File AlignmentTask.java

Branches:

Statements:

Methods:

Classes:

LOC:

217

NCLOC:

180

Total complexity:

Complexity density:

0.26

Statements/Method:

21.75

Methods/Class:

Average method complexity:

5.75

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentTask	39	87	23	0.00%

Class AlignmentTask

Class AlignmentTask	Line # 39	Total Statements 87	Complexity 23	TOTAL Coverage 0.00%
AlignmentTask(AlignmentWebServiceClientI,AlignmentAction,List<ArgumentI>,Credentials,AlignViewportI,boolean) AlignmentTask(AlignmentWebServiceClientI,AlignmentAction,List<ArgumentI>,Credentials,AlignViewportI,boolean)	5858	11.011	2.02	0.0 0.00%
prepareJobs() : List<AlignmentJob> prepareJobs() : List<AlignmentJob>	7575	15.015	5.05	0.0 0.00%
collectResult(List<AlignmentJob>) : AlignmentResult collectResult(List<AlignmentJob>) : AlignmentResult	102102	54.054	12.012	0.0 0.00%
propagateDatasetMappings(AlignmentI) : void propagateDatasetMappings(AlignmentI) : void	199199	7.07	4.04	0.0 0.00%

Contributing tests

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package jalview.ws2.actions.alignment;

import static java.lang.String.format;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import jalview.analysis.AlignmentSorter;

import jalview.analysis.SeqsetUtils;

import jalview.analysis.SeqsetUtils.SequenceInfo;

import jalview.api.AlignViewportI;

import jalview.bin.Console;

import jalview.datamodel.AlignedCodonFrame;

import jalview.datamodel.Alignment;

import jalview.datamodel.AlignmentI;

import jalview.datamodel.AlignmentOrder;

import jalview.datamodel.AlignmentView;

import jalview.datamodel.HiddenColumns;

import jalview.datamodel.Sequence;

import jalview.datamodel.SequenceI;

import jalview.ws.params.ArgumentI;

import jalview.ws2.actions.BaseTask;

import jalview.ws2.actions.ServiceInputInvalidException;

import jalview.ws2.api.Credentials;

import jalview.ws2.api.JobStatus;

import jalview.ws2.client.api.AlignmentWebServiceClientI;

/**

* Implementation of an abstract pollable task used by alignment service

* actions.

* @author mmwarowny

class AlignmentTask extends BaseTask<AlignmentJob, AlignmentResult>

{

/* task parameters set in the constructor */

private final AlignmentWebServiceClientI client;

private final AlignmentAction action;

private final AlignmentView msa; // a.k.a. input

private final boolean submitGaps;

private final AlignmentI currentView;

private final AlignmentI dataset;

private final char gapChar;

private final List<AlignedCodonFrame> codonFrame = new ArrayList<>();

AlignmentTask(AlignmentWebServiceClientI client, AlignmentAction action,

List<ArgumentI> args, Credentials credentials,

AlignViewportI viewport, boolean submitGaps)

{

super(client, args, credentials);

this.client = client;

this.action = action;

this.msa = viewport.getAlignmentView(true);

this.submitGaps = submitGaps;

this.currentView = viewport.getAlignment();

this.dataset = viewport.getAlignment().getDataset();

this.gapChar = viewport.getGapCharacter();

List<AlignedCodonFrame> cf = viewport.getAlignment().getCodonFrames();

if (cf != null)

this.codonFrame.addAll(cf);

}

@Override

protected List<AlignmentJob> prepareJobs() throws ServiceInputInvalidException

{

Console.info(format("starting alignment service %s:%s",

client.getClientName(), action.getName()));

SequenceI[][] conmsa = msa.getVisibleContigs(gapChar);

if (conmsa == null)

{

throw new ServiceInputInvalidException("no visible contigs for alignment");

}

List<AlignmentJob> jobs = new ArrayList<>(conmsa.length);

boolean validInput = false;

for (int i = 0; i < conmsa.length; i++)

{

AlignmentJob job = AlignmentJob.create(conmsa[i], 2, submitGaps);

validInput |= job.isInputValid(); // at least one input is valid

job.setStatus(job.isInputValid() ? JobStatus.READY : JobStatus.INVALID);

jobs.add(job);

