|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.systemsbiology.jrap.MSXMLParser
public final class MSXMLParser
A generic utility class for reading an MSXML file in a random access fashion and utilizing a stored scan index for fast reads.
Field Summary | |
---|---|
protected static java.lang.String |
CONT_AFTER_FATAL_ERROR_ID
Continue after fatal error id. |
protected static boolean |
DEFAULT_CONT_AFTER_FATAL_ERROR
Default dynamic validation support (false). |
protected static boolean |
DEFAULT_DYNAMIC_VALIDATION
Default dynamic validation support (false). |
protected static boolean |
DEFAULT_NAMESPACE_PREFIXES
Default namespace prefixes (false). |
protected static boolean |
DEFAULT_NAMESPACES
Default namespaces support (false). |
protected static java.lang.String |
DEFAULT_PARSER_NAME
Default parser name. |
protected static boolean |
DEFAULT_SCHEMA_FULL_CHECKING
Default Schema full checking support (false). |
protected static boolean |
DEFAULT_SCHEMA_VALIDATION
Default Schema validation support (false). |
protected static boolean |
DEFAULT_VALIDATION
Default validation support (false). |
protected static java.lang.String |
DYNAMIC_VALIDATION_FEATURE_ID
Dynamic validation feature id (http://apache.org/xml/features/validation/dynamic). |
protected java.lang.String |
fileMD5
The MD5 signature found the last time we read the index |
protected java.lang.String |
fileName
The file we are in charge of reading |
protected java.util.ArrayList |
indexes
The indexes |
protected MZXMLFileInfo |
info
The information contained in the header of the mzXML file. |
protected static java.lang.String |
NAMESPACE_PREFIXES_FEATURE_ID
Namespace prefixes feature id (http://xml.org/sax/features/namespace-prefixes). |
protected static java.lang.String |
NAMESPACES_FEATURE_ID
Namespaces feature id (http://xml.org/sax/features/namespaces). |
protected org.xml.sax.XMLReader |
parser
A handle to the XML parser |
protected static java.lang.String |
SCHEMA_FULL_CHECKING_FEATURE_ID
Schema full checking feature id (http://apache.org/xml/features/validation/schema-full-checking). |
protected static java.lang.String |
SCHEMA_VALIDATION_FEATURE_ID
Schema validation feature id (http://apache.org/xml/features/validation/schema). |
protected static java.lang.String |
VALIDATION_FEATURE_ID
Validation feature id (http://xml.org/sax/features/validation). |
Constructor Summary | |
---|---|
MSXMLParser(java.lang.String fileName)
|
Method Summary | |
---|---|
MZXMLFileInfo |
getHeaderInfo()
Get the header information contained in the mzXML file, which is constant for every scan. |
int |
getScanCount()
Get the total number of scans in the mzXMLfile handled by this parser. |
long |
getScanOffset(int scanNumber)
get scan offset, scan number is 1 based. |
Scan |
rap(int scanNumber)
Read a particular scan from a MSXML file and return a generic Scan object with it's data. |
ScanHeader |
rapHeader(int scanNumber)
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected static final java.lang.String NAMESPACES_FEATURE_ID
protected static final java.lang.String NAMESPACE_PREFIXES_FEATURE_ID
protected static final java.lang.String VALIDATION_FEATURE_ID
protected static final java.lang.String SCHEMA_VALIDATION_FEATURE_ID
protected static final java.lang.String SCHEMA_FULL_CHECKING_FEATURE_ID
protected static final java.lang.String DYNAMIC_VALIDATION_FEATURE_ID
protected static final java.lang.String CONT_AFTER_FATAL_ERROR_ID
protected static final java.lang.String DEFAULT_PARSER_NAME
protected static final boolean DEFAULT_NAMESPACES
protected static final boolean DEFAULT_NAMESPACE_PREFIXES
protected static final boolean DEFAULT_VALIDATION
protected static final boolean DEFAULT_SCHEMA_VALIDATION
protected static final boolean DEFAULT_SCHEMA_FULL_CHECKING
protected static final boolean DEFAULT_DYNAMIC_VALIDATION
protected static final boolean DEFAULT_CONT_AFTER_FATAL_ERROR
protected org.xml.sax.XMLReader parser
protected java.lang.String fileName
protected java.lang.String fileMD5
protected java.util.ArrayList indexes
protected MZXMLFileInfo info
Constructor Detail |
---|
public MSXMLParser(java.lang.String fileName)
Method Detail |
---|
public ScanHeader rapHeader(int scanNumber)
public Scan rap(int scanNumber)
public int getScanCount()
public MZXMLFileInfo getHeaderInfo()
public long getScanOffset(int scanNumber)
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |