Package ubic.gemma.core.analysis.expression.coexpression

Class CoexpressionMetaValueObject

java.lang.Object
ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject
All Implemented Interfaces:
Serializable
public class CoexpressionMetaValueObject extends Object implements Serializable
Author:
luke
See Also:

  • Constructor Details

    • CoexpressionMetaValueObject

      public CoexpressionMetaValueObject()

  • Method Details

    • getErrorState

      public String getErrorState()

    • setErrorState

      public void setErrorState(String errorState)

    • getMaxEdges

      public int getMaxEdges()
      Returns:
      How many edges total are we allowed to have in the graph? Above this, they can get trimmed.

    • setMaxEdges

      public void setMaxEdges(int maxEdges)
      Override the value of gemma.cytoscapeweb.maxEdges (or DEFAULT_MAX_EDGES_PER_GRAPH )
      Parameters:
      maxEdges - max edges

    • getNumDatasetsQueried

      public int getNumDatasetsQueried()

    • setNumDatasetsQueried

      public void setNumDatasetsQueried(int numDatasetsQueried)
      Parameters:
      numDatasetsQueried - the number of data sets which were actually used in the query (a subset of those requested by the user if they didn't have coexpression analysis done)

    • getQueryGenes

      public Collection<GeneValueObject> getQueryGenes()

    • setQueryGenes

      public void setQueryGenes(Collection<GeneValueObject> queryGenes)

    • getQueryStringency

      public int getQueryStringency()

    • setQueryStringency

      public void setQueryStringency(int queryStringency)

    • getResults

      public List<CoexpressionValueObjectExt> getResults()
      A sorted list of the results (sorting must be done elsewhere!)
      Returns:
      coexp VOs

    • setResults

      public void setResults(List<CoexpressionValueObjectExt> results)
      Parameters:
      results - please be sorted.

    • getSearchSettings

      public CoexpressionSearchCommand getSearchSettings()
      The original search settings from the client. made to the stringency
      Returns:
      coexp search command

    • setSearchSettings

      public void setSearchSettings(CoexpressionSearchCommand searchSettings)
      Parameters:
      searchSettings - , should be the original settings

    • getSummaries

      public Map<Long,CoexpressionSummaryValueObject> getSummaries()

    • setSummaries

      public void setSummaries(Map<Long,CoexpressionSummaryValueObject> summary)

    • isQueryGenesOnly

      public boolean isQueryGenesOnly()

    • setQueryGenesOnly

      public void setQueryGenesOnly(boolean queryGenesOnly)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • trim

      @Deprecated public void trim()
      Deprecated.
      because this is too ad hoc and messy
      This method just removes low stringency results until it goes below the limit, regardless of whether the genes involved were query genes or not. This means, in effect, the original query could have been done at this higher stringency. The other trim method only removes non-query gene edges, so it is suitable for large 'query genes only'. Warning, this method can remove results that user may have expected.