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Seq.c

/* 
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information. 
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-* 
-* 
-*
Z* -------------------------------------------------------------------
*/

#include "os_gl.h"
#include "os_std.h"

#include "Base.h"
#include "Seq.h"
#include "main.h"
#include "ScrollBar.h"
#include "MemoryDebug.h"
#include "PyMOLObject.h"
#include "Scene.h"
#include "Text.h"

#include "Seeker.h"

#include "Menu.h"
#include "Executive.h"

struct _CSeq {
  Block *Block;
  int DragFlag;
  int ScrollBarActive;
  int NSkip;
  struct CScrollBar *ScrollBar;
  CSeqRow *Row;
  int NRow;
  int Size;
  int VisSize;
  int Changed;
  int Dirty;
  int LineHeight;
  int CharWidth;
  int ScrollBarWidth;
  int ScrollBarMargin;
  int CharMargin;
  int LastRow;
  CSeqHandler *Handler;         /* borrowed pointer */
};

static int SeqFindRowCol(PyMOLGlobals * G, int x, int y, int *row_num_ptr,
                         int *col_num_ptr, int fixed_row)
{
  register CSeq *I = G->Seq;
  int result = 0;
  int row_num = 0;
  int col_num = 0;

  if(I->ScrollBarActive) {
    y -= I->ScrollBarWidth;
  }
  if(fixed_row >= 0) {
    row_num = fixed_row;
  } else {
    row_num = (y - I->Block->rect.bottom) / I->LineHeight;
    row_num = (I->NRow - 1) - row_num;
  }
  if((row_num >= 0) && (row_num < I->NRow)) {
    int char_num;
    CSeqRow *row;
    row = I->Row + row_num;
    char_num = (x - I->Block->rect.left - I->CharMargin) / I->CharWidth;
    if(row->nCol && !row->label_flag)
      if(char_num < I->VisSize) {
        char_num += I->NSkip;
        if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) {
          col_num = row->char2col[char_num];
          if(col_num) {
            col_num--;
            if(col_num < row->nCol) {
              result = true;
            } else if(fixed_row >= 0) {
              col_num = row->nCol - 1;
              result = true;
            }
          }
        } else if(char_num == 0) {
          col_num = 0;
          result = true;
        } else {
          col_num = row->nCol - 1;
          result = true;
        }
      }
  }
  if(result) {
    *row_num_ptr = row_num;
    *col_num_ptr = col_num;
  }
  return result;
}

void SeqUpdate(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;

  if(I->Changed) {
    SeekerUpdate(G);
    I->Changed = false;
    I->Dirty = true;
    OrthoReshape(G, -1, -1, false);     /* careful, this is recursive... */
  }
  if(I->Dirty) {
    if(I->Handler->fRefresh)
      I->Handler->fRefresh(G, I->Row);
    I->Dirty = false;
  }
}

static void SeqReshape(Block * block, int width, int height)
{
  PyMOLGlobals *G = block->G;
  register CSeq *I = G->Seq;
  BlockReshape(block, width, height);

  {                             /* get current sequence sizes */
    int a;
    I->Size = 0;
    for(a = 0; a < I->NRow; a++) {
      if(I->Row[a].ext_len > I->Size)
        I->Size = I->Row[a].ext_len;
    }
  }

  {
    int extra;
    I->VisSize = (I->Block->rect.right - I->Block->rect.left - 1) / I->CharWidth;
    /*    printf("%d %d %d %d %d\n",cw,I->Block->rect.right,I->Block->rect.left,I->VisSize,I->Size); */

    if(I->VisSize < 1)
      I->VisSize = 1;
    extra = I->Size - I->VisSize;
    if(extra <= 0) {
      I->ScrollBarActive = false;
    } else {
      I->ScrollBarActive = true;
      ScrollBarSetLimits(I->ScrollBar, I->Size, I->VisSize);
    }
  }
}

void SeqDirty(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;
  I->Dirty = true;
  SceneInvalidate(G);
}

void SeqChanged(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;
  I->Changed = true;
  SceneInvalidate(G);
}

static int SeqDrag(Block * block, int x, int y, int mod)
{
  PyMOLGlobals *G = block->G;
  register CSeq *I = G->Seq;
  int pass = 0;
  int row_num;
  int col_num;
  if(!pass) {
    if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) {
      CSeqRow *row;
      CSeqCol *col;
      row = I->Row + row_num;
      col = row->col + col_num;
      if(I->Handler)
        if(I->Handler->fDrag)
          I->Handler->fDrag(G, I->Row, row_num, col_num, mod);
      OrthoDirty(G);
    }
  }
  return (1);
}

