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Public Member Functions |
| | PlasmidCanvas (wxWindow *parent, const wxPoint &pos, const wxSize &size) |
| | Constructor.
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| virtual | ~PlasmidCanvas () |
| | Destructor.
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| virtual void | OnDraw (wxDC &pdc) |
| | Draws the map.
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| virtual void | Refresh () |
| | Redraws the map.
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| virtual void | print () |
| | Prints the map.
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| virtual void | setZoom (int factor) |
| | Sets the display zoom factor.
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| virtual wxString | getSelection () |
| | Returns the current sequence selection.
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| virtual void | RunPrimerEditor (vector< TPrimer > &pl, int mut=-1) |
| | Invokes the PCR/primer design module.
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| virtual void | invokeVectorEditor (wxString what=_T(""), int num=0, bool forceUpdate=false) |
| | Invokes the vector editor dialog.
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| virtual wxMenu * | invokeItemPopup (int item, wxPoint pt, bool doreturn=false) |
| | Generates the item/feature context menu.
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| virtual wxMenu * | invokeRsPopup (int rs, wxPoint pt, bool doreturn=false) |
| | Generates the restriction enzyme context menu.
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| virtual wxMenu * | invokeVectorPopup (wxPoint pt, bool doreturn=false, int pos=-1) |
| | Generates the vector context menu.
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| virtual void | invokeORFpopup (int item, wxPoint pt) |
| | Generates the open reading frame context menu.
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| virtual void | OnPrimerForward (wxCommandEvent &ev) |
| | "Run PCR with primer forward" event handler
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| virtual void | OnPrimerBackward (wxCommandEvent &ev) |
| | "Run PCR with primer backwards" event handler
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| virtual void | OnPrimerBoth (wxCommandEvent &ev) |
| | "Run PCR with both primers" event handler
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| virtual void | OnPrimerMutation (wxCommandEvent &ev) |
| | "Run PCR with mutation primers" event handler
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| virtual void | OnPaint (wxPaintEvent &event) |
| | Paint event handler.
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| virtual void | OnSaveImage (wxCommandEvent &ev) |
| | "Save as image" event handler
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| virtual void | OnStrandCopy35 (wxCommandEvent &event) |
| | "Copy 3'->5' strand" event handler
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| virtual void | OnStrandCopy53 (wxCommandEvent &event) |
| | "Copy 5'->3' strand" event handler
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| virtual void | OnStrandCopyBoth (wxCommandEvent &event) |
| | "Copy both strands" event handler
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| virtual void | OnStrandNew35 (wxCommandEvent &event) |
| | "New DNA module from 3'->5' strand" event handler
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| virtual void | OnStrandNew53 (wxCommandEvent &event) |
| | "New DNA module from 5'->3' strand" event handler
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| virtual void | OnStrandNewBoth (wxCommandEvent &event) |
| | "New DNA modules from both strands" event handler
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| virtual void | OnOpenFeature (wxCommandEvent &event) |
| | "Open feature" event handler
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| virtual void | OnCopyImage (wxCommandEvent &ev) |
| | "Copy as image" event handler
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| virtual void | itemMark (wxCommandEvent &ev) |
| | "Mark item" event handler
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| virtual void | itemMarkShow (wxCommandEvent &ev) |
| | "Mark item and show in sequence" event handler
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| virtual void | itemEdit (wxCommandEvent &ev) |
| | "Edit item" event handler
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| virtual void | itemAsNewSequence (wxCommandEvent &ev) |
| | "Make a new sequence from item" event handler
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| virtual void | itemDelete (wxCommandEvent &ev) |
| | "Delete item" event handler
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| virtual void | itemBlastDNA (wxCommandEvent &ev) |
| | "BLAST item DNA sequence" event handler
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| virtual void | itemBlastAA (wxCommandEvent &ev) |
| | "BLAST item amino acid sequence" event handler
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| virtual void | itemCopyDNA (wxCommandEvent &ev) |
| | "Copy item DNA sequence" event handler
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| virtual void | itemCopyAA (wxCommandEvent &ev) |
| | "Copy item amino acid sequence" event handler
