Package org.snpeff.fileIterator
Class LineClassFileIterator<T>
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<T>
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- org.snpeff.fileIterator.LineClassFileIterator<T>
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- All Implemented Interfaces:
java.lang.Iterable<T>
,java.util.Iterator<T>
- Direct Known Subclasses:
BlastResultFileIterator
,MatrixEntryFileIterator
,MicroCosmFileIterator
public class LineClassFileIterator<T> extends FileIterator<T>
Iterate on each line. Create and populate objects based on 'fieldNames' definition: a colon separated list of fields. Note: You can use empty names to skip columns- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description protected java.lang.Class
clazz
static boolean
debug
static char
FIELD_NAME_SEPARATOR
protected java.util.HashMap<java.lang.String,java.lang.reflect.Field>
fieldByName
protected java.lang.String[]
fieldNames
protected java.lang.String
fieldStr
protected java.lang.String
separator
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Constructor Summary
Constructors Constructor Description LineClassFileIterator(java.lang.String fileName, java.lang.Class clazz)
LineClassFileIterator(java.lang.String fileName, java.lang.Class clazz, java.lang.String fieldNames)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected T
createObject(java.lang.String line)
Create an object usingprotected void
fieldMap()
Map field names to Field objectsjava.util.Iterator<T>
iterator()
protected T
readNext()
Read a sequence from the filevoid
setSeparator(java.lang.String separator)
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Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
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Field Detail
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debug
public static boolean debug
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FIELD_NAME_SEPARATOR
public static final char FIELD_NAME_SEPARATOR
- See Also:
- Constant Field Values
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separator
protected java.lang.String separator
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fieldStr
protected java.lang.String fieldStr
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fieldNames
protected java.lang.String[] fieldNames
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fieldByName
protected java.util.HashMap<java.lang.String,java.lang.reflect.Field> fieldByName
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clazz
protected java.lang.Class clazz
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Method Detail
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createObject
protected T createObject(java.lang.String line)
Create an object using- Parameters:
line
-- Returns:
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fieldMap
protected void fieldMap()
Map field names to Field objects
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iterator
public java.util.Iterator<T> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<T>
- Overrides:
iterator
in classFileIterator<T>
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readNext
protected T readNext()
Read a sequence from the file- Specified by:
readNext
in classFileIterator<T>
- Returns:
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setSeparator
public void setSeparator(java.lang.String separator)
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