Class GeneMappingSummaryValueObject

java.lang.Object
ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject
All Implemented Interfaces:
Serializable
public class GeneMappingSummaryValueObject extends Object implements Serializable
One probe-to-gene mapping, as it goes over the wire: a single alignment plus the genes it supports.

The wire counterpart of GeneMappingSummary, which cannot be serialized as-is. That class predates the REST API and was shaped for a DWR/javascript client: it carries the same genes three times over (geneProductMap keyed by object, plus geneProductIdMap and geneProductIdGeneMap, two string-keyed mirrors that exist because "javascript clients cannot marshal maps unless the keys are strings"), and it holds a compositeSequence back-reference to the very value object that would contain it. Serializing it would emit each gene three times, key one of those maps by Object.toString(), and nest the parent inside its own child.

Alignment scores and the biological-sequence metadata both live on blatResult — its identity / score and its querySequence respectively — rather than being repeated at this level as GeneMappingSummary does.

Author:
paul
See Also:

  • Constructor Details

  • Method Details

    • getBlatResult

      @Nullable public BlatResultValueObject getBlatResult()
      The alignment this mapping rests on, carrying the scores (identity, score), the genomic coordinates, and the probe's biological sequence under querySequence.

      Null only for mappings that come from an annotation association rather than a real alignment.

    • getGenes

      public List<GeneReferenceValueObject> getGenes()
      Genes this alignment supports, deduplicated — a gene reached through several of its gene products appears once. Empty for an alignment that maps to no gene, which is a real and reportable outcome rather than a missing value.

    • setBlatResult

      public void setBlatResult(@Nullable BlatResultValueObject blatResult)
      The alignment this mapping rests on, carrying the scores (identity, score), the genomic coordinates, and the probe's biological sequence under querySequence.

      Null only for mappings that come from an annotation association rather than a real alignment.

    • setGenes

      public void setGenes(List<GeneReferenceValueObject> genes)
      Genes this alignment supports, deduplicated — a gene reached through several of its gene products appears once. Empty for an alignment that maps to no gene, which is a real and reportable outcome rather than a missing value.