Serialized Form

Class uk.ac.vamsas.objects.core.Alignment extends Vobject implements Serializable

Serialized Fields

_gapChar

java.lang.String _gapChar
Field _gapChar.


_aligned

boolean _aligned
Field _aligned.


_has_aligned

boolean _has_aligned
keeps track of state for field: _aligned


_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


_alignmentAnnotationList

java.util.Vector _alignmentAnnotationList
This is annotation over the coordinate frame defined by all the columns in the alignment.


_treeList

java.util.Vector _treeList
Field _treeList.


_alignmentSequenceList

java.util.Vector _alignmentSequenceList
Field _alignmentSequenceList.


_propertyList

java.util.Vector _propertyList
typical properties may be additional alignment score objects


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.AlignmentAnnotation extends RangeAnnotation implements Serializable

Serialized Fields

_graph

boolean _graph
TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph


_has_graph

boolean _has_graph
keeps track of state for field: _graph


_seqrefs

java.util.Vector _seqrefs
annotation is associated with a range on a particular group of alignment sequences


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.AlignmentSequence extends SequenceType implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_refid

java.lang.Object _refid
Dataset Sequence from which this alignment sequence is taken from


_alignmentSequenceAnnotationList

java.util.Vector _alignmentSequenceAnnotationList
Field _alignmentSequenceAnnotationList.


Class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation extends RangeAnnotation implements Serializable

Serialized Fields

_graph

boolean _graph
TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph


_has_graph

boolean _has_graph
keeps track of state for field: _graph


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.AnnotationElement extends Vobject implements Serializable

Serialized Fields

_position

long _position
position with respect to the coordinate frame defined by a rangeType specification


_has_position

boolean _has_position
keeps track of state for field: _position


_after

boolean _after
true means the annotation element appears between the specified position and the next


_has_after

boolean _has_after
keeps track of state for field: _after


_id

java.lang.String _id
Primary Key for vamsas object referencing


_description

java.lang.String _description
Free text at this position


_glyphList

java.util.Vector _glyphList
Discrete symbol - possibly graphically represented


_valueList

java.util.Vector _valueList
Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions


Class uk.ac.vamsas.objects.core.AppData extends Vobject implements Serializable

Serialized Fields

_choiceValue

java.lang.Object _choiceValue
Internal choice value storage


_data

byte[] _data
Field _data.


_dataReference

java.lang.String _dataReference
Field _dataReference.


Class uk.ac.vamsas.objects.core.ApplicationData extends AppData implements Serializable

Serialized Fields

_version

java.lang.String _version
Version string describing the application specific data storage version used


_name

java.lang.String _name
Canonical name of application


_userList

java.util.Vector _userList
Field _userList.


_common

Common _common
Field _common.


_instanceList

java.util.Vector _instanceList
Field _instanceList.


Class uk.ac.vamsas.objects.core.Attachment extends AppData implements Serializable

Serialized Fields

_compressed

boolean _compressed
true implies data will be decompresses with Zip before presenting to application


_has_compressed

boolean _has_compressed
keeps track of state for field: _compressed


_type

java.lang.String _type
Type of arbitrary data - TODO: decide format - use (extended) MIME types ?


_objectref

java.lang.Object _objectref
Object the arbitrary data is associated with


_id

java.lang.String _id
Primary Key for vamsas object referencing


Class uk.ac.vamsas.client.ClientHandle extends java.lang.Object implements Serializable

serialVersionUID: 0l

Serialized Fields

clientName

java.lang.String clientName
(non-unique) human readable vamsas client name


clientUrn

java.lang.String clientUrn
the unambiguous client identifier This may be rewritten by the Vorba object if other clients with the same name, version and user are involved in a session.


version

java.lang.String version
version modifier to tag application space


Class uk.ac.vamsas.objects.core.Common extends AppData implements Serializable


Class uk.ac.vamsas.objects.core.DataSet extends Vobject implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_sequenceList

java.util.Vector _sequenceList
Field _sequenceList.


_sequenceMappingList

java.util.Vector _sequenceMappingList
Field _sequenceMappingList.


_dataSetAnnotationsList

java.util.Vector _dataSetAnnotationsList
Field _dataSetAnnotationsList.


