"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer1/Seq.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

[ To the main PyMOL source changes report ]

Seq.cpp  (pymol-open-source-2.2.0):Seq.cpp  (pymol-open-source-2.3.0)
skipping to change at line 37 skipping to change at line 37
#include "Scene.h" #include "Scene.h"
#include "Text.h" #include "Text.h"
#include "Seeker.h" #include "Seeker.h"
#include "Menu.h" #include "Menu.h"
#include "Executive.h" #include "Executive.h"
#include "Ortho.h" #include "Ortho.h"
#include "CGO.h" #include "CGO.h"
struct _CSeq { struct CSeq : public Block {
::Block *Block; bool DragFlag { false };
int DragFlag; bool ScrollBarActive { true };
int ScrollBarActive; int NSkip {};
int NSkip; ScrollBar m_ScrollBar;
struct CScrollBar *ScrollBar; CSeqRow *Row { nullptr };
CSeqRow *Row; int NRow { 0 };
int NRow; int Size {};
int Size; int VisSize {};
int VisSize; int Changed {};
int Changed; bool Dirty { true };
int Dirty; int LineHeight { 13 };
int LineHeight; int CharWidth { 8 };
int CharWidth; int ScrollBarWidth { 16 };
int ScrollBarWidth; int ScrollBarMargin { 2 };
int ScrollBarMargin; int CharMargin { 2 };
int CharMargin; int LastRow { -1 };
int LastRow; CSeqHandler *Handler {}; /* borrowed pointer */
CSeqHandler *Handler; /* borrowed pointer */
CSeq(PyMOLGlobals * G) : Block(G), m_ScrollBar(G, true) {}
int click(int button, int x, int y, int mod) override;
void draw(CGO* orthoCGO) override;
int drag(int x, int y, int mod) override;
int release(int button, int x, int y, int mod) override;
void reshape(int width, int height) override;
}; };
static int SeqFindRowCol(PyMOLGlobals * G, int x, int y, int *row_num_ptr, static int SeqFindRowCol(PyMOLGlobals * G, int x, int y, int *row_num_ptr,
int *col_num_ptr, int fixed_row) int *col_num_ptr, int fixed_row)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
int result = 0; int result = 0;
int row_num = 0; int row_num = 0;
int col_num = 0; int col_num = 0;
if(I->ScrollBarActive) { if(I->ScrollBarActive) {
y -= DIP2PIXEL(I->ScrollBarWidth); y -= DIP2PIXEL(I->ScrollBarWidth);
} }
if(fixed_row >= 0) { if(fixed_row >= 0) {
row_num = fixed_row; row_num = fixed_row;
} else { } else {
row_num = (y - I->Block->rect.bottom) / DIP2PIXEL(I->LineHeight); row_num = (y - I->rect.bottom) / DIP2PIXEL(I->LineHeight);
row_num = (I->NRow - 1) - row_num; row_num = (I->NRow - 1) - row_num;
} }
if((row_num >= 0) && (row_num < I->NRow)) { if((row_num >= 0) && (row_num < I->NRow)) {
int char_num; int char_num;
CSeqRow *row; CSeqRow *row;
row = I->Row + row_num; row = I->Row + row_num;
char_num = (x - I->Block->rect.left - DIP2PIXEL(I->CharMargin)) / DIP2PIXEL( I->CharWidth); char_num = (x - I->rect.left - DIP2PIXEL(I->CharMargin)) / DIP2PIXEL(I->Char Width);
if(row->nCol && !row->label_flag) if(row->nCol && !row->label_flag)
if(char_num < I->VisSize) { if(char_num < I->VisSize) {
char_num += I->NSkip; char_num += I->NSkip;
if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) { if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) {
col_num = row->char2col[char_num]; col_num = row->char2col[char_num];
if(col_num) { if(col_num) {
