- a - Variable in class de.mpg.biochem.mars.kcp.KCPSegment
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- A - Static variable in class de.mpg.biochem.mars.kcp.KCPSegment
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- AbstractJsonConvertibleRecord - Class in de.mpg.biochem.mars.molecule
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Abstract superclass for JsonConvertibleRecords.
- AbstractJsonConvertibleRecord() - Constructor for class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord
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Constructor for creating a JsonConvertibleRecord.
- AbstractMarsMetadata - Class in de.mpg.biochem.mars.metadata
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Abstract superclass for storage of metadata, which includes all information
about specific data collections, imaging settings, frame timing.
- AbstractMarsMetadata() - Constructor for class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
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Constructor for creating an empty MarsMetadata record.
- AbstractMarsMetadata(String) - Constructor for class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
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Constructor for creating an empty MarsMetadata record with the specified
UID.
- AbstractMarsMetadata(String, OMEXMLMetadata) - Constructor for class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
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Constructor for creating a MarsMetadata record using OMEXMLMetadata.
- AbstractMarsMetadata(JsonParser) - Constructor for class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
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Constructor for loading a MarsMetadata record from a file.
- AbstractMarsRecord - Class in de.mpg.biochem.mars.molecule
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- AbstractMarsRecord() - Constructor for class de.mpg.biochem.mars.molecule.AbstractMarsRecord
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Constructor for creating an empty MarsRecord.
- AbstractMarsRecord(String) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMarsRecord
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Constructor for creating an empty MarsRecord with the specified UID.
- AbstractMolecule - Class in de.mpg.biochem.mars.molecule
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Abstract superclass for molecule records.
- AbstractMolecule() - Constructor for class de.mpg.biochem.mars.molecule.AbstractMolecule
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Constructor for creating an empty Molecule record.
- AbstractMolecule(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMolecule
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Constructor for loading a Molecule record from a file.
- AbstractMolecule(String) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMolecule
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Constructor for creating an empty Molecule record with the specified UID.
- AbstractMolecule(String, MarsTable) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMolecule
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Constructor for creating a new Molecule record with the specified UID and
the
MarsTable given as the DataTable.
- AbstractMoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>> - Class in de.mpg.biochem.mars.molecule
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Abstract superclass for the primary storage structure of Mars datasets.
- AbstractMoleculeArchive(String) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for creating an empty MoleculeArchive.
- AbstractMoleculeArchive(File) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for loading a MoleculeArchive.
- AbstractMoleculeArchive(URI) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for loading a MoleculeArchive.
- AbstractMoleculeArchive(MoleculeArchiveSource) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
- AbstractMoleculeArchive(String, File) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for loading a MoleculeArchive.
- AbstractMoleculeArchive(String, MarsTable) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for building a Molecule Archive from a MarsTable.
- AbstractMoleculeArchive(String, MarsTable, String) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Constructor for building a molecule archive from a MarsTable.
- AbstractMoleculeArchiveDialog - Class in de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector
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- AbstractMoleculeArchiveDialog(Context) - Constructor for class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
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- AbstractMoleculeArchiveDialog(String, Context) - Constructor for class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
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- AbstractMoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata> - Class in de.mpg.biochem.mars.molecule
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- AbstractMoleculeArchiveIndex() - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
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- AbstractMoleculeArchiveIndex(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
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- AbstractMoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata> - Class in de.mpg.biochem.mars.molecule
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Abstract superclass for MoleculeArchiveProperties objects that contain global
properties of the MoleculeArchive, including indexing, comments, and many
other global properties.
- AbstractMoleculeArchiveProperties() - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Creates an empty MoleculeArchiveProperties record.
- AbstractMoleculeArchiveProperties(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Constructor for loading MoleculeArchiveProperties record from a JsonParser
stream.
- accept(T) - Method in interface de.mpg.biochem.mars.util.MarsUtil.ThrowingConsumer
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- accumulator() - Method in class de.mpg.biochem.mars.table.MarsTableRowCollector
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- actionPerformed(ActionEvent) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveWidget
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- actionPerformed(ActionEvent) - Method in class de.mpg.biochem.mars.table.MarsTableWidget
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- add(MoleculeArchiveSwingTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
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- add(MoleculeArchiveTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode
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Adds a node as a child of this node.
- addAllChannels(Set<Integer>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add molecule channel indexes to the global set that contains a record of
all unique channel indexes that are represented in the archive.
- addAllChannels(Set<Integer>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add molecule channel indexes to the global set that contains a record of
all unique channel indexes that are represented in the archive.
- addAllColumns(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add column names to the unique set of column names in use in molecule
DataTables.
- addAllColumns(List<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add column names to the unique set of column names in use in molecule
DataTables.
- addAllColumns(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add column names to the unique set of column names in use in molecule
Tables.
- addAllColumns(List<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add column names to the unique set of column names in use in molecule
Tables.
- addAllParameters(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add molecule parameter names to the global set that contains a record of
all unique parameter names that are being used.
- addAllParameters(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add molecule parameter names to the global set that contains a record of
all unique parameter names that are being used.
- addAllPositions(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add molecule position names to the global set that contains a record of all
unique position names that are being used.
