aln_multi_cgi.cpp

来自「ncbi源码」· C++ 代码 · 共 285 行

/*
 * ===========================================================================
 * PRODUCTION $Log: aln_multi_cgi.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:07:35  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: aln_multi_cgi.cpp,v 1000.1 2004/06/01 21:07:35 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.
 *
 * ===========================================================================
 *
 * Author:  Andrey Yazhuk
 *
 * File Description:
 */

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

#include <cgi/cgictx.hpp>
#include <gui/opengl/mesa/glcgi_image.hpp>
#include <gui/opengl/mesa/gloscontext.hpp>
#include <gui/opengl/glutils.hpp>
#include <gui/opengl/glpane.hpp>

#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>


#include <gui/widgets/aln_multiple/align_row.hpp>
#include <gui/widgets/aln_multiple/alnvec_multi_ds.hpp>
#include <gui/widgets/aln_multiple/alnvec_multi_model.hpp>

#include <gui/widgets/aln_multiple/alnmulti_renderer.hpp>
#include <gui/widgets/aln_multiple/aln_scoring.hpp>


USING_SCOPE(ncbi);   //using namespace ncbi;
USING_SCOPE(objects);


static const int kColorGradNumber = 32; /// number of gradient colors in alignment


class CAlnMultiCGIException : public CException
{
public:
	enum EErrCode	{
		eInvalidAccession,
		eCannotLoadBioseq,
		eInvalidVisibleRange,
		eInvalidAnchor
	};
	
	virtual const char* GetErrCodeString(void) const
	{
		switch(GetErrCode())	{
		case eInvalidAccession: return "eInvalidException";
		case eCannotLoadBioseq: return "eCannotLoadBioseq";
		case eInvalidVisibleRange: return "eInvalidVisibleRange";
		case eInvalidAnchor: return "eInvalidAnchor";
		default:	return CException::GetErrCodeString();
		};
	}
	
	NCBI_EXCEPTION_DEFAULT(CAlnMultiCGIException, CException);
};

/////////////////////////////////////////////////////////////////////////////
//  CAlnMultiCGIApplication::
//

class CAlnMultiCGIApplication : public CGlCgiImageApplication
{
public:
    CAlnMultiCGIApplication();

    virtual void Render(CCgiContext& ctx);
protected:
	virtual void x_PreProcess(CCgiContext& ctx);
private:
	CRef<CObjectManager> 	m_ObjMgr;
  	CRef<CScope> 			m_Scope;
	CBioseq_Handle  		m_Handle;

	// Renderer setup
    CRowStyleCatalog    m_StyleCatalog;
    CAlnVecMultiDataSource m_DataSource;
    CAlnVecMultiModel   m_Model;
    CAlnMultiRenderer   m_Renderer;
	
	//parameter 
	int m_Start, m_Stop;
};



CAlnMultiCGIApplication::CAlnMultiCGIApplication()
: m_Renderer(TVPRect(0, 0, m_Width, m_Height))
{
    //setup ?
}

//extracting arguments, verifying and loading data
void	CAlnMultiCGIApplication::x_PreProcess(CCgiContext& ctx)
{
	SetEnvironment("NCBI_SERVICE_NAME_ID1",  "ID1LXA");
	
	// retrieve our CGI rendering params
    const CCgiRequest& request  = ctx.GetRequest();
    const TCgiEntries& entries = request.GetEntries();
	
	m_Start = m_Stop = -1;

	TCgiEntries::const_iterator it_acc = entries.find("acc");
	TCgiEntries::const_iterator it_start = entries.find("start");
	TCgiEntries::const_iterator it_stop = entries.find("stop");
	TCgiEntries::const_iterator it_anchor = entries.find("anchor");
	
	if(it_acc == entries.end()) {
		NCBI_THROW(CAlnMultiCGIException, eInvalidAccession, "Accession is not specified.");
	} else {			
		string s = "Accession: " + it_acc->second;
		LOG_POST(s);

		//extract other parameters
		if(it_start != entries.end()  &&  it_start->second.size()) {
			m_Start = NStr::StringToInt(it_start->second);
		}
		if(it_stop != entries.end()  &&  it_stop->second.size()) {
			m_Stop = NStr::StringToInt(it_stop->second);
		}

    	m_ObjMgr.Reset(new CObjectManager());		
    	m_ObjMgr->RegisterDataLoader(*new CGBDataLoader(), 
                                    	CObjectManager::eDefault);

    	m_Scope.Reset(new CScope(*m_ObjMgr));
    	m_Scope->AddDefaults();

