Coverage Report
File AtomSpecModel.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AtomSpecModel | 33 | 24 | 12 |
Contributing tests
This file is covered by 25 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.structure; | |
| 22 | ||
| 23 | import java.util.ArrayList; | |
| 24 | import java.util.BitSet; | |
| 25 | import java.util.List; | |
| 26 | import java.util.Map; | |
| 27 | import java.util.TreeMap; | |
| 28 | ||
| 29 | /** | |
| 30 | * A class to model a set of models, chains and atom range positions | |
| 31 | * | |
| 32 | */ | |
| 33 | public class AtomSpecModel | |
| 34 | { | |
| 35 | /* | |
| 36 | * { modelId, {chainCode, List<from-to> ranges} } | |
| 37 | */ | |
| 38 | private Map<String, Map<String, BitSet>> atomSpec; | |
| 39 | ||
| 40 | /** | |
| 41 | * Constructor | |
| 42 | */ | |
| 43 | 54 |  public AtomSpecModel() |
| 44 | { | |
| 45 | 54 | atomSpec = new TreeMap<>(); |
| 46 | } | |
| 47 | ||
| 48 | /** | |
| 49 | * Adds one contiguous range to this atom spec | |
| 50 | * | |
| 51 | * @param model | |
| 52 | * @param startPos | |
| 53 | * @param endPos | |
| 54 | * @param chain | |
| 55 | */ | |
| 56 | 480 | public void addRange(String model, int startPos, int endPos, String chain) |
| 57 | { | |
| 58 | /* | |
| 59 | * Get/initialize map of data for the colour and model | |
| 60 | */ | |
| 61 | 480 | Map<String, BitSet> modelData = atomSpec.get(model); |
| 62 | 480 | if (modelData == null) |
| 63 | { | |
| 64 | 83 | atomSpec.put(model, modelData = new TreeMap<>()); |
| 65 | } | |
| 66 | ||
| 67 | /* | |
| 68 | * Get/initialize map of data for colour, model and chain | |
| 69 | */ | |
| 70 | 480 | BitSet chainData = modelData.get(chain); |
| 71 | 480 | if (chainData == null) |
| 72 | { | |
| 73 | 116 | chainData = new BitSet(); |
| 74 | 116 | modelData.put(chain, chainData); |
| 75 | } | |
| 76 | ||
| 77 | /* | |
| 78 | * Add the start/end positions | |
| 79 | */ | |
| 80 | 480 | chainData.set(startPos, endPos + 1); |
| 81 | } | |
| 82 | ||
| 83 | 142 | public Iterable<String> getModels() |
| 84 | { | |
| 85 | 142 | return atomSpec.keySet(); |
| 86 | } | |
| 87 | ||
| 88 | 0 | public int getModelCount() |
| 89 | { | |
| 90 | 0 | return atomSpec.size(); |
| 91 | } | |
| 92 | ||
| 93 | 199 | public Iterable<String> getChains(String model) |
| 94 | { | |
| 95 | 199 | return atomSpec.containsKey(model) ? atomSpec.get(model).keySet() |
| 96 | : null; | |
| 97 | } | |
| 98 | ||
| 99 | /** | |
| 100 | * Returns a (possibly empty) ordered list of contiguous atom ranges for the | |
| 101 | * given model and chain. | |
| 102 | * | |
| 103 | * @param model | |
| 104 | * @param chain | |
| 105 | * @return | |
| 106 | */ | |
| 107 | 325 | public List<int[]> getRanges(String model, String chain) |
| 108 | { | |
| 109 | 325 | List<int[]> ranges = new ArrayList<>(); |
| 110 | 325 | if (atomSpec.containsKey(model)) |
| 111 | { | |
| 112 | 323 | BitSet bs = atomSpec.get(model).get(chain); |
| 113 | 323 | int start = 0; |
| 114 | 323 | if (bs != null) |
| 115 | { | |
| 116 | 322 | start = bs.nextSetBit(start); |
| 117 | 322 | int end = 0; |
| 118 | 736 | while (start != -1) |
| 119 | { | |
| 120 | 414 | end = bs.nextClearBit(start); |
| 121 | 414 | ranges.add(new int[] { start, end - 1 }); |
| 122 | 414 | start = bs.nextSetBit(end); |
| 123 | } | |
| 124 | } | |
| 125 | } | |
| 126 | 325 | return ranges; |
| 127 | } | |
| 128 | } |