A dataset that represents a Oxford Nanopore Measurement. @author: Sven Fillinger
| Modifiers | Name | Description |
|---|---|---|
private static enum |
OxfordNanoporeMeasurement.METADATA_FIELD |
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private static class |
OxfordNanoporeMeasurement.MetaData |
| Modifiers | Name | Description |
|---|---|---|
private static java.lang.String |
LIBRARY_PREP_KIT_SCHEMA |
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private java.util.Map<java.lang.String, DataFolder> |
folders |
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private java.util.List<DataFile> |
logFilesCollection |
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private MeasurementFolder |
measurementFolder |
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private java.util.Map<METADATA_FIELD, java.lang.String> |
metadata |
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private boolean |
pooledSamplesMeasurement |
| Constructor and description |
|---|
protected OxfordNanoporeMeasurement
(java.lang.String name, java.lang.String path, java.util.List children, java.util.Map metadata) |
| Type Params | Return Type | Name and description |
|---|---|---|
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private void |
assessFast5Content() |
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private void |
assessFastQContent() |
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private void |
assessPooledStatus() |
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private void |
assessState() |
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private static boolean |
containsAtLeastOneBarcodedFolder(DataFolder folder) |
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static OxfordNanoporeMeasurement |
create(java.lang.String name, java.lang.String path, java.util.List children, java.util.Map metadata) |
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private void |
createContent() |
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private static java.lang.String |
extractLibraryKit(java.lang.String text) |
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java.lang.String |
getAdapter()Provides access to the adapter type used in the measurement. |
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java.lang.String |
getAsicTemp()Provides access to the asic temperature. |
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java.lang.String |
getBaseCaller()Provides access to the base caller. |
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java.lang.String |
getBaseCallerVersion()Provides access to the base caller version. |
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java.lang.String |
getDeviceType()Provides access to the device type. |
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java.lang.String |
getFlowCellPosition()Provides access to the flow cell position. |
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java.lang.String |
getFlowCellType()Provides access to the flow cell type. |
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java.lang.String |
getFlowcellId()Provides access to the flow cell id. |
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java.lang.String |
getLibraryPreparationKit()Provides access to the library kit used. |
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private java.util.List<DataFile> |
getLogFileCollection() |
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java.util.List<DataFile> |
getLogFiles()This method returns a list of all log files from the Oxford Nanopore measurement. |
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java.lang.String |
getMachineHost()Provides access to the machine host name. |
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java.util.Map<java.lang.String, java.util.Map<java.lang.String, DataFolder>> |
getRawDataPerSample(ExperimentFolder experiment)This method aggregates all fast5 files and fastq files of an Oxford Nanopore measurement by sample code. |
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java.lang.String |
getRelativePath()This method is used to return the relative path of a Oxford Nanopore measurement. |
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java.lang.String |
getStartDate()Provides access to the experiment start date. |
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java.util.Map<java.lang.String, DataFolder> |
getUnclassifiedData()This method aggregates only *unclassified* fast5 files and fastq files of an Oxford Nanopore measurement. |
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private java.util.Map<java.lang.String, java.util.Map<java.lang.String, DataFolder>> |
prepareRawData(java.lang.String sampleId) |
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private java.util.Map<java.lang.String, java.util.Map<java.lang.String, DataFolder>> |
prepareRawDataFromPooledMeasurement() |
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private java.util.Map<java.lang.String, DataFolder> |
prepareUnclassifiedData() |
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private void |
readMetaData(java.util.Map<java.lang.String, java.lang.String> metadata) |
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private static void |
validateMetaData(java.util.Map metadata) |
null |
OxfordNanoporeMeasurement |
valueOf(java.lang.String name)Returns the enum constant of this type with the specified name. |
null |
OxfordNanoporeMeasurement[] |
values()Returns an array containing the constants of this enum type, in the order they are declared. |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Provides access to the adapter type used in the measurement. Is empty when no adapter was used.
Provides access to the asic temperature.
Provides access to the base caller.
Provides access to the base caller version.
Provides access to the device type.
Provides access to the flow cell position.
Provides access to the flow cell type.
Provides access to the flow cell id.
Provides access to the library kit used.
This method returns a list of all log files from the Oxford Nanopore measurement.
Provides access to the machine host name.
This method aggregates all fast5 files and fastq files of an Oxford Nanopore measurement by sample code. The DataFolder objects will not contain unclassified read information. The resulting data-structure follows this map schema: "QBiC sample code": "fast5fail": DataFolder "fast5pass": DataFolder "fastqfail": DataFolder "fastqpass": DataFolder "Other sample code": // In case of pooled samples ...
This method is used to return the relative path of a Oxford Nanopore measurement.
The path is always relative to the Oxford Nanopore experiment root folder.
Example:
QABCD001AE_nanopore_experiment
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- 20200219_1107_1-E3-H3_PAE26974_454b8dc6 (measurement)
| |
| - ...
- 20200219_1107_2-E4-H1_PAE00000_454b8dc6
The resulting relative path would be:
Provides access to the experiment start date.
This method aggregates only *unclassified* fast5 files and fastq files of an Oxford Nanopore measurement. The resulting data-structure follows this map schema: "fast5fail": DataFolder "fast5pass": DataFolder "fastqfail": DataFolder "fastqpass": DataFolder
Returns the enum constant of this type with the specified name.
Returns an array containing the constants of this enum type, in the order they are declared.