col_num--; col_num--;
if(col_num < row->nCol) { if(col_num < row->nCol) {
result = true; result = true;
} else if(fixed_row >= 0) { } else if(fixed_row >= 0) {
skipping to change at line 127 skipping to change at line 134
I->Dirty = true; I->Dirty = true;
OrthoReshape(G, -1, -1, false); /* careful, this is recursive... */ OrthoReshape(G, -1, -1, false); /* careful, this is recursive... */
} }
if(I->Dirty) { if(I->Dirty) {
if(I->Handler->fRefresh) if(I->Handler->fRefresh)
I->Handler->fRefresh(G, I->Row); I->Handler->fRefresh(G, I->Row);
I->Dirty = false; I->Dirty = false;
} }
} }
static void SeqReshape(Block * block, int width, int height) void CSeq::reshape(int width, int height)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = m_G;
CSeq *I = G->Seq; CSeq *I = G->Seq;
BlockReshape(block, width, height); Block::reshape(width, height);
{ /* get current sequence sizes */ { /* get current sequence sizes */
int a; int a;
I->Size = 0; I->Size = 0;
for(a = 0; a < I->NRow; a++) { for(a = 0; a < I->NRow; a++) {
if(I->Row[a].ext_len > I->Size) if(I->Row[a].ext_len > I->Size)
I->Size = I->Row[a].ext_len; I->Size = I->Row[a].ext_len;
} }
} }
{ {
int extra; int extra;
I->VisSize = (I->Block->rect.right - I->Block->rect.left - 1) / DIP2PIXEL(I- I->VisSize = (I->rect.right - I->rect.left - 1) / DIP2PIXEL(I->CharWidth);
>CharWidth); /* printf("%d %d %d %d %d\n",cw,I->rect.right,I->rect.left,I->VisSize,I->
/* printf("%d %d %d %d %d\n",cw,I->Block->rect.right,I->Block->rect.left, Size); */
I->VisSize,I->Size); */
if(I->VisSize < 1) if(I->VisSize < 1)
I->VisSize = 1; I->VisSize = 1;
extra = I->Size - I->VisSize; extra = I->Size - I->VisSize;
if(extra <= 0) { if(extra <= 0) {
I->ScrollBarActive = false; I->ScrollBarActive = false;
} else { } else {
I->ScrollBarActive = true; I->ScrollBarActive = true;
ScrollBarSetLimits(I->ScrollBar, I->Size, I->VisSize); m_ScrollBar.setLimits(I->Size, I->VisSize);
} }
} }
} }
void SeqDirty(PyMOLGlobals * G) void SeqDirty(PyMOLGlobals * G)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
I->Dirty = true; I->Dirty = true;
SceneInvalidate(G); SceneInvalidate(G);
} }
void SeqChanged(PyMOLGlobals * G) void SeqChanged(PyMOLGlobals * G)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
I->Changed = true; I->Changed = true;
SceneInvalidate(G); SceneInvalidate(G);
} }
static int SeqDrag(Block * block, int x, int y, int mod) int CSeq::drag(int x, int y, int mod)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = m_G;
CSeq *I = G->Seq; CSeq *I = G->Seq;
int pass = 0; int pass = 0;
int row_num; int row_num;
int col_num; int col_num;
if(!pass) { if(!pass) {
if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) { if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) {
if(I->Handler) if(I->Handler)
if(I->Handler->fDrag) if(I->Handler->fDrag)
I->Handler->fDrag(G, I->Row, row_num, col_num, mod); I->Handler->fDrag(G, I->Row, row_num, col_num, mod);
OrthoDirty(G); OrthoDirty(G);
} }
} }
return (1); return (1);
} }
static int SeqRelease(Block * block, int button, int x, int y, int mod) int CSeq::release(int button, int x, int y, int mod)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = m_G;
