public class MgfIndex extends ExperimentObject
Constructor and Description |
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MgfIndex(ArrayList<String> spectrumTitles,
HashMap<String,Long> indexMap,
String fileName,
double minRT,
double maxRT,
double maxMz,
double maxIntensity)
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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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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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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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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ArrayList<String> |
getSpectrumTitles()
Returns an ordered list of all spectrum titles
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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 |
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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addUrParam, getParameterKey, getUrParam
public MgfIndex(ArrayList<String> spectrumTitles, HashMap<String,Long> indexMap, String fileName, double minRT, double maxRT, double maxMz, double maxIntensity)
spectrumTitles
- an ordered list of all spectrum titlesindexMap
- map of all indexes: spectrum title -> index in the filefileName
- the mgf file namemaxRT
- the maximum retention timeminRT
- the minimum retention tomemaxMz
- the maximum m/z valuemaxIntensity
- the maximum precursor intensitypublic Long getIndex(String spectrumTitle)
spectrumTitle
- the desired spectrumpublic boolean containsSpectrum(String spectrumTitle)
spectrumTitle
- the spectrum titlepublic ArrayList<String> getSpectrumTitles()
public String getFileName()
public Double getMaxRT()
public void setMaxRT(Double maxRT)
maxRT
- the maximal RT in this filepublic Double getMaxMz()
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 int getNSpectra()
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