RNA3D_OpenGLEngine.cxx

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#include "RNA3D_GlobalHeader.hxx"
#include "RNA3D_Global.hxx"
#include "RNA3D_OpenGLEngine.hxx"
#include "RNA3D_OpenGLGraphics.hxx"
#include "RNA3D_StructureData.hxx"
#include "RNA3D_Textures.hxx"
#include "RNA3D_Renderer.hxx"
#include "RNA3D_Graphics.hxx"
#include "RNA3D_Interface.hxx"

#include <iostream>

#include <aw_root.hxx>
#include <aw_awars.hxx>
#include <BI_basepos.hxx>

#include <GL/aw_window_ogl.hxx>

// --------------------------------------------------------------------------------
// global data

RNA3D_Global *RNA3D = NULp;

void RNA3D_init_global_data(ED4_plugin_host& host) {
    if (!RNA3D) {
        RNA3D = new RNA3D_Global(host);
    }
}

RNA3D_Global::RNA3D_Global(ED4_plugin_host& host) {
    OpenGLEngineState = -1;
    iRotateMolecule   = 0;
    bPointSpritesSupported           = false;
    bEColiRefInitialized             = false;
    bMapSaiDispListCreated           = false;
    bAutoRotate                      = false;
    bRotateMolecule                  = false;
    bDisplayMask                     = false;
    bDisplayComments                 = false;
    bMapSearchStringsDispListCreated = false;

    ROTATION_SPEED = 0.5;
    scale = 0.01;

    cGraphics  = new OpenGLGraphics;
    cStructure = new Structure3D(host);
    cTexture   = new Texture2D;
    cRenderer  = new GLRenderer;

    Viewer = Vector3(0.0, 0.0, -2);
    Center = Vector3(0.0, 0.0, 0.0);
    Up     = Vector3(0.0, 1.0, 0.0);
}

RNA3D_Global::~RNA3D_Global() {
    delete cGraphics;
    delete cStructure;
    delete cTexture;
    delete cRenderer;
}

// end of global data section
// --------------------------------------------------------------------------------

static float fAspectRatio;
const float fViewAngle = 40.0;
const float fClipNear  = 0.5f;
const float fClipFar   = 100;

static Display *dpy;
static GLXContext glx_context;

static int DoubleBufferWithAlpha[] = { GLX_RGBA,
                                       GLX_DEPTH_SIZE, 12,
                                       GLX_RED_SIZE, 4,
                                       GLX_GREEN_SIZE, 4,
                                       GLX_BLUE_SIZE, 4,
                                       GLX_ALPHA_SIZE, 4,
                                       GLX_DOUBLEBUFFER,
                                       None };

static int DoubleBuffer[] = { GLX_RGBA,
                              GLX_DEPTH_SIZE, 12,
                              GLX_RED_SIZE, 4,
                              GLX_GREEN_SIZE, 4,
                              GLX_BLUE_SIZE, 4,
                              GLX_DOUBLEBUFFER,
                              None };

static int SingleBuffer[] = { GLX_RGBA,
                              GLX_DEPTH_SIZE, 12,
                              GLX_RED_SIZE, 4,
                              GLX_GREEN_SIZE, 4,
                              GLX_BLUE_SIZE, 4,
                              None };

static GLfloat rotation_matrix[16];
static GLfloat rot_x = 0.0, rot_y = 0.0;

static int iScreenWidth, iScreenHeight;

static bool bMapSpDispListCreated     = false;
static bool bCursorPosDispListCreated = false;
static bool bHelixNrDispListCreated   = false;

using namespace std;

static void ShowVendorInformation() {
    const GLubyte *vendor = NULp;
    vendor = glGetString(GL_VENDOR);   cout<<"Vendor  : "<<vendor<<endl;
    vendor = glGetString(GL_RENDERER); cout<<"Renderer: "<<vendor<<endl;
    vendor = glGetString(GL_VERSION);  cout<<"Version : "<<vendor<<endl;
}

static void initExtensions() {
    // check mandatory for extensions
    char missingExtensions[500]="";
    if (!GLEW_VERSION_1_2) {
        strcat(missingExtensions, "\nOpenGL Version 1.2");
    }
    if (strlen(missingExtensions) > 0) {
        GBK_terminatef("ERROR: Some needed extensions are not present:%s\n", missingExtensions);
    }

#ifdef DEBUG
    printf("DEBUG: All mandatory extensions seem to be ok.\n");
#endif // DEBUG

