htsjdk.samtools.filter

Class AbstractJavascriptFilter<HEADER,TYPE>

java.lang.Object

htsjdk.samtools.filter.AbstractJavascriptFilter<HEADER,TYPE>

Direct Known Subclasses:

JavascriptSamRecordFilter, JavascriptVariantFilter

public abstract class AbstractJavascriptFilter<HEADER,TYPE>
extends java.lang.Object

Javascript filter with HEADER type containing TYPE records. contains two static method to get a SAM Read filter or a VariantFilter. warning: tools, like galaxy, using this class are not safe because a script can access the filesystem.

Field Summary

Fields

Modifier and Type	Field and Description
protected javax.script.Bindings	bindings javascript bindings
static java.lang.String	DEFAULT_HEADER_KEY

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractJavascriptFilter(java.io.File scriptFile, HEADER header) constructor using a java.io.File script, compiles the script, puts 'header' in the bindings
protected	AbstractJavascriptFilter(java.io.Reader scriptReader, HEADER header) Constructor, compiles script, put header in the bindings
protected	AbstractJavascriptFilter(java.lang.String scriptExpression, HEADER header) constructor using a java.lang.String script, compiles the script, puts 'header' in the bindings

Method Summary

Modifier and Type	Method and Description
protected boolean	accept(TYPE record) Evaluates this predicate on the given argument
java.lang.String	getHeaderKey() returns key used for header binding
abstract java.lang.String	getRecordKey() returns key used for record binding

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_HEADER_KEY

public static final java.lang.String DEFAULT_HEADER_KEY

See Also:

Constant Field Values

bindings

protected javax.script.Bindings bindings

javascript bindings

Constructor Detail

AbstractJavascriptFilter

protected AbstractJavascriptFilter(java.io.File scriptFile,
                                   HEADER header)
                            throws java.io.IOException

constructor using a java.io.File script, compiles the script, puts 'header' in the bindings

Throws:

java.io.IOException

AbstractJavascriptFilter

protected AbstractJavascriptFilter(java.lang.String scriptExpression,
                                   HEADER header)

constructor using a java.lang.String script, compiles the script, puts 'header' in the bindings

AbstractJavascriptFilter

protected AbstractJavascriptFilter(java.io.Reader scriptReader,
                                   HEADER header)

Constructor, compiles script, put header in the bindings

Parameters:

scriptReader - reader containing the script. will be closed.

header - the header to be injected in the javascript context

Method Detail

getHeaderKey

public java.lang.String getHeaderKey()

returns key used for header binding

getRecordKey

public abstract java.lang.String getRecordKey()

returns key used for record binding

accept

protected boolean accept(TYPE record)

Evaluates this predicate on the given argument

Parameters:

record - the record to test. It will be inject in the javascript context using getRecordKey()

Returns:

true (keep) if the user script returned 1 or true, else false (reject).