public class SearchParametersInputBean extends Object
Modifier and Type | Class and Description |
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static class |
SearchParametersInputBean.ToolType
The tool type.
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Constructor and Description |
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SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine)
Takes all the arguments from a command line.
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Modifier and Type | Method and Description |
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boolean |
fixDuplicateSpectrumTitles()
Returns true if duplicate spectrum titles are to be corrected
automatically.
|
int |
getMgfMaxSize()
Returns the max mgf file size before splitting.
|
int |
getMgfNSpectra()
Get the max number of spectra in an mgf file.
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int |
getNThreads()
Returns the number of threads to use.
|
File |
getOmssaLocation()
Returns the OMSSA location, null if none is set.
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File |
getOutputFile()
Returns the output folder.
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File |
getPepNovoExecutable()
Returns the PepNovo+ executable.
|
SearchParameters |
getSearchParameters()
Returns the search parameters.
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ArrayList<File> |
getSpectrumFiles()
Return the spectrum files.
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static ArrayList<File> |
getSpectrumFiles(String optionInput)
Returns a list of spectrum files as imported from the command line
option.
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File |
getXtandemLocation()
Returns the X!Tandem location.
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boolean |
isOmssaEnabled()
Returns true if OMSSA is to be used.
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boolean |
isOmssaOutputAsOmx()
Returns true if OMSSA OMX is to be used as output, false if OMSSA CSV is
to be used.
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static boolean |
isValidStartup(org.apache.commons.cli.CommandLine aLine,
SearchParametersInputBean.ToolType currentToolType)
Verifies the command line start parameters.
|
boolean |
isXTandemEnabled()
Returns true if X!Tandem is to be used.
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void |
setFixDuplicateSpectrumTitles(boolean fixDuplicateSpectrumTitles)
Set if duplicate spectrum titles are to be corrected automatically.
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void |
setOmssaLocation(File omssaLocation)
Set the OMSSA location.
|
void |
setPepNovoExecutable(File pepNovoExecutable)
Set the PepNovo+ executable.
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void |
setXtandemLocation(File xtandemLocation)
Set the X!Tandem location.
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public SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine) throws FileNotFoundException, IOException, ClassNotFoundException
aLine
- the command lineFileNotFoundException
IOException
ClassNotFoundException
public ArrayList<File> getSpectrumFiles()
public File getOutputFile()
public SearchParameters getSearchParameters()
public static ArrayList<File> getSpectrumFiles(String optionInput) throws FileNotFoundException
optionInput
- the command line optionFileNotFoundException
- exception thrown whenever a file is not
foundpublic boolean isOmssaEnabled()
public boolean isXTandemEnabled()
public boolean isOmssaOutputAsOmx()
public File getOmssaLocation()
public void setOmssaLocation(File omssaLocation)
omssaLocation
- the omssaLocation to setpublic File getXtandemLocation()
public void setXtandemLocation(File xtandemLocation)
xtandemLocation
- the xtandemLocation to setpublic File getPepNovoExecutable()
public void setPepNovoExecutable(File pepNovoExecutable)
pepNovoExecutable
- the pepNovoExecutable to setpublic int getMgfMaxSize()
public int getMgfNSpectra()
public boolean fixDuplicateSpectrumTitles()
public void setFixDuplicateSpectrumTitles(boolean fixDuplicateSpectrumTitles)
fixDuplicateSpectrumTitles
- the fixDuplicateSpectrumTitles to setpublic int getNThreads()
public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine, SearchParametersInputBean.ToolType currentToolType) throws IOException
aLine
- the command line to validatecurrentToolType
- the tool type, used to check which parameters that
are mandatoryIOException
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