- addAllPositions(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add molecule position names to the global set that contains a record of all
unique position names that are being used.
- addAllRegions(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add molecule region names to the global set that contains a record of all
unique region names that are being used.
- addAllRegions(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add molecule region names to the global set that contains a record of all
unique region names that are being used.
- addAllSegmentsTableNames(Set<List<String>>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add segment table names to the unique set of segment table names found in
molecule records.
- addAllSegmentsTableNames(Set<List<String>>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add segment table names to the unique set of segment table names found in
molecule records.
- addAllTags(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add molecule tags to the global set that contains a record of all unique
tag names that are being used.
- addAllTags(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add molecule tags to the global set that contains a record of all unique
tag names that are being used.
- addArchive(MoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
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- addChannel(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a channel index to the global set that contains a record of all unique
indexes that are represented in the archive.
- addChannel(int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a channel index to the global set that contains a record of all unique
indexes that are represented in the archive.
- addChildPath(String) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
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- addColumn(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a column name to the unique set of column names in use in molecule
DataTables.
- addColumn(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a column name to the unique set of column names in use in molecule
DataTables.
- addComment(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add to archive comments.
- addComment(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add to archive comments.
- addIntegrationMap(String, int, Interval, Map<Integer, Map<String, Peak>>) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
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This method accepts maps the specify peak locations that should be
integrated in the form of a map first to T and then a Map From UID to Peak.
- addIntegrationMap(String, int, Interval, Map<Integer, Map<String, Peak>>) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
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This method accepts maps the specify peak locations that should be
integrated in the form of a map first to T and then a Map From UID to Peak.
- addMetadata(I) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
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- addMetadata(I) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex
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- addMetadataProperties(I) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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- addMetadataProperties(I) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Update global sets to include metadata properties.
- addMolecule(M) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
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- addMolecule(M) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex
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- addMoleculeProperties(M) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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- addMoleculeProperties(M) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Update global sets to include molecule properties.
- addMoleculeTags(Map<String, String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Add tags to molecules using UID to tag map.
- addMoleculeTags(Map<String, String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
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Add tags to molecules using UID to tag map.
- addNote(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
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Add to any notes already in the record.
- addNote(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
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Add to any notes already in the record.
- addParameter(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a molecule parameter name to the global set that contains a record of
all unique parameter names that are being used.
- addParameter(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a molecule parameter name to the global set that contains a record of
all unique parameter names that are being used.
- addParameter(String, boolean) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addParameter(String, int) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addParameter(String, Integer) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addParameter(String, double) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addParameter(String, Double) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addParameter(String, String) - Method in class de.mpg.biochem.mars.util.LogBuilder
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- addPath(String) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
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- addPath(String) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode
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Adds a node at the specified full path and any parent nodes along the path,
if they do not already exist.
- addPath(String, Function<String, MoleculeArchiveTreeNode>) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode
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Adds a node at the specified full path and any parent nodes along the path,
if they do not already exist.
- addPosition(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a molecule position name to the global set that contains a record of
all unique position names that are being used.
- addPosition(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a molecule position name to the global set that contains a record of
all unique position names that are being used.
- addRegion(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a molecule region name to the global set that contains a record of all
unique region names that are being used.
- addRegion(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a molecule region name to the global set that contains a record of all
unique region names that are being used.
- addRow(MarsTableRow) - Method in class de.mpg.biochem.mars.table.MarsTable
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Add MarsTableRow to the end of the table.
- addSegmentsTableNames(List<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a segment table name to the unique set of segment table names found in
molecule records.
- addSegmentsTableNames(List<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a segment table name to the unique set of segment table names found in
molecule records.
- addTable(MarsTable) - Method in class de.mpg.biochem.mars.table.MarsTableService
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- addTag(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
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Add a string tag to the record.
- addTag(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
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Add a string tag to the record.
- addTag(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
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Add a molecule tag to the global set that contains a record of all unique
tag names that are being used.
- addTag(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
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Add a string tag to the record.
- addTag(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
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Add a molecule tag to the global set that contains a record of all unique
tag names that are being used.
- addTime(SingleMoleculeArchive) - Static method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
-
- addTime(SingleMoleculeArchive, double) - Static method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
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- AddTimeCommand - Class in de.mpg.biochem.mars.molecule.commands
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- AddTimeCommand() - Constructor for class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
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- addTrailingSlash(String) - Static method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess
-
When listing children objects for a group, must append a delimiter to the path (e.g.
- addWidget(InputWidget<?, JPanel>) - Method in class de.mpg.biochem.mars.swingUI.MarsSwingInputPanel
-
- archiveIndex - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Record index used for virtual archives.
- archiveProperties - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
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Archive properties.
- ArchiveUtils - Class in de.mpg.biochem.mars.molecule
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- ArchiveUtils() - Constructor for class de.mpg.biochem.mars.molecule.ArchiveUtils
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- AREA - Static variable in class de.mpg.biochem.mars.image.Peak
-
- area() - Method in class de.mpg.biochem.mars.image.PeakShape
-
- at(int) - Method in class de.mpg.biochem.mars.table.MarsTableRow
-