aln_multi_cgi.cpp
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- /*
- * ===========================================================================
- * 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
- *
- * ===========================================================================
- */