void ShowHideManager::ShowDomainsWithHighlights(const StructureSet *set)
{
// first, show all highlighted stuff
MakeAllVisible();
if (!GlobalMessenger()->IsAnythingHighlighted()) return;
ShowSelectedResidues(set);
// then, also show all domains that contain highlighted residues
StructureSet::ObjectList::const_iterator o, oe = set->objects.end();
for (o=set->objects.begin(); o!=oe; ++o) {
ChemicalGraph::MoleculeMap::const_iterator m, me = (*o)->graph->molecules.end();
for (m=(*o)->graph->molecules.begin(); m!=me; ++m) {
Molecule::ResidueMap::const_iterator r, re = m->second->residues.end();
// find domains in this molecule that have highlights
map < int , bool > domains;
int domain;
for (r=m->second->residues.begin(); r!=re; ++r) {
if (GlobalMessenger()->IsHighlighted(m->second, r->first)) {
domain = m->second->residueDomains[r->first - 1];
if (domain != Molecule::NO_DOMAIN_SET)
domains[domain] = true;
}
}
// now show all residues in these domains
for (r=m->second->residues.begin(); r!=re; ++r) {
domain = m->second->residueDomains[r->first - 1];
if (domain != Molecule::NO_DOMAIN_SET && domains.find(domain) != domains.end())
Show(r->second, true);
}
}
}
}
void ViewerWindowBase::OnCacheHighlights(wxCommandEvent& event)
{
if (event.GetId() == MID_CACHE_HIGHLIGHTS)
GlobalMessenger()->CacheHighlights();
else if (event.GetId() == MID_RESTORE_CACHED_HIGHLIGHTS)
GlobalMessenger()->RestoreCachedHighlights();
}
void SequenceViewer::CreateSequenceWindow(bool showNow)
{
if (sequenceWindow) {
sequenceWindow->Show(showNow);
if (showNow)
GlobalMessenger()->PostRedrawSequenceViewer(this);
} else {
SequenceDisplay *display = GetCurrentDisplay();
if (display) {
sequenceWindow = new SequenceViewerWindow(this);
#ifdef __WXMAC__
// Nudge down a bit to compensate for the menubar at the top of the screen
wxPoint p = sequenceWindow->GetPosition();
p.y += 20;
sequenceWindow->Move(p);
#endif
sequenceWindow->NewDisplay(display, true);
sequenceWindow->ScrollToColumn(display->GetStartingColumn());
sequenceWindow->Show(showNow);
// ScrollTo causes immediate redraw, so don't need a second one
GlobalMessenger()->UnPostRedrawSequenceViewer(this);
}
}
}
void ShowHideManager::ShowSelectedResidues(const StructureSet *set)
{
MakeAllVisible();
if (!GlobalMessenger()->IsAnythingHighlighted()) return;
StructureSet::ObjectList::const_iterator o, oe = set->objects.end();
for (o=set->objects.begin(); o!=oe; ++o) {
bool anyResidueInObjectVisible = false;
ChemicalGraph::MoleculeMap::const_iterator m, me = (*o)->graph->molecules.end();
for (m=(*o)->graph->molecules.begin(); m!=me; ++m) {
Molecule::ResidueMap::const_iterator r, re = m->second->residues.end();
bool anyResidueInMoleculeVisible = false;
for (r=m->second->residues.begin(); r!=re; ++r) {
if (!GlobalMessenger()->IsHighlighted(m->second, r->first))
Show(r->second, false);
else
anyResidueInMoleculeVisible = anyResidueInObjectVisible = true;
}
if (!anyResidueInMoleculeVisible) {
for (r=m->second->residues.begin(); r!=re; ++r)
Show(r->second, true); // un-flag individual residues
Show(m->second, false); // flag whole molecule as hidden
}
}
if (!anyResidueInObjectVisible) {
for (m=(*o)->graph->molecules.begin(); m!=me; ++m)