static int SeqRelease(Block * block, int button, int x, int y, int mod)
{
  PyMOLGlobals *G = block->G;
  register CSeq *I = G->Seq;
  int pass = 0;
  /*
     if(I->ScrollBarActive) {
     if((y-I->Block->rect.bottom)<I->ScrollBarWidth) {
     pass = 1;
     ScrollBarDoRelease(I->ScrollBar,button,x,y,mod);
     OrthoUngrab(G);
     }
     } 
   */
  if(!pass) {
    int row_num;
    int col_num;
    if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) {
      CSeqRow *row;
      CSeqCol *col;
      row = I->Row + row_num;
      col = row->col + col_num;
      if(I->Handler)
        if(I->Handler->fRelease)
          I->Handler->fRelease(G, I->Row, button, row_num, col_num, mod);
      OrthoDirty(G);
    } else {
      if(I->Handler)
        if(I->Handler->fRelease)
          I->Handler->fRelease(G, I->Row, button, -1, -1, mod);
      OrthoDirty(G);
    }
  }
  I->DragFlag = false;
  I->LastRow = -1;
  return (1);
}

int SeqGetHeight(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;
  int height = 0;

  if(I->NRow) {
    height = 13 * I->NRow + 4;
    if(I->ScrollBarActive)
      height += I->ScrollBarWidth;
  }
  return (height);
}

void SeqSetHandler(PyMOLGlobals * G, CSeqHandler * handler)
{
  register CSeq *I = G->Seq;
  I->Handler = handler;
}

static int SeqClick(Block * block, int button, int x, int y, int mod)
{
  PyMOLGlobals *G = block->G;
  register CSeq *I = G->Seq;
  int pass = 0;
  int row_num;
  int col_num;
  if(I->ScrollBarActive) {
    if((y - I->Block->rect.bottom) < I->ScrollBarWidth) {
      pass = 1;
      ScrollBarDoClick(I->ScrollBar, button, x, y, mod);
    }
  }
  if(!pass) {
    if(SeqFindRowCol(G, x, y, &row_num, &col_num, -1)) {
      CSeqRow *row;
      CSeqCol *col;
      row = I->Row + row_num;
      col = row->col + col_num;
      if(I->Handler)
        if(I->Handler->fClick)
          I->Handler->fClick(G, I->Row, button, row_num, col_num, mod, x, y);
      I->DragFlag = true;
      I->LastRow = row_num;
      OrthoDirty(G);
    } else {
      switch (button) {
      case P_GLUT_RIGHT_BUTTON:
        {
          ObjectNameType name;
          if(ExecutiveGetActiveSeleName(G, name, false, false)) {
            MenuActivate2Arg(G, x, y + 20, x, y, false, "pick_sele", name, name);
          }
        }
        break;
      case P_GLUT_LEFT_BUTTON:
        if(I->Handler)
          if(I->Handler->fClick)
            I->Handler->fClick(G, I->Row, button, -1, -1, mod, x, y);
        break;
      }
    }
  }
  return (1);
}

static void SeqDraw(Block * block)
{
  PyMOLGlobals *G = block->G;
  register CSeq *I = G->Seq;

  if(G->HaveGUI && G->ValidContext) {

    int x = I->Block->rect.left;
    int y = I->Block->rect.bottom + I->ScrollBarMargin + 1;
    float *bg_color, overlay_color[3] = { 1.0F, 1.0F, 1.0F };
    int label_color_index = SettingGetGlobal_color(G, cSetting_seq_view_label_color);
    float *label_color = ColorGet(G, label_color_index);
    copy3f(label_color, overlay_color);
    bg_color = SettingGet_3fv(G, NULL, NULL, cSetting_bg_rgb);
    overlay_color[0] = overlay_color[0] - bg_color[0];
    overlay_color[1] = overlay_color[1] - bg_color[1];
    overlay_color[2] = overlay_color[2] - bg_color[2];
    if(diff3f(overlay_color, bg_color) < 0.25)
      zero3f(overlay_color);

