de.hu.berlin.wbi.objects

Class Transcript

java.lang.Object

de.hu.berlin.wbi.objects.Transcript

Direct Known Subclasses:

TranscriptNormalized

public class Transcript
extends Object

Class to represents a transcript (Protein as well as coding sequence) Therefore one gene usually contains one or more Transcript

Author:

Philippe Thomas

Field Summary

Fields

Modifier and Type	Field and Description
protected String	CDC_sequence Coding Sequence
protected String	ensg Ensemble gene ID.
protected String	ensp Ensemble protein ID.
protected String	enst Ensemble transcript ID.
protected int	entrez Gene-ID (Entrez in our case).
protected String	protein_sequence Protein Sequence
protected String	uniprot UniProt-ID.

Constructor Summary

Constructors

Constructor and Description
Transcript()
Transcript(int entrez, String uniprot, String ensg, String enst, String ensp, String protein_sequence, String CDC_sequence)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getCDC_sequence()
String	getEnsg()
String	getEnsp()
String	getEnst()
int	getEntrez()
String	getProtein_sequence()
static Set<Transcript>	getTranscripts(int entrez)
String	getUniprot()
int	hashCode()
static void	init(DatabaseConnection connection, String table) Initializes the prepared statements for retrieving sequence information for one Gene
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

entrez

protected int entrez

Gene-ID (Entrez in our case).

uniprot

protected String uniprot

UniProt-ID.

ensg

protected String ensg

Ensemble gene ID.

enst

protected String enst

Ensemble transcript ID.

ensp

protected String ensp

Ensemble protein ID.

protein_sequence

protected String protein_sequence

Protein Sequence

CDC_sequence

protected String CDC_sequence

Coding Sequence

Constructor Detail

Transcript

public Transcript()

Transcript

public Transcript(int entrez,
                  String uniprot,
                  String ensg,
                  String enst,
                  String ensp,
                  String protein_sequence,
                  String CDC_sequence)

Method Detail

init

public static void init(DatabaseConnection connection,
                        String table)
                 throws SQLException

Initializes the prepared statements for retrieving sequence information for one Gene

Parameters:

connection - Database connection

Throws:

SQLException

getTranscripts

public static Set<Transcript> getTranscripts(int entrez)

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getEntrez

public int getEntrez()

getUniprot

public String getUniprot()

getEnst

public String getEnst()

getProtein_sequence

public String getProtein_sequence()

getCDC_sequence

public String getCDC_sequence()

getEnsg

public String getEnsg()

getEnsp

public String getEnsp()