| aaa | TAlignment | [private] |
| Activate() | ChildBase | [virtual] |
| algorithm | TAlignment | |
| allow_copy | ChildBase | |
| allow_cut | ChildBase | |
| allow_find | ChildBase | |
| allow_paste | ChildBase | |
| allow_print | ChildBase | |
| allow_save | ChildBase | |
| allow_undo | ChildBase | |
| arrangedExport(wxFile &out, wxString n, wxString s, int l) | ChildBase | [protected, virtual] |
| bold | TAlignment | |
| callMiddleMouseButton(int id, int pos, wxString _mode=_T("")) | TAlignment | [virtual] |
| caniclose(wxCloseEvent &event) | ChildBase | [virtual] |
| ChildBase() | ChildBase | |
| ChildBase(wxWindow *parent, const wxString &title, const wxPoint &pos, const wxSize &size, const long style) | ChildBase | |
| ChildBase(wxWindow *parent, const wxString &title) | ChildBase | |
| colAA | TAlignment | |
| colCur | TAlignment | |
| colDNA | TAlignment | |
| cons | TAlignment | |
| consensusSequence | TAlignment | |
| CreateToolBar(int i) | ChildBase | [virtual] |
| CreateToolBar(int i, int j, wxString s) | ChildBase | [virtual] |
| cSequence | ChildBase | |
| database | TAlignment | |
| def | ChildBase | |
| doExport(wxString filename, int filter) | TAlignment | [protected, virtual] |
| editAppearance(int from, int to, int firstline, int lastline) | TAlignment | |
| EnforceRefesh() | ChildBase | [inline, virtual] |
| Entry() | TAlignment | [virtual] |
| exportVector(TVector *vec, wxFile &out, int filter, wxString filename=_T("")) | ChildBase | [protected, virtual] |
| findColors(char c1, char c2, bool fg) | TAlignment | [virtual] |
| fixMenus(int i) | TAlignment | [private, virtual] |
| fontsize | TAlignment | [private] |
| fromVector(TVector *nv) | TAlignment | [virtual] |
| gap | TAlignment | |
| gap_penalty | TAlignment | |
| generateConsensusSequence(bool addit=true) | TAlignment | [private, virtual] |
| getCharMarkup(SequenceCharMarkup &scm, int vline, int pos, int vfirst) | TAlignment | |
| getExportFilters() | TAlignment | [protected, virtual] |
| GetMenuBar() | ChildBase | [virtual] |
| getName() | TAlignment | [virtual] |
| GetToolBar() | ChildBase | [virtual] |
| init() | ChildBase | [virtual] |
| initHelp() | ChildBase | [virtual] |
| initme() | TAlignment | [virtual] |
| inMainTree | ChildBase | |
| invokeOriginal(int id, int pos) | TAlignment | [virtual] |
| invs | TAlignment | |
| isAA() | TAlignment | [virtual] |
| isDNA() | TAlignment | [virtual] |
| isThreadRunning() | TAlignment | [inline, virtual] |
| keepIdentity | TAlignment | [private] |
| lines | TAlignment | |
| match | TAlignment | |
| matrix | TAlignment | |
| MatrixAlignment(wxString &_s1, wxString &_s2, bool local) | TAlignment | [virtual] |
| MatrixBacktrack(vector< wxArrayInt > &back, wxString s1, wxString s2, wxString &t1, wxString &t2, int i, int j) | TAlignment | [virtual] |
| Maximize(bool isit=true) | ChildBase | [virtual] |
| menubar | ChildBase | [protected] |
| mismatch | TAlignment | |
| mmb | TAlignment | [private] |
| mono | TAlignment | |
| MoveUpDown(int what, int where) | TAlignment | [virtual] |
| myDelete(int line, int pos) | TAlignment | [private, virtual] |
| MyFrame class | ChildBase | [friend] |
| myInsert(int line, int pos, char what) | TAlignment | [private, virtual] |
| name | TAlignment | |
| NeedlemanWunsch(wxString &s1, wxString &s2) | TAlignment | [virtual] |
| OnClose(wxCloseEvent &event) | ChildBase | [virtual] |
| OnCopy(wxCommandEvent &event) | TAlignment | [virtual] |
| OnDummy(wxCommandEvent &WXUNUSED(event)) | ChildBase | [inline, virtual] |
| OnExport(wxCommandEvent &WXUNUSED(event)) | ChildBase | [virtual] |
| OnFileSave(wxCommandEvent &ev) | TAlignment | [virtual] |
| ChildBase::OnFileSave(wxCommandEvent &WXUNUSED(event)) | ChildBase | [inline, virtual] |
| OnFocus(wxFocusEvent &event) | ChildBase | [virtual] |
| OnFontsize(wxCommandEvent &event) | TAlignment | [virtual] |
| OnHorizontal(wxCommandEvent &event) | TAlignment | [virtual] |
| OnMarkAll(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuBold(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuCons(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuFeat(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuIdent(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuInvs(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuMono(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuNorm(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuRNA(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuSeq(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuSiml(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuSoa(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnMenuSoaI(wxCommandEvent &ev) | TAlignment | [virtual] |
| OnPaste(wxCommandEvent &WXUNUSED(event)) | ChildBase | [inline, virtual] |
| OnSeqPrint(wxCommandEvent &event) | TAlignment | [virtual] |
| OnSettings(wxCommandEvent &ev) | TAlignment | [virtual] |
| prealigned(wxArrayString &vs, wxArrayChildBase &vc) | TAlignment | [virtual] |
| readTabColors(wxString filename) | TAlignment | [protected, virtual] |
| recalcAlignments() | TAlignment | [virtual] |
| redoAlignments(bool doRecalc=true) | TAlignment | [virtual] |
| RunPhylip(int cmd) | TAlignment | [virtual] |
| sc | TAlignment | |
| SetIcon(wxIcon icon) | ChildBase | [virtual] |
| SetMenuBar(wxMenuBar *menu_bar) | ChildBase | [virtual] |
| SetMyMenuBar() | ChildBase | [virtual] |
| showIdentity | TAlignment | |
| showName(wxString x=_T("")) | ChildBase | [virtual] |
| SmithWaterman(wxString &s1, wxString &s2) | TAlignment | [virtual] |
| TAlignment(wxWindow *parent, const wxString &title) | TAlignment | |
| threadRunning | TAlignment | [private] |
| toolbar | ChildBase | [protected] |
| updateSequence() | TAlignment | [private, virtual] |
| updateSequenceCanvas(bool remember=false) | ChildBase | [virtual] |
| updateToolbar() | ChildBase | [protected, virtual] |
| updateUndoMenu() | ChildBase | [virtual] |
| vec | ChildBase | |
| ~TAlignment() | TAlignment | [virtual] |
