org.fhcrc.cpl.viewer.amt
Class AmtTsvReader

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AmtTsvReader

public class AmtTsvReader
extends java.lang.Object

A class for writing AMT TSV files.

Nested Class Summary

protected static class

AmtTsvReader.AmtTsvRow Used by TabLoader to represent one row.

Field Summary

protected static java.text.DateFormat

dateParser

Constructor Summary

AmtTsvReader()

Method Summary

protected static AmtRunEntry	createRunEntry(java.util.List<AmtTsvReader.AmtTsvRow> amtTsvRowList, java.lang.String commentLineForRun, boolean useTimesInsteadOfScans) Create a run entry from a comment row in the tsv file
protected static java.util.List<MS2Modification>[]	identifyAllModifications(java.lang.String strippedPeptide, java.lang.String peptideWithMods, AmtRunEntry run, java.util.Map<java.lang.String,MS2Modification> thisRunSymbolModMap) Figure out what modifications exist in this peptide string
static AmtDatabase	read(java.io.File file) Read an AMT database from a tsv file
protected static java.lang.String	stripPeptide(java.lang.String peptideWithMods) Return a version of the peptide string that contains only the residues
protected static java.lang.String	stripTrypticEnds(java.lang.String peptideString) Strip tryptic ends off a raw peptide string

Methods inherited from class java.lang.Object

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

Field Detail

dateParser

protected static java.text.DateFormat dateParser

Constructor Detail

AmtTsvReader

public AmtTsvReader()

Method Detail

read

public static AmtDatabase read(java.io.File file)
                        throws java.io.IOException

Read an AMT database from a tsv file

Parameters:

file -

Throws:

java.io.IOException

stripTrypticEnds

protected static java.lang.String stripTrypticEnds(java.lang.String peptideString)

Strip tryptic ends off a raw peptide string

Parameters:

peptideString -

Returns:

stripPeptide

protected static java.lang.String stripPeptide(java.lang.String peptideWithMods)

Return a version of the peptide string that contains only the residues

Parameters:

peptideWithMods -

Returns:

identifyAllModifications

protected static java.util.List<MS2Modification>[] identifyAllModifications(java.lang.String strippedPeptide,
                                                                            java.lang.String peptideWithMods,
                                                                            AmtRunEntry run,
                                                                            java.util.Map<java.lang.String,MS2Modification> thisRunSymbolModMap)

Figure out what modifications exist in this peptide string

Parameters:

strippedPeptide -

peptideWithMods -

run -

thisRunSymbolModMap -

Returns:

createRunEntry

protected static AmtRunEntry createRunEntry(java.util.List<AmtTsvReader.AmtTsvRow> amtTsvRowList,
                                            java.lang.String commentLineForRun,
                                            boolean useTimesInsteadOfScans)

Create a run entry from a comment row in the tsv file

Parameters:

amtTsvRowList -

commentLineForRun -

useTimesInsteadOfScans -

Returns: