block_multiple_alignment.hpp

ncbi源码

    // intended for volatile storage of row-associated info (e.g. for alignment scores, etc.)
    mutable std::vector < double > rowDoubles;
    mutable std::vector < std::string > rowStrings;

    // for flagging residues (e.g. for geometry violations)
    typedef std::vector < std::vector < bool > > RowSeqIndexFlags;
    RowSeqIndexFlags geometryViolations;
    bool showGeometryViolations;

public:

    // NULL if block before is aligned; if NULL passed, retrieves last block (if unaligned; else NULL)
    const UnalignedBlock * GetUnalignedBlockBefore(const UngappedAlignedBlock *aBlock) const;

    int NBlocks(void) const { return blocks.size(); }
    int NAlignedBlocks(void) const;
    int NRows(void) const { return sequences->size(); }
    int AlignmentWidth(void) const { return totalWidth; }

    // return a number from 1..n for aligned blocks, -1 for unaligned
    int GetAlignedBlockNumber(int alignmentIndex) const { return blockMap[alignmentIndex].alignedBlockNum; }

    // for storing/querying info
    double GetRowDouble(int row) const { return rowDoubles[row]; }
    void SetRowDouble(int row, double value) const { rowDoubles[row] = value; }
    const std::string& GetRowStatusLine(int row) const { return rowStrings[row]; }
    void SetRowStatusLine(int row, const std::string& value) const { rowStrings[row] = value; }

    // empties all rows' infos
    void ClearRowInfo(void) const
    {
        for (int r=0; r<NRows(); ++r) {
            rowDoubles[r] = 0.0;
            rowStrings[r].erase();
        }
    }

    // kludge for now for storing allowed alignment regions, e.g. when demoted from multiple.
    // (only two ranges for now, since this is used only with pairwise alignments)
    int alignMasterFrom, alignMasterTo, alignSlaveFrom, alignSlaveTo;
};


// static function to create Seq-aligns out of multiple
ncbi::objects::CSeq_align * CreatePairwiseSeqAlignFromMultipleRow(const BlockMultipleAlignment *multiple,
    const BlockMultipleAlignment::UngappedAlignedBlockList& blocks, int slaveRow);


// base class for Block - BlockMultipleAlignment is made up of a list of these
class Block
{
public:
    int width;

    virtual bool IsAligned(void) const = 0;

    typedef struct {
        int from, to;
    } Range;

    // get sequence index for a column, which must be in block range (0 ... width-1)
    virtual int GetIndexAt(int blockColumn, int row,
        BlockMultipleAlignment::eUnalignedJustification justification) const = 0;

    // delete a row
    virtual void DeleteRow(int row) = 0;
    virtual void DeleteRows(std::vector < bool >& removeRows, int nToRemove) = 0;

    // makes a new copy of itself
    virtual Block * Clone(const BlockMultipleAlignment *newMultiple) const = 0;

protected:
    Block(const BlockMultipleAlignment *multiple) :
        parentAlignment(multiple), ranges(multiple->NRows()) { }

    typedef std::vector < Range > RangeList;
    RangeList ranges;

    const BlockMultipleAlignment *parentAlignment;

public:
    virtual ~Block(void) { }    // virtual destructor for base class

    bool IsFrom(const BlockMultipleAlignment *alignment) const { return (alignment == parentAlignment); }

    // given a row number (from 0 ... nSequences-1), give the sequence range covered by this block
    const Range* GetRangeOfRow(int row) const { return &(ranges[row]); }

    // set range
    void SetRangeOfRow(int row, int from, int to)
    {
        ranges[row].from = from;
        ranges[row].to = to;
    }

    // resize - add new (empty) rows at end
    void AddRows(int nNewRows) { ranges.resize(ranges.size() + nNewRows); }

    int NSequences(void) const { return ranges.size(); }
};


// a gapless aligned block; width must be >= 1
class UngappedAlignedBlock : public Block
{
public:
    UngappedAlignedBlock(const BlockMultipleAlignment *multiple) : Block(multiple) { }

    bool IsAligned(void) const { return true; }

    int GetIndexAt(int blockColumn, int row,
        BlockMultipleAlignment::eUnalignedJustification justification =
            BlockMultipleAlignment::eCenter) const  // justification ignored for aligned block
        { return (GetRangeOfRow(row)->from + blockColumn); }

    char GetCharacterAt(int blockColumn, int row) const;

    void DeleteRow(int row);
    void DeleteRows(std::vector < bool >& removeRows, int nToRemove);

    Block * Clone(const BlockMultipleAlignment *newMultiple) const;
};


