Roger Pettett > Bio-Das-ProServer > Bio::Das::ProServer::SourceAdaptor

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NAME ^

Bio::Das::ProServer::SourceAdaptor - base class for sources

VERSION ^

$Revision: 688 $

SYNOPSIS ^

A base class implementing stubs for all SourceAdaptors.

DESCRIPTION ^

SourceAdaptor.pm generates XML and manages callouts for DAS request handling.

If you're extending ProServer, this class is probably what you need to inherit. The build_* methods are probably the ones you need to extend. build_features() in particular.

AUTHOR ^

Roger Pettett <rmp@sanger.ac.uk>

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

SUBROUTINES/METHODS ^

new - Constructor

  my $oSourceAdaptor = Bio::Das::ProServer::SourceAdaptor::<implementation>->new({
    'dsn'      => q(),
    'port'     => q(),
    'hostname' => q(),
    'protocol' => q(),
    'baseuri'  => q(),
    'config'   => q(),
    'debug'    => 1,
  });

  Generally this would only be invoked on a subclass

init - Post-construction initialisation, passed the first argument to new()

  $oSourceAdaptor->init();

length - Returns the segment-length given a segment

  my $sSegmentLength = $oSourceAdaptor->length('DYNA_CHICK');
  
  By default returns 0

mapmaster - Mapmaster for this source.

  my $sMapMaster = $oSourceAdaptor->mapmaster();
  
  By default returns configuration 'mapmaster' setting

description - Description for this source.

  my $sDescription = $oSourceAdaptor->description();
  
  By default returns configuration 'description' setting or $self->title

doc_href - Location of a homepage for this source.

  my $sDocHref = $oSourceAdaptor->doc_href();
  
  By default returns configuration 'doc_href' setting

title - Short title for this source.

  my $title = $oSourceAdaptor->title();
  
  By default returns configuration 'title' setting or $self->source_uri

source_uri - URI for all versions of a source.

  my $uriS = $oSourceAdaptor->source_uri();
  
  By default returns configuration 'source_uri' setting or $self->dsn

version_uri - URI for a specific version of a source.

  my $uriV = $oSourceAdaptor->version_uri();
  
  By default returns configuration 'version_uri' setting or $self->source_uri

maintainer - Contact email for this source.

  my $email = $oSourceAdaptor->maintainer();
  
  By default returns configuration 'maintainer' setting, server setting or an empty string

strict_boundaries - Whether to return error segments for out-of-range queries

  my $strict = $oSourceAdaptor->strict_boundaries(); # boolean
  
  By default returns configuration 'strict_boundaries' setting, server setting or nothing (false)

build_features - (subclasses only) Fetch feature data

This call is made by das_features(). It is passed one of:

 { 'segment'    => $,
   'start'      => $,
   'end'        => $,
   'types'      => [$,$,...],
   'categories' => [$,$,...],
   'maxbins'    => $ }        # if support is indicated by the 'maxbins' capability

OR, if support is indicated by the 'feature-by-id' capability:

 { 'feature_id' => $,
   'types'      => [$,$,...],
   'categories' => [$,$,...],
   'maxbins'    => $ }        # if support is indicated by the 'maxbins' capability

When running in legacy mode, it may also be passed:

 { 'group_id'   => $,
   'types'      => [$,$,...],
   'categories' => [$,$,...],
   'maxbins'    => $ }        # if support is indicated by the 'maxbins' capability

The 'types' and 'categories' parameters are filters. They do not need to be honoured as the das_features method will do this for you. They are included in case you wish to use them to improve performance.