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| virtual void | itemAsNewAA (wxCommandEvent &ev) |
| | "Make new amino acid sequence from item" event handler
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| virtual void | rsInfo (wxCommandEvent &ev) |
| | "Go to ReBase web page for this restriction enzyme" event handler
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| virtual void | rsEdit (wxCommandEvent &ev) |
| | "Edit this restriction enzyme" event handler
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| virtual void | rsDel (wxCommandEvent &ev) |
| | "Delete this restriction enzyme" event handler
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| virtual void | rsShowHide (wxCommandEvent &ev) |
| | "Toggle restriction enzyme visibility" event handler
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| virtual void | rsHideLimit (wxCommandEvent &ev) |
| | "Limit maximum number of cuts per restriction enzyme" event handler
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| virtual void | rsMark (wxCommandEvent &ev) |
| | "Mark sequence" event handler
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| virtual void | rsMarkShow (wxCommandEvent &ev) |
| | "Mark and show in sequence display" event handler
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| virtual void | rsAdd2Cocktail (wxCommandEvent &ev) |
| | "Add to restriction enzyme cocktail" event handler
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| virtual void | rsAddAndCut (wxCommandEvent &ev) |
| | "Add to restriction enzyme cocktail and cut with it" event handler
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| virtual void | rsCutWithCocktail (wxCommandEvent &ev) |
| | "Cut with restriction enzyme cocktail" event handler
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| virtual void | orfCopyDNA (wxCommandEvent &ev) |
| | "Copy open reading frame DNA sequence" event handler
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| virtual void | orfCopyAA (wxCommandEvent &ev) |
| | "Copy open reading frame amino acid sequence" event handler
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| virtual void | orfAsNewItem (wxCommandEvent &ev) |
| | "Open reading frame as new item" event handler
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| virtual void | orfAsNewDNA (wxCommandEvent &ev) |
| | "Open reading frame as new DNA sequence" event handler
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| virtual void | orfAsNewAA (wxCommandEvent &ev) |
| | "Open reading frame as new amino acid sequence" event handler
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| virtual void | orfBlastDNA (wxCommandEvent &ev) |
| | "BLAST open reading frame DNA sequence" event handler
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| virtual void | orfBlastAA (wxCommandEvent &ev) |
| | "BLAST open reading frame amino acid sequence" event handler
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| virtual void | OnFillKlenow (wxCommandEvent &event) |
| | "Klenow-fill sticky ends" event handler
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| virtual void | OnWhatCuts (wxCommandEvent &event) |
| | "List enzymes that cut here" event handler
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| virtual void | OnRunPCR (wxCommandEvent &event) |
| | "Run PCR" event handler
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| virtual void | vecEdit (wxCommandEvent &ev) |
| | "Edit vector" event handler
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| virtual void | blastDNA (wxCommandEvent &ev) |
| | "BLAST DNA sequence" event handler
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| virtual void | blastAA (wxCommandEvent &ev) |
| | "BLAST amino acid sequence" event handler
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| virtual void | itemShowHide (wxCommandEvent &ev) |
| | "Toggle item visibility" event handler
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| virtual void | OnTurningPoint (wxCommandEvent &ev) |
| | "Turning point (12 o'clock)" event handler
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| virtual void | setPrinting (bool _b) |
| | Sets the printing mode on/off.
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| virtual void | setLastContextItem (long _l) |
| | Sets the last item the mouse was over.
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| virtual int | getMarkFrom () |
| | Returns the first selected position, or -1.
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| virtual int | getMarkTo () |
| | Returns the last selected position, or -1.
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| virtual void | getMark (int &i1, int &i2) |
| | Sets i1 and i2 to the first/last selected positions, or to -1.
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| virtual void | setMark (int i1, int i2) |
| | Sets the selection.
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| virtual void | setRootChild (MyChild *_p) |
| | Sets the MyChild parent.
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| virtual int | getZoom () |
| | Returns the current zoom factor.
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Private Member Functions |
| virtual void | OnDrawLinear (wxDC &dc) |
| | Draw a linear sequence.
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| virtual void | OnDrawCircular (wxDC &dc) |
| | Draw a circular sequence.
