JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api

[jalview.git] / src / intervalstore / nonc / IntervalStore.java

diff --git a/src/intervalstore/nonc/IntervalStore.java b/src/intervalstore/nonc/IntervalStore.java
index bc9ca83..5c013ad 100644 (file)
--- a/src/intervalstore/nonc/IntervalStore.java
+++ b/src/intervalstore/nonc/IntervalStore.java
@@ -224,8 +224,8 @@ public class IntervalStore<T extends IntervalI>
           Comparator<? super IntervalI> comparator, boolean bigendian)
   {
     icompare = (comparator != null ? comparator
-            : bigendian ? IntervalI.COMPARATOR_BIGENDIAN
-                    : IntervalI.COMPARATOR_LITTLEENDIAN);
+            : bigendian ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+                    : IntervalI.COMPARE_BEGIN_ASC_END_ASC);
     this.bigendian = bigendian;
 
     if (intervals != null)
@@ -259,7 +259,7 @@ public class IntervalStore<T extends IntervalI>
   }
 
   /**
-   * Adds one interval to the store, allowing duplicates.
+   * Adds one interval to the store, allowing duplicates
    * 
    * @param interval
    */
@@ -320,9 +320,6 @@ public class IntervalStore<T extends IntervalI>
         else
         {
           index = findInterval(interval);
-          // System.out.println("index = " + index + " for " + interval + "\n"
-          // + Arrays.toString(intervals) + "\n"
-          // + Arrays.toString(offsets));
           if (!allowDuplicates && index >= 0)
           {
             return false;
@@ -405,7 +402,7 @@ public class IntervalStore<T extends IntervalI>
       int pt0 = pt;
       while (--pt >= 0 && offsets[pt] == 0)
       {
-        ;
+        
       }
       if (pt < 0)
       {
@@ -484,7 +481,7 @@ public class IntervalStore<T extends IntervalI>
       case 0:
         IntervalI iv = intervals[mid];
         if ((bsIgnore == null || !bsIgnore.get(mid))
-                && iv.equalsInterval(interval))
+                && sameInterval(interval, iv))
         {
           return mid;
           // found one; just scan up and down now, first checking the range, but
@@ -498,7 +495,7 @@ public class IntervalStore<T extends IntervalI>
             break;
           }
           if ((bsIgnore == null || !bsIgnore.get(i))
-                  && iv.equalsInterval(interval))
+                  && sameInterval(interval, iv))
           {
             return i;
           }
@@ -511,7 +508,7 @@ public class IntervalStore<T extends IntervalI>
             return -1 - ++i;
           }
           if ((bsIgnore == null || !bsIgnore.get(i))
-                  && iv.equalsInterval(interval))
+                  && sameInterval(interval, iv))
           {
             return i;
           }
@@ -522,10 +519,21 @@ public class IntervalStore<T extends IntervalI>
     return -1 - start;
   }
 
-  @Override
-  public boolean canCheckForDuplicates()
+  /**
+   * Answers true if the two intervals are equal (as determined by
+   * {@code i1.equals(i2)}, else false
+   * 
+   * @param i1
+   * @param i2
+   * @return
+   */
+  static boolean sameInterval(IntervalI i1, IntervalI i2)
   {
-    return true;
+    /*
+     * for speed, do the fast check for begin/end equality before
+     * the equals check which includes type checking
+     */
+    return i1.equalsInterval(i2) && i1.equals(i2);
   }
 
   /**
@@ -766,21 +774,6 @@ public class IntervalStore<T extends IntervalI>
   }
 
   /**
-   * return the i-th interval in the designated order (bigendian or
-   * littleendian)
-   */
-  @Override
-  public IntervalI get(int i)
-  {
-    if (i < 0 || i >= intervalCount + added)
-    {
-      return null;
-    }
-    ensureFinalized();
-    return intervals[i];
-  }
-
-  /**
    * Return the deepest level of nesting.
    * 
    */
@@ -821,26 +814,6 @@ public class IntervalStore<T extends IntervalI>
   }
 
   /**
-   * Get the number of root-level nests.
-   * 
-   */
-  @Override
-  public int getWidth()
-  {
-    ensureFinalized();
-    // System.out.println(
-    // "ISList w[0]=" + nestCounts[0] + " w[1]=" + nestCounts[1]);
-    return nestCounts[0] + (createUnnested ? nestCounts[1] : 0);
-  }
-
-  @Override
-  public boolean isValid()
-  {
-    ensureFinalized();
-    return true;
-  }
-
-  /**
    * Answers an iterator over the intervals in the store, with no particular
    * ordering guaranteed. The iterator does not support the optional
    * <code>remove</code> operation (throws
@@ -915,17 +888,15 @@ public class IntervalStore<T extends IntervalI>
     {
       sb.append(sep).append(nests[pt + i].toString());
       if (nestCounts[pt + i] > 0)
+      {
         dump(pt + i, sb, sep + "  ");
+      }
     }
   }
 
   @Override
   public synchronized boolean remove(Object o)
   {
-    // if (o == null)
-    // {
-    // throw new NullPointerException();
-    // }
     return (o != null && intervalCount > 0
             && removeInterval((IntervalI) o));
   }
@@ -964,7 +935,7 @@ public class IntervalStore<T extends IntervalI>
         case -1:
           break;
         case 0:
-          if (iv.equalsInterval(interval))
+          if (sameInterval(interval, iv))
           {
             return pt;
           }
@@ -979,9 +950,9 @@ public class IntervalStore<T extends IntervalI>
     else
     {
       int i = intervalCount;
-      while (--i >= 0 && !intervals[i].equalsInterval(interval))
+      while (--i >= 0 && !sameInterval(intervals[i], interval))
       {
-        ;
+        
       }
       return i;
     }
@@ -1067,7 +1038,6 @@ public class IntervalStore<T extends IntervalI>
    * Recreate the key nest arrays.
    * 
    */
-  @Override
   public boolean revalidate()
   {
     isTainted = true;
@@ -1186,7 +1156,6 @@ public class IntervalStore<T extends IntervalI>
     int beginLast2 = beginLast;
 
     // Phase One: Get the temporary container array myContainer.
-
     for (int i = 1; i < intervalCount; i++)
     {
       int pt = i - 1;