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java.lang.Object net.sf.basedb.core.AbstractBatcher net.sf.basedb.core.SpotBatcher
public class SpotBatcher
Batcher class for per-spot intensity values for bioassaysets. This batcher is normally used when a new bioassayset has been created that uses a different cube and/or layer to store it's data than the source bioassayset.
Code example: Swap the intensities of channel 1 and 2
// Get source bioassayset DbControl dc = ... BioAssaySet source = ... // Create new transformation and bioassayset to hold the // new intensities, we use the same data cube as the source // but a different layer Transformation t = source.newTransformation(); dc.saveItem(t); BioAssaySet bas = t.newProduct(null, "new", true); dc.saveItem(bas); // Create a query that selects the data of // the source bioassayset DynamicSpotQuery query = source.getSpotData(); // Execute the query, and use the batcher to swap the // intensities SpotBatcher batcher = bas.getSpotBatcher(); DynamicResultIterator result = query.iterate(dc); int column = result.getIndex(VirtualColumn.COLUMN.getName()); int position = result.getIndex(VirtualColumn.POSITION.getName()); int ch1 = result.getIndex(VirtualColumn.channel(1).getName()); int ch2 = result.getIndex(VirtualColumn.channel(2).getName()); while (result.hasNext()) { SqlResult r = result.next(); batcher.insert(r.getShort(column), r.getInt(position), r.getFloat(ch2), r.getFloat(ch1)); } // Close and commit batcher.close(); dc.commit();
BioAssaySet.getSpotBatcher()
Field Summary | |
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private BioAssaySet |
bioAssaySet
The bioassayset this batcher inserts data for. |
private long |
bytes
The number of bytes this batcher has added to the experiment. |
private long |
bytesPerRow
The number of bytes used by a single row. |
private int |
numChannels
The number of channels used in the raw data type of the experiment where the bioassayset belongs. |
private int |
queuedInsertCount
The number of queued inserts. |
private PreparedStatement |
spotSql
The statement that inserts spot data. |
private String |
spotSqlStatement
The SQL string for the spotSql statement. |
private int |
totalInsertCount
The total number of inserts done by this batcher. |
Fields inherited from class net.sf.basedb.core.AbstractBatcher |
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debugSqlEnabled, logSql |
Constructor Summary | |
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SpotBatcher(DbControl dc,
BioAssaySet bioAssaySet)
Create a new spot batcher for a bioassayset. |
Method Summary | |
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private String |
buildInsertSelectSql(String selectSql)
Build the INSERT INTO ... |
private void |
buildSpotSql()
Builds the insert SQL statement. |
void |
flush()
Flush the batcher and send all remaining items in memory to the database. |
int |
insert(AbstractSqlQuery query)
Insert spot intensities using a query. |
void |
insert(short column,
int position,
float... intensities)
Insert intensities for a given column/position coordinate. |
(package private) void |
onBeforeClose()
Update disk usage and close open SQL statements |
Methods inherited from class net.sf.basedb.core.AbstractBatcher |
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analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final BioAssaySet bioAssaySet
private final int numChannels
private int queuedInsertCount
private int totalInsertCount
private long bytes
private final long bytesPerRow
private PreparedStatement spotSql
INSERT INTO Dynamic#PerSpot (cube, layer, column, position, ch1, ch2, ...) VALUES (cube, layer, ?, ?, ?, ?, ...)
private String spotSqlStatement
spotSql
statement.
Constructor Detail |
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SpotBatcher(DbControl dc, BioAssaySet bioAssaySet)
Method Detail |
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public void flush() throws BaseException
Batcher
BaseException
- If there is an errorBatcher.close()
void onBeforeClose() throws BaseException
onBeforeClose
in class AbstractBatcher
BaseException
public void insert(short column, int position, float... intensities) throws BaseException
column
- The column coordinateposition
- The position coordinateintensities
- An array holding the intensities for the coordinate,
the length must match the number of channels of the raw data type
InvalidDataException
- If the intensities array is null or
of the incorrect length
BaseException
- If there is another errorpublic int insert(AbstractSqlQuery query) throws BaseException
Internally this method converts the query into a
INSERT INTO ... SELECT ...
query, making it very fast,
since the data for each spot doesn't have to be retreived, processed and
then inserted one row at a time. It is possible to call
this method multiple times with the same or different query.
Here is an alternative to the example above:
// Get source bioassayset DbControl dc = ... BioAssaySet source = ... // Create new transformation and bioassayset to hold the // new intensities, we use the same data cube as the source // but a different layer Transformation t = source.newTransformation(); dc.saveItem(t); BioAssaySet bas = t.newProduct(null, "new", true); dc.saveItem(bas); // Create a query that selects the data of // the source bioassayset, swap the order of the channels DynamicSpotQuery query = source.getSpotData(); query.select(Dynamic.select(VirtualColumn.COLUMN)); query.select(Dynamic.select(VirtualColumn.POSITION)); query.select(Dynamic.select(VirtualColumn.channel(2))); query.select(Dynamic.select(VirtualColumn.channel(1))); // Execute the query, and use the batcher to insert the result SpotBatcher batcher = bas.getSpotBatcher(); batcher.insert(query); // Close and commit batcher.close(); dc.commit();
query
- The query that selects the data to be inserted
BaseException
- If there is an errorprivate void buildSpotSql() throws SQLException, BaseException
SQLException
BaseException
BatchUtil.buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[])
private String buildInsertSelectSql(String selectSql) throws BaseException
selectSql
- The SELECT part of the query
BaseException
BatchUtil.buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String)
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