+++ /dev/null
-/*
- * 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.ext.rbvi.chimera;
-
-import jalview.util.IntRangeComparator;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-/**
- * A class to model a Chimera atomspec pattern, for example
- *
- * <pre>
- * #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
- * </pre>
- *
- * where
- * <ul>
- * <li>#0 is a model number</li>
- * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
- * <li>.A is a chain identifier</li>
- * <li>residue ranges are separated by comma</li>
- * <li>atomspecs for distinct models are separated by | (or)</li>
- * </ul>
- *
- * <pre>
- * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
- * </pre>
- */
-public class AtomSpecModel
-{
- private Map<Integer, Map<String, List<int[]>>> atomSpec;
-
- /**
- * Constructor
- */
- public AtomSpecModel()
- {
- atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
- }
-
- /**
- * Adds one contiguous range to this atom spec
- *
- * @param model
- * @param startPos
- * @param endPos
- * @param chain
- */
- public void addRange(int model, int startPos, int endPos, String chain)
- {
- /*
- * Get/initialize map of data for the colour and model
- */
- Map<String, List<int[]>> modelData = atomSpec.get(model);
- if (modelData == null)
- {
- atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
- }
-
- /*
- * Get/initialize map of data for colour, model and chain
- */
- List<int[]> chainData = modelData.get(chain);
- if (chainData == null)
- {
- chainData = new ArrayList<int[]>();
- modelData.put(chain, chainData);
- }
-
- /*
- * Add the start/end positions
- */
- chainData.add(new int[] { startPos, endPos });
- // TODO add intelligently, using a RangeList class
- }
-
- /**
- * Returns the range(s) formatted as a Chimera atomspec
- *
- * @return
- */
- public String getAtomSpec()
- {
- StringBuilder sb = new StringBuilder(128);
- boolean firstModel = true;
- for (Integer model : atomSpec.keySet())
- {
- if (!firstModel)
- {
- sb.append("|");
- }
- firstModel = false;
- sb.append("#").append(model).append(":");
-
- boolean firstPositionForModel = true;
- final Map<String, List<int[]>> modelData = atomSpec.get(model);
-
- for (String chain : modelData.keySet())
- {
- chain = " ".equals(chain) ? chain : chain.trim();
-
- List<int[]> rangeList = modelData.get(chain);
-
- /*
- * sort ranges into ascending start position order
- */
- Collections.sort(rangeList, IntRangeComparator.ASCENDING);
-
- int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
- int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
-
- Iterator<int[]> iterator = rangeList.iterator();
- while (iterator.hasNext())
- {
- int[] range = iterator.next();
- if (range[0] <= end + 1)
- {
- /*
- * range overlaps or is contiguous with the last one
- * - so just extend the end position, and carry on
- * (unless this is the last in the list)
- */
- end = Math.max(end, range[1]);
- }
- else
- {
- /*
- * we have a break so append the last range
- */
- appendRange(sb, start, end, chain, firstPositionForModel);
- firstPositionForModel = false;
- start = range[0];
- end = range[1];
- }
- }
-
- /*
- * and append the last range
- */
- if (!rangeList.isEmpty())
- {
- appendRange(sb, start, end, chain, firstPositionForModel);
- firstPositionForModel = false;
- }
- }
- }
- return sb.toString();
- }
-
- /**
- * @param sb
- * @param start
- * @param end
- * @param chain
- * @param firstPositionForModel
- */
- protected void appendRange(StringBuilder sb, int start, int end,
- String chain, boolean firstPositionForModel)
- {
- if (!firstPositionForModel)
- {
- sb.append(",");
- }
- if (end == start)
- {
- sb.append(start);
- }
- else
- {
- sb.append(start).append("-").append(end);
- }
-
- sb.append(".");
- if (!" ".equals(chain)) {
- sb.append(chain);
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff