Coverage Report
File SecStructPredMsaTask.java
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0% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| SecStructPredMsaTask | 32 | 38 | 8 | ||
| SecStructPredMsaTask.SecStructPredJob | 118 | 6 | 3 |
Contributing tests
This file is covered by 10 tests.
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Source view
| 1 | package jalview.ws2.actions.secstructpred; | |
| 2 | ||
| 3 | import java.io.IOException; | |
| 4 | import java.util.ArrayList; | |
| 5 | import java.util.Arrays; | |
| 6 | import java.util.List; | |
| 7 | import java.util.Map; | |
| 8 | ||
| 9 | import jalview.analysis.AlignmentAnnotationUtils; | |
| 10 | import jalview.analysis.SeqsetUtils; | |
| 11 | import jalview.analysis.SeqsetUtils.SequenceInfo; | |
| 12 | import jalview.api.AlignViewportI; | |
| 13 | import jalview.bin.Console; | |
| 14 | import jalview.datamodel.Alignment; | |
| 15 | import jalview.datamodel.AlignmentAnnotation; | |
| 16 | import jalview.datamodel.AlignmentI; | |
| 17 | import jalview.datamodel.AlignmentView; | |
| 18 | import jalview.datamodel.HiddenColumns; | |
| 19 | import jalview.datamodel.SeqCigar; | |
| 20 | import jalview.datamodel.SequenceI; | |
| 21 | import jalview.io.AlignFile; | |
| 22 | import jalview.io.JPredFile; | |
| 23 | import jalview.io.JnetAnnotationMaker; | |
| 24 | import jalview.ws.params.ArgumentI; | |
| 25 | import jalview.ws2.actions.BaseJob; | |
| 26 | import jalview.ws2.actions.BaseTask; | |
| 27 | import jalview.ws2.actions.ServiceInputInvalidException; | |
| 28 | import jalview.ws2.api.Credentials; | |
| 29 | import jalview.ws2.api.JobStatus; | |
| 30 | import jalview.ws2.client.api.SecStructPredWebServiceClientI; | |
| 31 | ||
| 32 | public class SecStructPredMsaTask | |
| 33 | extends BaseTask<SecStructPredMsaTask.SecStructPredJob, AlignmentI> | |
| 34 | { | |
| 35 | private final SecStructPredWebServiceClientI client; | |
| 36 | ||
| 37 | private final AlignmentView alignmentView; | |
| 38 | ||
| 39 | private final AlignmentI currentView; | |
| 40 | ||
| 41 | private final char gapChar; | |
| 42 | ||
| 43 | 10 |  SecStructPredMsaTask(SecStructPredWebServiceClientI client, |
| 44 | List<ArgumentI> args, Credentials credentials, | |
| 45 | AlignViewportI viewport) | |
| 46 | { | |
| 47 | 10 | super(client, args, credentials); |
| 48 | 10 | this.client = client; |
| 49 | 10 | this.alignmentView = viewport.getAlignmentView(true); |
| 50 | 10 | this.currentView = viewport.getAlignment(); |
| 51 | 10 | this.gapChar = viewport.getGapCharacter(); |
| 52 | } | |
| 53 | ||
| 54 | 10 | @Override |
| 55 | protected List<SecStructPredJob> prepareJobs() | |
| 56 | throws ServiceInputInvalidException | |
| 57 | { | |
| 58 | 10 | SeqCigar[] msf = alignmentView.getSequences(); |
| 59 | 10 | SequenceI referenceSeq = msf[0].getSeq('-'); |
| 60 | 10 | int[] delMap = alignmentView |
| 61 | .getVisibleContigMapFor(referenceSeq.gapMap()); | |
| 62 | ||
| 63 | // TODO: assume MSA for now | |
| 64 | 10 | SequenceI[] sequences = new SequenceI[msf.length]; |
| 65 | 37 | for (int i = 0; i < msf.length; i++) |
