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| CCdd (void) |
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| ~CCdd (void) |
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| CCdd_Base (void) |
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virtual | ~CCdd_Base (void) |
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| DECLARE_INTERNAL_TYPE_INFO () |
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bool | IsSetName (void) const |
| a short name (can be the accession..) Check if a value has been assigned to Name data member. More...
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bool | CanGetName (void) const |
| Check if it is safe to call GetName method. More...
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void | ResetName (void) |
| Reset Name data member. More...
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const TName & | GetName (void) const |
| Get the Name member data. More...
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void | SetName (const TName &value) |
| Assign a value to Name data member. More...
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void | SetName (TName &&value) |
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TName & | SetName (void) |
| Assign a value to Name data member. More...
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bool | IsSetId (void) const |
| this CD's Ids Check if a value has been assigned to Id data member. More...
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bool | CanGetId (void) const |
| Check if it is safe to call GetId method. More...
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void | ResetId (void) |
| Reset Id data member. More...
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const TId & | GetId (void) const |
| Get the Id member data. More...
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void | SetId (TId &value) |
| Assign a value to Id data member. More...
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TId & | SetId (void) |
| Assign a value to Id data member. More...
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bool | IsSetDescription (void) const |
| status, references, etc. More...
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bool | CanGetDescription (void) const |
| Check if it is safe to call GetDescription method. More...
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void | ResetDescription (void) |
| Reset Description data member. More...
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const TDescription & | GetDescription (void) const |
| Get the Description member data. More...
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void | SetDescription (TDescription &value) |
| Assign a value to Description data member. More...
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TDescription & | SetDescription (void) |
| Assign a value to Description data member. More...
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bool | IsSetSeqannot (void) const |
| contains the CD alignment Check if a value has been assigned to Seqannot data member. More...
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bool | CanGetSeqannot (void) const |
| Check if it is safe to call GetSeqannot method. More...
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void | ResetSeqannot (void) |
| Reset Seqannot data member. More...
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const TSeqannot & | GetSeqannot (void) const |
| Get the Seqannot member data. More...
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TSeqannot & | SetSeqannot (void) |
| Assign a value to Seqannot data member. More...
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bool | IsSetFeatures (void) const |
| contains structure alignment data or "core" definitions Check if a value has been assigned to Features data member. More...
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bool | CanGetFeatures (void) const |
| Check if it is safe to call GetFeatures method. More...
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void | ResetFeatures (void) |
| Reset Features data member. More...
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const TFeatures & | GetFeatures (void) const |
| Get the Features member data. More...
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void | SetFeatures (TFeatures &value) |
| Assign a value to Features data member. More...
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TFeatures & | SetFeatures (void) |
| Assign a value to Features data member. More...
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bool | IsSetSequences (void) const |
| store as bioseq-set inside seq-entry Check if a value has been assigned to Sequences data member. More...
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bool | CanGetSequences (void) const |
| Check if it is safe to call GetSequences method. More...
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void | ResetSequences (void) |
| Reset Sequences data member. More...
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const TSequences & | GetSequences (void) const |
| Get the Sequences member data. More...
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void | SetSequences (TSequences &value) |
| Assign a value to Sequences data member. More...
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TSequences & | SetSequences (void) |
| Assign a value to Sequences data member. More...
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bool | IsSetProfile_range (void) const |
| profile for this region only also stores the Seq-id of the master Check if a value has been assigned to Profile_range data member. More...
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bool | CanGetProfile_range (void) const |
| Check if it is safe to call GetProfile_range method. More...
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void | ResetProfile_range (void) |
| Reset Profile_range data member. More...
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const TProfile_range & | GetProfile_range (void) const |
| Get the Profile_range member data. More...
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void | SetProfile_range (TProfile_range &value) |
| Assign a value to Profile_range data member. More...
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TProfile_range & | SetProfile_range (void) |
| Assign a value to Profile_range data member. More...
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bool | IsSetTrunc_master (void) const |
| holds the truncated master, which may be something like a consensus, uses the same sequence coordinate frame as the profile-range Check if a value has been assigned to Trunc_master data member. More...
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bool | CanGetTrunc_master (void) const |
| Check if it is safe to call GetTrunc_master method. More...
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void | ResetTrunc_master (void) |
| Reset Trunc_master data member. More...
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const TTrunc_master & | GetTrunc_master (void) const |
| Get the Trunc_master member data. More...
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void | SetTrunc_master (TTrunc_master &value) |
| Assign a value to Trunc_master data member. More...
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TTrunc_master & | SetTrunc_master (void) |
| Assign a value to Trunc_master data member. More...
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bool | IsSetPosfreq (void) const |
| relative residue frequencies Check if a value has been assigned to Posfreq data member. More...
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bool | CanGetPosfreq (void) const |
| Check if it is safe to call GetPosfreq method. More...
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void | ResetPosfreq (void) |
| Reset Posfreq data member. More...