_alignmentList

java.util.Vector _alignmentList
Field _alignmentList.


_treeList

java.util.Vector _treeList
Field _treeList.


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.DataSetAnnotations extends RangeAnnotation implements Serializable

Serialized Fields

_seqRef

java.util.Vector _seqRef
annotation is associated with a particular dataset sequence


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.DbRef extends Vobject implements Serializable

Serialized Fields

_source

java.lang.String _source
TODO Database Naming Convention: either start using LSID (so change type to URI) or leave this as an uncontrolled/unspecified string ID


_version

java.lang.String _version
Version must be specified -


_accessionId

java.lang.String _accessionId
TODO: make some specification of the database field from which this accessionId is taken from - should that be a special property of the dbRef object ?


_id

java.lang.String _id
Primary Key for vamsas object referencing


_mapList

java.util.Vector _mapList
the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. The mapped mapType is the mapped range defined on the dbRef element's reference frame. Conventionally, the unit attribute defaults to 1, or will be inferred from the local sequence's dictionary type and any dictionary type associated with the database being mapped to. However, it may be used to avoid ambiguity.


_linkList

java.util.Vector _linkList
Field _linkList.


_propertyList

java.util.Vector _propertyList
Field _propertyList.


Class uk.ac.vamsas.objects.core.Entry extends Vobject implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_user

java.lang.String _user
Who


_app

java.lang.String _app
With which application


_action

java.lang.String _action
Did what


_date

java.util.Date _date
When


_propertyList

java.util.Vector _propertyList
additional information


_paramList

java.util.Vector _paramList
parameter for the action


_inputList

java.util.Vector _inputList
bioinformatic objects input to action


Class uk.ac.vamsas.objects.core.Glyph extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_dict

java.lang.String _dict
specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here


Class uk.ac.vamsas.objects.core.Input extends RangeType implements Serializable

Serialized Fields

_name

java.lang.String _name
Field _name.


_objRef

java.util.Vector _objRef
Reference Frame for rangeType specfication


Class uk.ac.vamsas.objects.core.Instance extends AppData implements Serializable

Serialized Fields

_urn

java.lang.String _urn
Field _urn.


Class uk.ac.vamsas.client.InvalidSessionDocumentException extends java.lang.Exception implements Serializable


Class uk.ac.vamsas.client.InvalidSessionUrnException extends java.lang.Exception implements Serializable


Class uk.ac.vamsas.objects.core.Link extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_href

java.lang.String _href
The URI


Class uk.ac.vamsas.objects.core.Local extends MapRangeType implements Serializable


Class uk.ac.vamsas.objects.core.LockFile extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


Class uk.ac.vamsas.client.simpleclient.LockTimeoutException extends java.lang.Exception implements Serializable

serialVersionUID: 1l


Class uk.ac.vamsas.objects.core.Map extends MapType implements Serializable

Serialized Fields

_id

java.lang.String _id
Field _id.


Class uk.ac.vamsas.objects.core.MapList extends Vobject implements Serializable

Serialized Fields

_from

long _from
Offset to first position in dataset sequence record that start position on 'onto' maps to


_has_from

boolean _has_from
keeps track of state for field: _from


_to

long _to
Offset to last position in dataset sequence record that end position on 'onto' maps to


_has_to

boolean _has_to
keeps track of state for field: _to


_start

long _start
Offset to first position in database entry that first (or offset) position in sequence maps to


_has_start

boolean _has_start
keeps track of state for field: _start


_end

long _end
Offset to last position in database entry that last (offset) position in sequence maps to


_has_end

boolean _has_end
keeps track of state for field: _end


Class uk.ac.vamsas.objects.core.Mapped extends MapRangeType implements Serializable


Class uk.ac.vamsas.objects.core.Mapping extends MapList implements Serializable

Serialized Fields

_onto

java.lang.Object _onto
object to which the mapping is being mapped


Class uk.ac.vamsas.objects.core.MapRangeType extends RangeType implements Serializable

Serialized Fields

_unit

long _unit
number of dictionary symbol widths involved in each mapped position on this sequence (for example, 3 for a dna sequence exon region that is being mapped to a protein sequence). This is optional, since the unit can be usually be inferred from the dictionary type of each sequence involved in the mapping.


