Package htsjdk.samtools.seekablestream
Class SeekableFTPStream
- java.lang.Object
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- java.io.InputStream
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- htsjdk.samtools.seekablestream.SeekableStream
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- htsjdk.samtools.seekablestream.SeekableFTPStream
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- All Implemented Interfaces:
Closeable
,AutoCloseable
public class SeekableFTPStream extends SeekableStream
Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both. This class is for use with Tribble and delegates all the work to a helper.
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Field Summary
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Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream
mark
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Constructor Summary
Constructors Constructor Description SeekableFTPStream(URL url)
SeekableFTPStream(URL url, UserPasswordInput userPasswordInput)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
boolean
eof()
String
getSource()
long
length()
static void
main(String[] args)
long
position()
int
read()
int
read(byte[] buffer, int offset, int len)
void
seek(long position)
Seeks the stream to the provided position.long
skip(long n)
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Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream
available, mark, markSupported, readFully, reset
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Methods inherited from class java.io.InputStream
nullInputStream, read, readAllBytes, readNBytes, readNBytes, transferTo
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Constructor Detail
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SeekableFTPStream
public SeekableFTPStream(URL url) throws IOException
- Throws:
IOException
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SeekableFTPStream
public SeekableFTPStream(URL url, UserPasswordInput userPasswordInput) throws IOException
- Throws:
IOException
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Method Detail
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seek
public void seek(long position)
Description copied from class:SeekableStream
Seeks the stream to the provided position.- Specified by:
seek
in classSeekableStream
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position
public long position()
- Specified by:
position
in classSeekableStream
- Returns:
- the current byte position of the stream.
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eof
public boolean eof() throws IOException
- Specified by:
eof
in classSeekableStream
- Returns:
true
if the stream is already consumed;false
otherwise.- Throws:
IOException
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getSource
public String getSource()
- Specified by:
getSource
in classSeekableStream
- Returns:
- String representation of source (e.g. URL, file path, etc.), or null if not available.
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length
public long length()
- Specified by:
length
in classSeekableStream
- Returns:
- the length of the stream; 0 if not available or empty.
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skip
public long skip(long n) throws IOException
- Overrides:
skip
in classInputStream
- Throws:
IOException
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read
public int read(byte[] buffer, int offset, int len) throws IOException
- Specified by:
read
in classSeekableStream
- Throws:
IOException
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close
public void close() throws IOException
- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in classSeekableStream
- Throws:
IOException
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read
public int read() throws IOException
- Specified by:
read
in classInputStream
- Throws:
IOException
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main
public static void main(String[] args) throws IOException
- Throws:
IOException
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