Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / structure / AtomSpecModel.java

diff --git a/src/jalview/structure/AtomSpecModel.java b/src/jalview/structure/AtomSpecModel.java
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+++ b/src/jalview/structure/AtomSpecModel.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.structure;
+
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+/**
+ * A class to model a set of models, chains and atom range positions
+ * 
+ */
+public class AtomSpecModel
+{
+  /*
+   * { modelId, {chainCode, List<from-to> ranges} }
+   */
+  private Map<String, Map<String, BitSet>> atomSpec;
+
+  /**
+   * Constructor
+   */
+  public AtomSpecModel()
+  {
+    atomSpec = new TreeMap<>();
+  }
+
+  /**
+   * Adds one contiguous range to this atom spec
+   * 
+   * @param model
+   * @param startPos
+   * @param endPos
+   * @param chain
+   */
+  public void addRange(String model, int startPos, int endPos, String chain)
+  {
+    /*
+     * Get/initialize map of data for the colour and model
+     */
+    Map<String, BitSet> modelData = atomSpec.get(model);
+    if (modelData == null)
+    {
+      atomSpec.put(model, modelData = new TreeMap<>());
+    }
+
+    /*
+     * Get/initialize map of data for colour, model and chain
+     */
+    BitSet chainData = modelData.get(chain);
+    if (chainData == null)
+    {
+      chainData = new BitSet();
+      modelData.put(chain, chainData);
+    }
+
+    /*
+     * Add the start/end positions
+     */
+    chainData.set(startPos, endPos + 1);
+  }
+
+  public Iterable<String> getModels()
+  {
+    return atomSpec.keySet();
+  }
+
+  public int getModelCount()
+  {
+    return atomSpec.size();
+  }
+
+  public Iterable<String> getChains(String model)
+  {
+    return atomSpec.containsKey(model) ? atomSpec.get(model).keySet()
+            : null;
+  }
+
+  /**
+   * Returns a (possibly empty) ordered list of contiguous atom ranges for the
+   * given model and chain.
+   * 
+   * @param model
+   * @param chain
+   * @return
+   */
+  public List<int[]> getRanges(String model, String chain)
+  {
+    List<int[]> ranges = new ArrayList<>();
+    if (atomSpec.containsKey(model))
+    {
+      BitSet bs = atomSpec.get(model).get(chain);
+      int start = 0;
+      if (bs != null)
+      {
+        start = bs.nextSetBit(start);
+        int end = 0;
+        while (start != -1)
+        {
+          end = bs.nextClearBit(start);
+          ranges.add(new int[] { start, end - 1 });
+          start = bs.nextSetBit(end);
+        }
+      }
+    }
+    return ranges;
+  }
+}