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const TPosfreq & | GetPosfreq (void) const |
| Get the Posfreq member data. More...
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void | SetPosfreq (TPosfreq &value) |
| Assign a value to Posfreq data member. More...
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TPosfreq & | SetPosfreq (void) |
| Assign a value to Posfreq data member. More...
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bool | IsSetScoremat (void) const |
| Position dependent score matrix Check if a value has been assigned to Scoremat data member. More...
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bool | CanGetScoremat (void) const |
| Check if it is safe to call GetScoremat method. More...
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void | ResetScoremat (void) |
| Reset Scoremat data member. More...
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const TScoremat & | GetScoremat (void) const |
| Get the Scoremat member data. More...
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void | SetScoremat (TScoremat &value) |
| Assign a value to Scoremat data member. More...
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TScoremat & | SetScoremat (void) |
| Assign a value to Scoremat data member. More...
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bool | IsSetDistance (void) const |
| pairwise distances for all seqs. More...
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bool | CanGetDistance (void) const |
| Check if it is safe to call GetDistance method. More...
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void | ResetDistance (void) |
| Reset Distance data member. More...
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const TDistance & | GetDistance (void) const |
| Get the Distance member data. More...
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void | SetDistance (TDistance &value) |
| Assign a value to Distance data member. More...
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TDistance & | SetDistance (void) |
| Assign a value to Distance data member. More...
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bool | IsSetParent (void) const |
| this CD is the result of a split Check if a value has been assigned to Parent data member. More...
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bool | CanGetParent (void) const |
| Check if it is safe to call GetParent method. More...
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void | ResetParent (void) |
| Reset Parent data member. More...
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const TParent & | GetParent (void) const |
| Get the Parent member data. More...
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void | SetParent (TParent &value) |
| Assign a value to Parent data member. More...
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TParent & | SetParent (void) |
| Assign a value to Parent data member. More...
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bool | IsSetChildren (void) const |
| this CD has been split, not used Check if a value has been assigned to Children data member. More...
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bool | CanGetChildren (void) const |
| Check if it is safe to call GetChildren method. More...
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void | ResetChildren (void) |
| Reset Children data member. More...
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const TChildren & | GetChildren (void) const |
| Get the Children member data. More...
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void | SetChildren (TChildren &value) |
| Assign a value to Children data member. More...
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TChildren & | SetChildren (void) |
| Assign a value to Children data member. More...
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bool | IsSetSiblings (void) const |
| related CDs (common hits), clusters Check if a value has been assigned to Siblings data member. More...
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bool | CanGetSiblings (void) const |
| Check if it is safe to call GetSiblings method. More...
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void | ResetSiblings (void) |
| Reset Siblings data member. More...
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const TSiblings & | GetSiblings (void) const |
| Get the Siblings member data. More...
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void | SetSiblings (TSiblings &value) |
| Assign a value to Siblings data member. More...
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TSiblings & | SetSiblings (void) |
| Assign a value to Siblings data member. More...
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bool | IsSetNeighbors (void) const |
| co-occurring CDs, not used Check if a value has been assigned to Neighbors data member. More...
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bool | CanGetNeighbors (void) const |
| Check if it is safe to call GetNeighbors method. More...
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void | ResetNeighbors (void) |
| Reset Neighbors data member. More...
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const TNeighbors & | GetNeighbors (void) const |
| Get the Neighbors member data. More...
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void | SetNeighbors (TNeighbors &value) |
| Assign a value to Neighbors data member. More...
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TNeighbors & | SetNeighbors (void) |
| Assign a value to Neighbors data member. More...
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bool | IsSetPending (void) const |
| contains alignments from update or "lower panel" Check if a value has been assigned to Pending data member. More...
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bool | CanGetPending (void) const |
| Check if it is safe to call GetPending method. More...
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void | ResetPending (void) |
| Reset Pending data member. More...
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const TPending & | GetPending (void) const |
| Get the Pending member data. More...
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TPending & | SetPending (void) |
| Assign a value to Pending data member. More...
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bool | IsSetRejects (void) const |
| SeqIds of rejected CD- members, ignore in update Check if a value has been assigned to Rejects data member. More...
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bool | CanGetRejects (void) const |
| Check if it is safe to call GetRejects method. More...
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void | ResetRejects (void) |
| Reset Rejects data member. More...
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const TRejects & | GetRejects (void) const |
| Get the Rejects member data. More...
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TRejects & | SetRejects (void) |
| Assign a value to Rejects data member. More...
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bool | IsSetMaster3d (void) const |
| record if CD has a 3D representative Check if a value has been assigned to Master3d data member. More...
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bool | CanGetMaster3d (void) const |
| Check if it is safe to call GetMaster3d method. More...
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void | ResetMaster3d (void) |
| Reset Master3d data member. More...
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const TMaster3d & | GetMaster3d (void) const |
| Get the Master3d member data. More...
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TMaster3d & | SetMaster3d (void) |
| Assign a value to Master3d data member. More...