_has_unit

boolean _has_unit
keeps track of state for field: _unit


Class uk.ac.vamsas.objects.core.MapType extends Vobject implements Serializable

Serialized Fields

_local

Local _local

_mapped

Mapped _mapped


Class uk.ac.vamsas.objects.core.Newick extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_title

java.lang.String _title
Field _title.


_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


Class uk.ac.vamsas.client.NoDefaultSessionException extends java.lang.Exception implements Serializable


Class uk.ac.vamsas.objects.core.NodeType extends Vobject implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


_name

java.lang.String _name
Short name for this node


_description

java.lang.String _description
Descriptive text for this node


_vrefList

java.util.Vector _vrefList
Direct associations between this node and any vamsas objects


_propertyList

java.util.Vector _propertyList
Field _propertyList.


Class uk.ac.vamsas.objects.core.Param extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_name

java.lang.String _name
Field _name.


_type

java.lang.String _type
The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types


Class uk.ac.vamsas.objects.core.Pos extends Vobject implements Serializable

Serialized Fields

_i

int _i
Field _i.


_has_i

boolean _has_i
keeps track of state for field: _i


Class uk.ac.vamsas.objects.core.Property extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_name

java.lang.String _name
Field _name.


_type

java.lang.String _type
The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types


Class uk.ac.vamsas.objects.core.Provenance extends Vobject implements Serializable

Serialized Fields

_entryList

java.util.Vector _entryList
Field _entryList.


Class uk.ac.vamsas.objects.core.Range extends Vobject implements Serializable

Serialized Fields

_seqAStart

int _seqAStart
Field _seqAStart.


_has_seqAStart

boolean _has_seqAStart
keeps track of state for field: _seqAStart


_seqAEnd

int _seqAEnd
Field _seqAEnd.


_has_seqAEnd

boolean _has_seqAEnd
keeps track of state for field: _seqAEnd


_seqBStart

int _seqBStart
Field _seqBStart.


_has_seqBStart

boolean _has_seqBStart
keeps track of state for field: _seqBStart


_seqBEnd

int _seqBEnd
Field _seqBEnd.


_has_seqBEnd

boolean _has_seqBEnd
keeps track of state for field: _seqBEnd


Class uk.ac.vamsas.objects.core.RangeAnnotation extends RangeType implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


_group

java.lang.String _group
Annotation with the same non-empty group name are grouped together


_type

java.lang.String _type
A Das Feature has both a type and a Type ID. We go the route of requiring the type string to be taken from a controlled vocabulary if an application expects others to make sense of it. The type may qualified - so uniprot:CHAIN is a valid type name, and considered distinct from someotherDB:CHAIN


_label

java.lang.String _label
Short, meaningful name for the annotation - if this is absent, then the type string should be used in its place.


_description

java.lang.String _description
Human readable description of the annotation


_status

java.lang.String _status
TODO: specify this - we have considered taking the GO evidence codes as a model for assessing a measure of quality to an annotation.


_annotationElementList

java.util.Vector _annotationElementList
Annotation Element position maps to ordered positions defined by the sequence of rangeType pos positions or concatenated seg start/end segments.


_scoreList

java.util.Vector _scoreList
Ordered set of optionally named float values for the whole annotation


_linkList

java.util.Vector _linkList
Field _linkList.


_propertyList

java.util.Vector _propertyList
Note:These are mutable so an application should check them each time.


Class uk.ac.vamsas.objects.core.RangeType extends Vobject implements Serializable

Serialized Fields

_choiceValue

java.lang.Object _choiceValue
Internal choice value storage


_posList

java.util.Vector _posList
a position within the associated object's coordinate system


_segList

java.util.Vector _segList
a region from start to end, with flag for inclusivity of terminii


Class uk.ac.vamsas.objects.core.ReferenceType extends Vobject implements Serializable

Serialized Fields

_content

java.lang.String _content
internal content storage


_id

java.lang.String _id
Primary Key for vamsas object referencing


_refs

java.util.Vector _refs
List of one or more vamsas object references


Class uk.ac.vamsas.objects.core.Score extends Vobject implements Serializable

Serialized Fields

_content

float _content
internal content storage


_has_content

boolean _has_content
keeps track of state for field: _content


_name

java.lang.String _name
Field _name.


