AbstractJavascriptFilter (htsjdk 2.14.3 API)

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 String DEFAULT_HEADER_KEY

Fields
Modifier and Type	Field	Description
`protected Bindings`	`bindings`	javascript bindings
`static 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

All Methods Instance Methods Abstract Methods Concrete Methods
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 Detail
  - DEFAULT_HEADER_KEY
```
public static final String DEFAULT_HEADER_KEY
```
    See Also:
    
    Constant Field Values
  - bindings
```
protected Bindings bindings
```
    javascript bindings
- Constructor Detail
  - 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 Detail
  - 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).

Class AbstractJavascriptFilter<HEADER,TYPE>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_HEADER_KEY

bindings

Constructor Detail

AbstractJavascriptFilter

AbstractJavascriptFilter

AbstractJavascriptFilter

Method Detail

getHeaderKey

getRecordKey

accept