MarsRecord

All Superinterfaces:

JsonConvertibleRecord

All Known Subinterfaces:

MarsMetadata, Molecule

All Known Implementing Classes:

AbstractMarsMetadata, AbstractMarsRecord, AbstractMolecule, DefaultMolecule, DnaMolecule, MarsOMEMetadata, MartianObject, OLDMarsMetadata, SingleMolecule
```
public interface MarsRecord
extends JsonConvertibleRecord
```
Basic interface for Mars records.
All MarsRecords have a basic set of properties including a UID, notes, tags, parameters, MarsRegions, and MarsPositions. MarsRecords can be serialized to and from Json.
This basic set of properties is extended for storage of molecule information and metadata information in Molecule, AbstractMolecule, MarsMetadata, AbstractMarsMetadata.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`addNote(java.lang.String note)` Add to any notes already in the record.
`void`	`addTag(java.lang.String tag)` Add a string tag to the record.
`boolean`	`getBooleanParameter(java.lang.String parameter)` Get the value of a string parameter.
`java.lang.String`	`getNotes()` Get notes for this record.
`double`	`getParameter(java.lang.String parameter)` Get the value of a parameter.
`java.util.LinkedHashMap<java.lang.String,java.lang.Object>`	`getParameters()` Get the map for all parameters.
`MarsPosition`	`getPosition(java.lang.String name)` Get a `MarsPosition`.
`java.util.Set<java.lang.String>`	`getPositionNames()` Get the set of position names contained in this record.
`java.util.LinkedHashMap<java.lang.String,MarsPosition>`	`getPositions()` Get the map for all regions.
`MarsRegion`	`getRegion(java.lang.String name)` Get a `MarsRegion`.
`java.util.Set<java.lang.String>`	`getRegionNames()` Get the set of region names contained in this record.
`java.util.LinkedHashMap<java.lang.String,MarsRegion>`	`getRegions()` Get the map for all regions.
`java.lang.String`	`getStringParameter(java.lang.String parameter)` Get the value of a string parameter.
`java.util.LinkedHashSet<java.lang.String>`	`getTags()` Get the set of all tags.
`java.lang.String[]`	`getTagsArray()` Get an array list of all tags.
`java.lang.String`	`getUID()` Get the UID for this record.
`boolean`	`hasBooleanParameter(java.lang.String parameter)` Returns true if the boolean parameter exists.
`boolean`	`hasDoubleParameter(java.lang.String parameter)` Returns true if the double parameter exists.
`boolean`	`hasNoTags()` Check if the has no tags.
`boolean`	`hasParameter(java.lang.String parameter)` Returns true if any type of parameter has the name give.
`boolean`	`hasPosition(java.lang.String name)` Check if the record contains a `MarsPosition` using the name.
`boolean`	`hasRegion(java.lang.String name)` Check if the record contains a `MarsRegion` using the name.
`boolean`	`hasStringParameter(java.lang.String parameter)` Returns true if the string parameter exists.
`boolean`	`hasTag(java.lang.String tag)` Check if the record has a tag.
`void`	`merge(MarsRecord record)` Merge another MarsRecord into this one.
`void`	`putPosition(MarsPosition positionOfInterest)` Add or update a `MarsPosition`.
`void`	`putRegion(MarsRegion regionOfInterest)` Add or update a `MarsRegion`.
`void`	`removeAllParameters()` Remove all parameter values from the record.
`void`	`removeAllPositions()` Remove all `MarsPosition`s from the record.
`void`	`removeAllRegions()` Remove all `MarsRegion`s from the record.
`void`	`removeAllTags()` Remove all tags from the record.
`void`	`removeParameter(java.lang.String parameter)` Remove parameter.
`void`	`removePosition(java.lang.String name)` Remove a `MarsPosition` from the record using the name.
`void`	`removeRegion(java.lang.String name)` Remove a `MarsRegion` from the record using the name.
`void`	`removeTag(java.lang.String tag)` Remove a string tag from the record.
`void`	`setNotes(java.lang.String notes)` Sets the notes for this record.
`void`	`setParameter(java.lang.String parameter, boolean value)` Add or update a parameter value.
`void`	`setParameter(java.lang.String parameter, double value)` Add or update a parameter value.
`void`	`setParameter(java.lang.String parameter, java.lang.String value)` Add or update a parameter value.
`void`	`setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive)` Set the parent `MoleculeArchive` that this record is stored in.

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord
dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

- Method Detail
  - getUID
```
java.lang.String getUID()
```
    Get the UID for this record.
    