The method must return an array of hash references, i.e. ( {},{}...{} )

Each hash returned represents a single feature and should contain a subset of the following keys and types. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.

 segment                       => $               # segment ID (if not provided)
 id       || feature_id        => $               # feature ID
 label    || feature_label     => $               # feature text label
 start                         => $               # feature start position
 end                           => $               # feature end position
 ori                           => $               # feature strand
 phase                         => $               # feature phase
 type                          => $               # feature type ID
 type_cvid                     => $               # feature type controlled vocabulary ID
 typetxt                       => $               # feature type text label
 typecategory || type_category => $               # feature type category
 typesubparts                  => $               # feature has subparts
 typesuperparts                => $               # feature has superparts
 typereference                 => $               # feature is reference
 method                        => $               # annotation method ID
 method_cvid                   => $               # annotation method controlled vocabulary ID
 method_label                  => $               # annotation method text label
 score                         => $               # annotation score
 note                          => $ or [$,$,$...] # feature text note
 ##########################################################################
 # For one or more links:
 link                          => $ or [$,$,$...] # feature link href
 linktxt                       => $ or [$,$,$...] # feature link label
 # For hash-based links:
 link                          => {
                                   $ => $,        # href => label
                                   ...
                                  }
 ###############################################################################
 # For a single target:
 target_id                     => $               # target ID
 target_start                  => $               # target start position
 target_stop                   => $               # target end position
 targettxt                     => $               # target text label
 # For multiple targets:
 target                        => scalar or [{
                                              id        => $,
                                              start     => $,
                                              stop      => $,
                                              targettxt => $,
                                             },{}...]
 ###############################################################################
 # For hierarchical relationships:
 parent                        => $ or [$,$,$...] # parent feature IDs
 part                          => $ or [$,$,$...] # child feature IDs
 ###############################################################################

When running in legacy mode, the following may also be included:

 # For a single group:
 group_id                      => $               # feature group ID
 grouplabel                    => $               # feature group text label
 grouptype                     => $               # feature group type ID
 groupnote                     => $               # feature group text note
 grouplink                     => $               # feature group ID
 grouplinktxt                  => $               # feature group ID
 # For multiple groups:
 group                         => [{
                                    grouplabel   => $
                                    grouptype    => $
                                    groupnote    => $
                                    grouplink    => $
                                    grouplinktxt => $
                                    note         => $ or [$,$,$...]
                                    target       => [{
                                                      id        => $
                                                      start     => $
                                                      stop      => $
                                                      targettxt => $
                                                     }],
                                   }, {}...]
 ###############################################################################

sequence - (Subclasses only) fetch sequence data

This call is made by das_sequence(). It is passed:

 { 'segment'    => $, 'start' => $, 'end' => $ }

It is expected to return a hash reference:

 {
  seq     => $,
  version => $, # can also be specified with the segment_version method
  label   => $, # optional human readable label
 }

For details of the data constraints refer to the specification on biodas.org.

build_types - (Subclasses only) fetch type data

This call is made by das_types(). If no specific segments are requested by the client, it is passed no arguments. Otherwise it is passed:

 { 'segment'    => $, 'start' => $, 'end' => $ }

It is expected to return an array of hash references, i.e. ( {},{}...{} )

Each hash returned represents a single type and should contain a subset of the following keys and values. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.

 type                                       => $ # required
 type_cvid || c_ontology                    => $
 typetxt   || description                   => $
 category  || typecategory || type_category => $
 count                                      => $

build_entry_points - (Subclasses only) fetch entry_points data

This call is made by das_entry_points(). It is not passed any args

and is expected to return an array of hash references, i.e. ( {},{}...{} )

Each hash returned represents a single entry_point and should contain a subset of the following keys and values. For scalar types (i.e. numbers and strings) refer to the specification on biodas.org.

 segment  => $
 length   => $
 subparts => $
 start    => $
 stop     => $
 ori      => $

build_alignment - (Subclasses only) fetch alignment data

This call is made by das_alignment(). It is passed these arguments:

 (
  $,        # query ID (either subject or alignment, depending on the source)
  $,        # range of rows (X-Y)
  [ $, $ ], # subjects (ID[:X,Y])
  $,        # subject coordinate system
  $         # range of columns (X-Y)
 )

The that the query ID is required; all other arguments are optional. The optional arguments pertain to restricting parts of the alignment(s). This method must perform that restriction and should consider the most efficient mechanism to do so, but default implementations exist if needed (see the restrict_alignment_rows and restrict_alignment_columns methods).

