blast_hitmatrix.cpp

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/*  $Id: blast_hitmatrix.cpp 46176 2021-01-28 17:07:49Z grichenk $
 * ===========================================================================
 *
 *                            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:  Irena Zaretskaya
 *
 * File Description:
 */
 
#include <ncbi_pch.hpp>
 
#include <corelib/ncbistl.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
 
#include <util/image/image.hpp>
#include <util/image/image_util.hpp>
#include <util/image/image_io.hpp>
 
#include <objmgr/util/sequence.hpp>
 
#include <connect/services/netcache_api.hpp>
#include <gui/opengl/ftglfontmanager.hpp>
#include <gui/opengl/gltexturefont.hpp>
#include <gui/opengl/glrender.hpp>
#include <gui/opengl/glresmgr.hpp>
#include "blast_hitmatrix.hpp"
 
BEGIN_NCBI_SCOPE
 
void CBlastHitMatrix::x_InitObjectManager()
{
    m_ObjMgr = CObjectManager::GetInstance();
    CGBDataLoader::RegisterInObjectManager(*m_ObjMgr);
 
    // create our object manager
    m_Scope.Reset(new CScope(*m_ObjMgr));
    m_Scope->AddDefaults();
}
 
 
void CBlastHitMatrix::x_InitPort()
{
    m_Port.SetViewport(TVPRect(0, 0, m_Width, m_Height));
            
    TModelRect rc_m(0, 0, 1000, 1000);
    CBioseq_Handle s_handle = m_DataSource->GetSubjectHandle();
    if(s_handle)    {
       rc_m.SetHorz(0, s_handle.GetBioseqLength());
    } else {
       TSeqRange s_r = m_DataSource->GetSubjectHitsRange();
       rc_m.SetHorz(s_r.GetFrom(), s_r.GetToOpen());
    }
 
    CBioseq_Handle q_handle = m_DataSource->GetQueryHandle();
    if(q_handle)    {
       rc_m.SetVert(0, q_handle.GetBioseqLength());
    } else {
       TSeqRange q_r = m_DataSource->GetQueryHitsRange();
       rc_m.SetVert(q_r.GetFrom(), q_r.GetToOpen());
    }
    
    m_Port.SetModelLimitsRect(rc_m);
}
 
 
CBlastHitMatrix::CBlastHitMatrix(const list< CRef< CSeq_align > > &seqAligns, 
                                 int height,
                                 int width,
                                 CImageIO::EType format,
                                 const string& font_path)
{
    ITERATE (CSeq_annot::TData::TAlign, iter, seqAligns) {
        CRef< CSeq_align > seq_align = *iter;
        m_Aligns.push_back(CConstRef<CSeq_align>(seq_align));
    }
    m_Height = height;
    m_Width = width;
    m_Format = format;
    m_FileOut = false;
    m_Thumbnail = false;
 
    x_InitGraphics(font_path);
    m_Renderer.reset(new CHitMatrixRenderer);
}
 
 
void CBlastHitMatrix::x_GetLabels(void)
{
    for(size_t i=0; i < m_Aligns.size();i++) {        
        const CSeq_id& queryID = m_Aligns[i]->GetSeq_id(0);                        
        /* Somehow code for IsLocal stopped working
        if(queryID.IsLocal()) {        
            (*sequence::GetId(queryID,*m_Scope,sequence:: eGetId_Best).GetSeqId()).GetLabel(&m_QueryID);                  
       }
       else {
            CLabel::GetLabel(queryID,&m_QueryID,CLabel::eDefault,m_Scope.GetPointer());
       }
       */
       CLabel::GetLabel(queryID,&m_QueryID,CLabel::eDefault,m_Scope.GetPointer());
       if(queryID.IsLocal()) {
           m_QueryID = "lcl|" + m_QueryID;
       }
        
        const CSeq_id& subjectID = m_Aligns[i]->GetSeq_id(1);         
        /*
        if(subjectID.IsLocal()) {
            (*sequence::GetId(subjectID,*m_Scope,sequence:: eGetId_Best).GetSeqId()).GetLabel(&m_SubjectID);    
        }
        else {
            CLabel::GetLabel(subjectID,&m_SubjectID,CLabel::eDefault,m_Scope.GetPointer());
        }
        */
        CLabel::GetLabel(subjectID,&m_SubjectID,CLabel::eDefault,m_Scope.GetPointer());
        if(subjectID.IsLocal()) {
            m_SubjectID = "lcl|" + m_SubjectID;
        }
        //m_SubjectID = "Subj: " + m_SubjectID;
        break;
    }
}
 
 
//extracting arguments, verifying and loading data
void CBlastHitMatrix::x_PreProcess(void)
{
    
    x_InitObjectManager();
    x_GetLabels();
        
    // create a Data Source
    CHitMatrixDSBuilder builder;
    //builder.Init(*m_Scope, *m_Annot);
    builder.Init(*m_Scope, m_Aligns);       
    m_DataSource = builder.CreateDataSource();          
    m_DataSource->SelectDefaultIds();
 
    x_InitPort();       
    
    m_Renderer->ShowRulers(!m_Thumbnail);
    m_Renderer->ShowGrid(!m_Thumbnail);
    CRgbaColor cl("236 255 243");
    m_Renderer->SetBackgroundColor(cl);
    m_Renderer->Update(m_DataSource.GetPointer(), m_Port);
}
 
