cn3d_ba_interface.cpp

ncbi源码

                if (nRowsAddedToMultiple)
                    (*nRowsAddedToMultiple)++;
                else
                    ERRORMSG("BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment() "
                        "called with merge on, but NULL nRowsAddedToMultiple pointer");
                // recalculate PSSM
                dpPSSM = multiple->GetPSSM();

            } else {
                newAlignments->push_back(dpAlignment);
            }
        }

        // no alignment or block aligner failed - add old alignment to list so it doesn't get lost
        else {
            string status;
            if (dpStatus == STRUCT_DP_NO_ALIGNMENT) {
                WARNINGMSG("block aligner found no significant alignment - current alignment unchanged");
                status = "alignment unchanged";
            } else {
                WARNINGMSG("block aligner encountered a problem - current alignment unchanged");
                errorsEncountered = true;
                status = "block aligner error!";
            }
            BlockMultipleAlignment *newAlignment = (*s)->Clone();
            newAlignment->SetRowDouble(0, -1.0);
            newAlignment->SetRowDouble(1, -1.0);
            newAlignment->SetRowStatusLine(0, status);
            newAlignment->SetRowStatusLine(1, status);
            newAlignments->push_back(newAlignment);
        }

        // cleanup
        DP_DestroyAlignmentResult(dpResult);
    }

    if (errorsEncountered)
        ERRORMSG("Block aligner encountered problem(s) - see message log for details");

    // cleanup
    DP_DestroyBlockInfo(dpBlocks);
    dpBlocks = NULL;
    dpPSSM = NULL;
    dpQuery = NULL;

    return true;
}

bool BlockAligner::SetOptions(wxWindow* parent)
{
    BlockAlignerOptionsDialog dialog(parent, currentOptions);
    bool ok = (dialog.ShowModal() == wxOK);
    if (ok && !dialog.GetValues(&currentOptions))
        ERRORMSG("Error getting options from dialog!");
    return ok;
}


/////////////////////////////////////////////////////////////////////////////////////
////// BlockAlignerOptionsDialog stuff
////// taken (and modified) from block_aligner_dialog.wdr code
/////////////////////////////////////////////////////////////////////////////////////

#define ID_TEXT 10000
#define ID_T_PERCENT 10001
#define ID_S_EXT 10002
#define ID_T_EXTENSION 10003
#define ID_S_PERCENT 10004
#define ID_T_CUTOFF 10005
#define ID_S_LAMBDA 10006
#define ID_C_GLOBAL 10007
#define ID_C_KEEP 10008
#define ID_C_MERGE 10009
#define ID_B_OK 10010
#define ID_B_CANCEL 10011

BEGIN_EVENT_TABLE(BlockAlignerOptionsDialog, wxDialog)
    EVT_BUTTON(-1,  BlockAlignerOptionsDialog::OnButton)
    EVT_CLOSE (     BlockAlignerOptionsDialog::OnCloseWindow)
END_EVENT_TABLE()

BlockAlignerOptionsDialog::BlockAlignerOptionsDialog(
    wxWindow* parent, const BlockAligner::BlockAlignerOptions& init) :
        wxDialog(parent, -1, "Set Block Aligner Options", wxPoint(100,100), wxDefaultSize,
            wxCAPTION | wxSYSTEM_MENU) // not resizable
{
    wxPanel *panel = new wxPanel(this, -1);
    wxBoxSizer *item0 = new wxBoxSizer( wxVERTICAL );
    wxStaticBox *item2 = new wxStaticBox( panel, -1, wxT("Block Aligner Options") );
    wxStaticBoxSizer *item1 = new wxStaticBoxSizer( item2, wxVERTICAL );
    wxFlexGridSizer *item3 = new wxFlexGridSizer( 3, 0, 0 );
    item3->AddGrowableCol( 1 );

    wxStaticText *item4 = new wxStaticText( panel, ID_TEXT, wxT("Loop percentile:"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    fpPercent = new FloatingPointSpinCtrl(panel,
        0.0, 100.0, 0.6, init.loopPercentile,
        wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,
        wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));
    item3->Add(fpPercent->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);
    item3->Add(fpPercent->GetSpinButton(), 0, wxALIGN_CENTER_VERTICAL|wxRIGHT|wxTOP|wxBOTTOM, 5);

