org.expasy.mzjava.core.io.ms.spectrum

Class AbstractMgfReader<A extends PeakAnnotation,S extends Spectrum<A>>

java.lang.Object

org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<A,S>

org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader<A,S>

All Implemented Interfaces:

IterativeReader<S>

Direct Known Subclasses:

MgfReader

public abstract class AbstractMgfReader<A extends PeakAnnotation,S extends Spectrum<A>>
extends AbstractMsReader<A,S>

To extend how the TITLE line is handled add more TitleParser instances using addTitleParser

Version:

1.0

Author:

Oliver Horlacher, fnikitin

Nested Class Summary

Nested classes/interfaces inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

AbstractMsReader.ParseContext

Field Summary

Fields inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, precision

Fields inherited from interface org.expasy.mzjava.core.io.IterativeReader

EMPTY_READER

Constructor Summary

Constructors

Constructor and Description
AbstractMgfReader(Reader reader, URI spectraSource, PeakList.Precision precision, PeakProcessorChain<A> processorChain)

Method Summary

Methods

Modifier and Type	Method and Description
String	getExtension()
protected boolean	handleBeginIonLine(S spectrum, String line) Handle Begin Ion line
protected boolean	handleComment(S spectrum, String line) Handle comment line.
protected boolean	handleEndIonLine(S spectrum, String line) Handle end ion line, which is a line that starts with "END IONS".
protected void	handleIntermediaryLine(String line) Allows subclasses to handle lines that occur between BEGIN IONS and END IONS tags.
protected boolean	handlePeakLine(S spectrum, String line, AbstractMsReader.ParseContext context) Handle peak line, which is any line that starts with a digit
protected boolean	handleTagLine(String tag, String value, S spectrum) Handle tag value line.
protected boolean	handleUnknownLine(S spectrum, String line) Handle line that is not a comment, begin ion, tag, peak or end ion.
protected abstract S	newSpectrum(AbstractMsReader.ParseContext context, PeakList.Precision precision) Create a new spectrum.
protected boolean	parseChargeTag(String value, S spectrum) Parse the line that starts with CHARGE
protected String	parseHeader(AbstractMsReader.ParseContext context) This is called on reader initialization.
protected S	parseNextEntry(AbstractMsReader.ParseContext context)
protected void	parseNextMs1Entry(S spectrum, AbstractMsReader.ParseContext context) Parse all the lines that belong to one MS1 spectrum and the metadata and peaks to the spectrum.
protected void	parseNextMs2Entry(S spectrum, AbstractMsReader.ParseContext context) Parse all lines that correspond to the next MS2 entry and the metadata and peaks to the spectrum.
protected boolean	parsePepMassTag(String value, S spectrum) Parse the line that starts with PEPMASS
protected boolean	parseRetentionTimeTag(String value, S spectrum) Parse the line that starts with RTINSECONDS
protected boolean	parseScanTag(String value, S spectrum) Parse the line that starts with CHARGE
protected abstract boolean	parseTitleTag(String value, S spectrum) Parse the line that starts with a TITLE tag.
protected boolean	parseUnknownTag(String tag, String value, S spectrum) Called if there are any tags that are not handled by MgfReader This is meant to be over ridden by subclasses that want to parse tags that the MgfReader does not know about
protected abstract void	setRetentionTimes(S spectrum, RetentionTimeList retentionTimeList) Add the retention times contained in the retentionTimeList to the spectrum.
protected abstract void	setScanNumbers(S spectrum, ScanNumberList scanNumbers) Add the scan numbers contained in the scanNumbers to the spectrum.
protected boolean	skipIntermediaryLine(String line) Handle intermediary lines between BEGIN IONS and END IONS.

Methods inherited from class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

acceptUnsortedSpectra, addPeaksToSpectrum, addPeakToSpectrum, close, getContext, getHeader, hasNext, init, next

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMgfReader

public AbstractMgfReader(Reader reader,
                 URI spectraSource,
                 PeakList.Precision precision,
                 PeakProcessorChain<A> processorChain)
                  throws IOException

Throws:

IOException

Method Detail

getExtension

public String getExtension()

parseHeader

protected String parseHeader(AbstractMsReader.ParseContext context)
                      throws IOException

Description copied from class: AbstractMsReader

This is called on reader initialization. Subclasses should parse any information that occurs before the first spectrum. The information can returned as a string

Specified by:

parseHeader in class AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>>

Parameters:

context - the parser context

Returns:

the data that is before the first spectrum

Throws:

IOException

parseNextMs1Entry

protected void parseNextMs1Entry(S spectrum,
                     AbstractMsReader.ParseContext context)
                          throws IOException

Parse all the lines that belong to one MS1 spectrum and the metadata and peaks to the spectrum.

