A B C D E F G H I J K L M N O P Q R S T U V W X Z

O

Oligo - class trans.main.Oligo.

Container to hold information about a particular oligo.

Oligo(int, int, int, ArrayList, String) - Constructor for class trans.main.Oligo

OligoBase - class bioroot.oligo.OligoBase.

OligoBase() - Constructor for class bioroot.oligo.OligoBase

OligoBean - class bioroot.oligo.OligoBean.

OligoBean() - Constructor for class bioroot.oligo.OligoBean

OligoBean(int, DBUtil) - Constructor for class bioroot.oligo.OligoBean

OligoBean(ResultSet) - Constructor for class bioroot.oligo.OligoBean

OligoBean(String[], IdNameMatch[], IdNameMatch[], UserBean, DBUtil) - Constructor for class bioroot.oligo.OligoBean

For bulk file upload should be 17? cells Name, Alias Oligo Sequence, Matching Gene Sequence, uM Stock Concentration, ng/uL Stock Concentration, Volume(uL), Purification, 0 1 2 3 4 5 6 7 Modifications, Orientation, Type, Storage Location, Availibility, Visibility, Handling Instructions, Target Gene Name, Organism, Notes 8 9 10 11 12 13 14 15 16 17

OligoFlipper - class trans.tpmap.OligoFlipper.

This reversed the oligo sequence and orientation in a tpmap file.

OligoFlipper(String[]) - Constructor for class trans.tpmap.OligoFlipper

OligoIntensityPrinter - class trans.main.OligoIntensityPrinter.

Prints out the oligo intensity values, split by chromosome, as '.sgr' files for import into Affy's IGB.

OligoIntensityPrinter(String[]) - Constructor for class trans.main.OligoIntensityPrinter

OligoMatch - class bioroot.plasmid.OligoMatch.

OligoMatch(BlastMatcher) - Constructor for class bioroot.plasmid.OligoMatch

OligoMatch(ResultSet) - Constructor for class bioroot.plasmid.OligoMatch

OligoModify - class bioroot.oligo.OligoModify.

Servlet to modify oligos using OligoBeans referenced from a Session object.

OligoModify() - Constructor for class bioroot.oligo.OligoModify

OligoSpreadSheet - class bioroot.oligo.OligoSpreadSheet.

OligoSpreadSheet() - Constructor for class bioroot.oligo.OligoSpreadSheet

OligoUpload - class bioroot.oligo.OligoUpload.

OligoUpload() - Constructor for class bioroot.oligo.OligoUpload

OligoUploadBean - class bioroot.oligo.OligoUploadBean.

Oligo bulk file upload bean.

OligoUploadBean() - Constructor for class bioroot.oligo.OligoUploadBean

OligoViewPreferences - class bioroot.oligo.OligoViewPreferences.

OligoViewPreferences() - Constructor for class bioroot.oligo.OligoViewPreferences

Organism - class bioroot.Organism.

Organism() - Constructor for class bioroot.Organism

OrganismBean - class bioroot.OrganismBean.

OrganismBean() - Constructor for class bioroot.OrganismBean

OrganismBean(int, DBUtil) - Constructor for class bioroot.OrganismBean

Organization - class bioroot.Organization.

Container for holding info about Organization membership.

Organization(DBUtil, int) - Constructor for class bioroot.Organization

OverlapCounter - class trans.main.OverlapCounter.

Provides an intersection analysis on multiple Interval[]s.

OverlapCounter(String[]) - Constructor for class trans.main.OverlapCounter

OverlappingWindowScoreExtractor - class trans.main.OverlappingWindowScoreExtractor.

Finds the best overlapping Window for each region and prints that score with the region information.

OverlappingWindowScoreExtractor(String[]) - Constructor for class trans.main.OverlappingWindowScoreExtractor

For each validation region, finds the single test window that 'best' overlaps.

Owner - class com.amazon.s3.Owner.

A structure representing the owner of an object, used as a part of ListEntry.

Owner() - Constructor for class com.amazon.s3.Owner

object - Variable in class com.amazon.s3.GetResponse

objectArrayToArrayList(Object[]) - Static method in class util.gen.Misc

Converts an Object[] to an ArrayList

objectArraytoAL(Object[]) - Static method in class gata.main.GATAUtil

Converts an Object[] to an ArrayList

optimizeAlignmentScore(String, String, int, int, int, int, int) - Static method in class gata.main.GATAUtil

optimizeScores(int[][]) - Method in class gata.aligner.LocalAlignment

orderAntibodies(String, UserBean, AntibodyBean[], DBUtil) - Static method in class bioroot.antibody.AntibodySpreadSheet

Orders antibodys, sort of nasty, can't figure another way, reflection is way too slow.

orderOligos(String, Preference, OligoBean[], DBUtil) - Static method in class bioroot.oligo.OligoSpreadSheet

Orders oligos, sort of nasty, can't figure another way, reflection is way too slow.

orderPlasmids(String, UserBean, PlasmidBean[], DBUtil) - Static method in class bioroot.plasmid.PlasmidSpreadSheet

Orders plasmids, sort of nasty, can't figure another way, reflection is way too slow.

orderStrains(String, UserBean, StrainBean[], DBUtil) - Static method in class bioroot.strain.StrainSpreadSheet

Orders strains, sort of nasty, can't figure another way, reflection is way too slow.

ordered() - Method in class trans.cel.ControlStats

overlap(ArrayList, int, int) - Static method in class trans.anno.AnnotateRegions

Tests whether any startEnd int[] in the ArrayList of ints ovelaps a region defined by the startRegion and endRegion.

overlap(ArrayList, int, int) - Static method in class trans.anno.AnnotateRegionsWithGeneList

Tests whether any startEnd int[] in the ArrayList of ints ovelaps a region defined by the startRegion and endRegion.

overlap(BindingRegion) - Method in class trans.anno.BindingRegion

Returns -1 for no overlap, 0 for complete overlap, or a positive int for the # bases of overlap.

overlap(Interval) - Method in class trans.anno.Region

Returns -1 for no overlap, or a positive int for the # bases of overlap.

overlap(GenomicRegion, int) - Method in class trans.graphics.GenomicRegion

checks to see if regions overlap by the minimum maxGap, can set maxGap negative to require an overlap.

overlap(Interval, Interval) - Method in class trans.main.OverlapCounter

checks to see if intervals overlap by the minimum maxGap, can set maxGap negative to require an overlap.

overlap(Window) - Method in class trans.main.Window

overlapOrAbut(Window, Window) - Method in class trans.main.WindowBlockMakerTwoColor

Assumes right window is to right of left or abuts or doesn't overlap.

overlapPeaks(Interval, Interval) - Method in class trans.main.OverlapCounter

Returns distance between top peaks.

owner - Variable in class com.amazon.s3.ListEntry

The object's owner