org.proteios.core
Class PolyPeptide<D extends PolyPeptideData>

java.lang.Object
  org.proteios.core.BasicItem<D>
      org.proteios.core.OwnedItem<D>
          org.proteios.core.SharedItem<D>
              org.proteios.core.CommonItem<D>
                  org.proteios.core.AnnotatedItem<D>
                      org.proteios.core.PolyPeptide<D>

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Removable, Shareable

Direct Known Subclasses:

Peptide, Protein

public abstract class PolyPeptide<D extends PolyPeptideData>
extends AnnotatedItem<D>

This is the base class for for the two types of polypeptide: Protein and Peptide.

Version:

2.0

Author:

Fredrik

Field Summary

static int	MAX_ACCESSION_NUMBER_LENGTH The maximum length of the accessionNumber that can be stored in the database.
static int	MAX_LSID_LENGTH The maximum length of the lsid that can be stored in the database.
static int	MAX_SEQUENCE_LENGTH The maximum length of the sequence that can be stored in the database.

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

void	addObservedModification(ObservedModification modification) Add a Modification
String	getAccessionNumber() Get the accessionNumber of the polypeptide.
String	getLsid() Get the lsid of the polypeptide.
Set<ObservedModification>	getObservedModifications()
SearchResult	getSearchResult() Get the SearchResult this PolyPeptide is associated with.
String	getSequence() Get the sequence of the polypeptide.
void	setAccessionNumber(String accessionNumber) Set the accession number of the polypeptide.
void	setLsid(String lsid) Set the LSID of the polypeptide.
void	setObservedModifications(Set<ObservedModification> modifications) Set the ObservedModification modifications set.
void	setSearchResult(SearchResult searchResult) Set the SearchResult this PolyPeptide is associated with.
void	setSequence(String sequence) Set the sequecne of the PolyPeptide.

Methods inherited from class org.proteios.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class org.proteios.core.SharedItem

getItemKey, getProjectKey, isShared, setItemKey, setProjectKey

Methods inherited from class org.proteios.core.OwnedItem

getOwner, setOwner

Methods inherited from class org.proteios.core.BasicItem

checkPermission, equals, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.proteios.core.Identifiable

getId, getType, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

MAX_SEQUENCE_LENGTH

public static final int MAX_SEQUENCE_LENGTH

The maximum length of the sequence that can be stored in the database.

See Also:

setSequence(String), Constant Field Values

MAX_LSID_LENGTH

public static final int MAX_LSID_LENGTH

The maximum length of the lsid that can be stored in the database.

See Also:

setLsid(String), Constant Field Values

MAX_ACCESSION_NUMBER_LENGTH

public static final int MAX_ACCESSION_NUMBER_LENGTH

The maximum length of the accessionNumber that can be stored in the database.

See Also:

setAccessionNumber(String), Constant Field Values

Method Detail

getSequence

public String getSequence()

Get the sequence of the polypeptide.

Returns:

The sequence for the polypeptide

setSequence

public void setSequence(String sequence)
                 throws PermissionDeniedException,
                        InvalidDataException

Set the sequecne of the PolyPeptide. The value may be null but must not be longer than the value specified by the MAX_SEQUENCE_LENGTH constant.

Parameters:

sequence - The new value for the sequence

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the string is too long

getLsid

public String getLsid()

Get the lsid of the polypeptide.

Returns:

The lsid for the polypeptide

setLsid

public void setLsid(String lsid)
             throws PermissionDeniedException,
                    InvalidDataException

Set the LSID of the polypeptide. The value may be null but must not be longer than the value specified by the MAX_LSID_LENGTH constant.

Parameters:

lsid - The new value for the Lsid

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the string is too long

getAccessionNumber

public String getAccessionNumber()

Get the accessionNumber of the polypeptide.

Returns:

The accessionNumber for the polypeptide

setAccessionNumber

public void setAccessionNumber(String accessionNumber)
                        throws PermissionDeniedException,
                               InvalidDataException

Set the accession number of the polypeptide. The value may be null but must not be longer than the value specified by the MAX_ACCESSION_NUMBER_LENGTH constant.

Parameters:

accessionNumber - The new value for the accession number

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the string is too long

getSearchResult

public SearchResult getSearchResult()
                             throws BaseException

Get the SearchResult this PolyPeptide is associated with.

Returns:

The SearchResult item or null if not known

Throws:

BaseException - If there is another error

setSearchResult

public void setSearchResult(SearchResult searchResult)
                     throws BaseException

Set the SearchResult this PolyPeptide is associated with.

Parameters:

searchResult - The new SearchResult item

Throws:

BaseException - If there is another error

getObservedModifications

public Set<ObservedModification> getObservedModifications()
                                                   throws ItemNotFoundException,
                                                          BaseException

Returns:

Returns the modifications.

Throws:

ItemNotFoundException

BaseException

setObservedModifications

public void setObservedModifications(Set<ObservedModification> modifications)

Set the ObservedModification modifications set.

Parameters:

modifications - The new Set item.

Throws:

InvalidDataException - If dataProcessingStep is null

BaseException - If there is another error

addObservedModification

public void addObservedModification(ObservedModification modification)

Add a Modification

Parameters:

modification - The Search Database to add to the Set