Coverage Report
File StructuresFile.java
Coverage histogram
13% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| StructuresFile | 19 | 55 | 24 |
Contributing tests
This file is covered by 3 tests.
.
Source view
| 1 | package jalview.bin.argparser; | |
| 2 | ||
| 3 | import java.io.File; | |
| 4 | import java.util.ArrayList; | |
| 5 | import java.util.List; | |
| 6 | ||
| 7 | import jalview.bin.Cache; | |
| 8 | import jalview.bin.Console; | |
| 9 | import jalview.datamodel.AlignmentI; | |
| 10 | import jalview.datamodel.PDBEntry; | |
| 11 | import jalview.datamodel.SequenceI; | |
| 12 | import jalview.gui.AssociatePdbFileWithSeq; | |
| 13 | import jalview.gui.Desktop; | |
| 14 | import jalview.gui.StructureChooser; | |
| 15 | import jalview.gui.StructureViewer.ViewerType; | |
| 16 | import jalview.io.AppletFormatAdapter; | |
| 17 | import jalview.io.DataSourceType; | |
| 18 | ||
| 19 | public class StructuresFile | |
| 20 | { | |
| 21 | private boolean superpose = Cache | |
| 22 | .getDefault(StructureChooser.AUTOSUPERIMPOSE, true); | |
| 23 | ||
| 24 | private String viewerid = null; | |
| 25 | ||
| 26 | private ViewerType viewerType = ViewerType.JMOL; | |
| 27 | ||
| 28 | private List<StructureLine> structureLines; | |
| 29 | ||
| 30 | private List<SequenceI> seqs = new ArrayList<>(); | |
| 31 | ||
| 32 | private List<PDBEntry> pdbs = new ArrayList<>(); | |
| 33 | ||
| 34 | private AlignmentI alignment; | |
| 35 | ||
| 36 | 5 |  public StructuresFile(AlignmentI al, String filename) |
| 37 | { | |
| 38 | 5 | alignment = al; |
| 39 | 5 | setStructureLines(parseStructuresFile(new File(filename))); |
| 40 | } | |
| 41 | ||
| 42 | 5 | public boolean isSuperpose() |
| 43 | { | |
| 44 | 5 | return superpose; |
| 45 | } | |
| 46 | ||
| 47 | 5 | public void setSuperpose(boolean superpose) |
| 48 | { | |
| 49 | 5 | this.superpose = superpose; |
| 50 | } | |
| 51 | ||
| 52 | 20 | public String getViewerid() |
| 53 | { | |
| 54 | 20 | return viewerid; |
| 55 | } | |
| 56 | ||
| 57 | 5 | public void setViewerid(String viewerid) |
| 58 | { | |
| 59 | 5 | this.viewerid = viewerid; |
| 60 | } | |
| 61 | ||
| 62 | 5 | public ViewerType getViewerType() |
| 63 | { | |
| 64 | 5 | return viewerType; |
| 65 | } | |
| 66 | ||
| 67 | 5 | public void setViewerType(ViewerType viewerType) |
| 68 | { | |
| 69 | 5 | this.viewerType = viewerType; |
| 70 | } | |
| 71 | ||
| 72 | 0 | public List<StructureLine> getStructureLines() |
| 73 | { | |
| 74 | 0 | return structureLines; |
| 75 | } | |
| 76 | ||
| 77 | 5 | public void setStructureLines(List<StructureLine> structureLines) |
| 78 | { | |
| 79 | 5 | this.structureLines = structureLines; |
| 80 | } | |
| 81 | ||
| 82 | 5 | public List<StructureLine> parseStructuresFile(File structuresFile) |
| 83 | { | |
| 84 | 5 | if (!structuresFile.exists()) |
| 85 | { | |
| 86 | 0 | String message = Arg.STRUCTURESFILE.argString() + ArgParser.EQUALS |
| 87 | + "\"" + structuresFile.getPath() | |
| 88 | + "\": File does not exist."; | |
| 89 | 0 | Console.warn(message); |