    // the following code checks if point sprites could be used and activates them if possible
    missingExtensions[0] = 0;
    if (!GLEW_EXT_point_parameters) strcat(missingExtensions, "\nGL_EXT_point_parameters");
    if (!GLEW_ARB_point_sprite)     strcat(missingExtensions, "\nGL_ARB_point_sprite");
    if (strlen(missingExtensions) > 0) {
        printf("Some extra extensions are not present:%s\n", missingExtensions);
        printf("Molecule Display: Quality of Rendering is LOW!!\n");
        RNA3D->bPointSpritesSupported = false;
    }
    else {
#ifdef DEBUG
        printf("DEBUG: All extra extensions seem to be ok as well.\n");
#endif // DEBUG
        RNA3D->bPointSpritesSupported = true;
    }
}

void ReshapeOpenGLWindow(GLint width, GLint height) {
    iScreenWidth  = width;
    iScreenHeight = height;

    fAspectRatio = (float) width / (float) height;

    glViewport(0, 0, width, height);
    glMatrixMode(GL_PROJECTION);
    glLoadIdentity();
    gluPerspective(fViewAngle, fAspectRatio, fClipNear, fClipFar);
    glMatrixMode(GL_MODELVIEW);
    glLoadIdentity();
}

static void CalculateRotationMatrix() {
    static int initialized = 0;
    GLfloat new_rotation_matrix[16];

    // calculate new rotation matrix
    glPushMatrix();
    glLoadIdentity();
    glRotatef(-rot_x, 1.0, 0.0, 0.0);
    glRotatef(rot_y, 0.0, 1.0, 0.0);
    glGetFloatv(GL_MODELVIEW_MATRIX, new_rotation_matrix);
    glPopMatrix();

    // calculate total rotation
    glPushMatrix();
    glLoadIdentity();
    glMultMatrixf(new_rotation_matrix);
    if (initialized) {
        glMultMatrixf(rotation_matrix);
    }

    glGetFloatv(GL_MODELVIEW_MATRIX, rotation_matrix);
    initialized = 1;
    glPopMatrix();
}

void InitializeOpenGLEngine(GLint width, GLint height) {
    cout<<"RNA3D: Initializing OpenGLEngine : "<<width<<" x "<<height<<endl;

    RNA3D->saved_x = RNA3D->saved_y = 2.0f;
    ComputeRotationXY(1, 1);

    // Get Information about Vendor & Version
    ShowVendorInformation();

    GLenum err = glewInit();
    if (GLEW_OK != err) {
        // problem: glewInit failed, something is seriously wrong
        fprintf(stderr, "Error: %s\n", glewGetErrorString(err));
    }
    fprintf(stdout, "Status: Using GLEW %s\n", glewGetString(GLEW_VERSION));

    initExtensions();

    // Prepare the structure Data  and Generate Display Lists

    RNA3D->cStructure->ReadCoOrdinateFile();    // Reading Structure information
    RNA3D->cStructure->GetSecondaryStructureInfo();  // Getting Secondary Structure Information
    RNA3D->cStructure->Combine2Dand3DstructureInfo(); // Combining Secondary Structure data with 3D Coordinates

    RNA3D->cStructure->GenerateDisplayLists(); // Generating Display Lists for Rendering

    // Generate Textures
    RNA3D->cTexture->LoadGLTextures();  // Load The Texture(s)

    glShadeModel(GL_SMOOTH);
    glClearColor(0, 0, 0, 1);
    glClearDepth(1.0f);

    glEnable(GL_DEPTH_TEST);         // Enables Depth Testing
    glDepthFunc(GL_LEQUAL);          // The Type Of Depth Test To Do

    glHint(GL_PERSPECTIVE_CORRECTION_HINT, GL_NICEST);
    glEnable(GL_TEXTURE_2D);    // Enable Texture Mapping

    ReshapeOpenGLWindow(width, height);

    CalculateRotationMatrix();
}

void ComputeRotationXY(int x, int y) {
    rot_y = (GLfloat)(x - RNA3D->saved_x) * RNA3D->ROTATION_SPEED;
    rot_x = (GLfloat)(y - RNA3D->saved_y) * RNA3D->ROTATION_SPEED;
    RNA3D->saved_x = x;
    RNA3D->saved_y = y;
}

static void update_HelixNrDispList() {
    // update of DisplayLists for displaying Helix Numbers
    GLRenderer  *cRenderer  = RNA3D->cRenderer;
    Structure3D *cStructure = RNA3D->cStructure;

    if (!bHelixNrDispListCreated && (cRenderer->iHelixNrs || cRenderer->iHelixMidPoint)) {
        cStructure->GenerateHelixNrDispList(cRenderer->iStartHelix, cRenderer->iEndHelix);
        bHelixNrDispListCreated = true;
    }
}

void MapDisplayParameters(AW_root *root) {
    GLRenderer  *cRenderer  = RNA3D->cRenderer;
    Structure3D *cStructure = RNA3D->cStructure;

