Package ca.corefacility.bioinformatics.irida.model.sample

Class CoverageQCEntry

  • @Entity
public class CoverageQCEntry
extends QCEntry
    a QCEntry relating to the coverage of a sequence

    • Constructor Detail

      • CoverageQCEntry

        public CoverageQCEntry()

      • CoverageQCEntry

        public CoverageQCEntry​(SequencingObject sequencingObject,
                       long totalBases)

    • Method Detail

      • getType

        public QCEntry.QCEntryType getType()
        Description copied from class: QCEntry
        Return the type of qc entry. This will be used for display and grouping in the UI.
        Specified by:
        getType in class QCEntry
        Returns:
        the type of qc entry

      • getMessage

        public java.lang.String getMessage()
        Description copied from class: QCEntry
        Get the message for the qc entry
        Specified by:
        getMessage in class QCEntry
        Returns:
        the qc entry message to display

      • getCoverage

        public int getCoverage()
        Get the coverage number for this QCEntry
        Returns:
        coverage

      • getTotalBases

        public long getTotalBases()

      • setTotalBases

        public void setTotalBases​(long totalBases)

      • addProjectSettings

        public void addProjectSettings​(Project project)
        Enhance the QCEntry with a Project if required. This way a QCEntry can read project's settings to decide whether it's positive or negative.
        Specified by:
        addProjectSettings in class QCEntry
        Parameters:
        project - the Project to read from