| 90 | 0 | return null; |
| 91 | } | |
| 92 | 5 | List<String> lines = ArgParser.readArgFile(structuresFile); |
| 93 | 5 | List<StructureLine> structurelines = new ArrayList<>(); |
| 94 | 5 | if (lines != null) |
| 95 | { | |
| 96 | 5 | for (String line : lines) |
| 97 | { | |
| 98 | 28 | if (line.startsWith(ArgParser.DOUBLEDASH)) |
| 99 | { | |
| 100 | 13 | String val = getArgVal(Arg.VIEWERID, line); |
| 101 | 13 | if (val != null) |
| 102 | { | |
| 103 | 3 | setViewerid(val); |
| 104 | 3 | continue; |
| 105 | } | |
| 106 | 10 | val = getArgVal(Arg.STRUCTUREVIEWER, line); |
| 107 | 10 | if (val != null) |
| 108 | { | |
| 109 | 5 | setViewerType(ViewerType.getFromString(val)); |
| 110 | 5 | continue; |
| 111 | } | |
| 112 | 5 | Boolean b = getArgBoolean(Arg.SUPERPOSE, line); |
| 113 | 5 | if (b != null) |
| 114 | { | |
| 115 | 5 | setSuperpose(b); |
| 116 | 5 | continue; |
| 117 | } | |
| 118 | } | |
| 119 | 15 | StructureLine sl = new StructureLine(line); |
| 120 | 15 | structurelines.add(sl); |
| 121 | 15 | String structureLocationRef = sl.getSource(); |
| 122 | 15 | DataSourceType structureLocationType = AppletFormatAdapter |
| 123 | .checkProtocol(structureLocationRef); | |
| 124 | 15 | if (DataSourceType.FILE.equals(structureLocationType)) |
| 125 | { | |
| 126 | 15 | structureLocationRef = new File(structureLocationRef) |
| 127 | .getAbsolutePath(); | |
| 128 | } | |
| 129 | 15 | SequenceI seq = alignment.findName(sl.getSeqid()); |
| 130 | ||
| 131 | // TODO get global or subval values for TFT and notempfac | |
| 132 | ||
| 133 | 15 | PDBEntry pdbEntry = AssociatePdbFileWithSeq |
| 134 | .associatePdbWithSeq(structureLocationRef, | |
| 135 | structureLocationType, seq, false, Desktop.getInstance(), | |
| 136 | null, null, false); | |
| 137 | ||
| 138 | 15 | pdbs.add(pdbEntry); |
| 139 | 15 | seqs.add(seq); |
| 140 | ||
| 141 | } | |
| 142 | } | |
| 143 | 5 | return structurelines; |
| 144 | } | |
| 145 | ||
| 146 | 10 | public SequenceI[] getSeqs() |
| 147 | { | |
| 148 | 10 | SequenceI[] array = new SequenceI[seqs.size()]; |
| 149 | 10 | return seqs.toArray(array); |
| 150 | } | |
| 151 | ||
| 152 | 5 | public PDBEntry[] getPdbEntries() |
| 153 | { | |
| 154 | 5 | PDBEntry[] array = new PDBEntry[pdbs.size()]; |
| 155 | 5 | return pdbs.toArray(array); |
| 156 | } | |
| 157 | ||
| 158 | 23 | private static String getArgVal(Arg a, String line) |
| 159 | { | |
| 160 | 23 | String s = new StringBuilder(a.argString()).append(ArgParser.EQUALS) |
| 161 | .toString(); | |
| 162 | 23 | if (line.startsWith(s)) |
| 163 | { | |
| 164 | 8 | return line.substring(s.length()); |
| 165 | } | |
| 166 | 15 | return null; |
| 167 | } | |
| 168 | ||
| 169 | 5 | private static Boolean getArgBoolean(Arg a, String line) |
| 170 | { | |
| 171 | 5 | if (line.equals(a.argString())) |
| 172 | { | |
| 173 | 2 | return true; |
| 174 | } | |
| 175 | 3 | if (line.equals(a.negateArgString())) |
| 176 | { | |
| 177 | 3 | return false; |
| 178 | } | |
| 179 | 0 | return null; |
| 180 | } | |
| 181 | ||
| 182 | } |