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java.lang.Objectcom.compomics.util.experiment.identification.SearchParametersInputBean
public class SearchParametersInputBean
This class contains the parses parameters from a command line and stores them in a SearchParameters object.
Nested Class Summary | |
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static class |
SearchParametersInputBean.ToolType
The tool type. |
Constructor Summary | |
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SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine)
Takes all the arguments from a command line. |
Method Summary | |
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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. |
File |
getOmssaLocation()
Returns the OMSSA location, null if none is set. |
File |
getOutputFile()
Returns the output folder. |
File |
getPepNovoExecutable()
Returns the PepNovo+ executable. |
SearchParameters |
getSearchParameters()
Returns the search parameters. |
ArrayList<File> |
getSpectrumFiles()
Return the spectrum files. |
static ArrayList<File> |
getSpectrumFiles(String optionInput)
Returns a list of spectrum files as imported from the command line option. |
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(File omssaLocation)
Set the OMSSA location. |
void |
setPepNovoExecutable(File pepNovoExecutable)
Set the PepNovo+ executable. |
void |
setXtandemLocation(File xtandemLocation)
Set the X!Tandem location. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SearchParametersInputBean(org.apache.commons.cli.CommandLine aLine) throws FileNotFoundException, IOException, ClassNotFoundException
aLine
- the command line
FileNotFoundException
IOException
ClassNotFoundException
Method Detail |
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public ArrayList<File> getSpectrumFiles()
public File getOutputFile()
public SearchParameters getSearchParameters()
public static ArrayList<File> getSpectrumFiles(String optionInput) throws FileNotFoundException
optionInput
- the command line option
FileNotFoundException
- 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 mandatory
IOException
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