Coverage Report
File StructureImportSettings.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| StructureImportSettings | 36 | 19 | 16 | ||
| StructureImportSettings.StructureParser | 58 | 0 | 0 | ||
| StructureImportSettings.TFType | 63 | 1 | 1 |
Contributing tests
This file is covered by 49 tests.
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Source view
| 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.Locale; | |
| 24 | ||
| 25 | import jalview.datamodel.PDBEntry; | |
| 26 | import jalview.datamodel.PDBEntry.Type; | |
| 27 | import jalview.util.MessageManager; | |
| 28 | ||
| 29 | /** | |
| 30 | * bean holding settings for structure IO. TODO: tests for validation of values | |
| 31 | * TODO: tests for race conditions (all fields are static, is that correct ?) | |
| 32 | * | |
| 33 | * @author tcofoegbu | |
| 34 | * | |
| 35 | */ | |
| 36 | public class StructureImportSettings | |
| 37 | { | |
| 38 | /** | |
| 39 | * set to true to add derived sequence annotations (temp factor read from | |
| 40 | * file, or computed secondary structure) to the alignment | |
| 41 | */ | |
| 42 | private static boolean visibleChainAnnotation = false; | |
| 43 | ||
| 44 | /** | |
| 45 | * Set true to predict secondary structure (using JMol for protein, Annotate3D | |
| 46 | * for RNA) | |
| 47 | */ | |
| 48 | private static boolean processSecStr = false; | |
| 49 | ||
| 50 | /** | |
| 51 | * Set true (with predictSecondaryStructure=true) to predict secondary | |
| 52 | * structure using an external service (currently Annotate3D for RNA only) | |
| 53 | */ | |
| 54 | private static boolean externalSecondaryStructure = false; | |
| 55 | ||
| 56 | private static boolean showSeqFeatures = true; | |
| 57 | ||
| 58 | public enum StructureParser | |
| 59 | { | |
| 60 | JMOL_PARSER, JALVIEW_PARSER | |
| 61 | } | |
| 62 | ||
| 63 | public static enum TFType | |
| 64 | { | |
| 65 | DEFAULT, PLDDT; | |
| 66 | ||
| 67 | 33 |  @Override |
| 68 | public String toString() | |
| 69 | { | |
| 70 | 33 | return MessageManager.getString( |
| 71 | "label.tftype_" + this.name().toLowerCase(Locale.ROOT)); | |
| 72 | } | |
| 73 | } | |
| 74 | ||
| 75 | /** | |
| 76 | * Determines the default file format for structure files to be downloaded | |
| 77 | * from the PDB sequence fetcher. Possible options include: PDB|mmCIF | |
| 78 | */ | |
| 79 | private static PDBEntry.Type defaultStructureFileFormat = Type.PDB; | |
| 80 | ||
| 81 | /** | |
| 82 | * Determines the parser used for parsing PDB format file. Possible options | |
| 83 | * are : JMolParser|JalveiwParser | |
| 84 | */ | |
| 85 | private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER; | |
| 86 | ||
| 87 | private static TFType temperatureFactorType; | |
| 88 | ||
| 89 | 13 | public static void addSettings(boolean addAlignmentAnnotations, |
| 90 | boolean processSecStr, boolean externalSecStr) | |
| 91 | { | |
| 92 | 13 | StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations; |
| 93 | 13 | StructureImportSettings.processSecStr = processSecStr; |
| 94 | 13 | StructureImportSettings.externalSecondaryStructure = externalSecStr; |
| 95 | 13 | StructureImportSettings.showSeqFeatures = true; |
| 96 | } | |
| 97 | ||
| 98 | 40 | public static boolean isVisibleChainAnnotation() |
| 99 | { | |
| 100 | 40 | return visibleChainAnnotation; |
| 101 | } | |
| 102 | ||
| 103 | 5 | public static void setTemperatureFactorType(TFType t) |
| 104 | { | |
| 105 | 5 | StructureImportSettings.temperatureFactorType = t; |
| 106 | } | |
| 107 | ||
| 108 | 6 | public static void setVisibleChainAnnotation( |
| 109 | boolean visibleChainAnnotation) | |
| 110 | { | |
| 111 | 6 | StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation; |
| 112 | } | |
| 113 | ||
| 114 | 40 | public static boolean isProcessSecondaryStructure() |
| 115 | { | |
| 116 | 40 | return processSecStr; |
| 117 | } | |
| 118 | ||
| 119 | 6 | public static void setProcessSecondaryStructure( |
| 120 | boolean processSecondaryStructure) | |
| 121 | { | |
| 122 | 6 | StructureImportSettings.processSecStr = processSecondaryStructure; |
| 123 | } | |
| 124 | ||
| 125 | 40 | public static boolean isExternalSecondaryStructure() |
| 126 | { | |
| 127 | 40 | return externalSecondaryStructure; |
| 128 | } | |
| 129 | ||
| 130 | 5 | public static void setExternalSecondaryStructure( |
| 131 | boolean externalSecondaryStructure) | |
| 132 | { | |
| 133 | 5 | StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure; |
| 134 | } | |
| 135 | ||
| 136 | 141 | public static boolean isShowSeqFeatures() |
| 137 | { | |
| 138 | 141 | return showSeqFeatures; |
| 139 | } | |
| 140 | ||
| 141 | 29 | public static void setShowSeqFeatures(boolean showSeqFeatures) |
| 142 | { | |
| 143 | 29 | StructureImportSettings.showSeqFeatures = showSeqFeatures; |
| 144 | } | |
| 145 | ||
| 146 | 0 | public static PDBEntry.Type getDefaultStructureFileFormat() |
| 147 | { | |
| 148 | 0 | return defaultStructureFileFormat; |
| 149 | } | |
| 150 | ||
| 151 | 158 | public static void setDefaultStructureFileFormat( |
| 152 | String defaultStructureFileFormat) | |
| 153 | { | |
| 154 | 158 | StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type |
| 155 | .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT)); | |
| 156 | } | |
| 157 | ||
| 158 | 13 | public static String getDefaultPDBFileParser() |
| 159 | { | |
| 160 | 13 | return defaultPDBFileParser.toString(); |
| 161 | } | |
| 162 | ||
| 163 | 6 | public static void setDefaultPDBFileParser( |
| 164 | StructureParser defaultPDBFileParser) | |
| 165 | { | |
| 166 | 6 | StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser; |
| 167 | } | |
| 168 | ||
| 169 | 143 | public static void setDefaultPDBFileParser(String defaultPDBFileParser) |
| 170 | { | |
| 171 | 143 | StructureImportSettings.defaultPDBFileParser = StructureParser |
| 172 | .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT)); | |
| 173 | } | |
| 174 | ||
| 175 | 50 | public static TFType getTemperatureFactorType() |
| 176 | { | |
| 177 | 50 | return temperatureFactorType; |
| 178 | } | |
| 179 | ||
| 180 | } |