Parameters:

spectrum - the spectrum

context - the parse context

Throws:

IOException - if there are IO exceptions

parseNextMs2Entry

protected void parseNextMs2Entry(S spectrum,
                     AbstractMsReader.ParseContext context)
                          throws IOException

Parse all lines that correspond to the next MS2 entry and the metadata and peaks to the spectrum.

Parameters:

spectrum - the spectrum

context - the parse context

Throws:

IOException - if there are IO exceptions

handleIntermediaryLine

protected void handleIntermediaryLine(String line)

Allows subclasses to handle lines that occur between BEGIN IONS and END IONS tags. Default implementation does nothing

Parameters:

line - the line

skipIntermediaryLine

protected boolean skipIntermediaryLine(String line)

Handle intermediary lines between BEGIN IONS and END IONS.

Parameters:

line - the intermediary line to handle

Returns:

true if this line must be skipped

parseNextEntry

protected S parseNextEntry(AbstractMsReader.ParseContext context)
                                        throws IOException

Specified by:

parseNextEntry in class AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>>

Returns:

the next T-object or null if no more object to read.

Throws:

IOException

newSpectrum

protected abstract S newSpectrum(AbstractMsReader.ParseContext context,
            PeakList.Precision precision)

Create a new spectrum. This method allows subclasses to specify what type of spectra is read.

Parameters:

context - the parse context

precision - the precision for the new spectrum

Returns:

the newly created spectrum

handleComment

protected boolean handleComment(S spectrum,
                    String line)

Handle comment line. Comment lies start with #, ;, ! or /. Default implementation does nothing.

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

handleBeginIonLine

protected boolean handleBeginIonLine(S spectrum,
                         String line)

Handle Begin Ion line

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

handleTagLine

protected boolean handleTagLine(String tag,
                    String value,
                    S spectrum)

Handle tag value line. The tag and value is separated by =

Parameters:

spectrum - the spectrum currently being read

tag - the string from the start of the lien to the = character

value - the string from the character after the = to the end of the line

Returns:

true if the information in the line was processed, false otherwise

handlePeakLine

protected boolean handlePeakLine(S spectrum,
                     String line,
                     AbstractMsReader.ParseContext context)

Handle peak line, which is any line that starts with a digit

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

handleEndIonLine

protected boolean handleEndIonLine(S spectrum,
                       String line)

Handle end ion line, which is a line that starts with "END IONS". Default implementation does nothing

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

handleUnknownLine

protected boolean handleUnknownLine(S spectrum,
                        String line)

Handle line that is not a comment, begin ion, tag, peak or end ion. Default implementation does nothing

Parameters:

spectrum - the spectrum currently being read

line - the line

Returns:

true if the information in the line was processed, false otherwise

parseTitleTag

protected abstract boolean parseTitleTag(String value,
                    S spectrum)

Parse the line that starts with a TITLE tag. This uses the list of title parsers to find a parser that can parse the title. Note that the title parsed value is assign to the spectrum metadata comment by default.

Parameters:

value - the title value

spectrum - the spectrum being parsed

Returns:

true if any of the registered title parses extracted information from the title

parseUnknownTag

protected boolean parseUnknownTag(String tag,
                      String value,
                      S spectrum)

Called if there are any tags that are not handled by MgfReader

This is meant to be over ridden by subclasses that want to parse tags that the MgfReader does not know about

Parameters:

tag - the characters in the line before the first =

value - the characters in the line after the first =

spectrum - the spectrum that is being read

Returns:

true of this handled the tag, false otherwise

parseRetentionTimeTag

protected boolean parseRetentionTimeTag(String value,
                            S spectrum)

Parse the line that starts with RTINSECONDS

Parameters:

value - the value

spectrum - the spectrum being parsed

Returns:

true if the tag was handled, false otherwise

setRetentionTimes

protected abstract void setRetentionTimes(S spectrum,
                     RetentionTimeList retentionTimeList)

Add the retention times contained in the retentionTimeList to the spectrum.

Parameters:

spectrum - the spectrum that is currently being read

retentionTimeList - the retention times that were read

parseScanTag

protected boolean parseScanTag(String value,
                   S spectrum)

Parse the line that starts with CHARGE

Parameters:

value - the value

spectrum - the spectrum being parsed

Returns:

true if the tag was handled, false otherwise

setScanNumbers

protected abstract void setScanNumbers(S spectrum,
                  ScanNumberList scanNumbers)

Add the scan numbers contained in the scanNumbers to the spectrum.

Parameters:

spectrum - the spectrum that is currently being read

scanNumbers - the scan numbers that were read

parseChargeTag

protected boolean parseChargeTag(String value,
                     S spectrum)

Parse the line that starts with CHARGE

Parameters:

value - the value

spectrum - the spectrum being parsed

Returns:

true if the tag was handled, false otherwise

parsePepMassTag

protected boolean parsePepMassTag(String value,
                      S spectrum)

Parse the line that starts with PEPMASS

Parameters:

value - the value

spectrum - the spectrum being parsed

Returns:

true if the tag was handled, false otherwise