Custom UI form

Visual Gene Developer allows a user to develop a custom UI (user interface) form (or window).

o What is 'Custom UI form (or window)'?

 In order to analyze the CAI profile or mRNA binding energy profile of the test sequence, you may click on the menu item 'CAI profile v2' or 'mRNA profile v2' in the 'Toolbox' window. When done, the custom UI form will be pop-up as shown in the following figure. The diagram was drawn by executing a user-defined module that encodes algorithms to plot GC contents or mRNA energy profiles. Because all graphic functions are defined in the special class 'CustomUI', a user can easily make use of those functions to draw lines or text. Therefore, Visual Gene Developer gives a great advantage to expand software functionality by adding new graphical analysis windows designed by users.

Let's check the source code of 'CAI profile v2'.

It is easy to recognize that the class 'CustomUI' was used many times to draw line, string, or rectangle.

o Custom UI form (window)

The custom UI window consists of a caption, toolbar, and canvas. A user can set 'form caption', define 'canvas' size, and plot figures in the 'canvas'.

Visual Gene Developer provides a toolbar to export the image and raw data. Clicking on the 'Clone' menu button, a user can duplicate the current Custom UI form. Regarding X Y coordinates on canvas, left top corresponds to (0,0). X values increase from the left to right and Y value increases from top to bottom.

o Specialized class 'CustomUI'

The class 'CustomUI' has the ability to generate new Custom UI forms  and contains many graphic functions. The current version offers 27 functions such as Define_Canvas, Clear_Canvas, Update_Canvas, DrawLine, DrawPie, DrawRectangle, DrawBezier, and etc.

Check the complete list of functions

Visual Gene Developer provides 5 instances of the class 'CustomUI': 'CustomUI', 'CustomUI2', 'CustomUI3', 'CustomUI4', 'CustomUI5'.

Each instance represents and can operate a single independent 'active Custom UI window'. Thus, a user can handle a maximum five 'active Custom UI windows' at the same time. 'Active Custom UI window' is the window where a user draws graphics. It is different from the 'Cloned custom UI window' that can be generated by clicking on the 'Clone' button in the custom UI window.

Every module may use the same 'Active custom UI windows' and a user may need to add one line code to duplicate the 'Active custom UI window' to keep the image and raw data. The duplicated custom UI window can be called as 'cloned custom UI window'.

o How to generate custom UI form

Step 1: Define canvas and set 'Form caption'

Function: Sub Define_Canvas (Width As Integer, Height As Integer, Optional ShowToolStrip As Boolean)

              Property Form_Caption () As String

Step 2 (optional): Bring the form to front and clear canvas

Function: Sub Form_BringToFront ()

              Sub Clear_Canvas (Optional Color_byName As String)

Step 3: Draw graphics and update the canvas

Function: Sub DrawLine (X1 As Integer, Y1 As Integer, X2 As Integer, Y2 As Integer, Optional ForeColor_byName As String)

              Sub DrawString (X As Integer, Y As Integer, TextStr As String, Optional ForeColor_byName As String)

              Sub Update_Canvas ()

When you call 'Update_Canvas' function, Visual Gene Developer refreshes canvas to show an updated image. However, it doesn't need to update the canvas every time. When you draw graphics like line, pie, or rectangle, the canvas is already internally updated even if it doesn't show the updated image in real-time. Please remember that frequent calling of 'Update_Canvas' function may delay processing time. However, a user may prefer it to give an animation effect.

Step 4 (optional): Store raw data for data export

Function: Property RawData () As String

Grammar: Chr(9) generates Tab key,

                Chr(13) + Chr(10) generates Carriage return

A user store raw data (not image) to the custom UI window. When you call this function, the 'Copy raw data' toolbar button in the custom UI window will be activated. Now, a user can export text raw data to the clipboard anytime once he stores it.

Step 5 (recommended): Generate 'custom UI clone' and close 'active custom UI window'

Function: Sub Make_Clone ()

When a user calls this function, Visual Gene Developer duplicates the current 'active custom UI form (window)' and then close 'active UI form'. Apparently, a user may not distinguish between 'active custom UI form' and 'cloned custom UI window' because the duplicated custom UI window will be shown exactly at the same location with the same size. This function is important to keep the user's data in a separate UI form. We remind you that there are five instances of the class 'CustomUI' and consequently five active Custom UI windows. Active custom UI windows can be shared with other modules.

o Advanced example 1: Codon bias diagram

* Imitation of the job done by Plotkin and Kudla (Nature, 2011, p32-42)

* The algorithm was developed using VBScript. Check the code in the 'Module Library' and 'Module Editor' windows 

