edu.upenn.crimson.io
Class Queries

java.lang.Object
  edu.upenn.crimson.io.Queries

public class Queries
extends java.lang.Object

Functions related to QUERIES table.

Version:

$Id: Queries.java,v 1.66 2009/07/21 01:19:12 fisher Exp $

Notes:

Should see if can optimize db access by maintaining one Statement that is created every time a database connection is made.

Field Summary

(package private) static boolean	DEBUG_OUTPUT If true, then whenever a (bp or codon) position selection query is run, the list of positions selected will be output to the file 'positions.list'.
(package private) static int	SPECIES_CHUNK When writing data to a NEXUS file ('run()'), this is the number of species queried per SQL statement.

Constructor Summary

Queries()

Method Summary

static boolean	dbContains(java.lang.String id) This will return true if a query exists in QUERIES with an id equal to 'id'.
static java.util.ArrayList	dbList() This will return an ArrayList with id's for all queries in the QUERIES table.
static boolean	delete(java.lang.String id) Removes a query from the database.
static java.util.TreeSet	expandPositions(java.util.HashSet positionSet, boolean isCodons) This will convert a set of bp ranges to bp positions.
private static java.util.TreeSet	getRandomPositions(int partitionLength, int numSamples, boolean isCodons)
static void	load(java.lang.String id) This will load the specified query from the QUERIES table in the current database.
static void	publish(Query query) This will publish the specified query in the QUERIES table in the current database.
static void	publish(Query query, java.lang.String id, boolean overwrite) This will publish the specified query in the QUERIES table in the current database.
static Tree	run(java.lang.String queryID, java.lang.String filename, boolean incSequence, boolean incCrimson, int incTree, boolean incNotes) This will perform a tree query, generating a NEXUS file.
static void	run(java.lang.String queryID, java.lang.String filename, boolean incSequence, int numRuns) This will repeatedly run a query, generating a NEXUS file for each run.
static Tree	runPhylip(java.lang.String queryID, java.lang.String filename, int incTree) This will perform a tree query, generating a phylip formatted file.
java.lang.String	toString() Returns the non-Clob columns in the QUERIES table.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEBUG_OUTPUT

static final boolean DEBUG_OUTPUT

If true, then whenever a (bp or codon) position selection query is run, the list of positions selected will be output to the file 'positions.list'.

See Also:

Constant Field Values

SPECIES_CHUNK

static final int SPECIES_CHUNK

When writing data to a NEXUS file ('run()'), this is the number of species queried per SQL statement. If more than 'SPECIES_CHUNK' number of species to query, than multiple queries will be performed, each one with 'SPECIES_CHUNK' number of species.

See Also:

Constant Field Values

Constructor Detail

Queries

public Queries()

Method Detail

load

public static void load(java.lang.String id)

This will load the specified query from the QUERIES table in the current database. If no query is specified then all queries will be loaded.

publish

public static void publish(Query query)

This will publish the specified query in the QUERIES table in the current database. It will overwrite any query already in the table with the same name.

publish

public static void publish(Query query,
                           java.lang.String id,
                           boolean overwrite)

This will publish the specified query in the QUERIES table in the current database. If 'overwrite' is true then this will replace any query object with the same name, already in the table. If 'id' is not empty, then it will be used, instead of query.id, as the name of the query to be published (ie. QUERIES.id).

dbList

public static java.util.ArrayList dbList()

This will return an ArrayList with id's for all queries in the QUERIES table.

dbContains

public static boolean dbContains(java.lang.String id)

This will return true if a query exists in QUERIES with an id equal to 'id'.

delete

public static boolean delete(java.lang.String id)

Removes a query from the database.

run

public static void run(java.lang.String queryID,
                       java.lang.String filename,
                       boolean incSequence,
                       int numRuns)

This will repeatedly run a query, generating a NEXUS file for each run. The output will be a NEXUS file that includes the Crimson and tree blocks. Query notes will not be included.

Parameters:

queryID - string ID for query to be run

filename - filename for NEXUS output

incSequence - when true, inner sequence IDs will be included in the NEXUS file

numRuns - number of runs

run

public static Tree run(java.lang.String queryID,
                       java.lang.String filename,
                       boolean incSequence,
                       boolean incCrimson,
                       int incTree,
                       boolean incNotes)

This will perform a tree query, generating a NEXUS file. If Query.onlyStruct is true then incCrimson and incTree will be ignored.

Parameters:

queryID - string ID for query to be run

filename - filename for NEXUS output

incSequence - when true, inner sequence IDs will be included in the NEXUS file

incCrimson - when true, the CRIMSON block will be included in the NEXUS file

incTree - There are multiple options dictated by incTree: 0 = no tree will be output; 1 = tree is included in NEXUS file; 2 = tree ouptut to second NEXUS file ("*.tree"); 3 = rooted tree ouptut to a newick file ("*.newick"); 4 = unrooted tree ouptut to a newick file ("*.newick")

incNotes - When true, the Query.notes will be appended to the end of the NEXUS file. The notes can, for example, contain a PAUP block. It is assumed that the notes are properly formatted for the NEXUS file.

Returns:

The found tree object is returned (null when errors).

runPhylip

public static Tree runPhylip(java.lang.String queryID,
                             java.lang.String filename,
                             int incTree)

This will perform a tree query, generating a phylip formatted file.

Parameters:

queryID - string ID for query to be run

filename - filename for NEXUS output

incTree - There are multiple options dictated by incTree: 0 = no tree will be output; 1 = no tree will be output; 2 = tree ouptut to second NEXUS file ("*.tree"); 3 = rooted tree ouptut to a newick file ("*.newick"); 4 = unrooted tree ouptut to a newick file ("*.newick")

Returns:

The found tree object is returned (null when errors).

getRandomPositions

private static java.util.TreeSet getRandomPositions(int partitionLength,
                                                    int numSamples,
                                                    boolean isCodons)

expandPositions

public static java.util.TreeSet expandPositions(java.util.HashSet positionSet,
                                                boolean isCodons)

This will convert a set of bp ranges to bp positions. If the set is codons, the underlying bp positions for the codons we be used. Note that the user enters positions going from (1 to N) but when we access the data we go from (0 to N-1). So we shift the user specified positions down by 1.

toString

public java.lang.String toString()

Returns the non-Clob columns in the QUERIES table. Each table record will be separated by a '\n' in the output.

Overrides:

toString in class java.lang.Object