public class SingleMolecule extends AbstractMolecule
AbstractMoleculeArchives
to allow for fast and efficient retrieval and optimal organization.
Molecule records are designed to allow for storage of many different kinds of
single-molecule time-series data. They contain a primary MarsTable
(or DataTable) with molecule properties typically as a function of time/slice
of a video. This may include position or intensity information. To facilitate
efficient and reproducible processing Molecule records may also contain
calculated parameters, tags, notes, and kinetic change point segment
MarsTables generated by KCPCommand. Molecule records are
assigned a random UID string at the time of creation derived from a base58
encoded UUID for readability. This serves as their primary identifier within
AbstractMoleculeArchives and for a range of transformations and
merging operations. Molecule records also have a UID string for corresponding
MarsMetadata records, which contain information about the imaging
settings, the timing of frames etc.. during data collection.
Molecule records can be saved to JSON for storage when done processing. They are then either stored as an array within MoleculeArchive .yama files or as individual json files within .yama.store directories.
parent| Constructor and Description |
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SingleMolecule()
Constructor for creating an empty Molecule record.
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SingleMolecule(com.fasterxml.jackson.core.JsonParser jParser)
Constructor for loading a Molecule record from a file.
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SingleMolecule(java.lang.String UID)
Constructor for creating an empty Molecule record with the specified UID.
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SingleMolecule(java.lang.String UID,
MarsTable dataTable)
Constructor for creating a new Molecule record with the specified UID and
the
MarsTable given as the DataTable. |
addTag, createIOMaps, getChannel, getImage, getMetadataUID, getSegmentsTable, getSegmentsTable, getSegmentsTable, getSegmentsTableNames, getTable, hasSegmentsTable, hasSegmentsTable, merge, putPosition, putRegion, putSegmentsTable, putSegmentsTable, removeSegmentsTable, removeSegmentsTable, removeSegmentsTable, setChannel, setImage, setMetadataUID, setParameter, setParameter, setParameter, setTableaddNote, getBooleanParameter, getNotes, getParameter, getParameters, getPosition, getPositionNames, getPositions, getRegion, getRegionNames, getRegions, getStringParameter, getTags, getTagsArray, getUID, hasBooleanParameter, hasDoubleParameter, hasNoTags, hasParameter, hasPosition, hasRegion, hasStringParameter, hasTag, merge, removeAllParameters, removeAllPositions, removeAllRegions, removeAllTags, removeParameter, removePosition, removeRegion, removeTag, setNotes, setParentdumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSONclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddNote, getBooleanParameter, getNotes, getParameter, getParameters, getPosition, getPositionNames, getPositions, getRegion, getRegionNames, getRegions, getStringParameter, getTags, getTagsArray, getUID, hasBooleanParameter, hasDoubleParameter, hasNoTags, hasParameter, hasPosition, hasRegion, hasStringParameter, hasTag, merge, removeAllParameters, removeAllPositions, removeAllRegions, removeAllTags, removeParameter, removePosition, removeRegion, removeTag, setNotes, setParentdumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSONpublic SingleMolecule()
public SingleMolecule(com.fasterxml.jackson.core.JsonParser jParser)
throws java.io.IOException
AbstractMoleculeArchive or when a record is retrieved from the
virtual store.jParser - A JsonParser at the start of the molecule record json for
loading the molecule record from a file.java.io.IOException - Thrown if unable to parse Json from JsonParser stream.public SingleMolecule(java.lang.String UID)
UID - The unique identifier for this Molecule record.public SingleMolecule(java.lang.String UID,
MarsTable dataTable)
MarsTable given as the DataTable.UID - The unique identifier for this Molecule record.dataTable - The MarsTable to use for initialization.