Show(m->second, true); // un-flag individual molecules
Show(*o, false); // flag whole object as hidden
}
}
}
void ViewerWindowBase::NewDisplay(SequenceDisplay *display, bool enableSelectByColumn)
{
viewerWidget->AttachAlignment(display);
GlobalMessenger()->PostRedrawAllSequenceViewers();
menuBar->EnableTop(menuBar->FindMenu("Edit"), display->IsEditable());
menuBar->EnableTop(menuBar->FindMenu("Unaligned Justification"), display->IsEditable());
menuBar->Enable(MID_SELECT_COLS, enableSelectByColumn);
viewer->SetUndoRedoMenuStates();
}
// same as hitting done button
void PreferencesDialog::OnCloseWindow(wxCloseEvent& event)
{
bool okay = true, qualityChanged = false;
// set values if changed
try {
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_ATOM_SLICES, iAtomSlices, &qualityChanged);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_ATOM_STACKS, iAtomStacks, &qualityChanged);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_BOND_SIDES, iBondSides, &qualityChanged);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_WORM_SIDES, iWormSides, &qualityChanged);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_WORM_SEGMENTS, iWormSegments, &qualityChanged);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_QUALITY_HELIX_SIDES, iHelixSides, &qualityChanged);
SET_BOOL_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_HIGHLIGHTS_ON, ID_C_HIGHLIGHT, &qualityChanged);
SET_RADIO_REGISTRY_VALUE_IF_DIFFERENT(REG_QUALITY_SECTION,
REG_PROJECTION_TYPE, ID_RADIOBOX, &qualityChanged);
SET_BOOL_REGISTRY_VALUE_IF_DIFFERENT(REG_CACHE_SECTION, REG_CACHE_ENABLED, ID_C_CACHE_ON, 0);
DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tCache, ID_T_CACHE_FOLDER, wxTextCtrl)
SET_STRING_REGISTRY_VALUE_IF_DIFFERENT(REG_CACHE_SECTION, REG_CACHE_FOLDER, tCache);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_CACHE_SECTION, REG_CACHE_MAX_SIZE, iCacheSize, 0);
SET_BOOL_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, ID_C_ANNOT_RO, 0);
#ifdef __WXGTK__
DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tLaunch, ID_T_LAUNCH, wxTextCtrl)
SET_STRING_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_BROWSER_LAUNCH, tLaunch);
#endif
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_MAX_N_STRUCTS, iMaxStructs, 0);
SET_INTEGER_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_FOOTPRINT_RES, iFootRes, 0);
SET_DOUBLE_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_STEREO_SEPARATION, fSeparation, 0);
SET_BOOL_REGISTRY_VALUE_IF_DIFFERENT(REG_ADVANCED_SECTION, REG_PROXIMAL_STEREO, ID_C_PROXIMAL, 0);
// Limit cache size to current value now
int size;
if (iCacheSize->GetInteger(&size)) TruncateCache(size);
} catch (const char *err) {
ERRORMSG("Error setting registry values - " << err);
okay = false;
}
// close dialog only if all user values are legit
if (okay) {
if (qualityChanged) GlobalMessenger()->PostRedrawAllStructures();
EndModal(wxOK);
} else {
if (event.CanVeto())
event.Veto();
}
}
void ViewerWindowBase::UpdateDisplay(SequenceDisplay *display)
{
int vsX, vsY; // to preserve scroll position
viewerWidget->GetScroll(&vsX, &vsY);
viewerWidget->AttachAlignment(display, vsX, vsY);
menuBar->EnableTop(menuBar->FindMenu("Edit"), display->IsEditable());
