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

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

diff --git a/src/jalview/datamodel/VisibleContigsIterator.java b/src/jalview/datamodel/VisibleContigsIterator.java
new file mode 100644 (file)
index 0000000..0185978
--- /dev/null
+++ b/src/jalview/datamodel/VisibleContigsIterator.java
@@ -0,0 +1,116 @@
+/*
+ * 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 visible regions in a range. Provides a
+ * special "endsAtHidden" indicator to allow callers to determine if the final
+ * visible column is adjacent to a hidden region.
+ */
+public class VisibleContigsIterator implements Iterator<int[]>
+{
+  private List<int[]> vcontigs = new ArrayList<>();
+
+  private int currentPosition = 0;
+
+  private boolean endsAtHidden = false;
+
+  VisibleContigsIterator(int start, int end,
+          List<int[]> hiddenColumns)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      int vstart = start;
+      int hideStart;
+      int hideEnd;
+
+      for (int[] region : hiddenColumns)
+      {
+        endsAtHidden = false;
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        // navigate to start
+        if (hideEnd < vstart)
+        {
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          if (end - 1 > hideStart - 1)
+          {
+            int[] contig = new int[] { vstart, hideStart - 1 };
+            vcontigs.add(contig);
+            endsAtHidden = true;
+          }
+          else
+          {
+            int[] contig = new int[] { vstart, end - 1 };
+            vcontigs.add(contig);
+          }
+        }
+        vstart = hideEnd + 1;
+
+        // exit if we're past the end
+        if (vstart >= end)
+        {
+          break;
+        }
+      }
+
+      if (vstart < end)
+      {
+        int[] contig = new int[] { vstart, end - 1 };
+        vcontigs.add(contig);
+        endsAtHidden = false;
+      }
+    }
+    else
+    {
+      int[] contig = new int[] { start, end - 1 };
+      vcontigs.add(contig);
+    }
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return (currentPosition < vcontigs.size());
+  }
+
+  @Override
+  public int[] next()
+  {
+    int[] result = vcontigs.get(currentPosition);
+    currentPosition++;
+    return result;
+  }
+
+  public boolean endsAtHidden()
+  {
+    return endsAtHidden;
+  }
+}
+