X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=3f5099bd3ac2dc4d151f0e3a4f0c9009207d49dd;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=1342bb273760f0efc2524e1d3e2840ddf30b2f9c;hpb=3027bfb4b1b13af8686abcd419888e03141bd672;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 1342bb2..3f5099b 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -27,7 +27,6 @@ import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 import jalview.util.Format;
 
-import java.util.ArrayList;
 import java.util.Hashtable;
 
 /**
@@ -94,11 +93,11 @@ public class StructureFrequency
    * @param rnaStruc
    */
   public static final void calculate(SequenceI[] sequences, int start,
-          int end, Hashtable[] result, boolean profile,
+          int end, Hashtable<String, Object>[] result, boolean profile,
           AlignmentAnnotation rnaStruc)
   {
 
-    Hashtable residueHash;
+    Hashtable<String, Object> residueHash;
     String maxResidue;
     char[] struc = rnaStruc.getRNAStruc().toCharArray();
 
@@ -149,7 +148,7 @@ public class StructureFrequency
           {
             if (sequences[j] == null)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
@@ -191,7 +190,7 @@ public class StructureFrequency
         }
       }
 
-      residueHash = new Hashtable();
+      residueHash = new Hashtable<>();
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
@@ -251,7 +250,7 @@ public class StructureFrequency
         maxResidue = maxResidue.equals("(") ? ")"
                 : maxResidue.equals("[") ? "]" : "}";
 
-        residueHash = new Hashtable();
+        residueHash = new Hashtable<>();
         if (profile)
         {
           residueHash.put(PROFILE,
@@ -288,7 +287,7 @@ public class StructureFrequency
    * @param includeAllConsSymbols
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
-          Hashtable[] hconsensus, int iStart, int width,
+          Hashtable<String, Object>[] hconsensus, int iStart, int width,
           boolean ignoreGapsInConsensusCalculation,
           boolean includeAllConsSymbols, long nseq)
   {
@@ -315,7 +314,7 @@ public class StructureFrequency
 
     for (int i = iStart; i < width; i++)
     {
-      Hashtable hci;
+      Hashtable<String, Object> hci;
       if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
       {
         // happens if sequences calculated over were shorter than alignment
@@ -415,7 +414,7 @@ public class StructureFrequency
    * @param hconsensus
    * @return profile of the given column
    */
-  public static int[] extractProfile(Hashtable hconsensus,
+  public static int[] extractProfile(Hashtable<String, Object> hconsensus,
           boolean ignoreGapsInConsensusCalculation)
   {
     int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
@@ -468,23 +467,4 @@ public class StructureFrequency
     System.arraycopy(rtnval, 0, result, 1, rtnval.length);
     return result;
   }
-
-  public static void main(String args[])
-  {
-    // Short test to see if checkBpType works
-    ArrayList<String> test = new ArrayList<String>();
-    test.add("A");
-    test.add("c");
-    test.add("g");
-    test.add("T");
-    test.add("U");
-    for (String i : test)
-    {
-      for (String j : test)
-      {
-        System.out.println(i + "-" + j + ": "
-                + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
-      }
-    }
-  }
 }