public class MgfIndex extends ExperimentObject
Constructor and Description |
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MgfIndex(ArrayList<String> spectrumTitles,
HashMap<String,Integer> duplicatedSpectrumTitles,
HashMap<String,Long> indexMap,
HashMap<String,Integer> spectrumNumberIndexMap,
HashMap<Integer,Double> precursorMzMap,
String fileName,
double minRT,
double maxRT,
double maxMz,
double maxIntensity,
int maxCharge,
int maxPeakCount,
boolean peakPicked,
boolean precursorChargesMissing,
long lastModified,
int spectrumCount)
Constructor.
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MgfIndex(ArrayList<String> spectrumTitles,
HashMap<String,Long> indexMap,
HashMap<String,Integer> spectrumNumberIndexMap,
HashMap<Integer,Double> precursorMzMap,
String fileName,
double minRT,
double maxRT,
double maxMz,
double maxIntensity,
int maxCharge,
int maxPeakCount,
boolean peakPicked,
boolean precursorChargesMissing,
long lastModified)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
containsSpectrum(String spectrumTitle)
Returns a boolean indicating whether the spectrum title is implemented in
this index.
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HashMap<String,Integer> |
getDuplicatedSpectrumTitles()
Returns a map of the duplicated spectrum titles, can be null.
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String |
getFileName()
Returns the name of the indexed file.
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Long |
getIndex(String spectrumTitle)
Returns the index corresponding to the desired spectrum.
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Long |
getLastModified()
Returns when the file was last modified.
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Integer |
getMaxCharge()
Returns the maximal charge found in the mgf file.
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Double |
getMaxIntensity()
Returns the maximum precursor intensity in this file.
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Double |
getMaxMz()
Returns the maximum m/z in this file.
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Integer |
getMaxPeakCount()
Returns the maximum peak count in this file.
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Double |
getMaxRT()
Returns the maximal RT in this file.
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Double |
getMinRT()
Returns the minimum RT in this file.
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int |
getNSpectra()
Returns the number of imported spectra.
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Double |
getPrecursorMz(int spectrumIndex)
Returns the precursor mz for the spectrum at the given index.
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Integer |
getSpectrumIndex(String spectrumTitle)
Returns the spectrum index corresponding to the desired spectrum, i.e.,
returns 0 for the first spectrum in the file, 1 for the second, etc.
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String |
getSpectrumTitle(int number)
Returns the spectrum title corresponding to the given spectrum number.
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ArrayList<String> |
getSpectrumTitles()
Returns an ordered list of all spectrum titles.
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Boolean |
isPeakPicked()
Returns true if the indexed file seems to contain only peak picked
spectra.
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Boolean |
isPrecursorChargesMissing()
Returns true if the at least one spectrum is missing the precursor
charge.
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void |
setMaxCharge(Integer maxCharge)
Sets the maximum charge in this file.
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void |
setMaxIntensity(Double maxIntensity)
Sets the maximum precursor intensity in this file.
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void |
setMaxMz(Double maxMz)
Sets the maximum m/z in this file.
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void |
setMaxPeakCount(Integer maxPeakCount)
Sets the maximum peak count in this file.
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void |
setMaxRT(Double maxRT)
Sets the maximal RT in this file.
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void |
setMinRT(Double minRT)
Sets the minimum RT in this file.
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void |
setPeakPicked(Boolean peakPicked)
Set if the indexed file seems to contain only peak picked spectra or not.
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void |
setPrecursorChargesMissing(Boolean precursorChargesMissing)
Set if at least one spectrum is missing the precursor charge.
