Merge branch 'develop' into bug/JAL-2510amendFeatures

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

diff --git a/src/jalview/datamodel/VisibleRowsIterator.java b/src/jalview/datamodel/VisibleRowsIterator.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/datamodel/VisibleRowsIterator.java
@@ -0,0 +1,99 @@
+/*
+ * 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.Iterator;
+import java.util.NoSuchElementException;
+
+/**
+ * An iterator which iterates over all visible rows in an alignment
+ * 
+ * @author kmourao
+ *
+ */
+public class VisibleRowsIterator implements Iterator<Integer>
+{
+  private int last;
+
+  private int current;
+
+  private int next;
+
+  private HiddenSequences hidden;
+
+  private AlignmentI al;
+
+  /**
+   * Create an iterator for all visible rows in the alignment
+   * 
+   * @param firstrow
+   *          absolute row index to start from
+   * @param lastrow
+   *          absolute row index to end at
+   * @param alignment
+   *          alignment to work with
+   */
+  public VisibleRowsIterator(int firstrow, int lastrow, AlignmentI alignment)
+  {
+    al = alignment;
+    current = firstrow;
+    last = lastrow;
+    hidden = al.getHiddenSequences();
+    while (last > current && hidden.isHidden(last))
+    {
+      last--;
+    }
+    current = firstrow;
+    while (current < last && hidden.isHidden(current))
+    {
+      current++;
+    }
+    next = current;
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return next <= last;
+  }
+
+  @Override
+  public Integer next()
+  {
+    if (next > last)
+    {
+      throw new NoSuchElementException();
+    }
+    current = next;
+    do
+    {
+      next++;
+    } while (next <= last && hidden.isHidden(next));
+    return current;
+  }
+
+  @Override
+  public void remove()
+  {
+    throw new UnsupportedOperationException();
+  }
+}
+