muscle_tool.cpp

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/*  $Id: muscle_tool.cpp 47479 2023-05-02 13:24:02Z ucko $
* ===========================================================================
*
*                            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:  Roman Katargin
*
*/
 
#include <ncbi_pch.hpp>
 
#include <gui/objutils/interface_registry.hpp>
#include <gui/objutils/gui_seq_info.hpp>
 
#include <gui/packages/pkg_alignment/muscle_tool.hpp>
#include <gui/packages/pkg_alignment/muscle_tool_job.hpp>
#include "muscle_tool_panel.hpp"
 
#include <wx/msgdlg.h>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);
 
///////////////////////////////////////////////////////////////////////////////
/// CMuscleTool
CMuscleTool::CMuscleTool()
:   CAlgoToolManagerBase("MUSCLE",
                         "",
                         "Create an alignment using MUSCLE",
                         "MUSCLE (Multiple Sequence Comparison by Log-Expectation). Suitable for medium alignments.",
                         "https://www.ncbi.nlm.nih.gov/tools/gbench/manual5/#MSATools",
                         "Multiple Sequence Aligners"),
                         m_Panel()
{
}
 
string CMuscleTool::GetExtensionIdentifier() const
{
    return "muscle_tool";
}
 
 
string CMuscleTool::GetExtensionLabel() const
{
    return "MUSCLE Tool";
}
 
void CMuscleTool::InitUI()
{
    CAlgoToolManagerBase::InitUI();
 
    m_Panel = NULL;
}
 
void CMuscleTool::CleanUI()
{
    m_Panel = NULL;
    CAlgoToolManagerBase::CleanUI();
}
 
bool CMuscleTool::x_CreateParamsPanelIfNeeded()
{
    if (m_Panel == NULL) {
        x_SelectCompatibleInputObjects();
 
        m_Panel = new CMuscleToolPanel(m_ParentWindow, wxID_ANY,
                                   wxDefaultPosition, wxSize(0, 0), SYMBOL_CMUSCLETOOLPANEL_STYLE, false);
        m_Panel->SetData(m_Params);
        m_Panel->SetObjects(&m_Objects);
 
        m_Panel->SetRegistryPath(m_RegPath + ".ParamsPanel");
        m_Panel->LoadSettings();
    }
    return true;
}
 
bool CMuscleTool::x_ValidateParams()
{
    return true;
}
 
void CMuscleTool::x_SelectCompatibleInputObjects()
{
    x_ConvertInputObjects(CSeq_loc::GetTypeInfo(), m_Objects);
}
 
wxPanel* CMuscleTool::GetMaxPanel()
{
    CMuscleToolPanel* panel = new CMuscleToolPanel();
    panel->Create(m_ParentWindow);
    return panel;
}
 
CAlgoToolManagerParamsPanel* CMuscleTool::x_GetParamsPanel()
{
    return m_Panel;
}
 
IRegSettings* CMuscleTool::x_GetParamsAsRegSetting()
{
    return &m_Params;
}
 
CDataLoadingAppJob* CMuscleTool::x_CreateLoadingJob()
{
    if (m_Panel) m_Params = m_Panel->GetData();
    CMuscleToolJob* job = new CMuscleToolJob(m_Params);
    return job;
}
 
IAppTask* CMuscleTool::QuickLaunch()
{
    x_SelectCompatibleInputObjects();
 
    if (m_Objects.empty()) {
        wxMessageBox(wxT("No objects that can be proccessed were selected."),
                     wxT("MUSCLE Tool Error"), wxOK | wxICON_ERROR);
        return 0;
    }
 
    TConstScopedObjects objects;
 
    {{
        TConstScopedObjects genomic, proteins;
 
        NON_CONST_ITERATE (TObjects, it, m_Objects) {
            NON_CONST_ITERATE(TConstScopedObjects, it2, it->second) {
                CIRef<IGuiSeqInfo> gui_seq_info(CreateObjectInterface<IGuiSeqInfo>(*it2, NULL));
                if( gui_seq_info ) {
                    if (gui_seq_info->IsProtein()) {
                        proteins.push_back(*it2);
                    }
                    else {
                        genomic.push_back(*it2);
                    }
                }
            }
        }
        objects = (proteins.size() > genomic.size()) ? proteins : genomic;
    }}
 
    if (objects.size() < 2) {
        wxMessageBox(wxT("You have to select at least 2 either genomic or protein locations to run MUSCLE tool."),
                     wxT("MUSCLE Tool Error"), wxOK | wxICON_ERROR);
        return 0;
    }
 
    m_Params.SetObjects() = objects;
 
    CRef<CDataLoadingAppJob> job(x_CreateLoadingJob());
 
    CProjectService* prj_srv =
        m_SrvLocator->GetServiceByType<CProjectService>();
 
    vector<CSelectProjectOptions::TProjectId> projects;
    prj_srv->GetObjProjects(objects, projects);
 
    CSelectProjectOptions options;
    if (projects.empty())
        options.Set_CreateNewProject();
    else
        options.Set_AddToExistingProject(projects.front());
 
    CRef<CDataLoadingAppTask> task(new CDataLoadingAppTask(prj_srv, options, *job));
    return task.Release();
}
 
END_NCBI_SCOPE