The method is expected to return an array of alignment hash references:

 (
  {
   name        => $,
   description => $,
   type        => $,
   max         => $,
   position    => $,
   alignObj => [
                {
                 id              => $, # internal object ID
                 version         => $,
                 dbSource        => $,
                 dbVersion       => $,
                 dbAccession     => $,
                 chain           => $, # structure chain ID, if applicable
                 dbCoordSys      => $,
                 sequence        => $,
                 aliObjectDetail => [
                                     {
                                      property => $,
                                      value    => $,
                                      dbSource => $,
                                     },
                                    ],
                },
               ],
   scores   => [
                {
                 method => $,
                 score  => $,
                },
               ],
   blocks   => [
                {
                 blockOrder => $,
                 blockScore => $,
                 segments   => [
                                {
                                 id          => $, # internal object ID
                                 start       => $,
                                 end         => $,
                                 orientation => $, # + / - / undef
                                 cigar       => $,
                                },
                               ],
               ],
   geo3D    => [
                {
                 id
                 vector => {
                            x => $,
                            y => $,
                            z => $,
                           },
                 matrix => [
                            [$,$,$], # mat11, mat12, mat13
                            [$,$,$], # mat21, mat22, mat23
                            [$,$,$], # mat31, mat32, mat33
                           ],
                },
               ],
  }
 )

restrict_alignment_rows - Filter an alignment according to row/subject

This method may be called by subclasses in the build_alignment method. It exists as a helper to enable subclasses to easily implement the row filtering capability of the alignment command. It expects these arguments:

 (
  $,        # alignment hashref
  $,        # rows, of format START-END
  [ $, $ ], # subjects, of format ID[:BEFORE,AFTER]
  $         # subject coordinate system
 )

Subclasses can pass these arguments as they are received from the das_alignment method verbatim, without modification. This method will modify the alignment hashref and return.

The algorithm will apply two filters: one for each of the 'subjects' and 'rows' arguments. In the former case, the row identified by a subject ID (looking first at the object's dbAccession and then its internal ID) plus a surrounding range (if specified) will be retained. In the latter case, the specific requested rows will be retained. All other rows are discarded. Note that the filter acts on both the alignObjects and segments within the alignment. If after filtering a block contains no segments, it is not retained.

restrict_alignment_columns - Filter an alignment according to column

This method may be called by subclasses in the build_alignment method. It exists as a helper to enable subclasses to easily implement the column filtering capability of the alignment command. It expects these arguments:

 (
  $,        # alignment hashref
  $,        # cols, of format START-END
 )

Subclasses can pass these arguments as they are received from the das_alignment method verbatim, without modification. This method will modify the alignment hashref and return.

The algorithm will modify the alignment such that only alignment blocks that at least partially lie within the requested range of columns will be retained. Within such blocks, only segments that lie at least partially within the requested range will be retained. Finally, the segment start, end and cigar properties will be adjusted to reflect the new composition of the alignment. Note that the sequence of an alignObject (if present) is never changed - this refers to the entire object rather than a segment of it and is therefore not affected.

build_structure - (Subclasses only) fetch structure data

This call is made by das_structure(). It is passed these arguments:

 (
  $,        # query ID
  [ $, $ ], # chain ID filters
  [ $, $ ], # model number filters
 )

Note that the query ID is required, the other arguments may be empty arrayrefs.

It is expected to return a hash reference representing a structure:

