Package ubic.gemma.core.loader.expression.arrayDesign
package ubic.gemma.core.loader.expression.arrayDesign
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ClassDescriptionExtract the chip type from Affymetrix CEL files.Reads Affymetrix Probe files, including exon arrays.Co-bean carrying the
ArrayDesignMergeEventemission thatArrayDesignMergeHelperServiceImpl.persistMerging(ArrayDesign, ArrayDesign, Collection, boolean, Collection)records against each participating platform.Implementation ofArrayDesignMergeAuditService: a thin co-bean that exists so eachArrayDesignMergeAuditServiceImpl.recordMerge(ArrayDesign, String)call is invoked through a Spring proxy and theAuditedaspect can intercept it and emit theArrayDesignMergeEvent.Make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergeesFor an array design, generate gene product mappings for the sequences.Aligns sequences from array designs to the genome, using blat, and persists the blat results.Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.Parse the "old" array description format.Parse an Illumina "manifest.txt" file (tab-delimited).A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and reporters, and all analysis would take place at the level of CompositeSequences.