		CSeq_id id(it_acc->second);		
    	m_Handle = m_Scope->GetBioseqHandle(id);
		
		if(m_Handle)	{ // setup data source and visible range

			m_DataSource.Init(m_Handle, m_Scope.GetObject());    
		
			// attempt to set anchor
			if(it_anchor != entries.end()  &&  it_anchor->second.size())	{ 
				CSeq_id anchor_id(it_anchor->second);		

				bool b_set = false;
				CAlnVec::TNumrow n_rows = m_DataSource.GetNumRows();				
				for( CAlnVec::TNumrow row = 0;  row < n_rows  &&  ! b_set;  row++ )	{
					const CBioseq_Handle& row_handle = m_DataSource.GetBioseqHandle(row);
					if(row_handle.GetSeqId()->Match(anchor_id))	{
						m_DataSource.SetAnchor(row);
						b_set = true;
					}
				}
				if(! b_set) {
					NCBI_THROW(CAlnMultiCGIException, eInvalidAnchor,
								"Anchor accession is invalid."); 
				}
				
			}
		
			//calculate visible range
			int aln_start = m_DataSource.GetAlnStart();
			int aln_stop = m_DataSource.GetAlnStop();
			if(m_Start > -1)	{
				if(m_Start < 0  ||  m_Start > aln_stop)	{
					NCBI_THROW(CAlnMultiCGIException, eInvalidVisibleRange, 
							   "Visible start out of range.");
				}

			} else m_Start = aln_start;
			if(m_Stop > -1)	{
				if(m_Stop < 0  ||  m_Stop > aln_stop)	{					
					NCBI_THROW(CAlnMultiCGIException, eInvalidVisibleRange,
								"Visible end out of range.");	
				}

			} else m_Stop = aln_stop;
			
			//setup model
        	m_StyleCatalog.SetDefaultStyle(new CAlnVecRowDisplayStyle());
    		m_StyleCatalog.SetWidgetStyle(m_Model.GetDisplayStyle());

			m_Model.EnableScoring(false);
    		m_Model.SetStyleCatalog(&m_StyleCatalog);
        	m_Model.SetDataSource(&m_DataSource);

			m_Renderer.SetContext(&m_Model);
			TModelRect rc_vis = m_Model.GetAlignPort().GetModelLimitsRect();
			size_t h = (size_t) -rc_vis.Height();
			m_Height = min(m_Height, h);			
		}
    	else {
		   string msg = "Cannot load Bioseq for accession \"";
		   msg += it_acc->second;
		   msg += "\"";
		   NCBI_THROW(CAlnMultiCGIException, eCannotLoadBioseq, msg.c_str());
	   }

	}
}

void CAlnMultiCGIApplication::Render(CCgiContext& ctx)
{
    if(m_Handle)  {
		m_Renderer.Resize(TVPRect(0, 0, m_Width, m_Height));
		
		//adjus visible space
		CGlPane& port = m_Model.GetAlignPort();			
        port.SetViewport(TVPRect(0, 0, m_Width, m_Height)); ///### this have to be eliminated
        port.ZoomAll();

		// adjust visible range
		TModelRect rc_vis = port.GetVisibleRect();
		rc_vis.SetHorz(m_Start, m_Stop + 1);			
		port.SetVisibleRect(rc_vis);


        m_Renderer.Render();
    }
	//debugging trick
    //CImageIO::WriteImage(m_Context->GetBuffer(), "test.png", m_Format);
}



/////////////////////////////////////////////////////////////////////////////
//  MAIN
//

int main(int argc, const char* argv[])
{
    int result = CAlnMultiCGIApplication().AppMain(argc, argv, 0, eDS_Default, 0);
    _TRACE("back to normal diags");
    return result;
}


/*
 * ===========================================================================
 * $Log: aln_multi_cgi.cpp,v $
 * Revision 1000.1  2004/06/01 21:07:35  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/21 22:27:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.3  2004/03/26 16:51:09  yazhuk
 * Disabled scoring
 *
 * Revision 1.2  2004/03/22 19:23:44  yazhuk
 * Implemented argumnent handling; error handling; image size adjustment
 *
 * ===========================================================================
 */