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java.lang.Objectorg.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
public abstract static class RichSequenceFormat.BasicFormat
Provides a basic format with simple things like line-widths precoded.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat |
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RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat |
Constructor Summary | |
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RichSequenceFormat.BasicFormat()
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Method Summary | |
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boolean |
canRead(File file)
Check to see if a given file is in our format. |
boolean |
getElideComments()
Is the format going to emit events when comments data or remarks from bibliographic references are read? |
boolean |
getElideFeatures()
Is the format going to emit events when feature data is read? |
boolean |
getElideReferences()
Is the format going to emit events when bibliographic reference data is read? |
boolean |
getElideSymbols()
Is the format going to emit events when sequence data is read? |
int |
getLineWidth()
Retrive the current line width. |
PrintStream |
getPrintStream()
Gets the print stream currently being written to. |
SymbolTokenization |
guessSymbolTokenization(File file)
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. |
void |
setElideComments(boolean elideComments)
Use this method to toggle reading of comments data. |
void |
setElideFeatures(boolean elideFeatures)
Use this method to toggle reading of feature data. |
void |
setElideReferences(boolean elideReferences)
Use this method to toggle reading of bibliographic reference data. |
void |
setElideSymbols(boolean elideSymbols)
Use this method to toggle reading of sequence data. |
void |
setLineWidth(int width)
Set the line width. |
void |
setPrintStream(PrintStream os)
Sets the stream to write to. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat |
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beginWriting, canRead, finishWriting, guessSymbolTokenization, readRichSequence, writeSequence |
Methods inherited from interface org.biojava.bio.seq.io.SequenceFormat |
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getDefaultFormat, readSequence, writeSequence, writeSequence |
Constructor Detail |
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public RichSequenceFormat.BasicFormat()
Method Detail |
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public boolean canRead(File file) throws IOException
canRead
in interface RichSequenceFormat
file
- the File
to check.
IOException
- in case the file is inaccessible.public SymbolTokenization guessSymbolTokenization(File file) throws IOException
guessSymbolTokenization
in interface RichSequenceFormat
file
- the File
object to guess the format of.
SymbolTokenization
to read the file with.
IOException
- if the file is unrecognisable or inaccessible.public int getLineWidth()
getLineWidth
in interface RichSequenceFormat
public void setLineWidth(int width)
setLineWidth
in interface RichSequenceFormat
width
- the new line widthpublic boolean getElideSymbols()
getElideSymbols
in interface RichSequenceFormat
public void setElideSymbols(boolean elideSymbols)
setElideSymbols
in interface RichSequenceFormat
elideSymbols
- set to true if you don't want the sequence data.public boolean getElideFeatures()
getElideFeatures
in interface RichSequenceFormat
public void setElideFeatures(boolean elideFeatures)
setElideFeatures
in interface RichSequenceFormat
elideFeatures
- set to true if you don't want the feature data.public boolean getElideReferences()
getElideReferences
in interface RichSequenceFormat
public void setElideReferences(boolean elideReferences)
setElideReferences
in interface RichSequenceFormat
elideReferences
- set to true if you don't want the bibliographic reference data.public boolean getElideComments()
getElideComments
in interface RichSequenceFormat
public void setElideComments(boolean elideComments)
setElideComments
in interface RichSequenceFormat
elideComments
- set to true if you don't want the comments data.public void setPrintStream(PrintStream os)
setPrintStream
in interface RichSequenceFormat
os
- the PrintStream to write to.public PrintStream getPrintStream()
getPrintStream
in interface RichSequenceFormat
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