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] |