Package adams.db

Interface SpectrumIntf

All Superinterfaces:

adams.db.DatabaseConnectionProvider, adams.db.DatabaseConnectionUser, adams.db.DataProvider<Spectrum>, adams.db.TableInterface

All Known Implementing Classes:

SpectrumF, SpectrumT, SpectrumT, SpectrumT, SpectrumT, SpectrumT, SpectrumT, SpectrumT

public interface SpectrumIntf
extends adams.db.TableInterface, adams.db.DataProvider<Spectrum>

Interface for spectrum tables.

Author:

FracPete (fracpete at waikato dot ac dot nz)

Field Summary

Fields

Modifier and Type	Field	Description
static String	MAX_NUM_SPECTRUMS_CACHED
static String	TABLE_NAME	the table names.

Method Summary

Modifier and Type	Method	Description
Integer	add(Spectrum sp)	Adds a spectrum to the database.
Integer	add(Spectrum sp, boolean storeWaveNo)	Adds a spectrum to the database.
boolean	bulkAdd(Spectrum[] sp, boolean storeWaveNo, int batchSize, boolean autoCommit, boolean newConnection)	Stores the spectra in the database.
boolean	exists(int id)	Checks whether the container exists in the database.
boolean	exists(String id)	Checks whether the container exists in the database.
boolean	exists(String id, String format)	Checks whether the container exists in the database.
int	getDatabaseID(String id)	Returns the database ID for given spectrum ID.
int	getDatabaseID(String sample_id, String format)	Returns the database ID for given sample ID and type.
SampleDataIntf	getSampleDataHandler()	Returns the corresponding SampleData handler.
List<String>	getValues(String[] fields, SpectrumIDConditions cond)	returns all the specified fields in the database, separated by TABs.
List<String>	getValues(String[] fields, String where, SpectrumIDConditions cond)	returns all the specified fields in the database, separated by TABs.
List<String>	getValues(String[] fields, String tables, String where, SpectrumIDConditions cond)	returns all the specified fields in the database, separated by TABs.
boolean	init()	Initialise table & sub-tables.
Spectrum	load(int auto_id)	Load a spectrum with given database ID.
Spectrum	load(String id)	Load a spectrum with given ID.
Spectrum	load(String sample_id, String format)	Load a spectrum with given sample ID and type.
Spectrum	loadFromDB(int auto_id, String rlike, boolean raw)	Load a spectrum from DB with given auto_id.
Spectrum	loadFromDB(String sample_id, String format, boolean raw)	Load a spectrum from DB with given sample_id and format.
Spectrum	loadRaw(int auto_id)	Load a data container with given auto_id, without passing it through the global filter.
Spectrum	loadRaw(String sample_id, String format)	Load a spectrum with given sample ID and type, without filtering through the global container filter.
boolean	remove(int id, boolean keepReport)	Removes the spectrum and its sample data.
boolean	remove(String sample_id, boolean keepReport)	Removes the spectrum and its sample data.
boolean	remove(String sample_id, String format, boolean keepReport)	Removes the spectrum and its sample data.
void	stopBulkAdd()	Interrupts a currently running bulk store, if possible.

Methods inherited from interface adams.db.DatabaseConnectionProvider

getDatabaseConnection

Methods inherited from interface adams.db.TableInterface

getTableName

Field Detail

TABLE_NAME

static final String TABLE_NAME

the table names.

See Also:

Constant Field Values

MAX_NUM_SPECTRUMS_CACHED

static final String MAX_NUM_SPECTRUMS_CACHED

See Also:

Constant Field Values

Method Detail

getSampleDataHandler

SampleDataIntf getSampleDataHandler()

Returns the corresponding SampleData handler.

Returns:

the corresponding handler

init

boolean init()

Initialise table & sub-tables.

Returns:

success?

exists

boolean exists(int id)

Checks whether the container exists in the database.

Specified by:

exists in interface adams.db.DataProvider<Spectrum>

Parameters:

id - the database ID of the data container

Returns:

true if the container exists

exists

boolean exists(String id)

Checks whether the container exists in the database. Uses SampleData.DEFAULT_FORMAT as format.

Specified by:

exists in interface adams.db.DataProvider<Spectrum>

Parameters:

id - the ID of the data container

Returns:

true if the container exists

See Also:

exists(String, String)

exists

boolean exists(String id,
               String format)

Checks whether the container exists in the database.

Parameters:

id - the ID of the data container

Returns:

true if the container exists

load

Spectrum load(int auto_id)

Load a spectrum with given database ID. Get from cache if available

Specified by:

load in interface adams.db.DataProvider<Spectrum>

Parameters:

auto_id - the database ID

Returns:

Spectrum, or null if not found

load

Spectrum load(String id)

Load a spectrum with given ID. Get from cache if available Uses SampleData.DEFAULT_FORMAT as format.