    // General Molecule Display Section
    cRenderer->iBackBone       = root->awar(AWAR_3D_MOL_BACKBONE)->read_int();
    cRenderer->iColorise       = root->awar(AWAR_3D_MOL_COLORIZE)->read_int();
    cRenderer->fSkeletonSize   = root->awar(AWAR_3D_MOL_SIZE)->read_float();
    cRenderer->iDispPos        = root->awar(AWAR_3D_MOL_DISP_POS)->read_int();
    cStructure->iInterval      = root->awar(AWAR_3D_MOL_POS_INTERVAL)->read_int();
    cRenderer->iDispCursorPos  = root->awar(AWAR_3D_CURSOR_POSITION)->read_int();
    RNA3D->iRotateMolecule    = root->awar(AWAR_3D_MOL_ROTATE)->read_int();

    // Display Bases Section
    cRenderer->iDisplayBases     = root->awar(AWAR_3D_DISPLAY_BASES)->read_int();
    cRenderer->ObjectSize        = root->awar(AWAR_3D_DISPLAY_SIZE)->read_float();
    cRenderer->iBaseMode         = root->awar(AWAR_3D_BASES_MODE)->read_int();
    cRenderer->iBaseHelix        = root->awar(AWAR_3D_BASES_HELIX)->read_int();
    cRenderer->iBaseUnpairHelix  = root->awar(AWAR_3D_BASES_UNPAIRED_HELIX)->read_int();
    cRenderer->iBaseNonHelix     = root->awar(AWAR_3D_BASES_NON_HELIX)->read_int();
    cRenderer->iShapeHelix       = root->awar(AWAR_3D_SHAPES_HELIX)->read_int();
    cRenderer->iShapeUnpairHelix = root->awar(AWAR_3D_SHAPES_UNPAIRED_HELIX)->read_int();
    cRenderer->iShapeNonHelix    = root->awar(AWAR_3D_SHAPES_NON_HELIX)->read_int();

    // Display Helices Section
    cRenderer->iDisplayHelix  = root->awar(AWAR_3D_DISPLAY_HELIX)->read_int();
    cRenderer->iHelixMidPoint = root->awar(AWAR_3D_HELIX_MIDPOINT)->read_int();
    cRenderer->iHelixNrs      = root->awar(AWAR_3D_HELIX_NUMBER)->read_int();
    cRenderer->fHelixSize     = root->awar(AWAR_3D_HELIX_SIZE)->read_float();
    cRenderer->iHelixBackBone = root->awar(AWAR_3D_HELIX_BACKBONE)->read_int();
    cRenderer->iStartHelix    = root->awar(AWAR_3D_HELIX_FROM)->read_int();
    cRenderer->iEndHelix      = root->awar(AWAR_3D_HELIX_TO)->read_int();
    cRenderer->iDispTerInt    = root->awar(AWAR_3D_DISPLAY_TERTIARY_INTRACTIONS)->read_int();

    // Mapping Sequence Data Section
    cStructure->iMapSAI           = root->awar(AWAR_3D_MAP_SAI)->read_int();
    cStructure->iMapSearch        = root->awar(AWAR_3D_MAP_SEARCH_STRINGS)->read_int();
    cStructure->iMapEnable        = root->awar(AWAR_3D_MAP_ENABLE)->read_int();
    cRenderer->iMapSpecies        = root->awar(AWAR_3D_MAP_SPECIES)->read_int();
    cRenderer->iMapSpeciesBase    = root->awar(AWAR_3D_MAP_SPECIES_DISP_BASE)->read_int();
    cRenderer->iMapSpeciesPos     = root->awar(AWAR_3D_MAP_SPECIES_DISP_POS)->read_int();
    cRenderer->iMapSpeciesDels    = root->awar(AWAR_3D_MAP_SPECIES_DISP_DELETIONS)->read_int();
    cRenderer->iMapSpeciesMiss    = root->awar(AWAR_3D_MAP_SPECIES_DISP_MISSING)->read_int();
    cRenderer->iMapSpeciesIns     = root->awar(AWAR_3D_MAP_SPECIES_DISP_INSERTIONS)->read_int();
    cRenderer->iMapSpeciesInsInfo = root->awar(AWAR_3D_MAP_SPECIES_DISP_INSERTIONS_INFO)->read_int();

    // force valid helix range (in case something is wrong with AWAR values)
    cRenderer->fixInvalidHelixPositions(cStructure->calc_helix_count());
    update_HelixNrDispList();

    // Validation of Base Position display
    if (cStructure->iInterval < 1) {
        cout<<"WARNING: Invalid POSITION Interval!! Setting it to Default Value (25)."<<endl;
        root->awar(AWAR_3D_MOL_POS_INTERVAL)->write_int(25);
    }

    if (cStructure->iMapEnable) {
        if (cStructure->iMapSearch) {
            if (!RNA3D->bMapSearchStringsDispListCreated) {
                cStructure->MapSearchStringsToEcoliTemplate(root);
            }
        }
        if (cStructure->iMapSAI) {
            if (!RNA3D->bMapSaiDispListCreated) {
                cStructure->MapSaiToEcoliTemplate();
            }
        }
        if (!bMapSpDispListCreated) {
            cStructure->MapCurrentSpeciesToEcoliTemplate(root);
            bMapSpDispListCreated = true;
        }
    }
}


void DisplayPostionsIntervalChanged_CB(AW_root *awr) {
    MapDisplayParameters(awr);
    glDeleteLists(STRUCTURE_POS, 2);
    RNA3D->cStructure->ComputeBasePositions();
    RefreshOpenGLDisplay();
}

void MapSelectedSpeciesChanged_CB(AW_root *awr) {

    // If Selected Species (in Primary Editor) changed and
    // the MapSpecies display lists created then,
    //  1. Delete the display lists;
    //  2. Recalculate the Display lists for current species;
    //  3. Map it to EColi Template;

    if (RNA3D->cStructure->iMapEnable &&
        RNA3D->cRenderer->iMapSpecies &&
        bMapSpDispListCreated)
    {
        glDeleteLists(MAP_SPECIES_BASE_DIFFERENCE, 9);
        RNA3D->cStructure->MapCurrentSpeciesToEcoliTemplate(awr);
    }

    // If selected species changed then regenerate the SearchStrings DisplayList
    MapSearchStringsToEcoliTemplateChanged_CB(awr);

    RefreshOpenGLDisplay();
}

void MapSaiToEcoliTemplateChanged_CB(AW_root */*awr*/) {
    // if SAI changed in EDIT4 then display lists should be recalculated

    if (RNA3D->cStructure->iMapEnable  &&
        RNA3D->cStructure->iMapSAI     &&
        RNA3D->bMapSaiDispListCreated)
    {
        RNA3D->bMapSaiDispListCreated = false;
        glDeleteLists(MAP_SAI_TO_STRUCTURE, 1);
        RNA3D->cStructure->MapSaiToEcoliTemplate();
    }

    RefreshOpenGLDisplay();
}

void MapSearchStringsToEcoliTemplateChanged_CB(AW_root *awr) {

    // If selected species changed then regenerate the
    // SearchStrings DisplayList

    if (RNA3D->cStructure->iMapEnable  &&
        RNA3D->cStructure->iMapSearch  &&
        RNA3D->bMapSearchStringsDispListCreated)
    {
        RNA3D->bMapSearchStringsDispListCreated = false;
        glDeleteLists(MAP_SEARCH_STRINGS_TO_STRUCTURE, 2);
        RNA3D->cStructure->MapSearchStringsToEcoliTemplate(awr);
    }
}

void CursorPositionChanged_CB(AW_root *awr) {

    if (RNA3D->bEColiRefInitialized) {
        long iCursorPos = awr->awar(AWAR_CURSOR_POSITION)->read_int();
        long EColiPos   = RNA3D->cStructure->EColiRef->abs_2_rel(iCursorPos); // @@@ calls abs_2_rel with biopos (1..N)! this is wrong

        if (!bCursorPosDispListCreated) {
            RNA3D->cStructure->GenerateCursorPositionDispList(EColiPos);
            bMapSpDispListCreated = true;
        }
        else {
            glDeleteLists(ECOLI_CURSOR_POSITION, 1);
            RNA3D->cStructure->GenerateCursorPositionDispList(EColiPos);
        }
        RefreshOpenGLDisplay();
    }
}

