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package net.sf.basedb.reggie.plugins.release; |
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import org.json.simple.JSONArray; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.DerivedBioAssay; |
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import net.sf.basedb.core.RawBioAssay; |
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import net.sf.basedb.reggie.dao.Annotationtype; |
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/** |
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Common functionality for various raw bioassay writer implementations (eg. StringTie and Cufflinks) |
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@since 4.5 |
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*/ |
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public abstract class RawBioAssayWriter |
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extends CohortWriter |
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{ |
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protected RawBioAssayWriter(DbControl dc, ReleaseWriterOptions options) |
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{ |
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super(dc, options); |
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} |
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protected void addCommonRawBioAssayAnnotations(CohortItem item, RawBioAssay raw, JSONArray jsonAnnotations) |
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{ |
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jsonAnnotations.add(item.createAnnotationJSON("ArrayDesign", getName(raw.getArrayDesign()))); |
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jsonAnnotations.add(item.createAnnotationJSON("FeatureSoftware", getName(raw.getSoftware()))); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.PIPELINE, raw, null)); |
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} |
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protected void addCommonAlignmentAnnotations(CohortItem item, DerivedBioAssay alignment, JSONArray jsonAnnotations) |
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{ |
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jsonAnnotations.add(item.createAnnotationJSON("AlignmentName", item.toReleaseId(alignment.getName()))); |
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jsonAnnotations.add(item.createAnnotationJSON("AlignSoftware", getName(alignment.getSoftware()))); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.ALIGNED_PAIRS, alignment, null)); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.FRACTION_DUPLICATION, alignment, null)); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.FRAGMENT_SIZE_AVG, alignment, null)); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.FRAGMENT_SIZE_STDEV, alignment, null)); |
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} |
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protected void addCommonMaskedAnnotations(CohortItem item, DerivedBioAssay masked, JSONArray jsonAnnotations) |
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{ |
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jsonAnnotations.add(item.createAnnotationJSON("MaskSoftware", getName(masked.getSoftware()))); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.PM_READS, masked, null)); |
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} |
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} |