Refactoring

beast-dev · Jan 28, 2025 · 204e952 · 204e952
1 parent d694fac
commit 204e952
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Showing 3 changed files with 16 additions and 28 deletions.
diff --git a/src/dr/app/tools/treeannotator/BiClade.java b/src/dr/app/tools/treeannotator/BiClade.java
@@ -165,18 +165,18 @@ public Object getKey() {
     }
 
     public static Object makeKey(Object key1, Object key2) {
-        FastBitSet bits = new FastBitSet();
+        BitSet bits = new BitSet();
         if (key1 instanceof Integer) {
             bits.set((Integer) key1);
         } else {
-            assert key1 instanceof FastBitSet;
-            bits.or((FastBitSet) key1);
+            assert key1 instanceof BitSet;
+            bits.or((BitSet) key1);
         }
         if (key2 instanceof Integer) {
             bits.set((Integer) key2);
         } else {
-            assert key2 instanceof FastBitSet;
-            bits.or((FastBitSet) key2);
+            assert key2 instanceof BitSet;
+            bits.or((BitSet) key2);
         }
         return bits;
     }

diff --git a/src/dr/app/tools/treeannotator/Embiggulator.java b/src/dr/app/tools/treeannotator/Embiggulator.java
@@ -142,7 +142,7 @@ public void embiggenBiClades(final int minCladeSize, final int minCladeCount) {
         long embiggulationCount = 0;
 
         // create and reuse a bitset to avoid reallocating it
-        final FastBitSet bits = new FastBitSet();
+        final BitSet bits = new BitSet();
 
         int rejectCount = 0;
 
@@ -157,7 +157,7 @@ public void embiggenBiClades(final int minCladeSize, final int minCladeCount) {
 //                if (superClades1 == null) {
 //                    continue;
 //                }
-                FastBitSet bits1 = ((FastBitSet) clade1.getKey());
+                BitSet bits1 = ((BitSet) clade1.getKey());
 
                 for (int j = Math.max(i + 1, sizeIndices[maxSize - clade1.getSize()]); j < n; j++) {
                     BiClade clade2 = clades[j];
@@ -173,14 +173,13 @@ public void embiggenBiClades(final int minCladeSize, final int minCladeCount) {
 //                        }
 //                    }
 
-//                    bits.clear();
-//                    bits.or(bits1);
-                    bits.set(bits1);
+                    bits.clear();
+                    bits.or(bits1);
 
                     if (clade2.key instanceof Integer) {
                         bits.set((Integer) clade2.key);
                     } else {
-                        bits.or((FastBitSet) clade2.key);
+                        bits.or((BitSet) clade2.key);
                     }
 
                     int size = clade1.size + clade2.size;

diff --git a/src/dr/app/tools/treeannotator/FastBitSet.java b/src/dr/app/tools/treeannotator/FastBitSet.java
@@ -370,28 +370,17 @@ public void and(FastBitSet set) {
      * @param set a bit set
      */
     public void or(FastBitSet set) {
-        if (this == set)
-            return;
-
-        int wordsInCommon = Math.min(wordsInUse, set.wordsInUse);
+//        int wordsInCommon = Math.min(wordsInUse, set.wordsInUse);
 
         if (wordsInUse < set.wordsInUse) {
             ensureCapacity(set.wordsInUse);
             wordsInUse = set.wordsInUse;
+            for (int i = 0; i < wordsInUse; i++)
+                words[i] |= set.words[i];
+        } else {
+            for (int i = 0; i < set.wordsInUse; i++)
+                words[i] |= set.words[i];
         }
-
-        // Perform logical OR on words in common
-        for (int i = 0; i < wordsInCommon; i++)
-            words[i] |= set.words[i];
-
-        // Copy any remaining words
-        if (wordsInCommon < set.wordsInUse)
-            System.arraycopy(set.words, wordsInCommon,
-                    words, wordsInCommon,
-                    wordsInUse - wordsInCommon);
-
-        // recalculateWordsInUse() is unnecessary
-        checkInvariants();
     }
 
     /**