Package org.snpeff.nextProt
Class NextProtDb
- java.lang.Object
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- org.snpeff.nextProt.NextProtDb
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public class NextProtDb extends java.lang.Object
Parse NetxProt XML file and build a database http://www.nextprot.org/- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static int
HIGHLY_CONSERVED_AA_COUNT
static double
HIGHLY_CONSERVED_AA_PERCENT
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Constructor Summary
Constructors Constructor Description NextProtDb(java.lang.String xmlDirName, Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
fatalError(java.lang.String message)
Show an error message and exitboolean
parse()
Parse XML filevoid
saveDatabase()
Save nextprot markers as databasesvoid
setDebug(boolean debug)
void
setTrIdFile(java.lang.String trIdFile)
void
setVerbose(boolean verbose)
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Field Detail
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HIGHLY_CONSERVED_AA_PERCENT
public static final double HIGHLY_CONSERVED_AA_PERCENT
- See Also:
- Constant Field Values
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HIGHLY_CONSERVED_AA_COUNT
public static final int HIGHLY_CONSERVED_AA_COUNT
- See Also:
- Constant Field Values
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Constructor Detail
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NextProtDb
public NextProtDb(java.lang.String xmlDirName, Config config)
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Method Detail
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fatalError
protected void fatalError(java.lang.String message)
Show an error message and exit
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parse
public boolean parse()
Parse XML file
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saveDatabase
public void saveDatabase()
Save nextprot markers as databases
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setDebug
public void setDebug(boolean debug)
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setTrIdFile
public void setTrIdFile(java.lang.String trIdFile)
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setVerbose
public void setVerbose(boolean verbose)
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