Coverage Report
File PDBEntryUtils.java
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12% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| PDBEntryUtils | 35 | 44 | 17 |
Contributing tests
This file is covered by 43 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.HashSet; | |
| 25 | import java.util.List; | |
| 26 | import java.util.Set; | |
| 27 | import java.util.regex.Matcher; | |
| 28 | import java.util.regex.Pattern; | |
| 29 | ||
| 30 | import jalview.datamodel.PDBEntry; | |
| 31 | import jalview.datamodel.SequenceI; | |
| 32 | import jalview.io.StructureFile; | |
| 33 | import mc_view.PDBChain; | |
| 34 | ||
| 35 | public class PDBEntryUtils | |
| 36 | { | |
| 37 | ||
| 38 | 172 |  public static String inferChainId(SequenceI seq) |
| 39 | { | |
| 40 | 172 | String targetChainId; |
| 41 | 172 | if (seq.getName().indexOf("|") > -1) |
| 42 | { | |
| 43 | 52 | targetChainId = seq.getName() |
| 44 | .substring(seq.getName().lastIndexOf("|") + 1); | |
| 45 | 52 | if (targetChainId.length() > 1) |
| 46 | { | |
| 47 | 1 | if (targetChainId.trim().length() == 0) |
| 48 | { | |
| 49 | 0 | targetChainId = " "; |
| 50 | } | |
| 51 | else | |
| 52 | { | |
| 53 | // not a valid chain identifier | |
| 54 | 1 | targetChainId = ""; |
| 55 | } | |
| 56 | } | |
| 57 | } | |
| 58 | else | |
| 59 | { | |
| 60 | 120 | targetChainId = ""; |
| 61 | } | |
| 62 | 172 | return targetChainId; |
| 63 | } | |
| 64 | protected static Pattern id_and_chain=Pattern.compile("(\\d[0-9A-Za-z]{3})[_:|]?([0-9A-Za-z]{1,2})?.*"); | |
| 65 | ||
| 66 | 471 | public static List<PDBEntry> inferPDBEntry(SequenceI seq) |
| 67 | { | |
| 68 | 471 | Matcher matcher = id_and_chain.matcher(seq.getName()); |
| 69 | ||
| 70 | 471 | if (matcher.matches()) |
| 71 | { | |
| 72 | 133 | String id = matcher.group(1); |
| 73 | 133 | PDBEntry pdbe = new PDBEntry(); |
| 74 | 133 | pdbe.setId(id); |
| 75 | 133 | if (matcher.groupCount() > 1) |
| 76 | { | |
| 77 | 133 | pdbe.setChainCode(matcher.group(2)); |
| 78 | } | |
| 79 | ||
| 80 | 133 | return List.of(pdbe); |
| 81 | } | |
| 82 | 338 | return List.of(); |
| 83 | } | |
| 84 | ||
| 85 | ||
| 86 | /** | |
| 87 | * generate likely PDB IDs & chain codes from seq and ds that fit pdb | |
| 88 | * @param seq | |
| 89 | * @param ds | |
| 90 | * @param pdb | |
| 91 | * @return empty list or one or more PDBEntry which match pdb.getId() | |
| 92 | */ | |
| 93 | 230 | public static List<PDBEntry> selectPutativePDBe(SequenceI seq, |
| 94 | SequenceI ds, StructureFile pdb) | |
| 95 | { | |
| 96 | 230 | List<PDBEntry> putativePDBe = new ArrayList<PDBEntry>(); |
| 97 | 230 | Set<PDBEntry> possiblePDBe=PDBEntryUtils.gatherPDBEntries(seq,true); |
| 98 | 230 | for (PDBEntry infPDBe: possiblePDBe) |
| 99 | { | |
| 100 | 350 | if (infPDBe.getId().equalsIgnoreCase(pdb.getId())) |
| 101 | { | |
| 102 | 281 | putativePDBe.add(infPDBe); |
| 103 | } | |
| 104 | } | |
| 105 | 230 | return putativePDBe; |
| 106 | } | |
| 107 | ||
| 108 | ||
| 109 | 236 | public static Set<PDBEntry> gatherPDBEntries(SequenceI seq,boolean inferFromName) |
| 110 | { | |
| 111 | 236 | Set<PDBEntry> possiblePDBe=new HashSet<PDBEntry>(); |
| 112 | 706 | while (seq!=null) |
| 113 | { | |
| 114 | 470 | if (seq.getAllPDBEntries()!=null) { |
| 115 | 470 | possiblePDBe.addAll(seq.getAllPDBEntries()); |
| 116 | } | |
| 117 | 470 | if (inferFromName) |
| 118 | { | |
| 119 | 470 | possiblePDBe.addAll(PDBEntryUtils.inferPDBEntry(seq)); |
| 120 | } | |
| 121 | 470 | seq = seq.getDatasetSequence(); |
| 122 | } | |
| 123 | 236 | return possiblePDBe; |
| 124 | } | |
| 125 | ||
| 126 | ||
| 127 | 189 | public static PDBEntry selectPutativePDBEntry(List<PDBEntry> putativePDBe, |
| 128 | PDBChain chain) | |
| 129 | { | |
| 130 | 189 | if (putativePDBe.isEmpty()) |
| 131 | { | |
| 132 | 0 | return null; |
| 133 | } | |
| 134 | ||
| 135 | // check if there's a chaincode | |
| 136 | 189 | PDBEntry putativeEntry = null; |
| 137 | 189 | boolean hasChainCodes; |
| 138 | // check for a chaincode mapping | |
| 139 | 189 | for (PDBEntry pdbe : putativePDBe) |
| 140 | { | |
| 141 | 209 | if (pdbe.getChainCode() != null) |
| 142 | { | |
| 143 | 166 | hasChainCodes = true; |
| 144 | 166 | if (pdbe.getChainCode().equals(chain.id)) |
| 145 | { | |
| 146 | 127 | putativeEntry = pdbe; |
| 147 | 127 | return putativeEntry; |
| 148 | } | |
| 149 | } else { | |
| 150 | 43 | return pdbe; |
| 151 | } | |
| 152 | } | |
| 153 | 19 | return null; |
| 154 | } | |
| 155 | } |