From: Mateusz Warowny Date: Fri, 2 Jun 2023 10:36:47 +0000 (+0200) Subject: JAL-3954 Add query sequence aligned to consensus to search result X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dc82563dc0d6752da31ade9031035854e5c33409;p=jalview.git JAL-3954 Add query sequence aligned to consensus to search result --- diff --git a/src/jalview/ws2/actions/hmmer/PhmmerTask.java b/src/jalview/ws2/actions/hmmer/PhmmerTask.java index 0565300..e077b61 100644 --- a/src/jalview/ws2/actions/hmmer/PhmmerTask.java +++ b/src/jalview/ws2/actions/hmmer/PhmmerTask.java @@ -3,13 +3,18 @@ package jalview.ws2.actions.hmmer; import static jalview.util.Comparison.GapChars; import java.io.IOException; +import java.util.Arrays; import java.util.List; import jalview.analysis.AlignSeq; import jalview.bin.Console; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; +import jalview.datamodel.Annotation; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.Comparison; import jalview.ws.params.ArgumentI; import jalview.ws2.actions.AbstractPollableTask; import jalview.ws2.actions.BaseJob; @@ -56,11 +61,51 @@ class PhmmerTask extends AbstractPollableTask protected AlignmentI done() throws IOException { var job = getSubJobs().get(0); - var jobId = job.getServerJob().getJobId(); - var status = job.getStatus(); Console.info(String.format("phmmer finished job \"%s\" with status %s", - jobId, status)); - return client.getAlignment(job.getServerJob()); + job.getServerJob().getJobId(), job.getStatus())); + var outputAlignment = client.getAlignment(job.getServerJob()); + var querySeq = job.getInputSequences().get(0).deriveSequence(); + { + AlignmentAnnotation refpos = null; + for (var annot : outputAlignment.getAlignmentAnnotation()) + { + if (annot.sequenceRef == null && annot.label.equals("Reference Positions")) + { + refpos = annot; + break; + } + } + if (refpos != null) + { + querySeq = alignQeuryToReferencePositions(querySeq, refpos); + } + } + outputAlignment.insertSequenceAt(0, querySeq); + return outputAlignment; } + private SequenceI alignQeuryToReferencePositions(SequenceI query, AlignmentAnnotation refpos) + { + var sequenceBuilder = new StringBuilder(); + var index = 0; + for (Annotation a : refpos.annotations) + { + // TODO: we assume that the number of "x" annotations is equal to the number + // of residues. may need a safeguard against invalid input + if (a != null && a.displayCharacter.equals("x")) + { + char c; + do + c = query.getCharAt(index++); + while (Comparison.isGap(c)); + sequenceBuilder.append(c); + } + else + { + sequenceBuilder.append(Comparison.GAP_DASH); + } + } + query.setSequence(sequenceBuilder.toString()); + return query; + } } diff --git a/src/jalview/ws2/client/ebi/PhmmerWSClient.java b/src/jalview/ws2/client/ebi/PhmmerWSClient.java index 0bcb2f9..9c5f14f 100644 --- a/src/jalview/ws2/client/ebi/PhmmerWSClient.java +++ b/src/jalview/ws2/client/ebi/PhmmerWSClient.java @@ -1,16 +1,22 @@ package jalview.ws2.client.ebi; +import java.io.BufferedReader; import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; import java.io.StringReader; import java.net.URI; import java.util.List; import jalview.bin.Console; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FileFormat; +import jalview.io.FileParse; import jalview.io.FormatAdapter; +import jalview.io.StockholmFile; import jalview.ws.params.ArgumentI; import jalview.ws.params.simple.BooleanOption; import jalview.ws.params.simple.DoubleParameter; @@ -243,6 +249,15 @@ public class PhmmerWSClient implements AlignmentWebServiceClientI public AlignmentI getAlignment(WebServiceJobHandle job) throws IOException { URI url = client.getResultURL(job.getJobId(), "sto"); - return new FormatAdapter().readFile(url.toString(), DataSourceType.URL, FileFormat.Stockholm); + try(InputStream stream = client.getResultStream(job.getJobId(), "sto")) + { + StockholmFile file = new StockholmFile(new FileParse( + new BufferedReader(new InputStreamReader(stream)), + url.toString(), DataSourceType.URL)); + var aln = new Alignment(file.getSeqsAsArray()); + for (var annotation : file.getAnnotations()) + aln.addAnnotation(annotation); + return aln; + } } }