| 66 | 27 | sequences[i] = msf[i].getSeq('-'); |
| 67 | 10 | var sequenceInfo = SeqsetUtils.uniquify(sequences, true); |
| 68 | 10 | referenceSeq.setSequence(alignmentView.getASequenceString('-', 0)); |
| 69 | 37 | for (int i = 0; i < sequences.length; i++) |
| 70 | 27 | sequences[i].setSequence(alignmentView.getASequenceString('-', i)); |
| 71 | 10 | var nonEmptySeqs = SeqsetUtils.getNonEmptySequenceSet(sequences); |
| 72 | 10 | var job = new SecStructPredJob(Arrays.asList(nonEmptySeqs), |
| 73 | referenceSeq, delMap, sequenceInfo); | |
| 74 | 10 | job.setStatus(JobStatus.READY); |
| 75 | 10 | return List.of(job); |
| 76 | } | |
| 77 | ||
| 78 | 2 | @Override |
| 79 | protected AlignmentI collectResult(List<SecStructPredJob> jobs) | |
| 80 | throws IOException | |
| 81 | { | |
| 82 | 2 | var job = jobs.get(0); // There shouldn't be more than one job |
| 83 | 2 | var status = job.getStatus(); |
| 84 | 2 | Console.info( |
| 85 | String.format("sec str pred job \"%s\" finished with status %s", | |
| 86 | job.getServerJob().getJobId(), status)); | |
| 87 | 2 | if (status != JobStatus.COMPLETED) |
| 88 | 0 | return null; |
| 89 | 2 | JPredFile predictionFile = client.getPredictionFile(job.getServerJob()); |
| 90 | 2 | AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob()); |
| 91 | ||
| 92 | 2 | Object[] alnAndHiddenCols = alignmentView |
| 93 | .getAlignmentAndHiddenColumns(gapChar); | |
| 94 | 2 | Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]); |
| 95 | 2 | aln.setDataset(currentView.getDataset()); |
| 96 | 2 | aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]); |
| 97 | 2 | try |
| 98 | { | |
| 99 | 2 | JnetAnnotationMaker.add_annotation(predictionFile, aln, 0, false, |
| 100 | job.getDelMap()); | |
| 101 | } catch (Exception e) | |
| 102 | { | |
| 103 | 0 | throw new IOException(e); |
| 104 | } | |
| 105 | ||
| 106 | 2 | for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation()) |
| 107 | { | |
| 108 | 18 | if (alnAnnot.sequenceRef != null) |
| 109 | { | |
| 110 | 18 | AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot, |
| 111 | alnAnnot.label, getClass().getSimpleName()); | |
| 112 | } | |
| 113 | } | |
| 114 | 2 | aln.setSeqrep(aln.getSequenceAt(0)); |
| 115 | 2 | return aln; |
| 116 | } | |
| 117 | ||
| 118 | public static class SecStructPredJob extends BaseJob | |
| 119 | { | |
| 120 | private final int[] delMap; | |
| 121 | ||
| 122 | private final SequenceI refSeq; | |
| 123 | ||
| 124 | final Map<String, SequenceInfo> seqNames; | |
| 125 | ||
| 126 | 10 | SecStructPredJob(List<SequenceI> sequences, SequenceI refSeq, |
| 127 | int[] delMap, Map<String, SequenceInfo> seqNames) | |
| 128 | { | |
| 129 | 10 | super(sequences); |
| 130 | 10 | this.refSeq = refSeq; |
| 131 | 10 | this.delMap = delMap; |
| 132 | 10 | this.seqNames = seqNames; |
| 133 | } | |
| 134 | ||
| 135 | 8 | @Override |
| 136 | public boolean isInputValid() | |
| 137 | { | |
| 138 | 8 | return true; |
| 139 | } | |
| 140 | ||
| 141 | 2 | public int[] getDelMap() |
| 142 | { | |
| 143 | 2 | return this.delMap; |
| 144 | } | |
| 145 | } | |
| 146 | ||
| 147 | } |