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Public Member Functions |
| TAlignment (wxWindow *parent, const wxString &title) |
| Constructor.
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virtual | ~TAlignment () |
| Destructor.
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virtual void | initme () |
| Initialization.
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virtual wxString | getName () |
| Returns "Alignment".
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virtual void * | Entry () |
virtual int | NeedlemanWunsch (wxString &s1, wxString &s2) |
| Needleman-Wunsch-align two sequences.
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virtual int | SmithWaterman (wxString &s1, wxString &s2) |
| Smith-Waterman-align two sequences.
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virtual int | MatrixAlignment (wxString &_s1, wxString &_s2, bool local) |
| Part of NW/SW alignment algorithm.
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virtual void | MatrixBacktrack (vector< wxArrayInt > &back, wxString s1, wxString s2, wxString &t1, wxString &t2, int i, int j) |
| Part of NW/SW alignment algorithm.
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virtual void | redoAlignments (bool doRecalc=true) |
| Repaint and (maybe) recalculate the alignment.
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virtual void | recalcAlignments () |
| Recalculate the alignment.
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virtual wxColour | findColors (char c1, char c2, bool fg) |
| Generate the appropriate foreground/background color, using current settings.
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virtual void | OnSettings (wxCommandEvent &ev) |
| Settings button event handler.
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virtual void | OnMarkAll (wxCommandEvent &ev) |
| "Mark all" event handler
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virtual void | OnSeqPrint (wxCommandEvent &event) |
| "Print sequence" event handler
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virtual void | OnFileSave (wxCommandEvent &ev) |
| Save event handler.
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virtual void | OnMenuBold (wxCommandEvent &ev) |
| "Display bold" event handler
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virtual void | OnMenuMono (wxCommandEvent &ev) |
| "Display monochrome" event handler
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virtual void | OnMenuNorm (wxCommandEvent &ev) |
| "Display normal" event handler
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virtual void | OnMenuInvs (wxCommandEvent &ev) |
| "Display inverse" event handler
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virtual void | OnMenuSoa (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuSoaI (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuSiml (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuSeq (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuFeat (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuRNA (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuCons (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnMenuIdent (wxCommandEvent &ev) |
| Some event handler.
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virtual void | OnHorizontal (wxCommandEvent &event) |
| "Display horizontal" event handler
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virtual void | OnCopy (wxCommandEvent &event) |
| Copy event handler.
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virtual void | OnFontsize (wxCommandEvent &event) |
| Fontsize event handler.
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virtual void | invokeOriginal (int id, int pos) |
| Open the original sequence at the given position.
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virtual void | callMiddleMouseButton (int id, int pos, wxString _mode=_T("")) |
| Perform the middle mouse button function (the gap orgy).
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virtual void | MoveUpDown (int what, int where) |
| Move a line into the given direction.
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virtual void | prealigned (wxArrayString &vs, wxArrayChildBase &vc) |
| Initialize with a prealigned list of sequences (for example, from a multi-sequence genbank file).
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virtual void | fromVector (TVector *nv) |
| Initialize from a single vector (???).
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virtual bool | isDNA () |
| Tries to determine wether this is a DNA or an amino acid alignment.
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virtual bool | isAA () |
| Tries to determine wether this is a DNA or an amino acid alignment.
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virtual void | RunPhylip (int cmd) |
| Takes Phylip commands (invoked from SequenceCanvas).
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virtual bool | isThreadRunning () |
| Is a thread (alignment calculation) currently running?
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void | getCharMarkup (SequenceCharMarkup &scm, int vline, int pos, int vfirst) |
void | editAppearance (int from, int to, int firstline, int lastline) |
Public Attributes |
SequenceCanvas * | sc |
| Pointer to the sequence canvas.
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vector< TAlignLine > | lines |
| The list of TAlignLine structures.
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wxColour | colDNA [256] |
wxColour | colAA [256] |
wxColour * | colCur |
wxString | gap |
wxString | matrix |
wxString | consensusSequence |
wxString | name |
wxString | database |
int | match |
int | mismatch |
int | gap_penalty |
int | algorithm |
bool | bold |
bool | mono |
bool | cons |
bool | invs |
bool | showIdentity |
Protected Member Functions |
virtual wxString | getExportFilters () |
virtual void | doExport (wxString filename, int filter) |
| Export data, depending on filename and export type.
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virtual void | readTabColors (wxString filename) |
Private Member Functions |
virtual void | myInsert (int line, int pos, char what) |
virtual void | myDelete (int line, int pos) |
virtual void | updateSequence () |
virtual void | generateConsensusSequence (bool addit=true) |
virtual void | fixMenus (int i) |
Private Attributes |
wxChoice * | mmb |
SeqAA * | aaa |
bool | threadRunning |
bool | keepIdentity |
wxChoice * | fontsize |