Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

[jalview.git] / src / jalview / datamodel / RangeIterator.java

diff --git a/src/jalview/datamodel/RangeIterator.java b/src/jalview/datamodel/RangeIterator.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/datamodel/RangeIterator.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over a list of ranges. Works with a copy of the
+ * collection of ranges.
+ */
+public class RangeIterator implements Iterator<int[]>
+{
+  // current index in rangeList
+  private int currentPosition = 0;
+
+  // current range in rangeList
+  private int[] currentRange;
+
+  // local copy or reference to rangeList
+  private List<int[]> localRanges;
+
+  /**
+   * Unbounded constructor
+   * 
+   * @param rangeList
+   *          list of ranges to iterate over
+   */
+  RangeIterator(List<int[]> rangeList)
+  {
+    if (!rangeList.isEmpty())
+    {
+      int last = rangeList.get(rangeList.size() - 1)[1];
+      init(0, last, rangeList);
+    }
+    else
+    {
+      init(0, 0, rangeList);
+    }
+  }
+
+  /**
+   * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+   * 
+   * @param lowerBound
+   *          lower bound to iterate from
+   * @param upperBound
+   *          upper bound to iterate to
+   * @param rangeList
+   *          list of ranges to iterate over
+   */
+  RangeIterator(int lowerBound, int upperBound,
+          List<int[]> rangeList)
+  {
+    init(lowerBound, upperBound, rangeList);
+  }
+
+  /**
+   * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+   * 
+   * @param lowerBound
+   *          lower bound to iterate from
+   * @param upperBound
+   *          upper bound to iterate to
+   */
+  private void init(int lowerBound, int upperBound,
+          List<int[]> rangeList)
+  {
+    int start = lowerBound;
+    int end = upperBound;
+
+    if (rangeList != null)
+    {
+      localRanges = new ArrayList<>();
+
+      // iterate until a range overlaps with [start,end]
+      int i = 0;
+      while ((i < rangeList.size()) && (rangeList.get(i)[1] < start))
+      {
+        i++;
+      }
+
+      // iterate from start to end, adding each range. Positions are
+      // absolute, and all ranges which *overlap* [start,end] are added.
+      while (i < rangeList.size() && (rangeList.get(i)[0] <= end))
+      {
+        int[] rh = rangeList.get(i);
+        int[] cp = new int[2];
+        System.arraycopy(rh, 0, cp, 0, rh.length);
+        localRanges.add(cp);
+        i++;
+      }
+    }
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return (localRanges != null) && (currentPosition < localRanges.size());
+  }
+
+  @Override
+  public int[] next()
+  {
+    currentRange = localRanges.get(currentPosition);
+    currentPosition++;
+    return currentRange;
+  }
+
+  @Override
+  public void remove()
+  {
+    localRanges.remove(--currentPosition);
+  }
+}