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| CParameters_Base (void) |
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virtual | ~CParameters_Base (void) |
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| DECLARE_INTERNAL_TYPE_INFO () |
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bool | IsSetMatrix (void) const |
| Matrix used (-M) Check if a value has been assigned to Matrix data member. More...
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bool | CanGetMatrix (void) const |
| Check if it is safe to call GetMatrix method. More...
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void | ResetMatrix (void) |
| Reset Matrix data member. More...
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const TMatrix & | GetMatrix (void) const |
| Get the Matrix member data. More...
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void | SetMatrix (const TMatrix &value) |
| Assign a value to Matrix data member. More...
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void | SetMatrix (TMatrix &&value) |
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TMatrix & | SetMatrix (void) |
| Assign a value to Matrix data member. More...
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bool | IsSetExpect (void) const |
| Expectation threshold (-e) Check if a value has been assigned to Expect data member. More...
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bool | CanGetExpect (void) const |
| Check if it is safe to call GetExpect method. More...
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void | ResetExpect (void) |
| Reset Expect data member. More...
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TExpect | GetExpect (void) const |
| Get the Expect member data. More...
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void | SetExpect (TExpect value) |
| Assign a value to Expect data member. More...
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TExpect & | SetExpect (void) |
| Assign a value to Expect data member. More...
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bool | IsSetInclude (void) const |
| Inclusion threshold (-h) Check if a value has been assigned to Include data member. More...
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bool | CanGetInclude (void) const |
| Check if it is safe to call GetInclude method. More...
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void | ResetInclude (void) |
| Reset Include data member. More...
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TInclude | GetInclude (void) const |
| Get the Include member data. More...
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void | SetInclude (TInclude value) |
| Assign a value to Include data member. More...
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TInclude & | SetInclude (void) |
| Assign a value to Include data member. More...
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bool | IsSetSc_match (void) const |
| match score for NT (-r) Check if a value has been assigned to Sc_match data member. More...
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bool | CanGetSc_match (void) const |
| Check if it is safe to call GetSc_match method. More...
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void | ResetSc_match (void) |
| Reset Sc_match data member. More...
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TSc_match | GetSc_match (void) const |
| Get the Sc_match member data. More...
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void | SetSc_match (TSc_match value) |
| Assign a value to Sc_match data member. More...
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TSc_match & | SetSc_match (void) |
| Assign a value to Sc_match data member. More...
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bool | IsSetSc_mismatch (void) const |
| mismatch score for NT (-q) Check if a value has been assigned to Sc_mismatch data member. More...
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bool | CanGetSc_mismatch (void) const |
| Check if it is safe to call GetSc_mismatch method. More...
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void | ResetSc_mismatch (void) |
| Reset Sc_mismatch data member. More...
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TSc_mismatch | GetSc_mismatch (void) const |
| Get the Sc_mismatch member data. More...
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void | SetSc_mismatch (TSc_mismatch value) |
| Assign a value to Sc_mismatch data member. More...
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TSc_mismatch & | SetSc_mismatch (void) |
| Assign a value to Sc_mismatch data member. More...
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bool | IsSetGap_open (void) const |
| Gap opening cost (-G) Check if a value has been assigned to Gap_open data member. More...
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bool | CanGetGap_open (void) const |
| Check if it is safe to call GetGap_open method. More...
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void | ResetGap_open (void) |
| Reset Gap_open data member. More...
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TGap_open | GetGap_open (void) const |
| Get the Gap_open member data. More...
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void | SetGap_open (TGap_open value) |
| Assign a value to Gap_open data member. More...
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TGap_open & | SetGap_open (void) |
| Assign a value to Gap_open data member. More...
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bool | IsSetGap_extend (void) const |
| Gap extension cost (-E) Check if a value has been assigned to Gap_extend data member. More...
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bool | CanGetGap_extend (void) const |
| Check if it is safe to call GetGap_extend method. More...
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void | ResetGap_extend (void) |
| Reset Gap_extend data member. More...
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TGap_extend | GetGap_extend (void) const |
| Get the Gap_extend member data. More...
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void | SetGap_extend (TGap_extend value) |
| Assign a value to Gap_extend data member. More...
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TGap_extend & | SetGap_extend (void) |
| Assign a value to Gap_extend data member. More...
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bool | IsSetFilter (void) const |
| Filtering options (-F) Check if a value has been assigned to Filter data member. More...
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bool | CanGetFilter (void) const |
| Check if it is safe to call GetFilter method. More...
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void | ResetFilter (void) |
| Reset Filter data member. More...
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const TFilter & | GetFilter (void) const |
| Get the Filter member data. More...
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void | SetFilter (const TFilter &value) |
| Assign a value to Filter data member. More...
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void | SetFilter (TFilter &&value) |
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TFilter & | SetFilter (void) |
| Assign a value to Filter data member. More...
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bool | IsSetPattern (void) const |
| PHI-BLAST pattern Check if a value has been assigned to Pattern data member. More...
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bool | CanGetPattern (void) const |
| Check if it is safe to call GetPattern method. More...
