void SequenceViewer::DisplayAlignment(BlockMultipleAlignment *alignment)
{
SequenceDisplay *display = new SequenceDisplay(true, viewerWindow);
for (unsigned int row=0; row<alignment->NRows(); ++row)
display->AddRowFromAlignment(row, alignment);
// set starting scroll to a few residues left of the first aligned block
display->SetStartingColumn(alignment->GetFirstAlignedBlockPosition() - 5);
AlignmentList alignments;
alignments.push_back(alignment);
InitData(&alignments, display);
if (sequenceWindow)
sequenceWindow->UpdateDisplay(display);
else if (IsWindowedMode())
CreateSequenceWindow(false);
}
void SequenceViewer::DisplaySequences(const SequenceList *sequenceList)
{
SequenceDisplay *display = new SequenceDisplay(false, viewerWindow);
// populate each line of the display with one sequence, with blank lines inbetween
SequenceList::const_iterator s, se = sequenceList->end();
for (s=sequenceList->begin(); s!=se; ++s) {
// only do sequences from structure if this is a single-structure data file
if (!(*s)->parentSet->IsMultiStructure() &&
(*s)->parentSet->objects.front()->mmdbID != (*s)->identifier->mmdbID) continue;
if (display->NRows() > 0) display->AddRowFromString("");
// whole sequence on one row
display->AddRowFromSequence(*s, 0, (*s)->Length() - 1);
}
InitData(NULL, display);
if (sequenceWindow)
sequenceWindow->UpdateDisplay(display);
else if (IsWindowedMode())
CreateSequenceWindow(false);
}
static void SetRegistryDefaults(void)
{
// default log window startup
RegistrySetBoolean(REG_CONFIG_SECTION, REG_SHOW_LOG_ON_START, false);
RegistrySetString(REG_CONFIG_SECTION, REG_FAVORITES_NAME, NO_FAVORITES_FILE);
RegistrySetInteger(REG_CONFIG_SECTION, REG_MT_DIALOG_POS_X, 50);
RegistrySetInteger(REG_CONFIG_SECTION, REG_MT_DIALOG_POS_Y, 50);
RegistrySetInteger(REG_CONFIG_SECTION, REG_MT_DIALOG_SIZE_W, 400);
RegistrySetInteger(REG_CONFIG_SECTION, REG_MT_DIALOG_SIZE_H, 400);
// default animation controls
RegistrySetInteger(REG_ANIMATION_SECTION, REG_SPIN_DELAY, 50);
RegistrySetDouble(REG_ANIMATION_SECTION, REG_SPIN_INCREMENT, 2.0),
RegistrySetInteger(REG_ANIMATION_SECTION, REG_FRAME_DELAY, 500);
// default quality settings
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_ATOM_SLICES, 10);
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_ATOM_STACKS, 8);
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_BOND_SIDES, 6);
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_WORM_SIDES, 6);
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_WORM_SEGMENTS, 6);
RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_HELIX_SIDES, 12);
RegistrySetBoolean(REG_QUALITY_SECTION, REG_HIGHLIGHTS_ON, true);
RegistrySetString(REG_QUALITY_SECTION, REG_PROJECTION_TYPE, "Perspective");
if (IsWindowedMode()) {
// default font for OpenGL (structure window)
wxFont *font = wxFont::New(
#if defined(__WXMSW__)
12,
#elif defined(__WXGTK__)
14,
#elif defined(__WXMAC__)
14,
#endif
wxSWISS, wxNORMAL, wxBOLD, false);
if (font && font->Ok())
RegistrySetString(REG_OPENGL_FONT_SECTION, REG_FONT_NATIVE_FONT_INFO,
font->GetNativeFontInfoDesc().c_str());
else
ERRORMSG("Can't create default structure window font");
if (font) delete font;
// default font for sequence viewers
font = wxFont::New(
#if defined(__WXMSW__)
10,
#elif defined(__WXGTK__)
14,
#elif defined(__WXMAC__)
12,
#endif
wxROMAN, wxNORMAL, wxNORMAL, false);
if (font && font->Ok())
RegistrySetString(REG_SEQUENCE_FONT_SECTION, REG_FONT_NATIVE_FONT_INFO,
font->GetNativeFontInfoDesc().c_str());
else
ERRORMSG("Can't create default sequence window font");
if (font) delete font;
}
// default cache settings
RegistrySetBoolean(REG_CACHE_SECTION, REG_CACHE_ENABLED, true);
if (GetPrefsDir().size() > 0)
RegistrySetString(REG_CACHE_SECTION, REG_CACHE_FOLDER, GetPrefsDir() + "cache");
else
RegistrySetString(REG_CACHE_SECTION, REG_CACHE_FOLDER, GetProgramDir() + "cache");
RegistrySetInteger(REG_CACHE_SECTION, REG_CACHE_MAX_SIZE, 25);
// default advanced options
RegistrySetBoolean(REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, true);
#ifdef __WXGTK__
RegistrySetString(REG_ADVANCED_SECTION, REG_BROWSER_LAUNCH,
// for launching netscape in a separate window
"( netscape -noraise -remote 'openURL(<URL>,new-window)' || netscape '<URL>' ) >/dev/null 2>&1 &"
// for launching netscape in an existing window
// "( netscape -raise -remote 'openURL(<URL>)' || netscape '<URL>' ) >/dev/null 2>&1 &"
);
#endif
RegistrySetInteger(REG_ADVANCED_SECTION, REG_MAX_N_STRUCTS, 10);
RegistrySetInteger(REG_ADVANCED_SECTION, REG_FOOTPRINT_RES, 0);
// default stereo options
RegistrySetDouble(REG_ADVANCED_SECTION, REG_STEREO_SEPARATION, 5.0);
RegistrySetBoolean(REG_ADVANCED_SECTION, REG_PROXIMAL_STEREO, true);
}