CSeq *I = G->Seq; CSeq *I = G->Seq;
int pass = 0; 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) { if(!pass) {
int row_num; int row_num;
int col_num; int col_num;
if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) { if(SeqFindRowCol(G, x, y, &row_num, &col_num, I->LastRow)) {
if(I->Handler) if(I->Handler)
if(I->Handler->fRelease) if(I->Handler->fRelease)
I->Handler->fRelease(G, I->Row, button, row_num, col_num, mod); I->Handler->fRelease(G, I->Row, button, row_num, col_num, mod);
OrthoDirty(G); OrthoDirty(G);
} else { } else {
if(I->Handler) if(I->Handler)
skipping to change at line 244 skipping to change at line 242
} }
return (height); return (height);
} }
void SeqSetHandler(PyMOLGlobals * G, CSeqHandler * handler) void SeqSetHandler(PyMOLGlobals * G, CSeqHandler * handler)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
I->Handler = handler; I->Handler = handler;
} }
static int SeqClick(Block * block, int button, int x, int y, int mod) int CSeq::click(int button, int x, int y, int mod)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = m_G;
CSeq *I = G->Seq; CSeq *I = G->Seq;
int pass = 0; int pass = 0;
int row_num; int row_num;
int col_num; int col_num;
switch(button) {
case P_GLUT_BUTTON_SCROLL_FORWARD:
I->m_ScrollBar.moveBy(-1);
return 1;
case P_GLUT_BUTTON_SCROLL_BACKWARD:
I->m_ScrollBar.moveBy(1);
return 1;
}
if(I->ScrollBarActive) { if(I->ScrollBarActive) {
if((y - I->Block->rect.bottom) < DIP2PIXEL(I->ScrollBarWidth)) { if((y - rect.bottom) < DIP2PIXEL(I->ScrollBarWidth)) {
pass = 1; pass = 1;
ScrollBarDoClick(I->ScrollBar, button, x, y, mod); I->m_ScrollBar.click(button, x, y, mod);
} }
} }
if(!pass) { if(!pass) {
if(SeqFindRowCol(G, x, y, &row_num, &col_num, -1)) { if(SeqFindRowCol(G, x, y, &row_num, &col_num, -1)) {
if(I->Handler) if(I->Handler)
if(I->Handler->fClick) if(I->Handler->fClick)
I->Handler->fClick(G, I->Row, button, row_num, col_num, mod, x, y); I->Handler->fClick(G, I->Row, button, row_num, col_num, mod, x, y);
I->DragFlag = true; I->DragFlag = true;
I->LastRow = row_num; I->LastRow = row_num;
OrthoDirty(G); OrthoDirty(G);
skipping to change at line 286 skipping to change at line 294
if(I->Handler) if(I->Handler)
if(I->Handler->fClick) if(I->Handler->fClick)
I->Handler->fClick(G, I->Row, button, -1, -1, mod, x, y); I->Handler->fClick(G, I->Row, button, -1, -1, mod, x, y);
break; break;
} }
} }
} }
return (1); return (1);
} }
static void SeqDraw(Block * block ORTHOCGOARG) void CSeq::draw(CGO* orthoCGO)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = m_G;
CSeq *I = G->Seq; CSeq *I = G->Seq;
if(G->HaveGUI && G->ValidContext) { if(G->HaveGUI && G->ValidContext) {
int x = I->Block->rect.left; int x = rect.left;
int y = I->Block->rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + 1; int y = rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + 1;
float bg_color[3] = { 0.f, 0.f, 0.f }, overlay_color[3] = { 1.0F, 1.0F, 1.0F }; float bg_color[3] = { 0.f, 0.f, 0.f }, overlay_color[3] = { 1.0F, 1.0F, 1.0F };
int label_color_index = SettingGetGlobal_color(G, cSetting_seq_view_label_co lor); int label_color_index = SettingGetGlobal_color(G, cSetting_seq_view_label_co lor);
