net.maizegenetics.pangenome.db_updateDelete

Class DeleteReadMappingPlugin

net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin

public class DeleteReadMappingPlugin

This method will delete read_mappings for a specified method used with the taxon indicated in the keyfile.

The keyfile should be the same format as used in the FastqToMappingPlugin. This allows the user to use the same keyfile if they later detemine there were errors and they need to delete these (or a subset of) these read-mapping entries.

The method parameter is optional: If present, the read_mapping entries will be further filtered based on associated method.

This method will delete from the read_mapping, read_mapping_paths and paths table all entries related to the taxon in the keyfile which were loaded with the specified method.

Assumptions: user loaded the ParmeterCache with config file connection values.

Constructor Detail

DeleteReadMappingPlugin

public DeleteReadMappingPlugin(@Nullable
                               java.awt.Frame parentFrame,
                               boolean isInteractive)

This method will delete read_mappings for a specified method used with the taxon indicated in the keyfile.

The keyfile should be the same format as used in the FastqToMappingPlugin. This allows the user to use the same keyfile if they later detemine there were errors and they need to delete these (or a subset of) these read-mapping entries.

The method parameter is optional: If present, the read_mapping entries will be further filtered based on associated method.

This method will delete from the read_mapping, read_mapping_paths and paths table all entries related to the taxon in the keyfile which were loaded with the specified method.

Assumptions: user loaded the ParmeterCache with config file connection values.

DeleteReadMappingPlugin

public DeleteReadMappingPlugin()

This method will delete read_mappings for a specified method used with the taxon indicated in the keyfile.

The keyfile should be the same format as used in the FastqToMappingPlugin. This allows the user to use the same keyfile if they later detemine there were errors and they need to delete these (or a subset of) these read-mapping entries.

The method parameter is optional: If present, the read_mapping entries will be further filtered based on associated method.

This method will delete from the read_mapping, read_mapping_paths and paths table all entries related to the taxon in the keyfile which were loaded with the specified method.

Assumptions: user loaded the ParmeterCache with config file connection values.

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

keyFile

@Nullable
public java.lang.String keyFile()

Name of the Keyfile to process. Must have columns cultivar, flowcell_lane, filename, and PlateID.Taxa names are created from the cultivar column

Returns:

keyFile

keyFile

@NotNull
public DeleteReadMappingPlugin keyFile(@Nullable
                                                java.lang.String value)

Set keyFile. Name of the Keyfile to process. Must have columns cultivar, flowcell_lane, filename, and PlateID.Taxa names are created from the cultivar column

Parameters:

value - keyFile

Returns:

this plugin

methodName

@NotNull
public java.lang.String methodName()

Method name assigned to read mappings that will be deleted.

Returns:

Method Name

methodName

@NotNull
public DeleteReadMappingPlugin methodName(@NotNull
                                                   java.lang.String value)

Set Method Name. Method name assigned to read mappings that will be deleted.

Parameters:

value - Method Name

Returns:

this plugin

deleteMethod

public boolean deleteMethod()

Whether to delete the associated read_mapping method. default=false.

Returns:

Delete Read Mapping Method

deleteMethod

@NotNull
public DeleteReadMappingPlugin deleteMethod(boolean value)

Set Delete Read Mapping Method. Whether to delete the associated read_mapping method. default=false.

Parameters:

value - Delete Read Mapping Method

Returns:

this plugin