 {
  # Structure objects:
  objects  => [
               dbAccessionId => $, # the ID of the object in the source database
               objectVersion => $, # the version of the object in the source database
               dbSource      => $, # the source database
               dbVersion     => $, # the version of the source database
               dbCoordSys    => $, # the name of the object's coordinate system
               objectDetails => [
                                 source   => $, # the source of the property
                                 property => $, # name
                                 detail   => $, # value
                                ]
              ],
  # Structural chains, containing groups and atoms:
  chains   => [
               id          => $,
               modelNumber => $,
               groups      => [
                               id    => $, # unique identifier in the structure
                               name  => $, # e.g. ALA
                               type  => $, # amino|nucleotide|hetatom
                               icode => $, # insertion code
                               atoms => [
                                         x          => $, # X coordinate
                                         y          => $,
                                         z          => $,
                                         atomId     => $, # unique ID within the structure
                                         atomName   => $, # label, e.g. "CA"
                                         occupancy  => $, # floating point
                                         tempFactor => $, # floating point
                                         altLoc     => $, # conformation ID
                                        ]
                              ],
              ],
  # Atom connections:
  connects => [
               type       => $, # e.g. bond
               atomSerial => $, # source atomId
               atom_ids   => [
                              $, $, $, # target atomId(s)
                             ],
              ],
 }

build_interaction - (Subclasses only) fetch interaction data

This call is made by das_interaction(). It is passed this structure:

 # For request:
 # /interaction?interactor=$;interactor=$;detail=property:$;detail=property:$,value:$
 {
  interactors => [$, $, ..],
  details     => {
                  $ => undef, # property exists
                  $ => $,     # property has a certain value
                 },
 }

It is expected to return a hash reference of interactions and interactors where all the requested interactors are part of the interaction:

 {
  interactors => [
                  {
                   id            => $,
                   label || name => $,
                   dbSource      => $,
                   dbSourceCvId  => $, # controlled vocabulary ID
                   dbVersion     => $,
                   dbAccession   => $,
                   dbCoordSys    => $, # co-ordinate system
                   sequence      => $,
                   details       => [
                                     {
                                      property        => $,
                                      value           => $,
                                      propertyCvId    => $,
                                      valueCvId       => $,
                                      start           => $, 
                                      end             => $,
                                      startStatus     => $,
                                      endStatus       => $,
                                      startStatusCvId => $,
                                      endStatusCvId   => $,
                                     },
                                     ..
                                    ],
                  },
                  ..
                 ],
  interactions => [
                   {
                    label || name => $,
                    dbSource      => $,
                    dbSourceCvId  => $,
                    dbVersion     => $,
                    dbAccession   => $,
                    details       => [
                                      {
                                       property     => $,
                                       value        => $,
                                       propertyCvId => $,
                                       valueCvId    => $,
                                      },
                                      ..
                                     ],
                    participants  => [
                                      {
                                       id      => $,
                                       details => [
                                                   {
                                                    property        => $,
                                                    value           => $,
                                                    propertyCvId    => $,
                                                    valueCvId       => $,
                                                    start           => $,
                                                    end             => $,
                                                    startStatus     => $,
                                                    endStatus       => $,
                                                    startStatusCvId => $,
                                                    endStatusCvId   => $,
                                                   },
                                                   ..
                                                  ],
                                      },
                                      ..
                                     ],
                   },
                   ..
                  ],
 }

build_volmap - (Subclasses only) fetch volume map data

This call is made by das_volmap(). It is passed a single 'query' argument.

It is expected to return a hash reference for a single volume map:

 {
  id      => $,
  class   => $,
  type    => $,
  version => $,
  link    => $,                  # href for data
  linktxt => $,                  # text
  note    => $  OR  [ $, $, .. ]
 }

init_segments - hook for optimising results to be returned.

  By default - do nothing
  Not necessary for most circumstances, but useful for deciding on what sort
  of coordinate system you return the results if more than one type is available.

  $self->init_segments() is called inside das_features() before build_features().

known_segments - returns a list of valid segments that this adaptor knows about

  my @aSegmentNames = $oSourceAdaptor->known_segments();

segment_version - gives the version of a segment (MD5 under certain circumstances) given a segment name

  my $sVersion = $oSourceAdaptor->segment_version($sSegment);

dsn - get accessor for this sourceadaptor's dsn

  my $sDSN = $oSourceAdaptor->dsn();

dsnversion - get accessor for this sourceadaptor's dsn version

  my $sDSNVersion = $oSourceAdaptor->dsnversion();
  