    Returns:
    
    Returns the UID.
  - getNotes
```
java.lang.String getNotes()
```
    Get notes for this record. Notes can be added during manual sorting to point out a feature or important detail about the current record.
    
    Returns:
    
    Returns a string containing any notes associated with this record.
  - setNotes
```
void setNotes(java.lang.String notes)
```
    Sets the notes for this record. Notes can be added during manual sorting to point out a feature or important detail about the current record.
    
    Parameters:
    
    notes - Any notes about this record.
  - addNote
```
void addNote(java.lang.String note)
```
    Add to any notes already in the record.
    
    Parameters:
    
    note - String with the note to add to the record.
  - addTag
```
void addTag(java.lang.String tag)
```
    Add a string tag to the record. Tags are used for marking individual record to sorting and processing with subsets of records.
    
    Parameters:
    
    tag - The string tag to be added.
  - hasTag
```
boolean hasTag(java.lang.String tag)
```
    Check if the record has a tag.
    
    Parameters:
    
    tag - The string tag to check for.
    
    Returns:
    
    Returns true if the has the tag and false if the record doesn't.
  - hasNoTags
```
boolean hasNoTags()
```
    Check if the has no tags.
    
    Returns:
    
    Returns true if the record has no tags.
  - getTags
```
java.util.LinkedHashSet<java.lang.String> getTags()
```
    Get the set of all tags.
    
    Returns:
    
    Returns the set of tags for this record.
  - getTagsArray
```
java.lang.String[] getTagsArray()
```
    Get an array list of all tags.
    
    Returns:
    
    Returns the set of tags for this record as an array.
  - removeTag
```
void removeTag(java.lang.String tag)
```
    Remove a string tag from the record.
    
    Parameters:
    
    tag - The string tag to remove.
  - removeAllTags
```
void removeAllTags()
```
    Remove all tags from the record.
  - setParameter
```
void setParameter(java.lang.String parameter,
                  double value)
```
    Add or update a parameter value. Parameters are used to store single values associated with the record. For example, this can be the start and stop times for a region of interest. Or calculated features such as the slope or variance. Storing parameters with the record data allows for easier and more efficient processing and data extraction.
    
    Parameters:
    
    parameter - The string parameter name.
    
    value - The double value to set for the parameter name.
  - setParameter
```
void setParameter(java.lang.String parameter,
                  java.lang.String value)
```
    Add or update a parameter value.
    
    Parameters:
    
    parameter - The string parameter name.
    
    value - The string value to set for the parameter name.
  - setParameter
```
void setParameter(java.lang.String parameter,
                  boolean value)
```
    Add or update a parameter value.
    
    Parameters:
    
    parameter - The string parameter name.
    
    value - The boolean value to set for the parameter name.
  - removeAllParameters
```
void removeAllParameters()
```
    Remove all parameter values from the record.
  - removeParameter
```
void removeParameter(java.lang.String parameter)
```
    Remove parameter. Removes the name and value pair.
    
    Parameters:
    
    parameter - The parameter name to remove.
  - getParameter
```
double getParameter(java.lang.String parameter)
```
    Get the value of a parameter.
    
    Parameters:
    
    parameter - The string parameter name to retrieve the value for.
    
    Returns:
    
    Returns the double value for the parameter name given.
  - getStringParameter
```
java.lang.String getStringParameter(java.lang.String parameter)
```
    Get the value of a string parameter.
    
    Parameters:
    
    parameter - The string parameter name to retrieve the value for.
    
    Returns:
    
    Returns the string value for the parameter name given.
  - getBooleanParameter
```
boolean getBooleanParameter(java.lang.String parameter)
```
    Get the value of a string parameter.
    
    Parameters:
    
    parameter - The string parameter name to retrieve the value for.
    
    Returns:
    
    Returns the boolean value for the parameter name given.
  - hasParameter
```
boolean hasParameter(java.lang.String parameter)
```
    Returns true if any type of parameter has the name give.
    
    Parameters:
    
    parameter - The parameter name to check for.
    
    Returns:
    
    Returns true if a parameter with the name exists.
  - hasDoubleParameter
```
boolean hasDoubleParameter(java.lang.String parameter)
```
    Returns true if the double parameter exists.
    
    Parameters:
    
    parameter - The double parameter name to check for.
    
    Returns:
    
    Returns true if a parameter with this name exists.
  - hasStringParameter
```
boolean hasStringParameter(java.lang.String parameter)
```
    Returns true if the string parameter exists.
    
    Parameters:
    
    parameter - The string parameter name to check for.
    
