1 package jalview.ws2.actions.alignment;
3 import static java.lang.String.format;
5 import java.io.IOException;
6 import java.util.ArrayList;
7 import java.util.Arrays;
8 import java.util.HashMap;
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;
33 * Implementation of an abstract pollable task used by alignment service
39 class AlignmentTask extends BaseTask<AlignmentJob, AlignmentResult>
41 /* task parameters set in the constructor */
42 private final AlignmentWebServiceClientI client;
44 private final AlignmentAction action;
46 private final AlignmentView msa; // a.k.a. input
48 private final AlignViewportI viewport;
50 private final boolean submitGaps;
52 private final AlignmentI currentView;
54 private final AlignmentI dataset;
56 private final char gapChar;
58 private final List<AlignedCodonFrame> codonFrame = new ArrayList<>();
60 AlignmentTask(AlignmentWebServiceClientI client, AlignmentAction action,
61 List<ArgumentI> args, Credentials credentials,
62 AlignViewportI viewport, boolean submitGaps)
64 super(client, args, credentials);
67 this.msa = viewport.getAlignmentView(true);
68 this.viewport = viewport;
69 this.submitGaps = submitGaps;
70 this.currentView = viewport.getAlignment();
71 this.dataset = viewport.getAlignment().getDataset();
72 this.gapChar = viewport.getGapCharacter();
73 List<AlignedCodonFrame> cf = viewport.getAlignment().getCodonFrames();
75 this.codonFrame.addAll(cf);
79 protected List<AlignmentJob> prepareJobs() throws ServiceInputInvalidException
81 Console.info(format("starting alignment service %s:%s",
82 client.getClientName(), action.getName()));
83 SequenceI[][] conmsa = msa.getVisibleContigs(gapChar);
86 throw new ServiceInputInvalidException("no visible contigs for alignment");
88 List<AlignmentJob> jobs = new ArrayList<>(conmsa.length);
89 boolean validInput = false;
90 for (int i = 0; i < conmsa.length; i++)
92 AlignmentJob job = AlignmentJob.create(conmsa[i], 2, submitGaps);
93 validInput |= job.isInputValid(); // at least one input is valid
94 job.setStatus(job.isInputValid() ? JobStatus.READY : JobStatus.INVALID);
100 throw new ServiceInputInvalidException("no valid sequences for alignment");
106 protected AlignmentResult collectResult(List<AlignmentJob> jobs) throws IOException
108 IOException lastIOE = null;
109 for (AlignmentJob job : jobs)
111 if (job.isInputValid() && job.getStatus() == JobStatus.COMPLETED &&
116 job.setAlignmentResult(client.getAlignment(job.getServerJob()));
117 } catch (IOException e)
124 throw lastIOE; // do not proceed unless all results has been retrieved
126 List<AlignmentOrder> alorders = new ArrayList<>();
127 SequenceI[][] results = new SequenceI[jobs.size()][];
128 AlignmentOrder[] orders = new AlignmentOrder[jobs.size()];
129 for (int i = 0; i < jobs.size(); i++)
131 /* alternative implementation of MsaWSJob#getAlignment */
132 AlignmentJob job = jobs.get(i);
133 if (!job.hasResult())
135 AlignmentI alignment = job.getAlignmentResult();
136 int alnSize = alignment.getSequences().size();
137 char gapChar = alnSize > 0 ? alignment.getGapCharacter() : '-';
138 List<SequenceI> emptySeqs = job.getEmptySequences();
139 List<SequenceI> alnSeqs = new ArrayList<>(alnSize);
140 // create copies of all sequences involved
141 for (SequenceI seq : alignment.getSequences())
143 alnSeqs.add(new Sequence(seq));
145 for (SequenceI seq : emptySeqs)
147 alnSeqs.add(new Sequence(seq));
149 // find the width of the longest sequence
151 for (var seq: alnSeqs)
152 width = Integer.max(width, seq.getLength());
153 // make a sequence of gaps only to cut/paste
156 char[] gaps = new char[width];
157 Arrays.fill(gaps, gapChar);
158 gapSeq = new String(gaps);
160 for (var seq: alnSeqs)
162 if (seq.getLength() < width)
164 // pad sequences shorter than the target width with gaps
165 seq.setSequence(seq.getSequenceAsString()
166 + gapSeq.substring(seq.getLength()));
169 SequenceI[] result = alnSeqs.toArray(new SequenceI[0]);
170 AlignmentOrder msaOrder = new AlignmentOrder(result);
171 AlignmentSorter.recoverOrder(result);
172 Map<String, SequenceInfo> names = new HashMap<>(job.getNames());
173 SeqsetUtils.deuniquify(names, result);
175 alorders.add(msaOrder);
177 orders[i] = msaOrder;
179 Object[] newView = msa.getUpdatedView(results, orders, gapChar);
180 // free references to original data
181 for (int i = 0; i < jobs.size(); i++)
186 SequenceI[] alignment = (SequenceI[]) newView[0];
187 HiddenColumns hidden = (HiddenColumns) newView[1];
188 Alignment aln = new Alignment(alignment);
189 aln.setProperty("Alignment Program", action.getName());
191 aln.setDataset(dataset);
193 propagateDatasetMappings(aln);
194 return new AlignmentResult(aln, alorders, hidden);
198 * Conserve dataset references to sequence objects returned from web services.
199 * Propagate AlignedCodonFrame data from {@code codonFrame} to {@code aln}.
200 * TODO: Refactor to datamodel
202 private void propagateDatasetMappings(AlignmentI aln)
204 if (codonFrame != null)
206 SequenceI[] alignment = aln.getSequencesArray();
207 for (final SequenceI seq : alignment)
209 for (AlignedCodonFrame acf : codonFrame)
211 if (acf != null && acf.involvesSequence(seq))
213 aln.addCodonFrame(acf);