X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;fp=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=cc97be092aeb2ffcc1ab9f98554a96224e879368;hb=042832306c7e7aa0484079f3bab1e141b2944de5;hp=546a2144bd0934404ed7378d0c4bbefcf234632a;hpb=5cbf11a75929325ead970d992f10ad7f3e84bab0;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 546a214..cc97be0 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();
 
@@ -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