Specified by:

load in interface adams.db.DataProvider<Spectrum>

Parameters:

id - the ID

Returns:

Spectrum, or null if not found

See Also:

load(String, String)

load

Spectrum load(String sample_id,
              String format)

Load a spectrum with given sample ID and type. Get from cache if available

Parameters:

sample_id - the sample ID

format - the format

Returns:

Spectrum, or null if not found

loadRaw

Spectrum loadRaw(int auto_id)

Load a data container with given auto_id, without passing it through the global filter.

Parameters:

auto_id - the databae ID

Returns:

the data container, or null if not found

loadRaw

Spectrum loadRaw(String sample_id,
                 String format)

Load a spectrum with given sample ID and type, without filtering through the global container filter.

Parameters:

sample_id - the sample ID

format - the format

Returns:

Spectrum, or null if not found

loadFromDB

Spectrum loadFromDB(int auto_id,
                    String rlike,
                    boolean raw)

Load a spectrum from DB with given auto_id.

Parameters:

auto_id - the databae ID

rlike - regex for chrom name

raw - whether to return the raw spectrum or filter it through the global container filter

Returns:

Spectrum, or null if not found

loadFromDB

Spectrum loadFromDB(String sample_id,
                    String format,
                    boolean raw)

Load a spectrum from DB with given sample_id and format.

Parameters:

sample_id - the sample ID

format - the format

raw - whether to return the raw spectrum or filter it through the global container filter

Returns:

Spectrum, or null if not found

getDatabaseID

int getDatabaseID(String id)

Returns the database ID for given spectrum ID. Get from cache if available Uses SampleData.DEFAULT_FORMAT as format.

Parameters:

id - the ID

Returns:

Spectrum, or null if not found

See Also:

load(String, String)

getDatabaseID

int getDatabaseID(String sample_id,
                  String format)

Returns the database ID for given sample ID and type. Get from cache if available

Parameters:

sample_id - the sample ID

format - the format

Returns:

the database ID, Constants.NO_ID

getValues

List<String> getValues(String[] fields,
                       SpectrumIDConditions cond)

returns all the specified fields in the database, separated by TABs.

Parameters:

fields - the field names

cond - the conditions for the retrieval

Returns:

list of tab-separated values

getValues

List<String> getValues(String[] fields,
                       String where,
                       SpectrumIDConditions cond)

returns all the specified fields in the database, separated by TABs.

Parameters:

fields - the field names

where - the where clause, can be null

cond - the conditions for the retrieval

Returns:

list of tab-separated values

getValues

List<String> getValues(String[] fields,
                       String tables,
                       String where,
                       SpectrumIDConditions cond)

returns all the specified fields in the database, separated by TABs.

Parameters:

fields - the field names

tables - the involved tables

where - the where clause, can be null

cond - the conditions for the retrieval

Returns:

list of tab-separated values

add

Integer add(Spectrum sp)

Adds a spectrum to the database. Returns the created auto-id, and sets in Spectrum. Wave numbers get stored.

Specified by:

add in interface adams.db.DataProvider<Spectrum>

Parameters:

sp - spectrum Header

Returns:

new ID, or null if fail

add

Integer add(Spectrum sp,
            boolean storeWaveNo)

Adds a spectrum to the database. Returns the created auto-id, and sets in Spectrum.

Parameters:

sp - spectrum Header

storeWaveNo - whether to store the wave numbers as well

Returns:

new ID, or null if fail

bulkAdd

boolean bulkAdd(Spectrum[] sp,
                boolean storeWaveNo,
                int batchSize,
                boolean autoCommit,
                boolean newConnection)

Stores the spectra in the database.

Parameters:

sp - the spectra to add

storeWaveNo - whether to store the wave numbers as well

batchSize - the maximum number of records in one batch

autoCommit - whether to use auto-commit or not (turning off may impact other transactions!)

newConnection - uses a separate database connection just for this connection (then no auto-commit doesn't affect the rest)

Returns:

true if successfully inserted/updated

stopBulkAdd

void stopBulkAdd()

Interrupts a currently running bulk store, if possible.

remove

boolean remove(String sample_id,
               boolean keepReport)

Removes the spectrum and its sample data. Uses SampleData.DEFAULT_FORMAT as format.

Specified by:

remove in interface adams.db.DataProvider<Spectrum>

Parameters:

sample_id - the sample ID of the spectrum

keepReport - if true does not delete associated report

Returns:

true if no error

See Also:

remove(String, String, boolean)

remove

boolean remove(String sample_id,
               String format,
               boolean keepReport)

Removes the spectrum and its sample data.

Parameters:

sample_id - the sample ID of the spectrum

format - the format of the spectrum (eg NIR)

keepReport - if true does not delete associated report

Returns:

true if no error

remove

boolean remove(int id,
               boolean keepReport)

Removes the spectrum and its sample data.

Specified by:

remove in interface adams.db.DataProvider<Spectrum>

Parameters:

id - the ID of the spectrum to remove from the database

keepReport - if true does not delete associated report

Returns:

true if no error