Access to mapped experimental data

Currently the access to mapping data is read-only via this API.


Graph -- Contains graph nodes and edges (gravisto API)
\==> Node -- A graph node (gravisto API)
\==> NodeHelper (extends Node)
     \==> MappingData
          \==> SeriesData
               \==> SampleData

ToDo: Add method descriptions


  • A helper object with additional helper functions. Use getGraphNode to retreive the corresponding Node object
  • This object acts like a Proxy to the corresponding Node object

boolean writeDatasetTable(String fileName, boolean useAverage) -- Write mapped dataset to a text file (may be read in R with the function read.table). Returns true, if successful. The file format is explained here.
ArrayList<MappingData> getDataMappings()
ArrayList<SeriesData> getMappedSeriesData() -- Series data from all data mappings
ArrayList<SampleData> getMappedSampleData() -- All mapped samples (from all series)
ArrayList<SampleData> getMappedSampleDataForTimePoint(int timeValue) -- All samples (with replicate values) mapped onto the node for the specified time point
ArrayList<Double> getMappedMeanValuesForTimePoint(int timeValue) -- The mean value of all mapped sample data for the specified time point
Set<Integer> getMappedTimePointsCoveredByAllLines() -- The timepoints where all mapped series have sample data
Set<Integer> getMappedUniqueTimePoints() -- The super-set of time points, all possible time points, which are available for any of the mapped series
Set<String> getMappedSeriesNames() -- The series names of all mappings
double getAverage() -- The average of the mapped average sample values

MappingData: Several mappings may be assigned to a node

double getAverage() -- The average of the average sample values, belonging to this mapping
ArrayList<SeriesData> getSeriesData()
String getExperimentName()
String getExperimentCoordinator()
String getExperimentStartDate()

SeriesData: A mapping consists of assigned series data (wild type, transgenic line 1, ...)

ArrayList<Double> getStdDevValues()
ArrayList<Double> getStdErrValues()
double calcBeta()
double calcAlpha()
ArrayList<Double> getMeanValues()
ArrayList<String> getMeanMeasurementUnits()
ArrayList<String> getMeanTimeUnits()
ArrayList<Integer> getMeanTimePoints()
Set<Integer> getUniqueTimePoints()
String getName()
ArrayList<SampleData> getSamples()
SampleData (implements Comparable)
  • A data series contains a number of samples. Each sample contains replicate data and may have time series information and has a measurement unit assigned
  • May be sorted according to the time point

ArrayList<Double> getValues()
ArrayList<String> getReplicateIDs()
String getUnit()
String getTimeUnit()
int getTimePoint()