { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4,
-          -2, 2, -2, -2, -1, -8 },
-      { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0,
-          7, -1, -4, -5, -2, -8 },
-      { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
-          -1, -1, 0, -1, -8 },
-      { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3,
-          -1, 0, 0, 0, -8 },
-      { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3,
-          0, 0, -1, 0, -8 },
-      { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5,
-          17, 0, -6, -5, -6, -4, -8 },
-      { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
-          10, -2, -3, -4, -2, -8 },
-      { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
-          -2, 4, -2, -2, -1, -8 },
-      { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3,
-          -2, 3, 2, -1, -8 },
-      { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4,
-          -2, 2, 3, -1, -8 },
-      { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
-          -2, -1, -1, -1, -1, -8 },
-      { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-          -8, -8, -8, -8, -8, -8, 1 }, };
-
   // not currently used
   // public static final Map<String, Color> ssHash = new Hashtable<String,
   // Color>();
@@ -592,34 +542,6 @@ public class ResidueProperties
    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
    */
 
-  // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA.
-  // Will equate sequences if working with mixed nucleotide sets.
-  // treats T and U identically. R and Y weak equivalence with AG and CTU.
-  // N matches any other base weakly
-  //
-  public static final float[][] DNA = {
-      { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
-      { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
-      { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
-      { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
-      { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // U
-      { 1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1 }, // I
-      { 1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1 }, // X
-      { 1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1 }, // R
-      { -8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1 }, // Y
-      { 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1 }, // N
-      { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // -
-  };
-  /**
-   * register matrices in list
-   */
-  static
-  {
-    // scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62));
-    // scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250));
-    // scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA));
-  }
-
   public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
 
   public static String START = "ATG";
@@ -1270,11 +1192,6 @@ public class ResidueProperties
     return ResidueProperties.BLOSUM62;
   }
 
-  public static float getPAM250(String A1, String A2)
-  {
-    return getPAM250(A1.charAt(0), A2.charAt(0));
-  }
-
   public static String codonTranslate(String lccodon)
   {
     String cdn = codonHash2.get(lccodon.toUpperCase());
@@ -1285,16 +1202,6 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static float getPAM250(char c, char d)
-  {
-    int a = aaIndex[c];
-    int b = aaIndex[d];
-
-    float pog = ResidueProperties.PAM250[a][b];
-
-    return pog;
-  }
-
   public static Hashtable<String, String> toDssp3State;
   static
   {

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 8bae5ba..6d961c0 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -21,6 +21,8 @@
 package jalview.ws.sifts;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.DBRefEntryI;
 import jalview.api.SiftsClientI;
 import jalview.datamodel.DBRefEntry;
@@ -943,7 +945,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuffer getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputPojo mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -965,7 +967,7 @@ public class SiftsClient implements SiftsClientI
     int nochunks = ((seqRes.length()) / len)
             + ((seqRes.length()) % len > 0 ? 1 : 0);
     // output mappings
-    StringBuffer output = new StringBuffer();
+    StringBuilder output = new StringBuilder(512);
     output.append(NEWLINE);
     output.append("Sequence \u27f7 Structure mapping details").append(
             NEWLINE);
@@ -986,6 +988,8 @@ public class SiftsClient implements SiftsClientI
     output.append(String.valueOf(pdbEnd));
     output.append(NEWLINE).append(NEWLINE);
 
+    PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
+            .getInstance().forName(ScoreModels.PAM250);
     int matchedSeqCount = 0;
     for (int j = 0; j < nochunks; j++)
     {
@@ -1004,27 +1008,29 @@ public class SiftsClient implements SiftsClientI
       output.append(NEWLINE);
       output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
 
-      // Print out the matching chars
+      /*
+       * Print out the match symbols:
+       * | for exact match (ignoring case)
+       * . if PAM250 score is positive
+       * else a space
+       */
       for (int i = 0; i < len; i++)
       {
         try
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            boolean sameChar = Comparison.isSameResidue(
-                    seqRes.charAt(i + (j * len)),
-                    strRes.charAt(i + (j * len)), false);
-            if (sameChar
-                    && !jalview.util.Comparison.isGap(seqRes.charAt(i
-                            + (j * len))))
+            char c1 = seqRes.charAt(i + (j * len));
+            char c2 = strRes.charAt(i + (j * len));
+            boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+            if (sameChar && !Comparison.isGap(c1))
             {
               matchedSeqCount++;
               output.append("|");
             }
             else if (type.equals("pep"))
             {
-              if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
-                      strRes.charAt(i + (j * len))) > 0)
+              if (pam250.getPairwiseScore(c1, c2) > 0)
               {
                 output.append(".");
               }