Coverage Report
File AlignmentTask.java
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13% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentTask | 39 | 87 | 23 |
Contributing tests
This file is covered by 27 tests.
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Source view
| 1 | package jalview.ws2.actions.alignment; | |
| 2 | ||
| 3 | import static java.lang.String.format; | |
| 4 | ||
| 5 | import java.io.IOException; | |
| 6 | import java.util.ArrayList; | |
| 7 | import java.util.Arrays; | |
| 8 | import java.util.HashMap; | |
| 9 | import java.util.List; | |
| 10 | import java.util.Map; | |
| 11 | ||
| 12 | import jalview.analysis.AlignmentSorter; | |
| 13 | import jalview.analysis.SeqsetUtils; | |
| 14 | import jalview.analysis.SeqsetUtils.SequenceInfo; | |
| 15 | import jalview.api.AlignViewportI; | |
| 16 | import jalview.bin.Console; | |
| 17 | import jalview.datamodel.AlignedCodonFrame; | |
| 18 | import jalview.datamodel.Alignment; | |
| 19 | import jalview.datamodel.AlignmentI; | |
| 20 | import jalview.datamodel.AlignmentOrder; | |
| 21 | import jalview.datamodel.AlignmentView; | |
| 22 | import jalview.datamodel.HiddenColumns; | |
| 23 | import jalview.datamodel.Sequence; | |
| 24 | import jalview.datamodel.SequenceI; | |
| 25 | import jalview.ws.params.ArgumentI; | |
| 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.AlignmentWebServiceClientI; | |
| 31 | ||
| 32 | /** | |
| 33 | * Implementation of an abstract pollable task used by alignment service | |
| 34 | * actions. | |
| 35 | * | |
| 36 | * @author mmwarowny | |
| 37 | * | |
| 38 | */ | |
| 39 | class AlignmentTask extends BaseTask<AlignmentJob, AlignmentResult> | |
| 40 | { | |
| 41 | /* task parameters set in the constructor */ | |
| 42 | private final AlignmentWebServiceClientI client; | |
| 43 | ||
| 44 | private final AlignmentAction action; | |
| 45 | ||
| 46 | private final AlignmentView msa; // a.k.a. input | |
| 47 | ||
| 48 | private final boolean submitGaps; | |
| 49 | ||
| 50 | private final AlignmentI currentView; | |
| 51 | ||
| 52 | private final AlignmentI dataset; | |
| 53 | ||
| 54 | private final char gapChar; | |
| 55 | ||
| 56 | private final List<AlignedCodonFrame> codonFrame = new ArrayList<>(); | |
| 57 | ||
| 58 | 26 |  AlignmentTask(AlignmentWebServiceClientI client, AlignmentAction action, |
| 59 | List<ArgumentI> args, Credentials credentials, | |
| 60 | AlignViewportI viewport, boolean submitGaps) | |
| 61 | { | |
| 62 | 26 | super(client, args, credentials); |
| 63 | 26 | this.client = client; |
| 64 | 26 | this.action = action; |
| 65 | 26 | this.msa = viewport.getAlignmentView(true); |
| 66 | 26 | this.submitGaps = submitGaps; |
| 67 | 26 | this.currentView = viewport.getAlignment(); |
| 68 | 26 | this.dataset = viewport.getAlignment().getDataset(); |
| 69 | 26 | this.gapChar = viewport.getGapCharacter(); |
| 70 | 26 | List<AlignedCodonFrame> cf = viewport.getAlignment().getCodonFrames(); |
| 71 | 26 | if (cf != null) |
| 72 | 26 | this.codonFrame.addAll(cf); |
| 73 | } | |
| 74 | ||
| 75 | 26 | @Override |
| 76 | protected List<AlignmentJob> prepareJobs() throws ServiceInputInvalidException | |
| 77 | { | |
| 78 | 26 | Console.info(format("starting alignment service %s:%s", |
| 79 | client.getClientName(), action.getName())); | |
| 80 | 26 | SequenceI[][] conmsa = msa.getVisibleContigs(gapChar); |
| 81 | 26 | if (conmsa == null) |
| 82 | { | |
| 83 | 0 | throw new ServiceInputInvalidException("no visible contigs for alignment"); |
| 84 | } | |
| 85 | 26 | List<AlignmentJob> jobs = new ArrayList<>(conmsa.length); |
| 86 | 26 | boolean validInput = false; |
| 87 | 52 | for (int i = 0; i < conmsa.length; i++) |
| 88 | { | |
| 89 | 26 | AlignmentJob job = AlignmentJob.create(conmsa[i], 2, submitGaps); |
| 90 | 26 | validInput |= job.isInputValid(); // at least one input is valid |
| 91 | 26 | job.setStatus(job.isInputValid() ? JobStatus.READY : JobStatus.INVALID); |
| 92 | 26 | jobs.add(job); |
| 93 | } | |
| 94 | 26 | this.jobs = jobs; |
| 95 | 26 | if (!validInput) |
| 96 | { | |
| 97 | 0 | throw new ServiceInputInvalidException("no valid sequences for alignment"); |
| 98 | } | |
| 99 | 26 | return jobs; |
| 100 | } | |
| 101 | ||
| 102 | 26 | @Override |
| 103 | protected AlignmentResult collectResult(List<AlignmentJob> jobs) throws IOException | |
| 104 | { | |
| 105 | 26 | IOException lastIOE = null; |