menuBar->EnableTop(menuBar->FindMenu("Unaligned Justification"), display->IsEditable());
GlobalMessenger()->PostRedrawAllSequenceViewers();
viewer->SetUndoRedoMenuStates();
UpdateGeometryViolations();
}
void ViewerWindowBase::OnFindPattern(wxCommandEvent& event)
{
// remember previous pattern
static wxString previousPattern;
static wxString previousMode("Replace");
// get pattern from user
PatternDialog dialog(this);
dialog.m_Pattern->SetValue(previousPattern);
dialog.m_Pattern->SetSelection(-1, -1);
dialog.m_Mode->SetStringSelection(previousMode);
int status = dialog.ShowModal();
wxString pattern = dialog.m_Pattern->GetValue();
if (status != wxID_OK || pattern.size() == 0)
return;
// add trailing period if not present (convenience for the user)
if (pattern[pattern.size() - 1] != '.') pattern += '.';
previousPattern = pattern;
previousMode = dialog.m_Mode->GetStringSelection();
// set up highlighting
Messenger::MoleculeHighlightMap restrictTo;
if (dialog.m_Mode->GetStringSelection() == "Within")
GlobalMessenger()->GetHighlights(&restrictTo);
if (dialog.m_Mode->GetStringSelection() == "Replace" || dialog.m_Mode->GetStringSelection() == "Within")
GlobalMessenger()->RemoveAllHighlights(true);
// highlight pattern from each (unique) sequence in the display
map < const Sequence * , bool > usedSequences;
const SequenceDisplay *display = viewer->GetCurrentDisplay();
for (unsigned int i=0; i<display->NRows(); ++i) {
const Sequence *sequence = display->GetSequenceForRow(i);
if (!sequence || usedSequences.find(sequence) != usedSequences.end()) continue;
usedSequences[sequence] = true;
if (!sequence->HighlightPattern(pattern.c_str(), restrictTo)) break;
}
}
static void PostRedrawEntity(const StructureObject *object, const Molecule *molecule, const Residue *residue)
{
if (residue) {
const Molecule *m;
if (residue->GetParentOfType(&m))
GlobalMessenger()->PostRedrawMolecule(m);
}
else if (molecule) {
GlobalMessenger()->PostRedrawMolecule(molecule);
}
else if (object) {
// redraw all prot/nuc molecules
ChemicalGraph::MoleculeMap::const_iterator m, me = object->graph->molecules.end();
for (m=object->graph->molecules.begin(); m!=me; ++m) {
if (m->second->IsProtein() || m->second->IsNucleotide())
GlobalMessenger()->PostRedrawMolecule(m->second);
}
}
GlobalMessenger()->PostRedrawAllSequenceViewers();
}
void ViewerWindowBase::OnJustification(wxCommandEvent& event)
{
for (int i=MID_LEFT; i<=MID_SPLIT; ++i)
menuBar->Check(i, (i == event.GetId()) ? true : false);
switch (event.GetId()) {
case MID_LEFT:
currentJustification = BlockMultipleAlignment::eLeft; break;
case MID_RIGHT:
currentJustification = BlockMultipleAlignment::eRight; break;
case MID_CENTER:
currentJustification = BlockMultipleAlignment::eCenter; break;
case MID_SPLIT:
currentJustification = BlockMultipleAlignment::eSplit; break;
}
GlobalMessenger()->PostRedrawSequenceViewer(viewer);
}
AnnotateDialog::AnnotateDialog(wxWindow *parent, StyleManager *manager, const StructureSet *set) :
wxDialog(parent, -1, "User Annotations", wxPoint(400, 100), wxDefaultSize, wxDEFAULT_DIALOG_STYLE),
styleManager(manager), structureSet(set)
{
// get the structure highlights present when this dialog is created