    if(I->ScrollBarActive) {
      ScrollBarSetBox(I->ScrollBar, I->Block->rect.bottom + I->ScrollBarWidth,
                      I->Block->rect.left + I->ScrollBarMargin,
                      I->Block->rect.bottom + 2,
                      I->Block->rect.right - I->ScrollBarMargin);
      ScrollBarDoDraw(I->ScrollBar);
      y += I->ScrollBarWidth;
      I->NSkip = (int) ScrollBarGetValue(I->ScrollBar);
    } else {
      I->NSkip = 0;
    }
    if(I->NRow) {               /* get current sequence sizes */
      int a, b;
      float black[3] = { 0, 0, 0 };
      float blue[3] = { 0.5, 0.5, 1.0 };
      float *cur_color;
      CSeqRow *row;
      CSeqCol *col;
      int xx, yy, ch_wid, pix_wid, tot_len;
      int y1 = y;
      int max_len = 0;
      int n_real = 0;
      int vis_size = I->VisSize;
      int first_allowed;
      int max_title_width = 0;
      char fill_char, *fill_str = SettingGetGlobal_s(G, cSetting_seq_view_fill_char);
      int unaligned_color_index =
        SettingGetGlobal_color(G, cSetting_seq_view_unaligned_color);
      int fill_color_index = SettingGetGlobal_color(G, cSetting_seq_view_fill_color);
      int unaligned_mode = SettingGetGlobal_i(G, cSetting_seq_view_unaligned_mode);
      float *unaligned_color;
      float *fill_color;

      if(unaligned_color_index == -1) {
        switch (unaligned_mode) {
        case 3:
          unaligned_color_index = -1;
          break;
        default:
          unaligned_color_index = fill_color_index;
          break;
        }
      }
      fill_color = ColorGet(G, fill_color_index);
      if(unaligned_color_index < 0) {
        unaligned_color = NULL;
      } else {
        unaligned_color = ColorGet(G, unaligned_color_index);
      }

      if(fill_str && fill_str[0]) {
        fill_char = fill_str[0];
        if(fill_char == ' ')
          fill_char = 0;
      } else
        fill_char = 0;
      /* measure titles */

      for(a = I->NRow - 1; a >= 0; a--) {
        row = I->Row + a;
        col = row->col;
        if(row->label_flag || row->column_label_flag) {
          row->title_width = col->offset + (col->stop - col->start);
          if(max_title_width < row->title_width)
            max_title_width = row->title_width;
        }
      }

      /* draw titles */

      cur_color = overlay_color;
      TextSetColor(G, cur_color);
      for(a = I->NRow - 1; a >= 0; a--) {
        row = I->Row + a;
        yy = y1 - 2;
        col = row->col;
        if((row->label_flag || row->column_label_flag) && row->nCol) {
          row->title_width = col->offset + (col->stop - col->start);
          xx =
            x + I->CharMargin + I->CharWidth * (col->offset +
                                                (max_title_width - row->title_width));
          ch_wid = (col->stop - col->start);
          pix_wid = I->CharWidth * ch_wid;
          tot_len = col->offset + ch_wid - I->NSkip;
          if(tot_len <= vis_size) {
            TextDrawSubStrFast(G, row->txt, xx, y1, col->start, ch_wid);
          }
        }
        y1 += I->LineHeight;
      }

      y1 = y;
      for(a = I->NRow - 1; a >= 0; a--) {
        row = I->Row + a;
        cur_color = overlay_color;
        glColor3fv(cur_color);
        yy = y1 - 2;
        if(max_len < row->ext_len)
          max_len = row->ext_len;
        if(!row->label_flag)
          n_real++;

        if(row->label_flag) {
          first_allowed = I->NSkip + max_title_width;
        } else if(row->column_label_flag) {
          first_allowed = I->NSkip + max_title_width + 1;
        } else
          first_allowed = I->NSkip;

        for(b = 1; b < row->nCol; b++) {

          if(row->label_flag && (b > 1))
            first_allowed = I->NSkip + max_title_width + 1;