    wxStaticText *item7 = new wxStaticText( panel, ID_TEXT, wxT("Loop extension:"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    iExtension = new IntegerSpinCtrl(panel,
        0, 100000, 10, init.loopExtension,
        wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,
        wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));
    item3->Add(iExtension->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);
    item3->Add(iExtension->GetSpinButton(), 0, wxALIGN_CENTER_VERTICAL|wxRIGHT|wxTOP|wxBOTTOM, 5);

    wxStaticText *item10 = new wxStaticText( panel, ID_TEXT, wxT("Loop cutoff (0=none):"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item10, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    iCutoff = new IntegerSpinCtrl(panel,
        0, 100000, 0, init.loopCutoff,
        wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,
        wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));
    item3->Add(iCutoff->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);
    item3->Add(iCutoff->GetSpinButton(), 0, wxALIGN_CENTER_VERTICAL|wxRIGHT|wxTOP|wxBOTTOM, 5);

    item3->Add( 5, 5, 0, wxALIGN_CENTRE|wxALL, 5 );
    item3->Add( 5, 5, 0, wxALIGN_CENTRE|wxALL, 5 );
    item3->Add( 5, 5, 0, wxALIGN_CENTRE|wxALL, 5 );

    wxStaticText *item13 = new wxStaticText( panel, ID_TEXT, wxT("Global alignment:"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    cGlobal = new wxCheckBox( panel, ID_C_GLOBAL, wxT(""), wxDefaultPosition, wxDefaultSize, 0 );
    cGlobal->SetValue(init.globalAlignment);
    item3->Add( cGlobal, 0, wxALIGN_CENTRE|wxALL, 5 );
    item3->Add( 5, 5, 0, wxALIGN_CENTRE, 5 );

    wxStaticText *item15 = new wxStaticText( panel, ID_TEXT, wxT("Keep existing blocks (global only):"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    cKeep = new wxCheckBox( panel, ID_C_KEEP, wxT(""), wxDefaultPosition, wxDefaultSize, 0 );
    cKeep->SetValue(init.keepExistingBlocks);
    item3->Add( cKeep, 0, wxALIGN_CENTRE|wxALL, 5 );
    item3->Add( 5, 5, 0, wxALIGN_CENTRE, 5 );

    wxStaticText *item17 = new wxStaticText( panel, ID_TEXT, wxT("Merge after each row aligned:"), wxDefaultPosition, wxDefaultSize, 0 );
    item3->Add( item17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );
    cMerge = new wxCheckBox( panel, ID_C_MERGE, wxT(""), wxDefaultPosition, wxDefaultSize, 0 );
    cMerge->SetValue(init.mergeAfterEachSequence);
    item3->Add( cMerge, 0, wxALIGN_CENTRE|wxALL, 5 );
    item3->Add( 5, 5, 0, wxALIGN_CENTRE, 5 );

    item1->Add( item3, 0, wxALIGN_CENTRE, 5 );
    item0->Add( item1, 0, wxALIGN_CENTRE|wxALL, 5 );
    wxBoxSizer *item19 = new wxBoxSizer( wxHORIZONTAL );
    wxButton *item20 = new wxButton( panel, ID_B_OK, wxT("OK"), wxDefaultPosition, wxDefaultSize, 0 );
    item19->Add( item20, 0, wxALIGN_CENTRE|wxALL, 5 );
    item19->Add( 20, 20, 0, wxALIGN_CENTRE|wxALL, 5 );
    wxButton *item21 = new wxButton( panel, ID_B_CANCEL, wxT("Cancel"), wxDefaultPosition, wxDefaultSize, 0 );
    item19->Add( item21, 0, wxALIGN_CENTRE|wxALL, 5 );
    item0->Add( item19, 0, wxALIGN_CENTRE|wxALL, 5 );

    panel->SetAutoLayout(true);
    panel->SetSizer(item0);
    item0->Fit(this);
    item0->Fit(panel);
    item0->SetSizeHints(this);
}

