cdd_annot_dialog.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: cdd_annot_dialog.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:27:54  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.39
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: cdd_annot_dialog.cpp,v 1000.2 2004/06/01 18:27:54 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Authors:  Paul Thiessen
*
* File Description:
*      dialogs for annotating CDD's
*
* ===========================================================================
*/

#ifdef _MSC_VER
#pragma warning(disable:4018)   // disable signed/unsigned mismatch warning in MSVC
#endif

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>

#include <objects/cdd/Align_annot.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Packed_seqint.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/biblio/PubMedId.hpp>
#include <objects/mmdb1/Biostruc_annot_set.hpp>
#include <objects/mmdb1/Biostruc_descr.hpp>
#include <objects/mmdb1/Biostruc_id.hpp>
#include <objects/mmdb1/Mmdb_id.hpp>
#include <objects/mmdb3/Biostruc_feature_set.hpp>
#include <objects/mmdb3/Biostruc_feature_set_descr.hpp>
#include <objects/mmdb3/Biostruc_feature.hpp>
#include <objects/mmdb3/Chem_graph_pntrs.hpp>
#include <objects/mmdb3/Residue_pntrs.hpp>
#include <objects/mmdb3/Residue_interval_pntr.hpp>
#include <objects/mmdb1/Molecule_id.hpp>
#include <objects/mmdb1/Residue_id.hpp>
#include <objects/cn3d/Cn3d_backbone_type.hpp>
#include <objects/cn3d/Cn3d_backbone_style.hpp>
#include <objects/cn3d/Cn3d_general_style.hpp>
#include <objects/cn3d/Cn3d_style_settings.hpp>

#include "cdd_annot_dialog.hpp"
#include "structure_set.hpp"
#include "messenger.hpp"
#include "alignment_manager.hpp"
#include "block_multiple_alignment.hpp"
#include "sequence_set.hpp"
#include "cn3d_tools.hpp"
#include "chemical_graph.hpp"
#include "molecule_identifier.hpp"
#include "opengl_renderer.hpp"
#include "show_hide_manager.hpp"


////////////////////////////////////////////////////////////////////////////////////////////////
// The following is taken unmodified from wxDesigner's C++ header from cdd_annot_dialog.wdr
////////////////////////////////////////////////////////////////////////////////////////////////

#include <wx/image.h>
#include <wx/statline.h>
#include <wx/spinbutt.h>
#include <wx/spinctrl.h>
#include <wx/splitter.h>
#include <wx/listctrl.h>
#include <wx/treectrl.h>
#include <wx/notebook.h>

// Declare window functions

#define ID_L_ANNOT 10000
#define ID_B_NEW_ANNOT 10001
#define ID_B_HIGHLIGHT 10002
#define ID_B_ANNOT_UP 10003
#define ID_B_EDIT_ANNOT 10004
#define ID_B_DEL_ANNOT 10005
#define ID_B_ANNOT_DOWN 10006
#define ID_L_EVID 10007
#define ID_B_NEW_EVID 10008
#define ID_B_SHOW 10009
#define ID_B_EVID_UP 10010
#define ID_B_EDIT_EVID 10011
#define ID_B_DEL_EVID 10012
#define ID_B_EVID_DOWN 10013
wxSizer *SetupCDDAnnotDialog( wxPanel *parent, bool call_fit = TRUE, bool set_sizer = TRUE );

#define ID_R_COMMENT 10014
#define ID_ST_COMMENT 10015
#define ID_T_COMMENT 10016
#define ID_LINE 10017
#define ID_R_PMID 10018
#define ID_ST_PMID 10019
#define ID_T_PMID 10020
#define ID_R_STRUCTURE 10021
#define ID_ST_STRUCTURE 10022
#define ID_T_STRUCTURE 10023
#define ID_B_RERANGE 10024
#define ID_B_EDIT_OK 10025
#define ID_B_EDIT_CANCEL 10026
wxSizer *SetupEvidenceDialog( wxPanel *parent, bool call_fit = TRUE, bool set_sizer = TRUE );

////////////////////////////////////////////////////////////////////////////////////////////////

USING_NCBI_SCOPE;
USING_SCOPE(objects);


BEGIN_SCOPE(Cn3D)

