From b53d11f22f9c5db694835ba27490e7c19671872d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 25 Feb 2019 13:46:27 +0000
Subject: [PATCH 1/1] JAL-3200 fast lookup of DSSP3 notation

---
 src/jalview/schemes/ResidueProperties.java      |   48 ++++++++++++-----------
 test/jalview/schemes/ResiduePropertiesTest.java |   10 +++++
 2 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a4e6480..18b11c1 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1156,47 +1156,51 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static Hashtable<String, String> toDssp3State;
+  /*
+   * lookup of (A-Z) alternative secondary structure symbols'
+   * equivalents in DSSP3 notation
+   */
+  private static char[] toDssp3State;
   static
   {
-    toDssp3State = new Hashtable<>();
-    toDssp3State.put("H", "H");
-    toDssp3State.put("E", "E");
-    toDssp3State.put("C", " ");
-    toDssp3State.put(" ", " ");
-    toDssp3State.put("T", " ");
-    toDssp3State.put("B", "E");
-    toDssp3State.put("G", "H");
-    toDssp3State.put("I", "H");
-    toDssp3State.put("X", " ");
+    toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
+    Arrays.fill(toDssp3State, ' ');
+    toDssp3State['B' - 'A'] = 'E';
+    toDssp3State['E' - 'A'] = 'E';
+    toDssp3State['G' - 'A'] = 'H';
+    toDssp3State['H' - 'A'] = 'H';
+    toDssp3State['I' - 'A'] = 'H';
   }
 
   /**
    * translate from other dssp secondary structure alphabets to 3-state
    * 
-   * @param ssstring
-   * @return ssstring as a three-state secondary structure assignment.
+   * @param ssString
+   * @return ssstring
    */
-  public static String getDssp3state(String ssstring)
+  public static String getDssp3state(String ssString)
   {
-    if (ssstring == null)
+    if (ssString == null)
     {
       return null;
     }
-    StringBuffer ss = new StringBuffer();
-    for (int i = 0; i < ssstring.length(); i++)
+    int lookupSize = toDssp3State.length;
+    int len = ssString.length();
+    char[] trans = new char[len];
+    for (int i = 0; i < len; i++)
     {
-      String ssc = ssstring.substring(i, i + 1);
-      if (toDssp3State.containsKey(ssc))
+      char c = ssString.charAt(i);
+      int index = c - 'A';
+      if (index < 0 || index >= lookupSize)
       {
-        ss.append(toDssp3State.get(ssc));
+        trans[i] = ' ';
       }
       else
       {
-        ss.append(" ");
+        trans[i] = toDssp3State[index];
       }
     }
-    return ss.toString();
+    return new String(trans);
   }
 
   static
diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index 7fbad50..180deaf 100644
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -1569,6 +1569,16 @@ public class ResiduePropertiesTest
   }
 
   @Test(groups = { "Functional" })
+  public void testGetDssp3State()
+  {
+    assertNull(ResidueProperties.getDssp3state(null));
+    assertEquals("", ResidueProperties.getDssp3state(""));
+    String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
+    String bar = "                                    E  E HHH                 ";
+    assertEquals(bar, ResidueProperties.getDssp3state(foo));
+  }
+
+  @Test(groups = { "Functional" })
   public void testPhysicoChemicalProperties()
   {
     checkProperty("aromatic", "FYWH-*");
-- 
1.7.10.2