Class SequenceInfo

java.lang.Object

org.episteme.natural.biology.loaders.SequenceInfo

public class SequenceInfo
extends Object

Data transfer object for biological sequence information from GenBank.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SequenceInfo.SequenceType

Method Summary

Modifier and Type	Method	Description
static SequenceInfo	fromFasta(String fasta)	Parses FASTA format string into SequenceInfo.
String	getAccession()
String	getComplement()	Returns complementary strand (for DNA only).
String	getDescription()
double	getGCContent()	Calculates GC content (for DNA/RNA sequences).
int	getLength()
String	getReverseComplement()	Returns reverse complement (for DNA only).
String	getSequence()
SequenceInfo.SequenceType	getType()
String	toString()

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Details

getAccession

public String getAccession()

getDescription

public String getDescription()

getSequence

public String getSequence()

getType

public SequenceInfo.SequenceType getType()

getLength

public int getLength()

getGCContent

public double getGCContent()

Calculates GC content (for DNA/RNA sequences).

Returns:

GC content as fraction (0.0-1.0)

getComplement

public String getComplement()

Returns complementary strand (for DNA only).

getReverseComplement

public String getReverseComplement()

Returns reverse complement (for DNA only).

fromFasta

public static SequenceInfo fromFasta(String fasta)

Parses FASTA format string into SequenceInfo.

toString

public String toString()

Overrides:

toString in class Object