const float *label_color = ColorGet(G, label_color_index); const float *label_color = ColorGet(G, label_color_index);
copy3f(label_color, overlay_color); copy3f(label_color, overlay_color);
if (SettingGetGlobal_b(G, cSetting_bg_gradient)){ if (SettingGetGlobal_b(G, cSetting_bg_gradient)){
if(SettingGetGlobal_b(G, cSetting_seq_view_location)) { if(SettingGetGlobal_b(G, cSetting_seq_view_location)) {
copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb_bottom)), bg _color); copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb_bottom)), bg _color);
} else { } else {
copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb_top)), bg_co lor); copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb_top)), bg_co lor);
} }
} else { } else {
copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb)), bg_color); copy3f(ColorGet(G, SettingGetGlobal_color(G, cSetting_bg_rgb)), bg_color);
} }
if(!SettingGetGlobal_b(G, cSetting_seq_view_overlay)) { if(!SettingGetGlobal_b(G, cSetting_seq_view_overlay)) {
if (orthoCGO){ if (orthoCGO){
CGOColorv(orthoCGO, bg_color); CGOColorv(orthoCGO, bg_color);
} else { } else {
glColor3fv(bg_color); glColor3fv(bg_color);
} }
BlockFill(I->Block ORTHOCGOARGVAR); fill(orthoCGO);
} }
if(I->ScrollBarActive) { if(I->ScrollBarActive) {
ScrollBarSetBox(I->ScrollBar, I->Block->rect.bottom + DIP2PIXEL(I->ScrollB I->m_ScrollBar.setBox(rect.bottom + DIP2PIXEL(I->ScrollBarWidth),
arWidth), rect.left + DIP2PIXEL(I->ScrollBarMargin),
I->Block->rect.left + DIP2PIXEL(I->ScrollBarMargin), rect.bottom + DIP2PIXEL(2),
I->Block->rect.bottom + DIP2PIXEL(2), rect.right - DIP2PIXEL(I->ScrollBarMargin));
I->Block->rect.right - DIP2PIXEL(I->ScrollBarMargin)); I->m_ScrollBar.draw(orthoCGO);
ScrollBarDoDraw(I->ScrollBar ORTHOCGOARGVAR);
y += DIP2PIXEL(I->ScrollBarWidth); y += DIP2PIXEL(I->ScrollBarWidth);
I->NSkip = (int) ScrollBarGetValue(I->ScrollBar); I->NSkip = static_cast<int>(I->m_ScrollBar.getValue());
} else { } else {
I->NSkip = 0; I->NSkip = 0;
} }
if(I->NRow) { /* get current sequence sizes */ if(I->NRow) { /* get current sequence sizes */
int a, b; int a, b;
float black[3] = { 0, 0, 0 }; float black[3] = { 0, 0, 0 };
float blue[3] = { 0.5, 0.5, 1.0 }; float blue[3] = { 0.5, 0.5, 1.0 };
const float *cur_color; const float *cur_color;
CSeqRow *row; CSeqRow *row;
CSeqCol *col; CSeqCol *col;
skipping to change at line 594 skipping to change at line 602
glVertex2i(xx2, yy + DIP2PIXEL(I->LineHeight) - 2); glVertex2i(xx2, yy + DIP2PIXEL(I->LineHeight) - 2);
glVertex2i(xx2, yy); glVertex2i(xx2, yy);
glEnd(); glEnd();
} }
} }
} }
} }
if(I->ScrollBarActive) { if(I->ScrollBarActive) {
int real_count = n_real; int real_count = n_real;
int mode = 0; int mode = 0;
float width = (float) (I->Block->rect.right - I->Block->rect.left); float width = (float) (rect.right - rect.left);
float start = 0, stop; float start = 0, stop;
int right = 0; int right = 0;
float bot, top, cent; float bot, top, cent;
float height = (float) DIP2PIXEL(I->ScrollBarWidth - I->ScrollBarMargin) ; float height = (float) DIP2PIXEL(I->ScrollBarWidth - I->ScrollBarMargin) ;
