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java.lang.Object | +--org.emboss.jemboss.editor.SequenceReader
This class reads sequences in FASTA and MSF format. The sequences are read and stored as a Vector.
Field Summary | |
private boolean |
reading
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private java.io.File |
seqFile
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private java.util.Vector |
seqs
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Constructor Summary | |
SequenceReader()
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SequenceReader(java.io.File seqFile)
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SequenceReader(java.lang.String seqString)
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Method Summary | |
int |
getNumberOfSequences()
Returns the number of sequences. |
Sequence |
getSequence(int index)
Returns the sequence at a given position in the Sequence Vector store. |
java.io.File |
getSequenceFile()
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java.util.Vector |
getSequenceVector()
Returns the Sequence Vector store |
boolean |
isReading()
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java.util.Vector |
readFastaFile(java.io.BufferedReader in)
Reads in the FASTA sequence file and creates a Vector containing the sequence(s). |
java.util.Vector |
readMSFFile(java.io.BufferedReader in)
Reads in the MSF sequence file and creates a Vector containing the sequence(s). |
java.util.Vector |
readSequenceFile()
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java.util.Vector |
readSequenceString(java.lang.String seqString)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
private java.io.File seqFile
private java.util.Vector seqs
private boolean reading
Constructor Detail |
public SequenceReader()
public SequenceReader(java.io.File seqFile)
public SequenceReader(java.lang.String seqString)
Method Detail |
public boolean isReading()
public java.util.Vector readSequenceFile()
public java.util.Vector readSequenceString(java.lang.String seqString)
public java.util.Vector readFastaFile(java.io.BufferedReader in)
public java.util.Vector readMSFFile(java.io.BufferedReader in)
public int getNumberOfSequences()
public Sequence getSequence(int index)
public java.util.Vector getSequenceVector()
public java.io.File getSequenceFile()
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