void DisplayHelixNrsChanged_CB(AW_root *awr, bool upper_limit_changed) {
    AW_awar *awar_lower  = awr->awar(AWAR_3D_HELIX_FROM);
    AW_awar *awar_upper  = awr->awar(AWAR_3D_HELIX_TO);
    long     NoOfHelices = RNA3D->cStructure->calc_helix_count();

    if (upper_limit_changed) {
        awar_upper->write_int(force_in_range(1L, awar_upper->read_int(), NoOfHelices));
        awar_lower->write_int(force_in_range(1L, awar_lower->read_int(), awar_upper->read_int()));
    }
    else {
        awar_lower->write_int(force_in_range(1L,                     awar_lower->read_int(), NoOfHelices));
        awar_upper->write_int(force_in_range(awar_lower->read_int(), awar_upper->read_int(), NoOfHelices));
    }

    if (bHelixNrDispListCreated) { // force update (done by MapDisplayParameters below)
        glDeleteLists(HELIX_NUMBERS, 2);
        bHelixNrDispListCreated = false;
    }
    MapDisplayParameters(awr);

    RefreshOpenGLDisplay();
}

static void DrawStructure() {
    GLRenderer *cRenderer = RNA3D->cRenderer;

    // Drawing Molecule Skeleton
    cRenderer->DisplayMolecule(RNA3D->cStructure);

    // Mapping Helices to The molecule
    cRenderer->DoHelixMapping();

    // Texture Mapping
    cRenderer->BeginTexturizer();
    cRenderer->TexturizeStructure(RNA3D->cTexture, RNA3D->cStructure);
    cRenderer->EndTexturizer();
}

void RenderOpenGLScene(Widget w) {
    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);

    // setting the BackGround Color of the OpenGL Scene
    RNA3D->cGraphics->SetOpenGLBackGroundColor();

    glLoadIdentity();

    gluLookAt(RNA3D->Viewer.x, RNA3D->Viewer.y, RNA3D->Viewer.z,
              RNA3D->Center.x, RNA3D->Center.y, RNA3D->Center.z,
              RNA3D->Up.x,     RNA3D->Up.y,     RNA3D->Up.z);

    { // Displaying Molecule Name
        RNA3D->cRenderer->DisplayMoleculeName(iScreenWidth, iScreenHeight, RNA3D->cStructure);
    }

    glScalef(RNA3D->scale, RNA3D->scale, RNA3D->scale);

    RNA3D->cRenderer->DisplayMoleculeMask(iScreenWidth, iScreenHeight);

    if (RNA3D->bRotateMolecule || RNA3D->bAutoRotate) {
        CalculateRotationMatrix();
    }

    glMultMatrixf(rotation_matrix);

    Vector3& strCen = *RNA3D->cStructure->strCen;
    glTranslatef(-strCen.x, -strCen.y, -strCen.z);

    DrawStructure();

    glFlush();
    glXWaitX();
    glXSwapBuffers (XtDisplay(w), XtWindow(w));
}

void InitializeOpenGLWindow(Widget w) {

    if (RNA3D->OpenGLEngineState == CREATED) return;

    Arg args[1];
    XVisualInfo *vi;

    XtSetArg(args[0], (char *) GLwNvisualInfo, &vi);
    XtGetValues(w, args, 1);

    dpy = XtDisplay(w);
    if (!dpy) {
        fprintf(stderr, "could not open display\n");
    }
    else {
        if (AW_alpha_Size_Supported) {
            vi = glXChooseVisual(dpy, DefaultScreen(dpy), DoubleBufferWithAlpha);
            printf("RNA3D: Double Buffered Visual With Alpha Size Supported !\n");
        }
        else {
            vi = glXChooseVisual(dpy, DefaultScreen(dpy), DoubleBuffer);
            printf("RNA3D: Double Buffered Visual Supported !\n");
        }

        if (!vi) {
            fprintf(stderr, "try to get a single buffered visual\n");
            vi = glXChooseVisual(dpy, DefaultScreen(dpy), SingleBuffer);
            if (!vi)
                fprintf(stderr, "could not get visual\n");
        }
        else {
            glx_context = glXCreateContext(dpy, vi, NULp, GL_TRUE);
            if (!glXIsDirect(dpy, glx_context))
                fprintf(stderr, "direct rendering not supported\n");
            else
                printf("RNA3D: Direct rendering supported\n");

            GLwDrawingAreaMakeCurrent(w, glx_context);

            RNA3D->glw = w;

            RNA3D->OpenGLEngineState = CREATED;

            // Initializing fonts
            char fontName[] = "fixed";
            RNA3D->cGraphics->InitMainFont(fontName);
        }
    }
}