public class SearchParametersInputBean
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
SearchParametersInputBean.ToolType
The tool type.
|
Constructor and Description |
---|
SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine)
Takes all the arguments from a command line.
|
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.
|
int |
getNThreads()
Returns the number of threads to use.
|
java.io.File |
getOmssaLocation()
Returns the OMSSA location, null if none is set.
|
java.io.File |
getOutputFile()
Returns the output folder.
|
java.io.File |
getPepNovoLocation()
Returns the PepNovo+ location.
|
SearchParameters |
getSearchParameters()
Returns the search parameters.
|
java.util.ArrayList<java.io.File> |
getSpectrumFiles()
Return the spectrum files.
|
static java.util.ArrayList<java.io.File> |
getSpectrumFiles(java.lang.String optionInput)
Returns a list of spectrum files as imported from the command line
option.
|
java.io.File |
getXtandemLocation()
Returns the X!Tandem location.
|
boolean |
isOmssaEnabled()
Returns true if OMSSA is to be used.
|
boolean |
isOmssaOutputAsOmx()
Returns true if OMSSA OMX is to be used as output, false if OMSSA CSV is
to be used.
|
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.
|
void |
setFixDuplicateSpectrumTitles(boolean fixDuplicateSpectrumTitles)
Set if duplicate spectrum titles are to be corrected automatically.
|
void |
setOmssaLocation(java.io.File omssaLocation)
Set the OMSSA location.
|
void |
setPepNovoLocation(java.io.File pepNovoLocation)
Set the PepNovo+ location.
|
void |
setXtandemLocation(java.io.File xtandemLocation)
Set the X!Tandem location.
|
public SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
aLine
- the command linejava.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public java.util.ArrayList<java.io.File> getSpectrumFiles()
public java.io.File getOutputFile()
public SearchParameters getSearchParameters()
public static java.util.ArrayList<java.io.File> getSpectrumFiles(java.lang.String optionInput) throws java.io.FileNotFoundException
optionInput
- the command line optionjava.io.FileNotFoundException
- exception thrown whenever a file is not
foundpublic boolean isOmssaEnabled()
public boolean isXTandemEnabled()
public boolean isOmssaOutputAsOmx()
public java.io.File getOmssaLocation()
public void setOmssaLocation(java.io.File omssaLocation)
omssaLocation
- the omssaLocation to setpublic java.io.File getXtandemLocation()
public void setXtandemLocation(java.io.File xtandemLocation)
xtandemLocation
- the xtandemLocation to setpublic java.io.File getPepNovoLocation()
public void setPepNovoLocation(java.io.File pepNovoLocation)
pepNovoLocation
- the pepNovoLocation 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 java.io.IOException
aLine
- the command line to validatecurrentToolType
- the tool type, used to check which parameters that
are mandatoryjava.io.IOException
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