Package net.bioclipse.managers

Class BiojavaManager

java.lang.Object

net.bioclipse.managers.BiojavaManager

All Implemented Interfaces:

IBactingManager, net.bioclipse.managers.business.IBioclipseManager

public class BiojavaManager
extends Object
implements IBactingManager

Bioclipse manager that provides BioJava functionality.

Constructor Summary

Constructors

Constructor	Description
BiojavaManager(String workspaceRoot)	Creates a new BiojavaManager.

Method Summary

Modifier and Type	Method	Description
net.bioclipse.core.domain.IDNA	DNAfromPlainSequence(String dnaString)
net.bioclipse.core.domain.IDNA	DNAfromPlainSequence(String dnaString, String name)
List<String>	doi()	Lists the DOIs of the articles associated to this manager.
String	getManagerName()
net.bioclipse.core.domain.IProtein	proteinFromPlainSequence(String proteinString)
net.bioclipse.core.domain.IProtein	proteinFromPlainSequence(String proteinString, String name)

Methods inherited from class java.lang.Object

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

Constructor Details

BiojavaManager

public BiojavaManager(String workspaceRoot)

Creates a new BiojavaManager.

Parameters:

workspaceRoot - location of the workspace, e.g. "."

Method Details

getManagerName

public String getManagerName()

Specified by:

getManagerName in interface net.bioclipse.managers.business.IBioclipseManager

doi

public List<String> doi()

Description copied from interface: IBactingManager

Lists the DOIs of the articles associated to this manager.

Specified by:

doi in interface IBactingManager

Returns:

a List of String with DOIs

DNAfromPlainSequence

public net.bioclipse.core.domain.IDNA DNAfromPlainSequence(String dnaString)

DNAfromPlainSequence

public net.bioclipse.core.domain.IDNA DNAfromPlainSequence(String dnaString,
 String name)

proteinFromPlainSequence

public net.bioclipse.core.domain.IProtein proteinFromPlainSequence(String proteinString)

proteinFromPlainSequence

public net.bioclipse.core.domain.IProtein proteinFromPlainSequence(String proteinString,
 String name)