}

this.jobs = jobs;

if (!validInput)

{

throw new ServiceInputInvalidException("no valid sequences for alignment");

}

return jobs;

}

@Override

protected AlignmentResult collectResult(List<AlignmentJob> jobs) throws IOException

104

{

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IOException lastIOE = null;

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for (AlignmentJob job : jobs)

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{

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if (job.isInputValid() && job.getStatus() == JobStatus.COMPLETED &&

!job.hasResult())

{

try

{

job.setAlignmentResult(client.getAlignment(job.getServerJob()));

114

} catch (IOException e)

{

lastIOE = e;

}

}

}

if (lastIOE != null)

throw lastIOE; // do not proceed unless all results has been retrieved

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List<AlignmentOrder> alorders = new ArrayList<>();

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SequenceI[][] results = new SequenceI[jobs.size()][];

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AlignmentOrder[] orders = new AlignmentOrder[jobs.size()];

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for (int i = 0; i < jobs.size(); i++)

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{

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/* alternative implementation of MsaWSJob#getAlignment */

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AlignmentJob job = jobs.get(i);

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if (!job.hasResult())

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continue;

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AlignmentI alignment = job.getAlignmentResult();

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int alnSize = alignment.getSequences().size();

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char gapChar = alnSize > 0 ? alignment.getGapCharacter() : '-';

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List<SequenceI> emptySeqs = job.getEmptySequences();

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List<SequenceI> alnSeqs = new ArrayList<>(alnSize);

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// create copies of all sequences involved

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for (SequenceI seq : alignment.getSequences())

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{

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alnSeqs.add(new Sequence(seq));

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}

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for (SequenceI seq : emptySeqs)

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{

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alnSeqs.add(new Sequence(seq));

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}

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// find the width of the longest sequence

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int width = 0;

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for (var seq: alnSeqs)

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width = Integer.max(width, seq.getLength());

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// make a sequence of gaps only to cut/paste

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String gapSeq;

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{

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char[] gaps = new char[width];

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Arrays.fill(gaps, gapChar);

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gapSeq = new String(gaps);

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}

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for (var seq: alnSeqs)

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{

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if (seq.getLength() < width)

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{

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// pad sequences shorter than the target width with gaps

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seq.setSequence(seq.getSequenceAsString()

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+ gapSeq.substring(seq.getLength()));

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}

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}

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SequenceI[] result = alnSeqs.toArray(new SequenceI[0]);

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AlignmentOrder msaOrder = new AlignmentOrder(result);

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AlignmentSorter.recoverOrder(result);

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Map<String, SequenceInfo> names = new HashMap<>(job.getNames());

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SeqsetUtils.deuniquify(names, result);

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alorders.add(msaOrder);

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results[i] = result;

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orders[i] = msaOrder;

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}

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Object[] newView = msa.getUpdatedView(results, orders, gapChar);

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// free references to original data

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for (int i = 0; i < jobs.size(); i++)

{

results[i] = null;

orders[i] = null;

}

SequenceI[] alignment = (SequenceI[]) newView[0];

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HiddenColumns hidden = (HiddenColumns) newView[1];

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Alignment aln = new Alignment(alignment);

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aln.setProperty("Alignment Program", action.getName());

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if (dataset != null)

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aln.setDataset(dataset);

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propagateDatasetMappings(aln);

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return new AlignmentResult(aln, alorders, hidden);

}

/**

* Conserve dataset references to sequence objects returned from web services.

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* Propagate AlignedCodonFrame data from {@code codonFrame} to {@code aln}.

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* TODO: Refactor to datamodel

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private void propagateDatasetMappings(AlignmentI aln)

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{

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if (codonFrame != null)

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{

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SequenceI[] alignment = aln.getSequencesArray();

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for (final SequenceI seq : alignment)

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{

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for (AlignedCodonFrame acf : codonFrame)

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{

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if (acf != null && acf.involvesSequence(seq))

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{

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aln.addCodonFrame(acf);

break;

}

}

}

}

}

}

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Class AlignmentTask

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