GlobalMessenger()->GetHighlightedResiduesWithStructure(&highlightedResidues);
// construct the panel
wxSizer *topSizer = SetupAnnotationControlDialog(this, false);
// fill in list boxes with available and displayed styles
ResetListBoxes();
// set initial button states
SetButtonStates();
// call sizer stuff
topSizer->Fit(this);
topSizer->SetSizeHints(this);
}
void ViewerWindowBase::OnShowGeomVltns(wxCommandEvent& event)
{
UpdateGeometryViolations();
GlobalMessenger()->PostRedrawSequenceViewer(viewer);
}
bool Sequence::HighlightPattern(const string& prositePattern, const MoleculeHighlightMap& restrictTo) const
{
bool retval = true;
try {
// update CRegexp if not the same pattern as before
static auto_ptr < CRegexp > regexp;
static string previousPrositePattern;
static int nGroups;
if (!regexp.get() || prositePattern != previousPrositePattern) {
// convert from ProSite syntax
string regexPattern;
if (!Prosite2Regex(prositePattern, ®exPattern, &nGroups))
throw "error converting ProSite to regex syntax";
// create pattern buffer
TRACEMSG("creating CRegexp with pattern '" << regexPattern << "'");
regexp.reset(new CRegexp(regexPattern, CRegexp::fCompile_ungreedy));
previousPrositePattern = prositePattern;
}
// do the search, finding all non-overlapping matches
int i, start = 0;
while (start < (int)Length()) {
// do the search
string ignore = regexp->GetMatch(sequenceString, start, 0, CRegexp::fMatch_default, true);
if (regexp->NumFound() <= 0)
break;
// TRACEMSG("got match, num (sub)patterns: " << regexp->NumFound());
// for (i=0; i<regexp->NumFound(); ++i)
// TRACEMSG(" " << i << ": " << (regexp->GetResults(i)[0] + 1) << '-' << regexp->GetResults(i)[1]);
// check to see if this entire match is within the restricted set
bool addMatch = true;
if (restrictTo.size() > 0) {
MoleculeHighlightMap::const_iterator r = restrictTo.find(identifier);
if (r != restrictTo.end()) {
for (i=1; i<regexp->NumFound(); ++i) {
for (int j=regexp->GetResults(i)[0]; j<=regexp->GetResults(i)[1]-1; ++j) {
if (!r->second[j]) {
addMatch = false;
break;
}
}
if (!addMatch)
break;
}
} else
addMatch = false;
}
// parse the match subpatterns, highlight each subpattern range
if (addMatch)
for (i=1; i<regexp->NumFound(); ++i)
GlobalMessenger()->AddHighlights(this, regexp->GetResults(i)[0], regexp->GetResults(i)[1] - 1);
// start next search after the end of this one
start = regexp->GetResults(regexp->NumFound() - 1)[1];
}
} catch (const char *err) {
ERRORMSG("Sequence::HighlightPattern() - " << err);
retval = false;
} catch (exception& e) {
ERRORMSG("Sequence::HighlightPattern() - caught exception: " << e.what());
retval = false;
}
return retval;
}
// draw atom spheres and residue labels here
bool Residue::Draw(const AtomSet *atomSet) const
{
if (!atomSet) {
ERRORMSG("Residue::Draw(data) - NULL AtomSet*");
return false;
}
// verify presense of OpenGLRenderer
if (!parentSet->renderer) {
WARNINGMSG("Residue::Draw() - no renderer");
return false;
}
// get Molecule parent
const Molecule *molecule;
if (!GetParentOfType(&molecule)) return false;
// get object parent
const StructureObject *object;
if (!GetParentOfType(&object)) return false;
// is this residue labeled?