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| virtual void | OnEvent (wxMouseEvent &event) |
| | Mouse event handler.
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| virtual int | deg2x (float deg, int r) |
| | Converts degree/radius to x coordinate.
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| virtual int | deg2y (float deg, int r) |
| | Converts degree/radius to y coordinate.
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| virtual float | xy2deg (float x, float y) |
| | Converts x/y coordinate to degrees.
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| virtual float | xy2r (float x, float y) |
| | Converts x/y coordinate to radius.
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| virtual int | findVectorObjectCircular (float angle, float radius) |
| | Returns the number of an item/feature at the given position, or -1.
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| virtual int | findRestrictionSite (int x, int y) |
| | Returns the number of the restriction site at the given position, or -1.
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| virtual wxPoint | makeLastRect (int a, wxDC &dc) |
| | Some internal function...
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| virtual void | arrangeRestrictionSitesCircular (wxDC &dc) |
| | Arranges the restriction site labels.
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| virtual bool | optimizeCircularRestrictionSites (int a, wxDC &dc) |
| | Rearranges the restriction site labels.
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| virtual int | findORFcircular (float angle, float radius) |
| | Returns the number of the open reading frame at the given position, or -1.
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| virtual void | drawCircularORFs (wxDC &dc) |
| | Draws open reading frames in circular mode.
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| virtual int | findVectorObjectLinear (wxPoint pp) |
| | Returns the number of an item/feature at the given position, or -1.
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| virtual void | drawLinearItem (wxDC &dc, int r1, int r2, float a1, float a2, TVectorItem *i) |
| | Draws an item/feature in linear mode.
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| virtual void | arrangeRestrictionSitesLinear (int a, wxDC &dc) |
| | Arranges the restriction site labels.
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| virtual bool | intersectsLine (wxRect &a, wxPoint p) |
| | Does the point lie within the rectangle, except for the top part?
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| virtual void | drawLinearORFs (wxDC &dc) |
| | Draws open reading frames in linear mode.
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| virtual int | findORFlinear (int x, int y) |
| | Returns the number of the open reading frame at the given position, or -1.
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| virtual bool | intersects (wxRect &a, wxRect &b) |
| | Does the point lie within the rectangle?
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| virtual bool | pointinrect (int x, int y, wxRect &a) |
| | Does the point lie within the rectangle?
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| virtual bool | isEnzymeVisible (wxString s) |
| | Is the enzyme visible (or was it set to "hidden")?
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| virtual void | updateLinkedItems (TVector *vec, int in) |
| | Update items that belong together (like exons).
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| virtual void | SetMyToolTip (wxString s, int mode) |
| | Sets the tool tip.
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| virtual wxString | getDNAorAA (int from, int to, int dir, bool dna=true) |
| | Returns the given DNA or amino acid sequence.
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| virtual int | circular_pos (float angle) |
| | Converts an angle to a DNA position in circular mode.
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| virtual void | push_rc_left (int a, wxDC &dc) |
| | Internally "push" a restriction site label to the "left".
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| virtual void | push_rc_right (int a, wxDC &dc) |
| | Internally "push" a restriction site label to the "right".
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| virtual void | recalc_rc (int a, wxDC &dc) |
| | Recalculates the position of the restriction cuts and labels.
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| virtual void | makeGCcolor (int percent, wxColour &col) |
| | Sets the color appropriate for the percentage of the GC contents.
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| virtual void | showGClegend (wxDC &dc) |
| | Draws the GC contents legend.
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Private Attributes |
| int | context_last_rs |
| int | lasttooltip |
| int | context_last_orf |
| int | lastvectorobject |
| int | lastrestrictionsite |
| int | lastbp |
| int | mousediffx |
| int | mousediffy |
| int | zoom |
| int | last_rightclick_base |
| long | context_last_item |
| int | r |
| int | w |
| int | h |
| bool | initialclick |
| bool | painting |
| bool | hasBeenPainted |
| bool | printing |
| wxToolTip * | tt |
| | The current/last tooptip.
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| MyChild * | p |
| | The MyChild structure containing this PlasmidCanvas.
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