Package org.snpeff.fileIterator
Class LineClassFileIterator<T>
java.lang.Object
org.snpeff.fileIterator.FileIterator<T>
org.snpeff.fileIterator.LineClassFileIterator<T>
- Direct Known Subclasses:
BlastResultFileIterator
,MatrixEntryFileIterator
,MicroCosmFileIterator
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 -
Constructor Summary
ConstructorsConstructorDescriptionLineClassFileIterator
(String fileName, Class clazz) LineClassFileIterator
(String fileName, Class clazz, String fieldNames) -
Method Summary
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
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Details
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debug
public static boolean debug -
FIELD_NAME_SEPARATOR
public static final char FIELD_NAME_SEPARATOR- See Also:
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separator
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fieldStr
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fieldNames
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fieldByName
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clazz
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Constructor Details
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LineClassFileIterator
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LineClassFileIterator
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Method Details
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createObject
Create an object using- Parameters:
line
-- Returns:
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fieldMap
protected void fieldMap()Map field names to Field objects -
iterator
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readNext
Read a sequence from the file- Specified by:
readNext
in classFileIterator<T>
- Returns:
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setSeparator
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