const StyleSettings& settings = parentSet->styleManager->GetStyleForResidue(object, molecule->id, id);
bool proteinLabel = (IsAminoAcid() && settings.proteinLabels.spacing > 0 &&
(id-1)%settings.proteinLabels.spacing == 0);
bool nucleotideLabel = (IsNucleotide() && settings.nucleotideLabels.spacing > 0 &&
(id-1)%settings.nucleotideLabels.spacing == 0);
bool overlayEnsembles = parentSet->showHideManager->OverlayConfEnsembles();
AtomStyle atomStyle;
const AtomCoord *atom, *l1 = NULL, *l2 = NULL, *l3 = NULL;
Vector labelColor;
bool alphaVisible = false, alphaOnly = false;
// iterate atoms; key is atomID
AtomInfoMap::const_iterator a, ae = atomInfos.end();
for (a=atomInfos.begin(); a!=ae; ++a) {
// get AtomCoord* for appropriate altConf
AtomPntr ap(molecule->id, id, a->first);
atom = atomSet->GetAtom(ap, overlayEnsembles, true);
if (!atom) continue;
// get Style
if (!parentSet->styleManager->GetAtomStyle(this, ap, atom, &atomStyle))
return false;
// highlight atom if necessary
if (atomStyle.isHighlighted)
atomStyle.color = GlobalColors()->Get(Colors::eHighlight);
// draw the atom
if (atomStyle.style != StyleManager::eNotDisplayed && atomStyle.radius > 0.0)
parentSet->renderer->DrawAtom(atom->site, atomStyle);
// store coords for positioning label, based on backbone coordinates
if ((proteinLabel || nucleotideLabel) && a->second->classification != eSideChainAtom) {
if (IsAminoAcid()) {
if (a->second->name == " CA ") {
l1 = atom;
labelColor = atomStyle.color;
alphaVisible = (atomStyle.style != StyleManager::eNotDisplayed);
}
else if (a->second->name == " C ") l2 = atom;
else if (a->second->name == " N ") l3 = atom;
} else if (IsNucleotide()) {
if (a->second->name == " P ") {
l1 = atom;
labelColor = atomStyle.color;
alphaVisible = (atomStyle.style != StyleManager::eNotDisplayed);
}
// labeling by alphas seems to work better for nucleotides
// else if (a->second->name == " C4*") l2 = atom;
// else if (a->second->name == " C5*") l3 = atom;
}
}
}
// if not all backbone atoms present (e.g. alpha only), use alpha coords of neighboring residues
if (l1 && (!l2 || !l3)) {
Molecule::ResidueMap::const_iterator prevRes, nextRes;
const AtomCoord *prevAlpha, *nextAlpha;
if ((prevRes=molecule->residues.find(id - 1)) != molecule->residues.end() &&
prevRes->second->alphaID != NO_ALPHA_ID &&
(prevAlpha=atomSet->GetAtom(AtomPntr(molecule->id, id - 1, prevRes->second->alphaID))) != NULL &&
(nextRes=molecule->residues.find(id + 1)) != molecule->residues.end() &&
nextRes->second->alphaID != NO_ALPHA_ID &&
(nextAlpha=atomSet->GetAtom(AtomPntr(molecule->id, id + 1, nextRes->second->alphaID))) != NULL)
{
l2 = prevAlpha;
l3 = nextAlpha;
alphaOnly = true;
}
}
// draw residue (but not terminus) labels, assuming we have the necessary coordinates and
// that alpha atoms are visible
if (alphaVisible && (proteinLabel|| nucleotideLabel)) {
Vector labelPosition;
CNcbiOstrstream oss;
double contrast = Colors::IsLightColor(settings.backgroundColor) ? 0 : 1;
// protein label
if (IsAminoAcid() && l1 && l2 && l3) {
// position
if (alphaOnly) {
Vector forward = - ((l2->site - l1->site) + (l3->site - l1->site));
forward.normalize();
labelPosition = l1->site + 1.5 * forward;
} else {
Vector up = vector_cross(l2->site - l1->site, l3->site - l1->site);
up.normalize();
Vector forward = (-((l2->site - l1->site) + (l3->site - l1->site)) / 2);
forward.normalize();
labelPosition = l1->site + 1.5 * forward + 1.5 * up;
}
// text
if (settings.proteinLabels.type == StyleSettings::eOneLetter) {
oss << code;
} else if (settings.proteinLabels.type == StyleSettings::eThreeLetter) {