| 106 | 26 | for (AlignmentJob job : jobs) |
| 107 | { | |
| 108 | 26 | if (job.isInputValid() && job.getStatus() == JobStatus.COMPLETED && |
| 109 | !job.hasResult()) | |
| 110 | { | |
| 111 | 20 | try |
| 112 | { | |
| 113 | 20 | job.setAlignmentResult(client.getAlignment(job.getServerJob())); |
| 114 | } catch (IOException e) | |
| 115 | { | |
| 116 | 0 | lastIOE = e; |
| 117 | } | |
| 118 | } | |
| 119 | } | |
| 120 | 26 | if (lastIOE != null) |
| 121 | 0 | throw lastIOE; // do not proceed unless all results has been retrieved |
| 122 | ||
| 123 | 26 | List<AlignmentOrder> alorders = new ArrayList<>(); |
| 124 | 26 | SequenceI[][] results = new SequenceI[jobs.size()][]; |
| 125 | 26 | AlignmentOrder[] orders = new AlignmentOrder[jobs.size()]; |
| 126 | 52 | for (int i = 0; i < jobs.size(); i++) |
| 127 | { | |
| 128 | /* alternative implementation of MsaWSJob#getAlignment */ | |
| 129 | 26 | AlignmentJob job = jobs.get(i); |
| 130 | 26 | if (!job.hasResult()) |
| 131 | 18 | continue; |
| 132 | 8 | AlignmentI alignment = job.getAlignmentResult(); |
| 133 | 8 | int alnSize = alignment.getSequences().size(); |
| 134 | 8 | char gapChar = alnSize > 0 ? alignment.getGapCharacter() : '-'; |
| 135 | 8 | List<SequenceI> emptySeqs = job.getEmptySequences(); |
| 136 | 8 | List<SequenceI> alnSeqs = new ArrayList<>(alnSize); |
| 137 | // create copies of all sequences involved | |
| 138 | 8 | for (SequenceI seq : alignment.getSequences()) |
| 139 | { | |
| 140 | 24 | alnSeqs.add(new Sequence(seq)); |
| 141 | } | |
| 142 | 8 | for (SequenceI seq : emptySeqs) |
| 143 | { | |
| 144 | 0 | alnSeqs.add(new Sequence(seq)); |
| 145 | } | |
| 146 | // find the width of the longest sequence | |
| 147 | 8 | int width = 0; |
| 148 | 8 | for (var seq: alnSeqs) |
| 149 | 24 | width = Integer.max(width, seq.getLength()); |
| 150 | // make a sequence of gaps only to cut/paste | |
| 151 | 8 | String gapSeq; |
| 152 | { | |
| 153 | 8 | char[] gaps = new char[width]; |
| 154 | 8 | Arrays.fill(gaps, gapChar); |
| 155 | 8 | gapSeq = new String(gaps); |
| 156 | } | |
| 157 | 8 | for (var seq: alnSeqs) |
| 158 | { | |
| 159 | 24 | if (seq.getLength() < width) |
| 160 | { | |
| 161 | // pad sequences shorter than the target width with gaps | |
| 162 | 0 | seq.setSequence(seq.getSequenceAsString() |
| 163 | + gapSeq.substring(seq.getLength())); | |
| 164 | } | |
| 165 | } | |
| 166 | 8 | SequenceI[] result = alnSeqs.toArray(new SequenceI[0]); |
| 167 | 8 | AlignmentOrder msaOrder = new AlignmentOrder(result); |
| 168 | 8 | AlignmentSorter.recoverOrder(result); |
| 169 | 8 | Map<String, SequenceInfo> names = new HashMap<>(job.getNames()); |
| 170 | 8 | SeqsetUtils.deuniquify(names, result); |
| 171 | ||
| 172 | 8 | alorders.add(msaOrder); |
| 173 | 8 | results[i] = result; |
| 174 | 8 | orders[i] = msaOrder; |
| 175 | } | |
| 176 | 26 | Object[] newView = msa.getUpdatedView(results, orders, gapChar); |
| 177 | // free references to original data | |
| 178 | 52 | for (int i = 0; i < jobs.size(); i++) |
| 179 | { | |
| 180 | 26 | results[i] = null; |
| 181 | 26 | orders[i] = null; |
| 182 | } | |
| 183 | 26 | SequenceI[] alignment = (SequenceI[]) newView[0]; |
| 184 | 26 | HiddenColumns hidden = (HiddenColumns) newView[1]; |
| 185 | 26 | Alignment aln = new Alignment(alignment); |
| 186 | 26 | aln.setProperty("Alignment Program", action.getName()); |
| 187 | 26 | if (dataset != null) |
| 188 | 0 | aln.setDataset(dataset); |
| 189 | ||
| 190 | 26 | propagateDatasetMappings(aln); |
| 191 | 26 | return new AlignmentResult(aln, alorders, hidden); |
| 192 | } | |
| 193 | ||
| 194 | /** | |
| 195 | * Conserve dataset references to sequence objects returned from web services. | |
| 196 | * Propagate AlignedCodonFrame data from {@code codonFrame} to {@code aln}. | |
| 197 | * TODO: Refactor to datamodel | |
| 198 | */ | |
| 199 | 26 | private void propagateDatasetMappings(AlignmentI aln) |
| 200 | { | |
| 201 | 26 | if (codonFrame != null) |
| 202 | { | |
| 203 | 26 | SequenceI[] alignment = aln.getSequencesArray(); |
| 204 | 26 | for (final SequenceI seq : alignment) |
| 205 | { | |
| 206 | 78 | for (AlignedCodonFrame acf : codonFrame) |
| 207 | { | |
| 208 | 0 | if (acf != null && acf.involvesSequence(seq)) |
| 209 | { | |
| 210 | 0 | aln.addCodonFrame(acf); |
| 211 | 0 | break; |
| 212 | } | |
| 213 | } | |
| 214 | } | |
| 215 | } | |
| 216 | } | |
| 217 | } |