          col = row->col + b;
          if(col->offset >= first_allowed) {
            xx = x + I->CharMargin + I->CharWidth * (col->offset - I->NSkip);
            ch_wid = (col->stop - col->start);
            pix_wid = I->CharWidth * ch_wid;
            tot_len = col->offset + ch_wid - I->NSkip;
            if(tot_len <= vis_size) {
              if(row->label_flag) {
                TextSetColor(G, cur_color);
                glColor3fv(cur_color);
              } else if(col->unaligned && unaligned_color) {
                float tmp_color[3];
                float *v = ColorGet(G, col->color);
                switch (unaligned_mode) {
                case 1:
                case 4:
                  average3f(v, bg_color, tmp_color);
                  TextSetColor(G, tmp_color);
                  glColor3fv(tmp_color);
                  break;
                case 2:
                case 5:
                  average3f(v, unaligned_color, tmp_color);
                  TextSetColor(G, tmp_color);
                  glColor3fv(tmp_color);
                  break;
                default:
                  TextSetColor(G, unaligned_color);
                  glColor3fv(unaligned_color);
                  break;
                }
              } else {
                float *v = ColorGet(G, col->color);
                TextSetColor(G, v);
                glColor3fv(v);
              }
              if(col->inverse) {
                glBegin(GL_POLYGON);
                glVertex2i(xx, yy);
                glVertex2i(xx, yy + I->LineHeight - 1);
                glVertex2i(xx + pix_wid, yy + I->LineHeight - 1);
                glVertex2i(xx + pix_wid, yy);
                glEnd();
                TextSetColor(G, black);
              }
              TextDrawSubStrFast(G, row->txt, xx, y1, col->start, ch_wid);
            }
          }
        }

        if(fill_char) {

          TextSetColor(G, fill_color);

          for(b = 0; b < row->nFill; b++) {

            col = row->fill + b;
            if(col->offset >= first_allowed) {
              xx = x + I->CharMargin + I->CharWidth * (col->offset - I->NSkip);
              ch_wid = (col->stop - col->start);
              pix_wid = I->CharWidth * ch_wid;
              tot_len = col->offset + ch_wid - I->NSkip;
              if(tot_len <= vis_size) {
                TextDrawCharRepeat(G, fill_char, xx, y1, col->start, ch_wid);
              }
            }
          }
        }

        y1 += I->LineHeight;
      }

      if(I->Handler->box_active) {
        int box_row = I->Handler->box_row;
        if((box_row >= 0) && (box_row < I->NRow)) {
          int start_col = I->Handler->box_start_col;
          int stop_col = I->Handler->box_stop_col;
          if(start_col > stop_col) {
            register int tmp = stop_col;
            stop_col = start_col;
            start_col = tmp;
          }
          row = I->Row + box_row;
          if((start_col >= 0) && (start_col < row->nCol) &&
             (stop_col >= 0) && (stop_col < row->nCol)) {
            int xx2;
            CSeqCol *col2;
            col = row->col + start_col;
            col2 = row->col + stop_col;

            /* trim spacers (if any) */
            while(col->spacer && (start_col < stop_col)) {
              start_col++;
              col = row->col + start_col;
            }
            while(col2->spacer && (start_col < stop_col)) {
              stop_col--;
              col2 = row->col + stop_col;
            }

            yy = y + ((I->NRow - 1) - box_row) * I->LineHeight - 2;
            xx = x + I->CharMargin + I->CharWidth * (col->offset - I->NSkip);
            xx2 =
              x + I->CharMargin + I->CharWidth * (col2->offset +
                                                  (col2->stop - col2->start) - I->NSkip);
            glColor3fv(overlay_color);
            glBegin(GL_LINE_LOOP);
            glVertex2i(xx, yy);
            glVertex2i(xx, yy + I->LineHeight - 2);
            glVertex2i(xx2, yy + I->LineHeight - 2);
            glVertex2i(xx2, yy);
            glEnd();

          }
        }
      }
      if(I->ScrollBarActive) {
        int real_count = n_real;
        int mode = 0;
        float width = (float) (I->Block->rect.right - I->Block->rect.left);
        float start = 0, stop;
        int right = 0;
        float bot, top, cent;
        float height = (float) (I->ScrollBarWidth - I->ScrollBarMargin);
        int last_color = -1;
        cur_color = blue;
        for(a = 0; a < I->NRow; a++) {
          row = I->Row + a;
          if(!row->label_flag) {
            top =
              I->Block->rect.bottom + I->ScrollBarMargin + (height * real_count) / n_real;
            real_count--;
            bot =
              I->Block->rect.bottom + I->ScrollBarMargin + (height * real_count) / n_real;
            mode = 0;
            for(b = 0; b < row->nCol; b++) {
              col = row->col + b;
              if(col->inverse && (!mode)) {
                start = (width * col->offset) / max_len;
                right = col->offset + (col->stop - col->start);
                mode = 1;
                last_color = col->color;
                if(row->label_flag)
                  cur_color = overlay_color;
                else
                  cur_color = ColorGet(G, col->color);  /* is this safe? should be for single-threading */
              } else if((!col->inverse) && (mode)) {
                if(b) {
                  stop =
                    (width * (col[-1].offset + col[-1].stop - col[-1].start)) / max_len;
                } else {
                  stop = (width * col->offset) / max_len;
                }
                if((stop - start) < 1.0F) {
                  cent = (stop + start) * 0.5F;
                  start = cent - 0.5F;
                  stop = cent + 0.5F;
                }