for (unsigned int i=0; i<nameGraph.size() && i<3; ++i)
oss << ((i == 0) ? (char) toupper((unsigned char) nameGraph[0]) : (char) tolower((unsigned char) nameGraph[i]));
}
// add number if necessary
if (settings.proteinLabels.numbering == StyleSettings::eSequentialNumbering)
oss << ' ' << id;
else if (settings.proteinLabels.numbering == StyleSettings::ePDBNumbering)
oss << namePDB;
// contrasting color? (default to CA's color)
if (settings.proteinLabels.white) labelColor.Set(contrast, contrast, contrast);
}
// nucleotide label
else if (IsNucleotide() && l2 && l3) {
if (alphaOnly) {
Vector forward = - ((l2->site - l1->site) + (l3->site - l1->site));
forward.normalize();
labelPosition = l1->site + 3 * forward;
} else {
labelPosition = l3->site + 3 * (l3->site - l2->site);
}
// text
if (settings.nucleotideLabels.type == StyleSettings::eOneLetter) {
oss << code;
} else if (settings.nucleotideLabels.type == StyleSettings::eThreeLetter) {
for (unsigned int i=0; i<3; ++i)
if (nameGraph.size() > i && nameGraph[i] != ' ')
oss << nameGraph[i];
}
// add number if necessary
if (settings.nucleotideLabels.numbering == StyleSettings::eSequentialNumbering)
oss << ' ' << id;
else if (settings.nucleotideLabels.numbering == StyleSettings::ePDBNumbering)
oss << namePDB;
// contrasting color? (default to C4*'s color)
if (settings.nucleotideLabels.white) labelColor.Set(contrast, contrast, contrast);
}
// draw label
if (oss.pcount() > 0) {
string labelText = (string) CNcbiOstrstreamToString(oss);
// apply highlight color if necessary
if (GlobalMessenger()->IsHighlighted(molecule, id))
labelColor = GlobalColors()->Get(Colors::eHighlight);
parentSet->renderer->DrawLabel(labelText, labelPosition, labelColor);
}
}
return true;
}
void AnnotateDialog::OnButton(wxCommandEvent& event)
{
switch (event.GetId()) {
case ID_B_NEW:
NewAnnotation();
break;
case ID_B_EDIT:
EditAnnotation();
break;
case ID_B_MOVE:
MoveAnnotation();
break;
case ID_B_DELETE:
DeleteAnnotation();
break;
case ID_B_SHOW: {
DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(available, ID_L_AVAILABLE, wxListBox)
if (available->GetSelection() >= 0) {
StyleManager::UserAnnotation *annotation = ANNOT_FROM_CLIENT_DATA(available);
if (annotation) {
GlobalMessenger()->SetHighlights(annotation->residues);
structureSet->showHideManager->ShowDomainsWithHighlights(structureSet);
highlightedResidues = annotation->residues;
} else
ERRORMSG("AnnotateDialog::OnButton() - error highlighting annotation #"
<< available->GetSelection());
}
break;
}
case ID_B_MOVE_UP: case ID_B_MOVE_DOWN: {
DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(available, ID_L_AVAILABLE, wxListBox)
if (available->GetSelection() >= 0) {
StyleManager::UserAnnotation *annotation = ANNOT_FROM_CLIENT_DATA(available);
if (annotation && styleManager->
MoveUserAnnotation(annotation, (event.GetId() == ID_B_MOVE_UP)))
ResetListBoxes();
else
ERRORMSG("AnnotateDialog::OnButton() - error reprioritizing annotation #"
<< available->GetSelection());
}
break;
}
case ID_B_TURN_OFF: case ID_B_TURN_ON: {
int listID = (event.GetId() == ID_B_TURN_OFF) ? ID_L_DISPLAYED : ID_L_AVAILABLE;
DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(listBox, listID, wxListBox)
if (listBox->GetSelection() >= 0) {
StyleManager::UserAnnotation *annotation = ANNOT_FROM_CLIENT_DATA(listBox);
if (annotation && styleManager->
DisplayUserAnnotation(annotation, (event.GetId() == ID_B_TURN_ON)))
ResetListBoxes();
else
ERRORMSG("AnnotateDialog::OnButton() - error toggling annotation #"
<< listBox->GetSelection());
}
break;
}
case ID_B_DONE:
EndModal(wxOK);
break;
default:
event.Skip();
}
SetButtonStates();
}