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addUrParam, getParameterKey, getUrParam
public MgfIndex(ArrayList<String> spectrumTitles, HashMap<String,Long> indexMap, HashMap<String,Integer> spectrumNumberIndexMap, HashMap<Integer,Double> precursorMzMap, String fileName, double minRT, double maxRT, double maxMz, double maxIntensity, int maxCharge, int maxPeakCount, boolean peakPicked, boolean precursorChargesMissing, long lastModified)
spectrumTitles
- an ordered list of all spectrum titlesindexMap
- map of all indexes: spectrum title > index in the filespectrumNumberIndexMap
- map of all spectrum index: spectrum title
> spectrum index in the fileprecursorMzMap
- map of the precursor mz values: spectrum index >
precursor mzfileName
- the mgf file namemaxRT
- the maximum retention timeminRT
- the minimum retention tomemaxMz
- the maximum m/z valuemaxIntensity
- the maximum precursor intensitymaxCharge
- the maximum peak precursor chargemaxPeakCount
- the maximum peak countpeakPicked
- indicates if the spectra seem to be peak picked or notprecursorChargesMissing
- indicates if at least one spectrum is
missing the precursor charge taglastModified
- a long indicating the last time the indexed file was
modifiedpublic MgfIndex(ArrayList<String> spectrumTitles, HashMap<String,Integer> duplicatedSpectrumTitles, HashMap<String,Long> indexMap, HashMap<String,Integer> spectrumNumberIndexMap, HashMap<Integer,Double> precursorMzMap, String fileName, double minRT, double maxRT, double maxMz, double maxIntensity, int maxCharge, int maxPeakCount, boolean peakPicked, boolean precursorChargesMissing, long lastModified, int spectrumCount)
spectrumTitles
- an ordered list of all spectrum titlesduplicatedSpectrumTitles
- a map of duplicated spectrum titles, and
how often each title is duplicatedindexMap
- map of all indexes: spectrum title > index in the filespectrumNumberIndexMap
- map of all spectrum index: spectrum title
> spectrum index in the fileprecursorMzMap
- map of the precursor mz values: spectrum index >
precursor mzfileName
- the mgf file namemaxRT
- the maximum retention timeminRT
- the minimum retention tomemaxMz
- the maximum m/z valuemaxIntensity
- the maximum precursor intensitymaxCharge
- the maximum peak precursor chargemaxPeakCount
- the maximum peak countpeakPicked
- indicates if the spectra seem to be peak picked or notprecursorChargesMissing
- indicates if at least one spectrum is
missing the precursor charge taglastModified
- a long indicating the last time the indexed file was
modifiedspectrumCount
- the number of spectra in the file counted by the
number of begin ion tagspublic Long getIndex(String spectrumTitle)
spectrumTitle
- the desired spectrumpublic Integer getSpectrumIndex(String spectrumTitle)
spectrumTitle
- the desired spectrumpublic Double getPrecursorMz(int spectrumIndex)
spectrumIndex
- the index of the spectrum, 0 for the first spectrum
in the file, 1 for the second, etcpublic String getSpectrumTitle(int number)
number
- the number of the spectrumpublic boolean containsSpectrum(String spectrumTitle)
spectrumTitle
- the spectrum titlepublic ArrayList<String> getSpectrumTitles()
public HashMap<String,Integer> getDuplicatedSpectrumTitles()
public String getFileName()
public Double getMaxRT()
public void setMaxRT(Double maxRT)
maxRT
- the maximal RT in this filepublic Double getMaxMz()
public void setMaxCharge(Integer maxCharge)
maxCharge
- the maximum charge in this filepublic Integer getMaxCharge()
public void setMaxMz(Double maxMz)
maxMz
- the maximum m/z in this filepublic Double getMaxIntensity()
public void setMaxIntensity(Double maxIntensity)
maxIntensity
- the maximum precursor intensity in this filepublic Double getMinRT()
public void setMinRT(Double minRT)
minRT
- the minimum RT in this filepublic Integer getMaxPeakCount()
public void setMaxPeakCount(Integer maxPeakCount)
maxPeakCount
- the maximum peak count in this filepublic int getNSpectra()
public Long getLastModified()
public Boolean isPeakPicked()
public void setPeakPicked(Boolean peakPicked)
peakPicked
- the peakPicked to setpublic Boolean isPrecursorChargesMissing()
public void setPrecursorChargesMissing(Boolean precursorChargesMissing)
precursorChargesMissing
- the precursorChargesMissing to setCopyright © 2016. All rights reserved.