apollo.dataadapter.genbank
Class GenbankReport

java.lang.Object
  apollo.dataadapter.genbank.GenbankReport

public class GenbankReport
extends java.lang.Object

GenbankReport.java Created: Mon Sep 1 16:04:06 2003

Version:

1.0 $Header: /tmp/rob/gmod/gmod_cvs/apollo/src/java/apollo/dataadapter/genbank/GenbankReport.java,v 1.16 2007-01-03 13:50:15 jcrabtree Exp $ Code from BCM for writing human-readable GenBank files. Fixed/extended by Nomi.

Author:

Shiran Pasternak, Ryan Lozado

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

GenbankReport(CurationSet cs)

Method Summary

java.lang.String	getAccession()
java.lang.String	getComment()
CurationSet	getCurationSet() Gets the value of cs
java.lang.String	getDefinition()
java.lang.String	getKeywords()
java.lang.String	getLocus() Properties that were saved from the GenBank-format input were saved verbatim, including newlines, and we don't need to add the keyword to the first line because it's there already.
java.lang.String	getOrganism()
java.io.PrintStream	getPrintStream()
java.lang.String	getReference()
java.lang.String	getSource()
java.lang.String	getVersion()
void	printDbXref(AnnotatedFeatureI annotation)
void	printFeatures()
void	printFooter()
void	printFunction(AnnotatedFeature annotation)
void	printGene(AnnotatedFeature gene)
void	printHeader()
void	printNotes(AnnotatedFeatureI annotation)
void	printTranscript(Transcript transcript)
static void	save(CurationSet cs, java.io.File file)
static void	save(CurationSet cs, java.lang.String filename)
void	setCurationSet(CurationSet cs) Sets the value of cs
void	setPrintStream(java.io.PrintStream out)
void	writeReport(java.io.PrintStream out)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

GenbankReport

public GenbankReport(CurationSet cs)

Method Detail

getCurationSet

public CurationSet getCurationSet()

Gets the value of cs

Returns:

the value of cs

setCurationSet

public void setCurationSet(CurationSet cs)

Sets the value of cs

Parameters:

cs - Value to assign to this.cs

getPrintStream

public java.io.PrintStream getPrintStream()

setPrintStream

public void setPrintStream(java.io.PrintStream out)

getLocus

public java.lang.String getLocus()

Properties that were saved from the GenBank-format input were saved verbatim, including newlines, and we don't need to add the keyword to the first line because it's there already.

getDefinition

public java.lang.String getDefinition()

getAccession

public java.lang.String getAccession()

getVersion

public java.lang.String getVersion()

getKeywords

public java.lang.String getKeywords()

getSource

public java.lang.String getSource()

getOrganism

public java.lang.String getOrganism()

getReference

public java.lang.String getReference()

getComment

public java.lang.String getComment()

printHeader

public void printHeader()

printTranscript

public void printTranscript(Transcript transcript)

printGene

public void printGene(AnnotatedFeature gene)

printNotes

public void printNotes(AnnotatedFeatureI annotation)

printFunction

public void printFunction(AnnotatedFeature annotation)

printDbXref

public void printDbXref(AnnotatedFeatureI annotation)

printFeatures

public void printFeatures()

printFooter

public void printFooter()

writeReport

public void writeReport(java.io.PrintStream out)

save

public static void save(CurationSet cs,
                        java.lang.String filename)

save

public static void save(CurationSet cs,
                        java.io.File file)