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bool | IsSetAlignannot (void) const |
| alignment annotation Check if a value has been assigned to Alignannot data member. More...
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bool | CanGetAlignannot (void) const |
| Check if it is safe to call GetAlignannot method. More...
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void | ResetAlignannot (void) |
| Reset Alignannot data member. More...
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const TAlignannot & | GetAlignannot (void) const |
| Get the Alignannot member data. More...
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void | SetAlignannot (TAlignannot &value) |
| Assign a value to Alignannot data member. More...
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TAlignannot & | SetAlignannot (void) |
| Assign a value to Alignannot data member. More...
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bool | IsSetStyle_dictionary (void) const |
| record rendering styles Check if a value has been assigned to Style_dictionary data member. More...
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bool | CanGetStyle_dictionary (void) const |
| Check if it is safe to call GetStyle_dictionary method. More...
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void | ResetStyle_dictionary (void) |
| Reset Style_dictionary data member. More...
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const TStyle_dictionary & | GetStyle_dictionary (void) const |
| Get the Style_dictionary member data. More...
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void | SetStyle_dictionary (TStyle_dictionary &value) |
| Assign a value to Style_dictionary data member. More...
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TStyle_dictionary & | SetStyle_dictionary (void) |
| Assign a value to Style_dictionary data member. More...
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bool | IsSetUser_annotations (void) const |
| user annotations in Cn3D Check if a value has been assigned to User_annotations data member. More...
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bool | CanGetUser_annotations (void) const |
| Check if it is safe to call GetUser_annotations method. More...
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void | ResetUser_annotations (void) |
| Reset User_annotations data member. More...
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const TUser_annotations & | GetUser_annotations (void) const |
| Get the User_annotations member data. More...
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void | SetUser_annotations (TUser_annotations &value) |
| Assign a value to User_annotations data member. More...
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TUser_annotations & | SetUser_annotations (void) |
| Assign a value to User_annotations data member. More...
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bool | IsSetAncestors (void) const |
| list of parents Check if a value has been assigned to Ancestors data member. More...
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bool | CanGetAncestors (void) const |
| Check if it is safe to call GetAncestors method. More...
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void | ResetAncestors (void) |
| Reset Ancestors data member. More...
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const TAncestors & | GetAncestors (void) const |
| Get the Ancestors member data. More...
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TAncestors & | SetAncestors (void) |
| Assign a value to Ancestors data member. More...
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bool | IsSetScoreparams (void) const |
| Check if a value has been assigned to Scoreparams data member. More...
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bool | CanGetScoreparams (void) const |
| Check if it is safe to call GetScoreparams method. More...
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void | ResetScoreparams (void) |
| Reset Scoreparams data member. More...
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const TScoreparams & | GetScoreparams (void) const |
| Get the Scoreparams member data. More...
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void | SetScoreparams (TScoreparams &value) |
| Assign a value to Scoreparams data member. More...
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TScoreparams & | SetScoreparams (void) |
| Assign a value to Scoreparams data member. More...
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bool | IsSetSeqtree (void) const |
| Check if a value has been assigned to Seqtree data member. More...
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bool | CanGetSeqtree (void) const |
| Check if it is safe to call GetSeqtree method. More...
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void | ResetSeqtree (void) |
| Reset Seqtree data member. More...
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const TSeqtree & | GetSeqtree (void) const |
| Get the Seqtree member data. More...
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void | SetSeqtree (TSeqtree &value) |
| Assign a value to Seqtree data member. More...
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TSeqtree & | SetSeqtree (void) |
| Assign a value to Seqtree data member. More...
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virtual void | Reset (void) |
| Reset the whole object. More...
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| CSerialObject (void) |
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virtual | ~CSerialObject (void) |
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virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
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virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More...
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virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More...
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virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More...
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void | ThrowUnassigned (TMemberIndex index) const |
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void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
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bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More...
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const string & | GetNamespaceName (void) const |
| Get namespace name. More...
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bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More...
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const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More...
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| CObject (void) |
| Constructor. More...
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| CObject (const CObject &src) |
| Copy constructor. More...
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virtual | ~CObject (void) |
| Destructor. More...
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CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More...
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bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More...
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bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More...
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bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More...
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bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More...
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void | AddReference (void) const |
| Add reference to object. More...
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void | RemoveReference (void) const |
| Remove reference to object. More...
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void | ReleaseReference (void) const |
| Remove reference without deleting object. More...
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virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More...
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virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More...
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void * | operator new (size_t size) |
| Define new operator for memory allocation. More...
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void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More...
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void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More...
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void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More...
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void * | operator new (size_t size, void *place) |
| Define new operator. More...
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void | operator delete (void *ptr, void *place) |
| Define delete operator. More...
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void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More...
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void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More...
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| CDebugDumpable (void) |
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virtual | ~CDebugDumpable (void) |
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void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
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void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
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void | DumpToConsole (void) const |
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