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package jalview.ext.rbvi.chimera; |
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import jalview.util.IntRangeComparator; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.TreeMap; |
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| 95.9% |
Uncovered Elements: 3 (73) |
Complexity: 16 |
Complexity Density: 0.36 |
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public class AtomSpecModel |
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{ |
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private Map<Integer, Map<String, List<int[]>>> atomSpec; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AtomSpecModel()... |
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{ |
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atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>(); |
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} |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
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public void addRange(int model, int startPos, int endPos, String chain)... |
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{ |
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Map<String, List<int[]>> modelData = atomSpec.get(model); |
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if (modelData == null) |
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{ |
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atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>()); |
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} |
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List<int[]> chainData = modelData.get(chain); |
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if (chainData == null) |
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chainData = new ArrayList<int[]>(); |
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modelData.put(chain, chainData); |
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} |
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chainData.add(new int[] { startPos, endPos }); |
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} |
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@return |
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| 92.9% |
Uncovered Elements: 3 (42) |
Complexity: 8 |
Complexity Density: 0.29 |
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public String getAtomSpec()... |
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{ |
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StringBuilder sb = new StringBuilder(128); |
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boolean firstModel = true; |
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for (Integer model : atomSpec.keySet()) |
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if (!firstModel) |
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sb.append("|"); |
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} |
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firstModel = false; |
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sb.append("#").append(model).append(":"); |
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boolean firstPositionForModel = true; |
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final Map<String, List<int[]>> modelData = atomSpec.get(model); |
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for (String chain : modelData.keySet()) |
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{ |
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chain = " ".equals(chain) ? chain : chain.trim(); |
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List<int[]> rangeList = modelData.get(chain); |
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Collections.sort(rangeList, IntRangeComparator.ASCENDING); |
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int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0]; |
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int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1]; |
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Iterator<int[]> iterator = rangeList.iterator(); |
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while (iterator.hasNext()) |
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int[] range = iterator.next(); |
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if (range[0] <= end + 1) |
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end = Math.max(end, range[1]); |
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} |
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else |
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{ |
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appendRange(sb, start, end, chain, firstPositionForModel); |
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firstPositionForModel = false; |
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start = range[0]; |
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end = range[1]; |
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} |
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} |
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if (!rangeList.isEmpty()) |
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{ |
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appendRange(sb, start, end, chain, firstPositionForModel); |
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firstPositionForModel = false; |
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} |
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} |
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} |
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return sb.toString(); |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
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protected void appendRange(StringBuilder sb, int start, int end,... |
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String chain, boolean firstPositionForModel) |
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{ |
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if (!firstPositionForModel) |
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sb.append(","); |
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} |
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if (end == start) |
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sb.append(start); |
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} |
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else |
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{ |
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sb.append(start).append("-").append(end); |
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} |
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sb.append("."); |
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if (!" ".equals(chain)) { |
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sb.append(chain); |
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} |
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} |
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} |