Class uk.ac.vamsas.objects.core.Seg extends Vobject implements Serializable

Serialized Fields

_start

int _start
Field _start.


_has_start

boolean _has_start
keeps track of state for field: _start


_end

int _end
Field _end.


_has_end

boolean _has_end
keeps track of state for field: _end


_inclusive

boolean _inclusive
when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2


_has_inclusive

boolean _has_inclusive
keeps track of state for field: _inclusive


Class uk.ac.vamsas.objects.utils.SeqAln extends Alignment implements Serializable


Class uk.ac.vamsas.objects.core.Sequence extends SequenceType implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_dictionary

java.lang.String _dictionary
symbol class for sequence


_dbRefList

java.util.Vector _dbRefList
Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record


_vxrefList

java.util.Vector _vxrefList
explicitly named cross reference to other objects in the document.


Class uk.ac.vamsas.objects.core.SequenceMapping extends MapType implements Serializable

Serialized Fields

_loc

java.lang.Object _loc
Object on which the local range is defined.


_map

java.lang.Object _map
Object on which the mapped range is defined.


_id

java.lang.String _id
Field _id.


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.SequenceType extends Vobject implements Serializable

Serialized Fields

_start

long _start
Field _start.


_has_start

boolean _has_start
keeps track of state for field: _start


_end

long _end
Field _end.


_has_end

boolean _has_end
keeps track of state for field: _end


_sequence

java.lang.String _sequence
Field _sequence.


_name

java.lang.String _name
Field _name.


_description

java.lang.String _description
Field _description.


_propertyList

java.util.Vector _propertyList
additional typed properties


Class uk.ac.vamsas.client.SessionHandle extends java.lang.Object implements Serializable

Serialized Fields

sessionUrn

java.lang.String sessionUrn
The path to the vamsas session file.


Class uk.ac.vamsas.objects.core.Tree extends Vobject implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


_title

java.lang.String _title
Field _title.


_newickList

java.util.Vector _newickList
Field _newickList.


_treenodeList

java.util.Vector _treenodeList
node identity and mapping data between tree representations and vamsas document objects


_propertyList

java.util.Vector _propertyList
Field _propertyList.


_provenance

Provenance _provenance
Field _provenance.


Class uk.ac.vamsas.objects.core.Treenode extends NodeType implements Serializable

Serialized Fields

_treeId

java.util.Vector _treeId
reference to one or more trees containing the node being described.


_nodespec

java.lang.String _nodespec
String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.


Class uk.ac.vamsas.objects.core.User extends AppData implements Serializable

Serialized Fields

_fullname

java.lang.String _fullname
Field _fullname.


_organization

java.lang.String _organization
Field _organization.


Class uk.ac.vamsas.objects.core.VAMSAS extends Vobject implements Serializable

Serialized Fields

_id

java.lang.String _id
Primary Key for vamsas object referencing


_modifiable

java.lang.String _modifiable
Field _modifiable.


_treeList

java.util.Vector _treeList
Field _treeList.


_dataSetList

java.util.Vector _dataSetList
Field _dataSetList.


Class uk.ac.vamsas.objects.core.VamsasDocument extends Vobject implements Serializable

Serialized Fields

_version

java.lang.String _version
Vamsas Document Version Number


_lockFile

LockFile _lockFile
Field _lockFile.


_provenance

Provenance _provenance
Field _provenance.


_VAMSASList

java.util.Vector _VAMSASList
contains unassociated trees and a number of analysis sets


_applicationDataList

java.util.Vector _applicationDataList
Field _applicationDataList.


_attachmentList

java.util.Vector _attachmentList
Field _attachmentList.


Class uk.ac.vamsas.client.VorbaId extends java.lang.Object implements Serializable

serialVersionUID: 1l

Serialized Fields

id

java.lang.String id


Class uk.ac.vamsas.objects.core.Vref extends ReferenceType implements Serializable


Class uk.ac.vamsas.objects.core.Vxref extends ReferenceType implements Serializable