VBScript

Sub Main()       '***** Setting *******************     MaxConstruct=99     LineWidth =7     LineHeight =5           '**** Ask target Gene Component ************     Info_Str=Get_ListOfComponents     Info_Str="List of Gene Component" + VBCrLF + VbCrLF +  Info_Str + VbCrLF + + VbCrLF + "Input number!"     ComponentIndex=InputBox(Info_Str,"Codon bias diagram")     ComponentCount=  GeneConstruct.ComponentCount     If  ComponentIndex <= 0  or -ComponentCount > -ComponentIndex Then              MsgBox "Incorrect number!"             Exit Sub            End If                '**** Set Range **********************************************************     Currnent_ConstructIndex=GeneConstruct.CurrentConstructIndex     Construct_Count=GeneConstruct.ConstructCount     Construct_End=Currnent_ConstructIndex + MaxConstruct     If Construct_End>Construct_Count Then Construct_End=Construct_Count                     '**** Initialize Graphics **********************      CustomUI.Define_Canvas 64*LineWidth+35,(Construct_End-Currnent_ConstructIndex)*LineHeight +40      CustomUI.Form_BringToFront      CustomUI.Clear_Canvas      CustomUI.Form_Caption="Codon bias diagram (based on RSCU)"              '**** Draw Codon text **********************     Output_Str="Number" + VBTab      CustomUI.Set_Font 8            For  Triplet_1st=1 to 4                  For Triplet_2nd=1 to 4                         For Triplet_3rd=1 to 4                                    CurrentTriplet=IndexToCGAT(Triplet_1st)+IndexToCGAT(Triplet_2nd)                                    CurrentTriplet=CurrentTriplet+IndexToCGAT(Triplet_3rd)                                      CurrentY=4                                    CurrentX=((Triplet_1st-1)*16+(Triplet_2nd-1)*4+(Triplet_3rd-1))*LineWidth +30                                    If Triplet_3rd=1 or Triplet_3rd=3 Then                                             CustomUI.Set_ForeColor_byName "Red"                                    Else                                             CustomUI.Set_ForeColor_byName "Blue"                                    End If                                                  CustomUI.DrawString CurrentX-1,CurrentY-3, IndexToCGAT(Triplet_1st)                                    CustomUI.DrawString CurrentX-1,CurrentY+4, IndexToCGAT(Triplet_2nd)                                    CustomUI.DrawString CurrentX-1,CurrentY+11, IndexToCGAT(Triplet_3rd)                                    Output_Str=Output_Str + CurrentTriplet + VbTab                         Next                        Next               Next                        Output_Str=Output_Str + VBCrLF          '**** Draw codon rscu diagram *************************************     CustomUI.Set_Font 8     For q = Currnent_ConstructIndex  to  Construct_End              SourceSeq=GeneConstruct.ParameterValue(q,ComponentIndex,"Modified DNA")            GeneService.Calculate_CodonUsage SourceSeq               CurrentY=(q-Currnent_ConstructIndex+1)*LineHeight +23            If   q=Int(q/5)*5 Then                               CustomUI.DrawString 5,CurrentY-1, CStr(q),"Black"            End If                   Output_Str=Output_Str + CStr(q) + VBTab              For  Triplet_1st=1 to 4                  For Triplet_2nd=1 to 4                         For Triplet_3rd=1 to 4                                    CurrentTriplet=IndexToCGAT(Triplet_1st)+IndexToCGAT(Triplet_2nd)                                    CurrentTriplet=CurrentTriplet+IndexToCGAT(Triplet_3rd)                                    CodonAddress64 =GeneService.Get_CodonAddress_Type64(CurrentTriplet)                                    CodonRSCU=GeneService.Get_CodonUsage_RSCU(CodonAddress64 )                                      CurrentX=((Triplet_1st-1)*16+(Triplet_2nd-1)*4+(Triplet_3rd-1))*LineWidth +30                                      CustomUI.Set_FillColor_byRGB CodonRSCU/3*255,0,255-CodonRSCU/3*255                                    CustomUI.FillRectangle CurrentX,CurrentY,LineWidth,LineHeight                                      Output_Str=Output_Str + CStr(CodonRSCU) + VbTab                         Next                        Next               Next               CustomUI.Update_Canvas              Output_Str=Output_Str + VBCrLF         Next          CustomUI.RawData=Output_Str      CustomUI.Make_Clone End Sub         Function IndexToCGAT(IndexNumber)     Select case IndexNumber            Case 1                     IndexToCGAT="C"            Case 2                     IndexToCGAT="G"            Case 3                     IndexToCGAT="A"            Case 4                     IndexToCGAT="T"            Case Else                       IndexToCGAT=""     End Select       End Function       Function Get_ListOfComponents      Buf_Str=""      ComponentCount=GeneConstruct.ComponentCount           For q=1 to ComponentCount             Buf_Str=Buf_Str + CStr(q) + ": " + GeneConstruct.ComponentName(1,q) + VBCrLf      Next                     Get_ListOfComponents=Buf_Str End Function