// a "structure evidence" biostruc-annot-set has these qualities - basically, a specific
// comment tag as the first entry in the set's description, and a 'name' descr in the feature set
static const string STRUCTURE_EVIDENCE_COMMENT = "Used as Structure Evidence for CDD Annotation";
#define IS_STRUCTURE_EVIDENCE_BSANNOT(evidence) \
    ((evidence).IsBsannot() && \
     (evidence).GetBsannot().IsSetDescr() && \
     (evidence).GetBsannot().GetDescr().size() > 0 && \
     (evidence).GetBsannot().GetDescr().front()->IsOther_comment() && \
     (evidence).GetBsannot().GetDescr().front()->GetOther_comment() == STRUCTURE_EVIDENCE_COMMENT && \
     (evidence).GetBsannot().GetFeatures().size() > 0 && \
     (evidence).GetBsannot().GetFeatures().front()->IsSetDescr() && \
     (evidence).GetBsannot().GetFeatures().front()->GetDescr().size() > 0 && \
     (evidence).GetBsannot().GetFeatures().front()->GetDescr().front()->IsName())


#define DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(var, id, type) \
    type *var; \
    var = wxDynamicCast(FindWindow(id), type); \
    if (!var) { \
        ERRORMSG("Can't find window with id " << id); \
        return; \
    }

#define DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(var, id, type) \
    type *var; \
    var = wxDynamicCast(FindWindow(id), type); \
    if (!var) { \
        ERRORMSG("Can't find window with id " << id); \
        return false; \
    }

BEGIN_EVENT_TABLE(CDDAnnotateDialog, wxDialog)
    EVT_BUTTON      (-1,    CDDAnnotateDialog::OnButton)
    EVT_LISTBOX     (-1,    CDDAnnotateDialog::OnSelection)
    EVT_CLOSE       (       CDDAnnotateDialog::OnCloseWindow)
END_EVENT_TABLE()

CDDAnnotateDialog::CDDAnnotateDialog(wxWindow *parent, CDDAnnotateDialog **handle, StructureSet *set) :
    wxDialog(parent, -1, "CDD Annotations", wxPoint(400, 100), wxDefaultSize,
        wxCAPTION | wxSYSTEM_MENU | wxDIALOG_MODELESS | wxFRAME_NO_TASKBAR),    // not resizable
    dialogHandle(handle), structureSet(set), annotSet(set->GetCDDAnnotSet())
{
    if (annotSet.Empty()) {
        Destroy();
        return;
    }

    // construct the panel
    wxPanel *panel = new wxPanel(this, -1);
    wxSizer *topSizer = SetupCDDAnnotDialog(panel, false);

    // call sizer stuff
    topSizer->Fit(panel);
    SetClientSize(topSizer->GetMinSize());

    // set initial GUI state
    SetupGUIControls(0, 0);
}

CDDAnnotateDialog::~CDDAnnotateDialog(void)
{
    // so owner knows that this dialog has been destroyed
    if (dialogHandle && *dialogHandle) *dialogHandle = NULL;
    TRACEMSG("destroyed CDDAnnotateDialog");
}

void CDDAnnotateDialog::OnCloseWindow(wxCloseEvent& event)
{
    Destroy();
}

void CDDAnnotateDialog::GetCurrentHighlightedIntervals(IntervalList *intervals)
{
    const BlockMultipleAlignment *alignment = structureSet->alignmentManager->GetCurrentMultipleAlignment();
    const Sequence *master = alignment->GetMaster();

    // find intervals of aligned residues of the master sequence that are currently highlighted
    intervals->clear();
    int first = 0, last = 0;
    while (first < master->Length()) {

        // find first highlighted residue
        while (first < master->Length() &&
               !(GlobalMessenger()->IsHighlighted(master, first) &&
                 alignment->IsAligned(0, first))) ++first;
        if (first >= master->Length()) break;

        // find last in contiguous stretch of highlighted residues
        last = first;
        while (last + 1 < master->Length() &&
               GlobalMessenger()->IsHighlighted(master, last + 1) &&
               alignment->IsAligned(0, last + 1)) ++last;

