Coverage Report
File AlignmentJob.java
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20% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentJob | 28 | 33 | 16 |
Contributing tests
This file is covered by 27 tests.
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Source view
| 1 | package jalview.ws2.actions.alignment; | |
| 2 | ||
| 3 | import java.util.ArrayList; | |
| 4 | import java.util.Collections; | |
| 5 | import java.util.LinkedHashMap; | |
| 6 | import java.util.List; | |
| 7 | import java.util.Map; | |
| 8 | ||
| 9 | import jalview.analysis.AlignSeq; | |
| 10 | import jalview.analysis.SeqsetUtils; | |
| 11 | import jalview.analysis.SeqsetUtils.SequenceInfo; | |
| 12 | import jalview.datamodel.AlignmentI; | |
| 13 | import jalview.datamodel.Sequence; | |
| 14 | import jalview.datamodel.SequenceI; | |
| 15 | import jalview.util.Comparison; | |
| 16 | import jalview.ws2.actions.BaseJob; | |
| 17 | import jalview.ws2.api.WebServiceJobHandle; | |
| 18 | ||
| 19 | /** | |
| 20 | * A wrapper class that extends basic job container with data specific to | |
| 21 | * alignment services. It stores input and empty sequences (with uniquified | |
| 22 | * names) along the original sequence information. {@link AlignmentJob} objects | |
| 23 | * are created by {@link AlignmentTask} during a preparation stage. | |
| 24 | * | |
| 25 | * @author mmwarowny | |
| 26 | * | |
| 27 | */ | |
| 28 | class AlignmentJob extends BaseJob | |
| 29 | { | |
| 30 | private final List<SequenceI> emptySeqs; | |
| 31 | ||
| 32 | private final Map<String, SequenceInfo> names; | |
| 33 | ||
| 34 | private AlignmentI alignmentResult; | |
| 35 | ||
| 36 | 26 |  AlignmentJob(List<SequenceI> inputSeqs, List<SequenceI> emptySeqs, |
| 37 | Map<String, SequenceInfo> names) | |
| 38 | { | |
| 39 | 26 | super(Collections.unmodifiableList(inputSeqs)); |
| 40 | 26 | this.emptySeqs = Collections.unmodifiableList(emptySeqs); |
| 41 | 26 | this.names = Collections.unmodifiableMap(names); |
| 42 | } | |
| 43 | ||
| 44 | 26 | public static AlignmentJob create(SequenceI[] seqs, int minlen, boolean keepGaps) |
| 45 | { | |
| 46 | 26 | int nseqs = 0; |
| 47 | 104 | for (int i = 0; i < seqs.length; i++) |
| 48 | { | |
| 49 | 78 | if (seqs[i].getEnd() - seqs[i].getStart() >= minlen) |
| 50 | 78 | nseqs++; |
| 51 | } | |
| 52 | 26 | boolean valid = nseqs > 1; // need at least two sequences |
| 53 | 26 | Map<String, SequenceInfo> names = new LinkedHashMap<>(); |
| 54 | 26 | List<SequenceI> inputSeqs = new ArrayList<>(); |
| 55 | 26 | List<SequenceI> emptySeqs = new ArrayList<>(); |
| 56 | 104 | for (int i = 0; i < seqs.length; i++) |
| 57 | { | |
| 58 | 78 | SequenceI seq = seqs[i]; |
| 59 | 78 | String newName = SeqsetUtils.unique_name(i); |
| 60 | 78 | names.put(newName, SeqsetUtils.SeqCharacterHash(seq)); |
| 61 | 78 | if (valid && seq.getEnd() - seq.getStart() >= minlen) |
| 62 | { | |
| 63 | // make new input sequence | |
| 64 | 78 | String seqString = seq.getSequenceAsString(); |
| 65 | 78 | if (!keepGaps) |
| 66 | 72 | seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString); |
| 67 | 78 | inputSeqs.add(new Sequence(newName, seqString)); |
| 68 | } | |
| 69 | else | |
| 70 | { | |
| 71 | 0 | String seqString = ""; |
| 72 | 0 | if (seq.getEnd() >= seq.getStart()) // true if gaps only |
| 73 | { | |
| 74 | 0 | seqString = seq.getSequenceAsString(); |
| 75 | 0 | if (!keepGaps) |
| 76 | 0 | seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString); |
| 77 | } | |
| 78 | 0 | emptySeqs.add(new Sequence(newName, seqString)); |
| 79 | } | |
| 80 | } | |
| 81 | 26 | return new AlignmentJob(inputSeqs, emptySeqs, names); |
| 82 | } | |
| 83 | ||
| 84 | 196 | @Override |
| 85 | public boolean isInputValid() | |
| 86 | { | |
| 87 | 196 | return inputSeqs.size() >= 2; |
| 88 | } | |
| 89 | ||
| 90 | 8 | List<SequenceI> getEmptySequences() |
| 91 | { | |
| 92 | 8 | return emptySeqs; |
| 93 | } | |
| 94 | ||
| 95 | 8 | Map<String, SequenceInfo> getNames() |
| 96 | { | |
| 97 | 8 | return names; |
| 98 | } | |
| 99 | ||
| 100 | 46 | boolean hasResult() |
| 101 | { | |
| 102 | 46 | return alignmentResult != null; |
| 103 | } | |
| 104 | ||
| 105 | 8 | AlignmentI getAlignmentResult() |
| 106 | { | |
| 107 | 8 | return alignmentResult; |
| 108 | } | |
| 109 | ||
| 110 | 20 | void setAlignmentResult(AlignmentI alignment) |
| 111 | { | |
| 112 | 20 | this.alignmentResult = alignment; |
| 113 | } | |
| 114 | } |