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void | ResetPattern (void) |
| Reset Pattern data member. More...
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const TPattern & | GetPattern (void) const |
| Get the Pattern member data. More...
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void | SetPattern (const TPattern &value) |
| Assign a value to Pattern data member. More...
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void | SetPattern (TPattern &&value) |
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TPattern & | SetPattern (void) |
| Assign a value to Pattern data member. More...
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bool | IsSetEntrez_query (void) const |
| Limit of request to Entrez query Check if a value has been assigned to Entrez_query data member. More...
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bool | CanGetEntrez_query (void) const |
| Check if it is safe to call GetEntrez_query method. More...
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void | ResetEntrez_query (void) |
| Reset Entrez_query data member. More...
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const TEntrez_query & | GetEntrez_query (void) const |
| Get the Entrez_query member data. More...
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void | SetEntrez_query (const TEntrez_query &value) |
| Assign a value to Entrez_query data member. More...
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void | SetEntrez_query (TEntrez_query &&value) |
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TEntrez_query & | SetEntrez_query (void) |
| Assign a value to Entrez_query data member. More...
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virtual void | Reset (void) |
| Reset the whole object. More...
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| CParameters_Base (void) |
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virtual | ~CParameters_Base (void) |
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| DECLARE_INTERNAL_TYPE_INFO () |
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bool | IsSetMatrix (void) const |
| Matrix used (-M) Check if a value has been assigned to Matrix data member. More...
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bool | CanGetMatrix (void) const |
| Check if it is safe to call GetMatrix method. More...
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void | ResetMatrix (void) |
| Reset Matrix data member. More...
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const TMatrix & | GetMatrix (void) const |
| Get the Matrix member data. More...
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void | SetMatrix (const TMatrix &value) |
| Assign a value to Matrix data member. More...
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void | SetMatrix (TMatrix &&value) |
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TMatrix & | SetMatrix (void) |
| Assign a value to Matrix data member. More...
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bool | IsSetExpect (void) const |
| Expectation threshold (-e) Check if a value has been assigned to Expect data member. More...
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bool | CanGetExpect (void) const |
| Check if it is safe to call GetExpect method. More...
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void | ResetExpect (void) |
| Reset Expect data member. More...
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TExpect | GetExpect (void) const |
| Get the Expect member data. More...
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void | SetExpect (TExpect value) |
| Assign a value to Expect data member. More...
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TExpect & | SetExpect (void) |
| Assign a value to Expect data member. More...
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bool | IsSetInclude (void) const |
| Inclusion threshold (-h) Check if a value has been assigned to Include data member. More...
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bool | CanGetInclude (void) const |
| Check if it is safe to call GetInclude method. More...
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void | ResetInclude (void) |
| Reset Include data member. More...
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TInclude | GetInclude (void) const |
| Get the Include member data. More...
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void | SetInclude (TInclude value) |
| Assign a value to Include data member. More...
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TInclude & | SetInclude (void) |
| Assign a value to Include data member. More...
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bool | IsSetSc_match (void) const |
| match score for NT (-r) Check if a value has been assigned to Sc_match data member. More...
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bool | CanGetSc_match (void) const |
| Check if it is safe to call GetSc_match method. More...
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void | ResetSc_match (void) |
| Reset Sc_match data member. More...
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TSc_match | GetSc_match (void) const |
| Get the Sc_match member data. More...
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void | SetSc_match (TSc_match value) |
| Assign a value to Sc_match data member. More...
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TSc_match & | SetSc_match (void) |
| Assign a value to Sc_match data member. More...
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bool | IsSetSc_mismatch (void) const |
| mismatch score for NT (-q) Check if a value has been assigned to Sc_mismatch data member. More...
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bool | CanGetSc_mismatch (void) const |
| Check if it is safe to call GetSc_mismatch method. More...
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void | ResetSc_mismatch (void) |
| Reset Sc_mismatch data member. More...
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TSc_mismatch | GetSc_mismatch (void) const |
| Get the Sc_mismatch member data. More...
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void | SetSc_mismatch (TSc_mismatch value) |
| Assign a value to Sc_mismatch data member. More...
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TSc_mismatch & | SetSc_mismatch (void) |
| Assign a value to Sc_mismatch data member. More...
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bool | IsSetGap_open (void) const |
| Gap opening cost (-G) Check if a value has been assigned to Gap_open data member. More...
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bool | CanGetGap_open (void) const |
| Check if it is safe to call GetGap_open method. More...
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void | ResetGap_open (void) |
| Reset Gap_open data member. More...
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TGap_open | GetGap_open (void) const |
| Get the Gap_open member data. More...
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void | SetGap_open (TGap_open value) |
| Assign a value to Gap_open data member. More...
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TGap_open & | SetGap_open (void) |
| Assign a value to Gap_open data member. More...
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bool | IsSetGap_extend (void) const |
| Gap extension cost (-E) Check if a value has been assigned to Gap_extend data member. More...