// an unaligned block; max width of block must be >=1, but range over any given
// sequence can be length 0 (but not <0). If length 0, "to" is the residue after
// the block, and "from" (=to - 1) is the residue before.
class UnalignedBlock : public Block
{
public:
    UnalignedBlock(const BlockMultipleAlignment *multiple) : Block(multiple) { }

    void Resize(void);  // recompute block width from current ranges

    bool IsAligned(void) const { return false; }

    int GetIndexAt(int blockColumn, int row,
        BlockMultipleAlignment::eUnalignedJustification justification) const;

    void DeleteRow(int row);
    void DeleteRows(std::vector < bool >& removeRows, int nToRemove);

    Block * Clone(const BlockMultipleAlignment *newMultiple) const;
};

END_SCOPE(Cn3D)

#endif // CN3D_BLOCK_MULTIPLE_ALIGNMENT__HPP

/*
* ---------------------------------------------------------------------------
* $Log: block_multiple_alignment.hpp,v $
* Revision 1000.2  2004/04/12 17:30:52  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.40
*
* Revision 1.40  2004/03/15 17:17:56  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.39  2004/02/19 17:04:44  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.38  2003/11/06 18:52:31  thiessen
* make geometry violations shown on/off; allow multiple pmid entry in ref dialog
*
* Revision 1.37  2003/07/14 18:37:07  thiessen
* change GetUngappedAlignedBlocks() param types; other syntax changes
*
* Revision 1.36  2003/02/03 19:20:01  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.35  2003/01/31 17:18:58  thiessen
* many small additions and changes...
*
* Revision 1.34  2003/01/28 21:07:56  thiessen
* add block fit coloring algorithm; tweak row dragging; fix style bug
*
* Revision 1.33  2003/01/23 20:03:05  thiessen
* add BLAST Neighbor algorithm
*
* Revision 1.32  2003/01/22 14:47:30  thiessen
* cache PSSM in BlockMultipleAlignment
*
* Revision 1.31  2002/10/23 01:29:25  thiessen
* fix block cache bug
*
* Revision 1.30  2002/07/26 15:28:44  thiessen
* add Alejandro's block alignment algorithm
*
* Revision 1.29  2002/06/13 13:32:38  thiessen
* add self-hit calculation
*
* Revision 1.28  2002/05/17 19:10:27  thiessen
* preliminary range restriction for BLAST/PSSM
*
* Revision 1.27  2002/03/28 14:06:02  thiessen
* preliminary BLAST/PSSM ; new CD startup style
*
* Revision 1.26  2002/02/21 22:01:49  thiessen
* remember alignment range on demotion
*
* Revision 1.25  2002/02/19 14:59:38  thiessen
* add CDD reject and purge sequence
*
* Revision 1.24  2002/02/05 18:53:24  thiessen
* scroll to residue in sequence windows when selected in structure window
*
* Revision 1.23  2001/09/27 15:36:47  thiessen
* decouple sequence import and BLAST
*
* Revision 1.22  2001/08/29 20:03:27  juran
* Heed warnings via static_cast.
*
* Revision 1.21  2001/08/15 20:52:57  juran
* Heed warnings.
*
* Revision 1.20  2001/07/19 19:12:46  thiessen
* working CDD alignment annotator ; misc tweaks
*
* Revision 1.19  2001/07/10 16:39:32  thiessen
* change selection control keys; add CDD name/notes dialogs
*
* Revision 1.18  2001/06/21 02:01:06  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.17  2001/06/02 17:22:58  thiessen
* fixes for GCC
*
* Revision 1.16  2001/06/01 13:35:39  thiessen
* add aligned block number to status line
*
* Revision 1.15  2001/05/17 18:34:00  thiessen
* spelling fixes; change dialogs to inherit from wxDialog
*
* Revision 1.14  2001/05/11 02:10:04  thiessen
* add better merge fail indicators; tweaks to windowing/taskbar
*
* Revision 1.13  2001/05/09 17:14:51  thiessen
* add automatic block removal upon demotion
*
* Revision 1.12  2001/05/02 13:46:15  thiessen
* major revision of stuff relating to saving of updates; allow stored null-alignments
*
* Revision 1.11  2001/04/05 22:54:50  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.10  2001/04/04 00:27:21  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.9  2001/03/30 03:07:08  thiessen
* add threader score calculation & sorting
*
* Revision 1.8  2001/03/22 00:32:35  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.7  2001/03/09 15:48:42  thiessen
* major changes to add initial update viewer
*
* Revision 1.6  2001/03/06 20:20:43  thiessen
* progress towards >1 alignment in a SequenceDisplay ; misc minor fixes
*
* Revision 1.5  2001/02/13 01:03:03  thiessen
* backward-compatible domain ID's in output; add ability to delete rows
*
* Revision 1.4  2001/02/02 20:17:42  thiessen
* can read in CDD with multi-structure but no struct. alignments
*
* Revision 1.3  2001/01/26 19:30:37  thiessen
* limit undo stack size ; fix memory leak
*
* Revision 1.2  2000/12/15 15:52:08  thiessen
* show/hide system installed
*
* Revision 1.1  2000/11/30 15:49:06  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
*/