BlockAlignerOptionsDialog::~BlockAlignerOptionsDialog(void)
{
    delete iCutoff;
    delete iExtension;
    delete fpPercent;
}

bool BlockAlignerOptionsDialog::GetValues(BlockAligner::BlockAlignerOptions *options)
{
    options->globalAlignment = cGlobal->IsChecked();
    options->keepExistingBlocks = cKeep->IsChecked();
    options->mergeAfterEachSequence = cMerge->IsChecked();
    return (
        fpPercent->GetDouble(&(options->loopPercentile)) &&
        iExtension->GetInteger(&(options->loopExtension)) &&
        iCutoff->GetInteger(&(options->loopCutoff))
    );
}

void BlockAlignerOptionsDialog::OnCloseWindow(wxCloseEvent& event)
{
    EndModal(wxCANCEL);
}

void BlockAlignerOptionsDialog::OnButton(wxCommandEvent& event)
{
    if (event.GetId() == ID_B_OK) {
		BlockAligner::BlockAlignerOptions dummy;
        if (GetValues(&dummy))  // can't successfully quit if values aren't valid
            EndModal(wxOK);
        else
            wxBell();
    } else if (event.GetId() == ID_B_CANCEL) {
        EndModal(wxCANCEL);
    } else {
        event.Skip();
    }
}

END_SCOPE(Cn3D)

/*
* ---------------------------------------------------------------------------
* $Log: cn3d_ba_interface.cpp,v $
* Revision 1000.2  2004/06/01 18:28:07  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.33
*
* Revision 1.33  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.32  2004/03/15 18:19:23  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.31  2004/03/10 23:15:51  thiessen
* add ability to turn off/on error dialogs; group block aligner errors in message log
*
* Revision 1.30  2004/02/19 17:04:48  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.29  2004/02/19 02:16:06  thiessen
* fix struct_dp.h path
*
* Revision 1.28  2003/08/23 22:26:23  thiessen
* switch to new dp block aligner, remove Alejandro's
*
* Revision 1.27  2003/07/21 19:54:10  thiessen
* fix firstBlock error
*
* Revision 1.26  2003/07/14 18:35:27  thiessen
* run DP and Alejandro's block aligners, and compare results
*
* Revision 1.25  2003/03/27 18:45:59  thiessen
* update blockaligner code
*
* Revision 1.24  2003/02/03 19:20:02  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.23  2003/01/23 20:03:05  thiessen
* add BLAST Neighbor algorithm
*
* Revision 1.22  2003/01/22 14:47:30  thiessen
* cache PSSM in BlockMultipleAlignment
*
* Revision 1.21  2002/12/20 02:51:46  thiessen
* fix Prinf to self problems
*
* Revision 1.20  2002/12/09 16:25:04  thiessen
* allow negative score threshholds
*
* Revision 1.19  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.18  2002/09/30 17:13:02  thiessen
* change structure import to do sequences as well; change cache to hold mimes; change block aligner vocabulary; fix block aligner dialog bugs
*
* Revision 1.17  2002/09/23 19:12:32  thiessen
* add option to allow long gaps between frozen blocks
*
* Revision 1.16  2002/09/21 12:36:28  thiessen
* add frozen block position validation; add select-other-by-distance
*
* Revision 1.15  2002/09/20 17:48:39  thiessen
* fancier trace statements
*
* Revision 1.14  2002/09/19 14:09:41  thiessen
* position options dialog higher up
*
* Revision 1.13  2002/09/19 12:51:08  thiessen
* fix block aligner / update bug; add distance select for other molecules only
*
* Revision 1.12  2002/09/16 21:24:58  thiessen
* add block freezing to block aligner
*
* Revision 1.11  2002/08/15 22:13:13  thiessen
* update for wx2.3.2+ only; add structure pick dialog; fix MultitextDialog bug
*
* Revision 1.10  2002/08/14 00:02:08  thiessen
* combined block/global aligner from Alejandro
*
* Revision 1.8  2002/08/09 18:24:08  thiessen
* improve/add magic formula to avoid Windows symbol clashes
*
* Revision 1.7  2002/08/04 21:41:05  thiessen
* fix GetObject problem
*
* Revision 1.6  2002/08/01 12:51:36  thiessen
* add E-value display to block aligner
*
* Revision 1.5  2002/08/01 01:55:16  thiessen
* add block aligner options dialog
*
* Revision 1.4  2002/07/29 19:22:46  thiessen
* another blockalign bug fix; set better parameters to block aligner
*
* Revision 1.3  2002/07/29 13:25:42  thiessen
* add range restriction to block aligner
*
* Revision 1.2  2002/07/27 12:29:51  thiessen
* fix block aligner crash
*
* Revision 1.1  2002/07/26 15:28:45  thiessen
* add Alejandro's block alignment algorithm
*
*/