Package 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 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	Description
protected Bindings	bindings	javascript bindings
static final String	DEFAULT_HEADER_KEY

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractJavascriptFilter(File scriptFile, HEADER header)	constructor using a java.io.File script, compiles the script, puts 'header' in the bindings
protected	AbstractJavascriptFilter(Reader scriptReader, HEADER header)	Constructor, compiles script, put header in the bindings
protected	AbstractJavascriptFilter(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	Description
protected boolean	accept(TYPE record)	Evaluates this predicate on the given argument
String	getHeaderKey()	returns key used for header binding
abstract 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 Details

DEFAULT_HEADER_KEY

public static final String DEFAULT_HEADER_KEY

See Also:

• Constant Field Values

bindings

protected Bindings bindings

javascript bindings

Constructor Details

AbstractJavascriptFilter

protected AbstractJavascriptFilter(File scriptFile,
 HEADER header)
                            throws IOException

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

Throws:

IOException

AbstractJavascriptFilter

protected AbstractJavascriptFilter(String scriptExpression,
 HEADER header)

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

AbstractJavascriptFilter

protected AbstractJavascriptFilter(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 Details

getHeaderKey

public String getHeaderKey()

returns key used for header binding

getRecordKey

public abstract 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).