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);
}
}
}
bool SequenceViewer::ReplaceAlignment(const BlockMultipleAlignment *origAln, BlockMultipleAlignment *newAln)
{
AlignmentList& alignments = GetCurrentAlignments();
SequenceDisplay *display = GetCurrentDisplay();
// sanity checks
if (alignments.size() != 1 || alignments.front() != origAln || !sequenceWindow || !sequenceWindow->EditorIsOn()) {
ERRORMSG("SequenceViewer::ReplaceAlignment() - bad parameters");
return false;
}
// empty out and then recreate the current alignment list and display (but not the undo stacks!)
DELETE_ALL_AND_CLEAR(alignments, AlignmentList);
alignments.push_back(newAln);
display->Empty();
display->AddBlockBoundaryRow(newAln);
for (unsigned int row=0; row<newAln->NRows(); ++row)
display->AddRowFromAlignment(row, newAln);
// set starting scroll to a few residues left of the first aligned block
display->SetStartingColumn(newAln->GetFirstAlignedBlockPosition() - 5);
Save(); // make this an undoable operation
if (sequenceWindow)
sequenceWindow->UpdateDisplay(display);
return true;
}
void SequenceViewer::SaveAlignment(void)
{
KeepCurrent();
// go back into the original pairwise alignment data and save according to the
// current edited BlockMultipleAlignment and display row order
vector < unsigned int > rowOrder;
const SequenceDisplay *display = GetCurrentDisplay();
for (unsigned int i=0; i<display->rows.size(); ++i) {
DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(display->rows[i]);
if (alnRow) rowOrder.push_back(alnRow->row);
}
alignmentManager->SavePairwiseFromMultiple(GetCurrentAlignments().back(), rowOrder);
}
void
GMApp::OpenMailbox
(
const JCharacter* filename,
const JBoolean beep,
const JBoolean iconify
)
{
if (JDirectoryExists(filename))
{
const JCharacter* map[] =
{
"dir", filename
};
const JString msg = JGetString("NameIsDirectoryNotFile::GMApp", map, sizeof(map));
JGetUserNotification()->ReportError(msg);
return;
}
if (MailboxOpen(filename, !iconify))
{
return;
}
JString mailbox(filename);
JBoolean locked = FileLocked(mailbox, kJFalse);
GMessageTableDir* dir;
if (!locked)
{
if (GLockFile(mailbox) && GMessageTableDir::Create(this, mailbox, &dir, iconify))
{
itsTableDirs->Append(dir);
GUnlockFile(mailbox);
Broadcast(MailboxOpened(mailbox));
if (beep && GGetPrefsMgr()->IsBeepingOnNewMail())
{
GetCurrentDisplay()->Beep();
}
}
}
}
void SequenceViewer::ExportAlignment(eExportType type)
{
// get filename
wxString extension, wildcard;
if (type == asFASTA) { extension = ".fsa"; wildcard = "FASTA Files (*.fsa)|*.fsa"; }
else if (type == asFASTAa2m) { extension = ".a2m"; wildcard = "A2M FASTA (*.a2m)|*.a2m"; }
else if (type == asText) { extension = ".txt"; wildcard = "Text Files (*.txt)|*.txt"; }
else if (type == asHTML) { extension = ".html"; wildcard = "HTML Files (*.html)|*.html"; }
else if (type == asPSSM) { extension = ".pssm"; wildcard = "PSSM Files (*.pssm)|*.pssm"; }
wxString outputFolder = wxString(GetUserDir().c_str(), GetUserDir().size() - 1); // remove trailing /
wxString baseName, outputFile;
wxFileName::SplitPath(GetWorkingFilename().c_str(), NULL, &baseName, NULL);
wxFileDialog dialog(sequenceWindow, "Choose a file for alignment export:", outputFolder,
#ifdef __WXGTK__
baseName + extension,
#else
baseName,
#endif
wildcard, wxFD_SAVE | wxFD_OVERWRITE_PROMPT);
dialog.SetFilterIndex(0);
if (dialog.ShowModal() == wxID_OK)
outputFile = dialog.GetPath();
if (outputFile.size() > 0) {
// create output stream
auto_ptr<CNcbiOfstream> ofs(new CNcbiOfstream(WX_TO_STD(outputFile).c_str(), IOS_BASE::out));
if (!(*ofs)) {
ERRORMSG("Unable to open output file " << outputFile.c_str());
return;
}
// map display row order to rows in BlockMultipleAlignment
vector < int > rowOrder;
const SequenceDisplay *display = GetCurrentDisplay();
for (unsigned int i=0; i<display->rows.size(); ++i) {
DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(display->rows[i]);
if (alnRow) rowOrder.push_back(alnRow->row);
}
// actually write the alignment
if (type == asFASTA || type == asFASTAa2m) {
INFOMSG("exporting" << (type == asFASTAa2m ? " A2M " : " ") << "FASTA to " << outputFile.c_str());
DumpFASTA((type == asFASTAa2m), alignmentManager->GetCurrentMultipleAlignment(),
rowOrder, sequenceWindow->GetCurrentJustification(), *ofs);
} else if (type == asText || type == asHTML) {
INFOMSG("exporting " << (type == asText ? "text" : "HTML") << " to " << outputFile.c_str());
DumpText((type == asHTML), alignmentManager->GetCurrentMultipleAlignment(),
rowOrder, sequenceWindow->GetCurrentJustification(), *ofs);
} else if (type == asPSSM) {
static string prevTitle;
if (prevTitle.size() == 0)
prevTitle = GetWorkingTitle();
string title = WX_TO_STD(wxGetTextFromUser(
"Enter a name for this PSSM (to be used by other applications like PSI-BLAST or RPS-BLAST):",
"PSSM Title?", prevTitle.c_str(), *viewerWindow).Strip(wxString::both));
if (title.size() > 0) {
INFOMSG("exporting PSSM (" << title << ") to " << outputFile.c_str());
alignmentManager->GetCurrentMultipleAlignment()->GetPSSM().OutputPSSM(*ofs, title);
prevTitle = title;
}
}
}
}