  By default returns $self->{'dsnversion'}, configuration 'dsnversion' setting or '1.0'

dsncreated - get accessor for this sourceadaptor's update time (variable format)

  # e.g. '2007-09-20T15:26:23Z'      -- ISO 8601, Coordinated Universal Time
  # e.g. '2007-09-20T16:26:23+01:00' -- ISO 8601, British Summer Time
  # e.g. '2007-09-20 07:26:23 -08'   -- indicating Pacific Standard Time
  # e.g. 1190301983                  -- UNIX
  # e.g. '2007-09-20'
  my $sDSNCreated = $oSourceAdaptor->dsncreated(); 
  
  By default tries and returns the following:
    1. $self->{'dsncreated'}
    2. configuration 'dsncreated' setting
    3. adaptor's 'last_modified' method (if it exists)
    4. zero (epoch)

dsncreated_unix - this sourceadaptor's update time, in UNIX format

  # e.g. 1190301983
  my $sDSNCreated = $oSourceAdaptor->dsncreated_unix();

dsncreated_iso - this sourceadaptor's update time, in ISO 8601 format

  # e.g. '2007-09-20T15:26:23Z'
  my $sDSNCreated = $oSourceAdaptor->dsncreated_iso();

coordinates - Returns this sourceadaptor's supported coordinate systems

  my $hCoords = $oSourceAdaptor->coordinates();
  
  Hash contains a key-value pair for each coordinate system, the key being
  either the URI or description, and the value being a suitable test range.
  
  By default returns an empty hash reference

_coordinates : Returns this sourceadaptor's supported coordinate systems in "full" format

  my $aCoords = $oSourceAdaptor->_coordinates();
  
  Returns the fully-annotated co-ordinate systems this adaptor supports, as an
  array or array reference (depending on context):
    [
     {
      'description' => 'NCBI_36,Chromosome,Homo sapiens',
      'uri'         => 'http://www.dasregistry.org/dasregistry/coordsys/CS_DS40',
      'taxid'       => '9606',
      'authority'   => 'NCBI',
      'source'      => 'Chromosome',
      'version'     => '36',
      'test_range'  => '1:11000000,12000000',
     },
     {
      ...
     },
    ]
  
  The co-ordinate system details are read in from disk by Bio::Das::ProServer.
  By default returns an empty array.

  DO NOT OVERRIDE THIS METHOD IN SUBCLASSES.

capabilities - Returns this sourceadaptor's supported capabilities

  my $hCapabilities = $oSourceAdaptor->capabilities();
  
  Hash contains a key-value pair for each command, the key being the command
  name, and the value being the implementation version.
  
  By default returns an empty hash.

_capabilities - Returns this sourceadaptor's supported capabilities, as rationalised by ProServer

  my $hCapabilities = $oSourceAdaptor->_capabilities();
  
  Hash contains a key-value pair for each command, the key being the command
  name, and the value being the implementation version.
  
  By default returns an empty hash.

  DO NOT OVERRIDE THIS METHOD IN SUBCLASSES.

properties - Returns custom properties for this sourceadaptor

  my $hProps = $oSourceAdaptor->properties();
  
  Hash contains key-scalar or key-array pairs for custom properties.
  
  By default returns an empty hash reference

start - get accessor for segment start given a segment

  my $sStart = $oSourceAdaptor->start('DYNA_CHICK');

  By default returns 1

end - get accessor for segment end given a segment

  my $sEnd = $oSourceAdaptor->end('DYNA_CHICK');
  
  By default returns $self->length

server_url - Get the URL for the server (not including the /das)

  my $sUrl = $oSourceAdaptor->server_url();

source_url - Get the full URL for the source

  my $sUrl = $oSourceAdaptor->source_url();

hydra - Get the relevant B::D::PS::SourceHydra::<...> configured for this adaptor, if there is one

  my $oHydra = $oSourceAdaptor->hydra();

transport - Build the relevant B::D::PS::SA::Transport::<...> configured for this adaptor

  my $oTransport = $oSourceAdaptor->transport();
  