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bool | CanGetGap_extend (void) const |
| Check if it is safe to call GetGap_extend method. More...
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void | ResetGap_extend (void) |
| Reset Gap_extend data member. More...
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TGap_extend | GetGap_extend (void) const |
| Get the Gap_extend member data. More...
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void | SetGap_extend (TGap_extend value) |
| Assign a value to Gap_extend data member. More...
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TGap_extend & | SetGap_extend (void) |
| Assign a value to Gap_extend data member. More...
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bool | IsSetFilter (void) const |
| Filtering options (-F) Check if a value has been assigned to Filter data member. More...
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bool | CanGetFilter (void) const |
| Check if it is safe to call GetFilter method. More...
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void | ResetFilter (void) |
| Reset Filter data member. More...
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const TFilter & | GetFilter (void) const |
| Get the Filter member data. More...
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void | SetFilter (const TFilter &value) |
| Assign a value to Filter data member. More...
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void | SetFilter (TFilter &&value) |
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TFilter & | SetFilter (void) |
| Assign a value to Filter data member. More...
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bool | IsSetPattern (void) const |
| PHI-BLAST pattern Check if a value has been assigned to Pattern data member. More...
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bool | CanGetPattern (void) const |
| Check if it is safe to call GetPattern method. More...
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void | ResetPattern (void) |
| Reset Pattern data member. More...
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const TPattern & | GetPattern (void) const |
| Get the Pattern member data. More...
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void | SetPattern (const TPattern &value) |
| Assign a value to Pattern data member. More...
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void | SetPattern (TPattern &&value) |
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TPattern & | SetPattern (void) |
| Assign a value to Pattern data member. More...
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bool | IsSetEntrez_query (void) const |
| Limit of request to Entrez query Check if a value has been assigned to Entrez_query data member. More...
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bool | CanGetEntrez_query (void) const |
| Check if it is safe to call GetEntrez_query method. More...
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void | ResetEntrez_query (void) |
| Reset Entrez_query data member. More...
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const TEntrez_query & | GetEntrez_query (void) const |
| Get the Entrez_query member data. More...
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void | SetEntrez_query (const TEntrez_query &value) |
| Assign a value to Entrez_query data member. More...
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void | SetEntrez_query (TEntrez_query &&value) |
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TEntrez_query & | SetEntrez_query (void) |
| Assign a value to Entrez_query data member. More...
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bool | IsSetCbs (void) const |
| composition-based stats (numbers correspond to numbering in stand-alone application parameter -comp_based_stats). More...
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bool | CanGetCbs (void) const |
| Check if it is safe to call GetCbs method. More...
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void | ResetCbs (void) |
| Reset Cbs data member. More...
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TCbs | GetCbs (void) const |
| Get the Cbs member data. More...
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void | SetCbs (TCbs value) |
| Assign a value to Cbs data member. More...
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TCbs & | SetCbs (void) |
| Assign a value to Cbs data member. More...
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bool | IsSetQuery_gencode (void) const |
| genetic code for query (blastx or tblastx) Check if a value has been assigned to Query_gencode data member. More...
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bool | CanGetQuery_gencode (void) const |
| Check if it is safe to call GetQuery_gencode method. More...
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void | ResetQuery_gencode (void) |
| Reset Query_gencode data member. More...
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TQuery_gencode | GetQuery_gencode (void) const |
| Get the Query_gencode member data. More...
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void | SetQuery_gencode (TQuery_gencode value) |
| Assign a value to Query_gencode data member. More...
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TQuery_gencode & | SetQuery_gencode (void) |
| Assign a value to Query_gencode data member. More...
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bool | IsSetDb_gencode (void) const |
| genetic code for db or subjects (tblastn or tblastx) Check if a value has been assigned to Db_gencode data member. More...
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bool | CanGetDb_gencode (void) const |
| Check if it is safe to call GetDb_gencode method. More...
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void | ResetDb_gencode (void) |
| Reset Db_gencode data member. More...
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TDb_gencode | GetDb_gencode (void) const |
| Get the Db_gencode member data. More...
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void | SetDb_gencode (TDb_gencode value) |
| Assign a value to Db_gencode data member. More...
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TDb_gencode & | SetDb_gencode (void) |
| Assign a value to Db_gencode data member. More...
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bool | IsSetBl2seq_mode (void) const |
| bl2seq mode Check if a value has been assigned to Bl2seq_mode data member. More...
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bool | CanGetBl2seq_mode (void) const |
| Check if it is safe to call GetBl2seq_mode method. More...
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void | ResetBl2seq_mode (void) |
| Reset Bl2seq_mode data member. More...
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const TBl2seq_mode & | GetBl2seq_mode (void) const |
| Get the Bl2seq_mode member data. More...
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void | SetBl2seq_mode (const TBl2seq_mode &value) |
| Assign a value to Bl2seq_mode data member. More...
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void | SetBl2seq_mode (TBl2seq_mode &&value) |
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TBl2seq_mode & | SetBl2seq_mode (void) |
| Assign a value to Bl2seq_mode 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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