 
 
 
void CBlastHitMatrix::x_Render(void)
{
    if(m_Aligns.size() > 0) {
        m_Renderer->Resize(m_Width, m_Height, m_Port);
        if(m_Thumbnail) {
            m_Renderer->GetBottomRuler().SetDisplayOptions(CRuler::fHideLabels);        
            m_Renderer->GetLeftRuler().SetDisplayOptions(CRuler::fHideLabels);            
            //m_Renderer.SetBackGroundColor(CRgbaColor("211 223 245"));
            //m_Renderer.SetBackGroundColor(CRgbaColor("238 238 238"));
        }
        else {
            m_Renderer->GetBottomRuler().SetDisplayOptions(CRuler::fShowTextLabel);        
            m_Renderer->GetLeftRuler().SetDisplayOptions(CRuler::fShowTextLabel);
            m_Renderer->GetBottomRuler().SetTextLabel(m_QueryID);        
            m_Renderer->GetLeftRuler().SetTextLabel(m_SubjectID);
        }
        
 
        //m_Renderer.GetBottomRuler().SetColor(CRuler::eText,CRgbaColor(24,0,0));        
        //m_Renderer.GetLeftRuler().SetColor(CRuler::eBackground,CRgbaColor(175,238,238));
        //m_Renderer.GetBottomRuler().SetColor(CRuler::eText,CRgbaColor(0,0,0));        
        //m_Renderer.GetLeftRuler().SetColor(CRuler::eBackground,CRgbaColor("173 255 47"));
        
        // adjust visible space
        m_Port.SetViewport(TVPRect(10, 10, m_Width, m_Height)); ///### this have to be eliminated
        m_Port.ZoomAll();
 
        m_Renderer->Render(m_Port);
    }   
}
 
bool CBlastHitMatrix::Display(CNcbiOstream & out)
{
    bool success = x_RenderImage();            
    if(success) {
        CImageIO::WriteImage(m_Context->GetBuffer(), out, m_Format);
    }
    return success;
}
 
 
bool CBlastHitMatrix::WriteToFile(void)
{
    bool success = x_RenderImage();
    if(success) {
        if(IsFileOut()) {
            CImageIO::WriteImage(m_Context->GetBuffer(), m_File, m_Format);
        }
        else {//netcache
            CNetCacheAPI nc_client("NC_HitMatrix", "blast_hitmatrix");
            m_ImageKey = nc_client.PutData(m_Context->GetBuffer().GetData(),  m_Width*m_Height*3);
        }
         
    }
    return success;
}
 
 
bool CBlastHitMatrix::x_RenderImage(void)
{
  bool success = false;
  try {
         // Clear any previously used OpenGL states
         IRender& gl = GetGl();
         gl.Clear();
 
         x_PreProcess();
 
         m_Context.Reset(new CGlOsContext(m_Width, m_Height));
         m_Context->MakeCurrent();         
 
         x_Render();
 
         glFinish();
         m_Context->SetBuffer().SetDepth(3);
         CImageUtil::FlipY(m_Context->SetBuffer());
         success = true;
    }
    catch (CException& e) {        
        m_ErrorMessage = "Error rendering image:" + e.GetMsg();                        
    }
    catch (exception& e) {        
        m_ErrorMessage = "Error rendering image:" + (string)e.what();                        
    }
    catch (...) {        
        m_ErrorMessage = "Error rendering image: unknown error";                
    }    
    return success;
}
 
void CBlastHitMatrix::x_InitGraphics(const string& font_path)
{
    try {
        m_Context.Reset(new CGlOsContext(m_Width, m_Height));
        m_Context->MakeCurrent();
#ifdef GLEW_MX
        GLEWContext  glew_context;
        GLenum err = glewContextInit(&glew_context);
        if (GLEW_OK != err) {
            // Problem: Error creating glew context
            _TRACE("Error creating glew context");
        } else {
            CGLGlewContext::GetInstance().SetGlewContext(&glew_context);
            err = glewInit();
            if (GLEW_OK != err) {
                // Problem: glewInit failed, something is seriously wrong.
                //   No extenstions will be available.
                _TRACE("Error loading opengl extensions");
            }
        }
#else 
    GLenum err = glewInit();
    if (GLEW_OK != err)
    {
       _TRACE("Error initializing glew: " << glewGetErrorString(err));
    } 
#endif
        // initialize OpenGL fonts
        CFtglFontManager::Instance().SetDeviceResolution(72);
        // path to find font files (they can be copied from svn
        // gbench/trunk/src/gui/res/share/gbench/fonts
        CFtglFontManager::Instance().SetFontPath(font_path.empty() ? "./"
                                                 : font_path);
        CFtglFontManager::Instance().Clear();
 
        CIRef<IRender>  mgr = CGlResMgr::Instance().
            GetRenderer( CGlResMgr::Instance().GetApiLevel());
        if (mgr.IsNull()) {
            ERR_POST(Error << "CGlRender object not available.");
            NCBI_THROW(CException, eUnknown,
                       string("no CGlRender object not available"));
 
        }
    }
    catch (CException& e) {
        m_ErrorMessage = "Error during initialization: " + e.GetMsg();
    }
    catch (...) {
        m_ErrorMessage = "Error during rendering initialization: unknown error";
    }
}
 
 
END_NCBI_SCOPE