    Returns:
    
    Returns true if a parameter with this name exists.
  - hasBooleanParameter
```
boolean hasBooleanParameter(java.lang.String parameter)
```
    Returns true if the boolean parameter exists.
    
    Parameters:
    
    parameter - The boolean parameter name to check for.
    
    Returns:
    
    Returns true if a parameter with this name exists.
  - getParameters
```
java.util.LinkedHashMap<java.lang.String,java.lang.Object> getParameters()
```
    Get the map for all parameters.
    
    Returns:
    
    Returns the map of parameter names to values.
  - putRegion
```
void putRegion(MarsRegion regionOfInterest)
```
    Add or update a MarsRegion. This can be a region of interest for further analysis steps: slope calculations or KCP calculations KCPCommand. Region names are unique. If a region that has this name already exists in the record it will be overwritten by this method.
    
    Parameters:
    
    regionOfInterest - The region to add to the record.
  - getRegion
```
MarsRegion getRegion(java.lang.String name)
```
    Get a MarsRegion. Region names are unique. Only one copy of each region can be stored in the record.
    
    Parameters:
    
    name - The name of the region to retrieve.
    
    Returns:
    
    The MarsRegion with the name given.
  - hasRegion
```
boolean hasRegion(java.lang.String name)
```
    Check if the record contains a MarsRegion using the name.
    
    Parameters:
    
    name - The name of the region to check for.
    
    Returns:
    
    True if a region with name exists, false otherwise.
  - removeRegion
```
void removeRegion(java.lang.String name)
```
    Remove a MarsRegion from the record using the name.
    
    Parameters:
    
    name - The name of the region to remove.
  - removeAllRegions
```
void removeAllRegions()
```
    Remove all MarsRegions from the record.
  - getRegionNames
```
java.util.Set<java.lang.String> getRegionNames()
```
    Get the set of region names contained in this record.
    
    Returns:
    
    The set of region names.
  - getRegions
```
java.util.LinkedHashMap<java.lang.String,MarsRegion> getRegions()
```
    Get the map for all regions.
    
    Returns:
    
    The map containing all regions.
  - putPosition
```
void putPosition(MarsPosition positionOfInterest)
```
    Add or update a MarsPosition. This can be a position of interest for further analysis steps. Position names are unique. If a position with has this name already exists in the record it will be overwritten by this method.
    
    Parameters:
    
    positionOfInterest - The position to add to the record.
  - getPosition
```
MarsPosition getPosition(java.lang.String name)
```
    Get a MarsPosition. Position names are unique. Only one copy of each region can be stored in the record.
    
    Parameters:
    
    name - The name of the position to retrieve.
    
    Returns:
    
    The MarsPosition with the name given.
  - hasPosition
```
boolean hasPosition(java.lang.String name)
```
    Check if the record contains a MarsPosition using the name.
    
    Parameters:
    
    name - The name of the position to check for.
    
    Returns:
    
    True if the position exists, false otherwise.
  - removePosition
```
void removePosition(java.lang.String name)
```
    Remove a MarsPosition from the record using the name.
    
    Parameters:
    
    name - The name of the position to remove.
  - getPositionNames
```
java.util.Set<java.lang.String> getPositionNames()
```
    Get the set of position names contained in this record.
    
    Returns:
    
    The set of MarsPosition names.
  - getPositions
```
java.util.LinkedHashMap<java.lang.String,MarsPosition> getPositions()
```
    Get the map for all regions.
    
    Returns:
    
    The map containing all positions.
  - removeAllPositions
```
void removeAllPositions()
```
    Remove all MarsPositions from the record.
  - merge
```
void merge(MarsRecord record)
```
    Merge another MarsRecord into this one.
    
    Parameters:
    
    record - The record to merge.
  - setParent
```
void setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive)
```
    Set the parent MoleculeArchive that this record is stored in.
    
    Parameters:
    
    archive - The MoleculeArchive holding this record.

Interface MarsRecord

Method Summary

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

Method Detail

getUID

getNotes

setNotes

addNote

addTag

hasTag

hasNoTags

getTags

getTagsArray

removeTag

removeAllTags

setParameter

setParameter

setParameter

removeAllParameters

removeParameter

getParameter

getStringParameter

getBooleanParameter

hasParameter

hasDoubleParameter

hasStringParameter

hasBooleanParameter

getParameters

putRegion

getRegion

hasRegion

removeRegion

removeAllRegions

getRegionNames

getRegions

putPosition

getPosition

hasPosition

removePosition

getPositionNames

getPositions

removeAllPositions

merge

setParent