  OR
  
  my $oTransport1 = $oSourceAdaptor->transport('foo');
  my $oTransport2 = $oSourceAdaptor->transport('bar');

authenticator : Build the B::D::PS::Authenticator::<...> configured for this adaptor

  my $oAuthenticator = $oSourceAdaptor->authenticator();

  Authenticators are built only if explicitly configured in the INI file, e.g.:
  [mysource]
  state         = on
  adaptor       = simple
  authenticator = ip
  
  See L<Bio::Das::ProServer::Authenticator|Bio::Das::ProServer::Authenticator> for more details.

config - get/set config settings for this adaptor

  $oSourceAdaptor->config($oConfig);

  my $oConfig = $oSourceAdaptor->config();

implements - helper to determine if an adaptor implements a request based on its capabilities

  my $bIsImplemented = $oSourceAdaptor->implements($sDASCall); # e.g. $sDASCall = 'sequence'

das_capabilities - DAS-response capabilities header support

  my $sHTTPHeader = $oSourceAdaptor->das_capabilities();

unknown_segment - DAS-response unknown/error segment error response

  my $sXMLResponse = $sa->unknown_segment();

  Reference sources (i.e. those implementing the 'sequence' command) will return an <ERRORSEGMENT> element.
  Annotation sources will return an <UNKNOWNSEGMENT> element.

error_segment - DAS-response error segment error response

  my $sXMLResponse = $sa->error_segment();

  Returns an <ERRORSEGMENT> element.

error_feature - DAS-response unknown feature error

  my $sXMLResponse = $sa->error_feature();

das_features - DAS-response for 'features' request

  my $sXMLResponse = $sa->das_features();

  See the build_features method for details of custom implementations.

das_sequence - DAS-response for sequence request

  my $sXMLResponse = $sa->das_sequence();

  See the sequence method for details of custom implementations.

das_types - DAS-response for 'types' request

  my $sXMLResponse = $sa->das_types();

  See the build_types method for details of custom implementations.

das_entry_points - DAS-response for 'entry_points' request

  my $sXMLResponse = $sa->das_entry_points();

  See the build_entry_points method for details of custom implementations.

das_interaction - DAS-response for 'interaction' request

  my $sXMLResponse = $sa->das_interaction();

  See the build_interaction method for details of custom implementations.

das_volmap - DAS-response for 'volmap' request

  my $sXMLResponse = $sa->das_volmap();

  See the build_volmap method for details of custom implementations.

das_stylesheet - DAS-response for 'stylesheet' request

  my $sXMLResponse = $sa->das_stylesheet();

  By default will use (in order of preference):
    the "stylesheet" INI property (inline XML)
    the "stylesheetfile" INI property (XML file location)
    the "stylesheetfile" INI property, prepended with the "styleshome" property
    a default stylesheet

das_sourcedata - DAS-response for 'sources' request

  my $sXMLResponse = $sa->das_sourcedata();

  Provides information about the DAS source for use in the sources command,
  such as title, description, coordinates and capabilities.

das_dsn - DAS-response (non-standard) for 'dsn' request

  my $sXMLResponse = $sa->das_dsn();

das_xsl - DAS-response (non-standard) for 'xsl' request

  my $sXSLResponse = $sa->das_xsl();

das_alignment - DAS-response for 'alignment' request

  my $sXMLResponse = $sa->das_alignment();

  See the build_alignment method for details of custom implementations.

  Example Response:

<alignment> <alignObject> <alignObjectDetail /> <sequence /> </alignObject> <score/> <block> <segment> <cigar /> </segment> </block> <geo3D> <vector /> <matrix mat11="float" mat12="float" mat13="float" mat21="float" mat22="float" mat23="float" mat31="float" mat32="float" mat33="float" /> </geo3D> </alignment>

_gen_align_object_response

 Title    : _gen_align_object_response
 Function : Formats alignment object into dasalignment xml
 Args     : align data structure
 Returns  : Das Response string encapuslating aliObject

_gen_align_score_response

 Title   : _gen_align_score_response
 Function: Formats input score data structure into dasalignment xml
 Args    : score data structure
 Returns : Das Response string from alignment score