int last_color = -1; int last_color = -1;
cur_color = blue; cur_color = blue;
for(a = 0; a < I->NRow; a++) { for(a = 0; a < I->NRow; a++) {
row = I->Row + a; row = I->Row + a;
if(!row->label_flag) { if(!row->label_flag) {
top = top =
I->Block->rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + (height * real_count) / n_real; rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + (height * real_count ) / n_real;
real_count--; real_count--;
bot = bot =
I->Block->rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + (height * real_count) / n_real; rect.bottom + DIP2PIXEL(I->ScrollBarMargin) + (height * real_count ) / n_real;
mode = 0; mode = 0;
for(b = 0; b < row->nCol; b++) { for(b = 0; b < row->nCol; b++) {
col = row->col + b; col = row->col + b;
if(col->inverse && (!mode)) { if(col->inverse && (!mode)) {
start = (width * col->offset) / max_len; start = (width * col->offset) / max_len;
right = col->offset + (col->stop - col->start); right = col->offset + (col->stop - col->start);
mode = 1; mode = 1;
last_color = col->color; last_color = col->color;
if(row->label_flag) if(row->label_flag)
cur_color = overlay_color; cur_color = overlay_color;
skipping to change at line 722 skipping to change at line 730
glVertex2f(start, bot); glVertex2f(start, bot);
glVertex2f(start, top); glVertex2f(start, top);
glVertex2f(stop, top); glVertex2f(stop, top);
glVertex2f(stop, bot); glVertex2f(stop, bot);
glEnd(); glEnd();
} }
} }
} }
} }
ScrollBarDrawHandle(I->ScrollBar, 0.35F ORTHOCGOARGVAR); I->m_ScrollBar.drawHandle(0.35F, orthoCGO);
} }
} }
} }
} }
int SeqInit(PyMOLGlobals * G) int SeqInit(PyMOLGlobals * G)
{ {
CSeq *I = NULL; CSeq *I = NULL;
if((I = (G->Seq = Calloc(CSeq, 1)))) { if((I = (G->Seq = new CSeq(G)))) {
I->Block = OrthoNewBlock(G, NULL); I->active = true;
I->Block->fClick = SeqClick; I->TextColor[0] = 1.0;
I->Block->fDraw = SeqDraw; I->TextColor[1] = 0.75;
I->Block->fDrag = SeqDrag; I->TextColor[2] = 0.75;
I->Block->fRelease = SeqRelease; OrthoAttach(G, I, cOrthoTool);
I->Block->fReshape = SeqReshape; I->m_ScrollBar.setValue(0);
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; return 1;
} else } else
return 0; return 0;
} }
static void SeqPurgeRowVLA(PyMOLGlobals * G) static void SeqPurgeRowVLA(PyMOLGlobals * G)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
if(I->Row) { if(I->Row) {
int a; int a;
skipping to change at line 793 skipping to change at line 783
SeqPurgeRowVLA(G); SeqPurgeRowVLA(G);
I->Row = row; I->Row = row;
I->NRow = nRow; I->NRow = nRow;
} }
void SeqFree(PyMOLGlobals * G) void SeqFree(PyMOLGlobals * G)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
SeqPurgeRowVLA(G); SeqPurgeRowVLA(G);
if(I->ScrollBar) DeleteP(G->Seq);
ScrollBarFree(I->ScrollBar);
OrthoFreeBlock(G, I->Block);
FreeP(G->Seq);
} }
Block *SeqGetBlock(PyMOLGlobals * G) Block *SeqGetBlock(PyMOLGlobals * G)
{ {
CSeq *I = G->Seq; CSeq *I = G->Seq;
{ {
return (I->Block); return (I);
} }
} }
 End of changes. 32 change blocks. 
92 lines changed or deleted 77 lines changed or added
To the C++ Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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