        // create Seq-interval
        CRef < CSeq_interval > interval(new CSeq_interval());
        interval->SetFrom(first);
        interval->SetTo(last);
        master->FillOutSeqId(&(interval->SetId()));
        intervals->push_back(interval);
        first = last + 2;
    }
}

void CDDAnnotateDialog::OnButton(wxCommandEvent& event)
{
    switch (event.GetId()) {
        // annotation buttons
        case ID_B_NEW_ANNOT:
            NewAnnotation();
            break;
        case ID_B_DEL_ANNOT:
            DeleteAnnotation();
            break;
        case ID_B_EDIT_ANNOT:
            EditAnnotation();
            break;
        case ID_B_HIGHLIGHT:
            HighlightAnnotation();
            break;
        case ID_B_ANNOT_UP: case ID_B_ANNOT_DOWN:
            MoveAnnotation(event.GetId() == ID_B_ANNOT_UP);
            break;

        // evidence buttons
        case ID_B_NEW_EVID:
            NewEvidence();
            break;
        case ID_B_DEL_EVID:
            DeleteEvidence();
            break;
        case ID_B_EDIT_EVID:
            EditEvidence();
            break;
        case ID_B_SHOW:
            ShowEvidence();
            break;
        case ID_B_EVID_UP: case ID_B_EVID_DOWN:
            MoveEvidence(event.GetId() == ID_B_EVID_UP);
            break;

        default:
            event.Skip();
    }
}

void CDDAnnotateDialog::OnSelection(wxCommandEvent& event)
{
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(evids, ID_L_EVID, wxListBox)

    if (event.GetEventObject() == annots)
        SetupGUIControls(annots->GetSelection(), 0);
    else
        SetupGUIControls(annots->GetSelection(), evids->GetSelection());
}

void CDDAnnotateDialog::SetupGUIControls(int selectAnnot, int selectEvidence)
{
    // get GUI control pointers
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(evids, ID_L_EVID, wxListBox)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bNewAnnot, ID_B_NEW_ANNOT, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bDelAnnot, ID_B_DEL_ANNOT, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bEditAnnot, ID_B_EDIT_ANNOT, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bHighlight, ID_B_HIGHLIGHT, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bAnnotUp, ID_B_ANNOT_UP, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bAnnotDown, ID_B_ANNOT_DOWN, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bNewEvid, ID_B_NEW_EVID, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bDelEvid, ID_B_DEL_EVID, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bEditEvid, ID_B_EDIT_EVID, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bShow, ID_B_SHOW, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bEvidUp, ID_B_EVID_UP, wxButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bEvidDown, ID_B_EVID_DOWN, wxButton)

    bool readOnly;
    RegistryGetBoolean(REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, &readOnly);

    // fill out annots listbox
    annots->Clear();
    CAlign_annot *selectedAnnot = NULL;
    CAlign_annot_set::Tdata::iterator a, ae = annotSet->Set().end();
    for (a=annotSet->Set().begin(); a!=ae; ++a) {
        if ((*a)->IsSetDescription())
            annots->Append((*a)->GetDescription().c_str(), a->GetPointer());
        else
            annots->Append("(no description)", a->GetPointer());
    }
    if (selectAnnot < annots->GetCount())
        annots->SetSelection(selectAnnot);
    else if (annots->GetCount() > 0)
        annots->SetSelection(0);
    if (annots->GetCount() > 0)
        selectedAnnot = reinterpret_cast<CAlign_annot*>(annots->GetClientData(annots->GetSelection()));

    // fill out evidence listbox
    evids->Clear();
    CFeature_evidence *selectedEvid = NULL;
    if (selectedAnnot && selectedAnnot->IsSetEvidence()) {
        CAlign_annot::TEvidence::iterator e, ee = selectedAnnot->SetEvidence().end();
        for (e=selectedAnnot->SetEvidence().begin(); e!=ee; ++e) {
            // get evidence "title" depending on type
            wxString evidTitle;
            if ((*e)->IsComment())
                evidTitle.Printf("Comment: %s", (*e)->GetComment().c_str());
            else if ((*e)->IsReference() && (*e)->GetReference().IsPmid())
                evidTitle.Printf("PMID: %i", (*e)->GetReference().GetPmid().Get());
            else if (IS_STRUCTURE_EVIDENCE_BSANNOT(**e))
                evidTitle.Printf("Structure: %s",