+/*
+ * 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;
+ }
+}