_gen_align_block_response

 Title   : _gen_align_block_response
 Function: Formats an input block data structure into 
         : dasalignment xml
 Args    : block data structure
 Returns : Das Response string from alignmentblock

_gen_align_geo3d_response

  Title    : genAlignGeo3d
  Function : Formats geo3d data structure into alignment matrix xml
  Args     : data structure containing the vector and matrix
  Returns  : String containing the DAS response xml

das_structure

 Title    : das_structure
 Function : This produces the das repsonse for a pdb structure
 Args     : query options.  Currently, this will that query, chain and modelnumber.
          : The only part of the specification that this does not adhere to is the range argument. 
          : However, I think this argument is a potential can of worms!
 returns  : string containing Das repsonse for the pdb structure
 comment  : See http://www.efamily.org.uk/xml/das/documentation/structure.shtml for more information 
          : on the das structure specification.

 Example Response:
<object dbAccessionId="1A4A" intObjectId="1A4A" objectVersion="29-APR-98" dbSource="PDB" dbVersion="20040621" dbCoordSys="PDBresnum,Protein Structure" />
<chain id="A" SwissprotId="null">
  <group name="ALA" type="amino" groupID="1">
    <atom atomID="1" atomName=" N  " x="-19.031" y="16.695" z="3.708" />
    <atom atomID="2" atomName=" CA " x="-20.282" y="16.902" z="4.404" />
    <atom atomID="3" atomName=" C  " x="-20.575" y="18.394" z="4.215" />
    <atom atomID="4" atomName=" O  " x="-20.436" y="19.194" z="5.133" />
    <atom atomID="5" atomName=" CB " x="-20.077" y="16.548" z="5.883" />
    <atom atomID="6" atomName="1H  " x="-18.381" y="17.406" z="4.081" />
    <atom atomID="7" atomName="2H  " x="-18.579" y="15.781" z="3.874" />
    <atom atomID="8" atomName="3H  " x="-19.018" y="16.844" z="2.68" />
  </group>
  <group name="HOH" type="hetatm" groupID="219">
    <atom atomID="3057" atomName=" O  " x="-17.904" y="13.635" z="-7.538" />
    <atom atomID="3058" atomName="1H  " x="-18.717" y="14.098" z="-7.782" />
    <atom atomID="3059" atomName="2H  " x="-17.429" y="13.729" z="-8.371" />
  </group>
</chain>
<connect atomSerial="26" type="bond">
  <atomID atomID="25" />
  <atomID atomID="242" />
</connect>

_gen_object_response

 Title    : _gen_object_response
 Function : Formats the supplied structure object data structure into dasstructure xml
 Args     : object data structure
 Returns  : Das Response string encapuslating 'object'
 Comment  : The object response allows the details of the coordinates to be descriped. For example
          : the fact that the coos are part of a pdb file.

_gen_chain_response

 Title    : _gen_chain_response
 Function : Formats the supplied chain object data structure into dasstructure xml
 Args     : chain data structure
 Returns  : Das Response string encapuslating 'chain'
 Comment  : Chain objects contain all of the atom positions (including hetatoms).
          : The groups are typically residues or ligands.

_gen_connect_response

 Title    : _gen_connect_response
 Function : Formats the supplied connect data structure into dasstructure xml
 Args     : connect data structure
 Returns  : Das Response string encapuslating "connect"
 Comment  : Such objects are specified to enable groups of atoms to be connected together.

cleanup : Post-request garbage collection

CONFIGURATION AND ENVIRONMENT ^

Used within Bio::Das::ProServer::Config, eg/proserver and of course all subclasses.

DIAGNOSTICS ^

set $self->{'debug'} = 1

DEPENDENCIES ^

HTML::Entities
HTTP::Date
English
Carp

INCOMPATIBILITIES ^

None reported

BUGS AND LIMITATIONS ^

None reported

LICENSE AND COPYRIGHT ^

Copyright (c) 2008 The Sanger Institute

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

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