                glColor3fv(cur_color);
                glBegin(GL_POLYGON);
                glVertex2f(start, bot);
                glVertex2f(start, top);
                glVertex2f(stop, top);
                glVertex2f(stop, bot);
                glEnd();
                mode = 0;
              } else if(col->inverse && mode) {
                if(last_color != col->color) {
                  if(b) {
                    stop =
                      (width * (col[-1].offset + col[-1].stop - col[-1].start)) / max_len;
                  } else {
                    stop = (width * col->offset) / max_len;
                  }
                  if((stop - start) < 1.0F) {
                    cent = (stop + start) * 0.5F;
                    start = cent - 0.5F;
                    stop = cent + 0.5F;
                  }
                  glColor3fv(cur_color);
                  glBegin(GL_POLYGON);
                  glVertex2f(start, bot);
                  glVertex2f(start, top);
                  glVertex2f(stop, top);
                  glVertex2f(stop, bot);
                  glEnd();
                  start = (width * col->offset) / max_len;
                  last_color = col->color;
                  if(row->label_flag)
                    cur_color = overlay_color;
                  else
                    cur_color = ColorGet(G, col->color);        /* is this safe? should be for single-threading */
                }
                right = col->offset + (col->stop - col->start);

              }
            }

            if(mode) {
              stop = width * right / max_len;
              if((stop - start) < 1.0F) {
                cent = (stop + start) * 0.5F;
                start = cent - 0.5F;
                stop = cent + 0.5F;
              }
              glColor3fv(cur_color);
              glBegin(GL_POLYGON);
              glVertex2f(start, bot);
              glVertex2f(start, top);
              glVertex2f(stop, top);
              glVertex2f(stop, bot);
              glEnd();
            }

          }
        }

        ScrollBarDrawHandle(I->ScrollBar, 0.35F);
      }
    }
  }
}

int SeqInit(PyMOLGlobals * G)
{
  register CSeq *I = NULL;
  if((I = (G->Seq = Calloc(CSeq, 1)))) {

    I->Block = OrthoNewBlock(G, NULL);
    I->Block->fClick = SeqClick;
    I->Block->fDraw = SeqDraw;
    I->Block->fDrag = SeqDrag;
    I->Block->fRelease = SeqRelease;
    I->Block->fReshape = SeqReshape;
    I->Block->active = true;
    I->Block->TextColor[0] = 1.0;
    I->Block->TextColor[1] = 0.75;
    I->Block->TextColor[2] = 0.75;
    OrthoAttach(G, I->Block, cOrthoTool);
    I->DragFlag = false;
    I->ScrollBarActive = true;
    I->ScrollBar = ScrollBarNew(G, true);
    ScrollBarSetValue(I->ScrollBar, 0);
    I->Row = NULL;
    I->NRow = 0;
    I->Dirty = true;
    I->ScrollBarWidth = 16;
    I->ScrollBarMargin = 2;
    I->LineHeight = 13;
    I->CharMargin = 2;
    I->LastRow = -1;
    I->CharWidth = 8;
    return 1;
  } else
    return 0;
}

static void SeqPurgeRowVLA(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;
  if(I->Row) {
    int a;
    CSeqRow *row;
    for(a = 0; a < I->NRow; a++) {
      row = I->Row + a;
      VLAFreeP(row->txt);
      VLAFreeP(row->col);
      VLAFreeP(row->fill);
      VLAFreeP(row->char2col);
      VLAFreeP(row->atom_lists);
    }
    VLAFreeP(I->Row);
  }
}

void SeqSetRowVLA(PyMOLGlobals * G, CSeqRow * row, int nRow)
{
  register CSeq *I = G->Seq;
  SeqPurgeRowVLA(G);
  I->Row = row;
  I->NRow = nRow;
}

void SeqFree(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;

  SeqPurgeRowVLA(G);
  if(I->ScrollBar)
    ScrollBarFree(I->ScrollBar);
  OrthoFreeBlock(G, I->Block);
  FreeP(G->Seq);
}

Block *SeqGetBlock(PyMOLGlobals * G)
{
  register CSeq *I = G->Seq;
  {
    return (I->Block);
  }
}

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