CG.frm

VERSION 5.00
Object = "{F9043C88-F6F2-101A-A3C9-08002B2F49FB}#1.2#0"; "COMDLG32.OCX"
Begin VB.Form PromKappa 
   Caption         =   "PromKappa v2.0: Analysis of DNA sequences through Objective Digital Stains"
   ClientHeight    =   14370
   ClientLeft      =   0
   ClientTop       =   270
   ClientWidth     =   17475
   Icon            =   "CG.frx":0000
   LinkTopic       =   "Form1"
   ScaleHeight     =   14370
   ScaleWidth      =   17475
   StartUpPosition =   2  'CenterScreen
   Begin VB.CommandButton Graph2_show 
      Caption         =   "Show pattern"
      Height          =   375
      Left            =   11520
      TabIndex        =   85
      Top             =   3600
      Width           =   1335
   End
   Begin VB.CommandButton Graph1_show 
      Caption         =   "Show distribution"
      Height          =   375
      Left            =   12960
      TabIndex        =   84
      Top             =   3600
      Width           =   1575
   End
   Begin VB.Frame MRP 
      Caption         =   "Master results"
      Height          =   9495
      Left            =   4200
      TabIndex        =   53
      Top             =   4080
      Visible         =   0   'False
      Width           =   10335
      Begin VB.Frame Frame6 
         Caption         =   "Setting for this graph"
         Height          =   3855
         Left            =   5160
         TabIndex        =   63
         Top             =   5520
         Width           =   4935
         Begin VB.CheckBox Save_Result_MR 
            Caption         =   "Save this graph"
            Height          =   375
            Left            =   240
            TabIndex        =   65
            Top             =   360
            Width           =   1815
         End
      End
      Begin VB.Frame Frame5 
         Caption         =   "Setting for this graph"
         Height          =   3855
         Left            =   120
         TabIndex        =   62
         Top             =   5520
         Width           =   4935
         Begin VB.CheckBox Show_center_PC 
            Caption         =   "Show center as points/ circles"
            Height          =   375
            Left            =   240
            TabIndex        =   69
            Top             =   720
            Width           =   3255
         End
         Begin VB.Frame Frame7 
            Caption         =   "Plot"
            Height          =   1215
            Left            =   240
            TabIndex        =   66
            Top             =   1200
            Width           =   4455
            Begin VB.OptionButton Option1 
               Caption         =   "Points"
               Height          =   255
               Left            =   240
               TabIndex        =   68
               Top             =   360
               Width           =   1575
            End
            Begin VB.OptionButton Option2 
               Caption         =   "Circles"
               Height          =   255
               Left            =   240
               TabIndex        =   67
               Top             =   720
               Value           =   -1  'True
               Width           =   1575
            End
         End
         Begin VB.CheckBox Save_Result_MP 
            Caption         =   "Save this graph"
            Height          =   375
            Left            =   240
            TabIndex        =   64
            Top             =   360
            Width           =   1815
         End
      End
      Begin VB.CommandButton Erase_Center_patt 
         Caption         =   "Erase"
         Height          =   375
         Left            =   120
         TabIndex        =   61
         Top             =   5040
         Width           =   5055
      End
      Begin VB.CommandButton Erase_MasterGraph 
         Caption         =   "Erase"
         Height          =   375
         Left            =   5160
         TabIndex        =   60
         Top             =   5040
         Width           =   5055
      End
      Begin VB.PictureBox MasterGraph 
         AutoRedraw      =   -1  'True
         BackColor       =   &H00FFFFFF&
         Height          =   4695
         Left            =   5160
         ScaleHeight     =   309
         ScaleMode       =   3  'Pixel
         ScaleWidth      =   333
         TabIndex        =   57
         Top             =   240
         Width           =   5055
         Begin VB.TextBox KIC_global_txt 
            BackColor       =   &H00FFC0C0&
            Height          =   285
            Left            =   120
            TabIndex        =   97
            Text            =   "0"
            Top             =   240
            Width           =   735
         End
         Begin VB.TextBox CG_global_txt 
            BackColor       =   &H0080C0FF&
            Height          =   285
            Left            =   4200
            TabIndex        =   96
            Text            =   "0"
            Top             =   4200
            Width           =   735
         End
         Begin VB.Label Label15 
            BackStyle       =   0  'Transparent
            Caption         =   "Global Kappa IC"
            BeginProperty Font 
               Name            =   "Lucida Console"
               Size            =   8.25
               Charset         =   0
               Weight          =   400
               Underline       =   0   'False
               Italic          =   0   'False
               Strikethrough   =   0   'False
            EndProperty
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   120
            TabIndex        =   59
            Top             =   0
            Width           =   2295
         End
         Begin VB.Label Label16 
            Alignment       =   1  'Right Justify
            BackStyle       =   0  'Transparent
            Caption         =   "Global C+G"
            BeginProperty Font 
               Name            =   "Lucida Console"
               Size            =   8.25
               Charset         =   0
               Weight          =   400
               Underline       =   0   'False
               Italic          =   0   'False
               Strikethrough   =   0   'False
            EndProperty
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   3600
            TabIndex        =   58
            Top             =   3960
            Width           =   1335
         End
         Begin VB.Line Line11 
            BorderStyle     =   3  'Dot
            X1              =   168
            X2              =   168
            Y1              =   0
            Y2              =   312
         End
         Begin VB.Line Line12 
            BorderStyle     =   3  'Dot
            X1              =   336
            X2              =   -8
            Y1              =   160
            Y2              =   160
         End
      End
      Begin VB.PictureBox Center_patt 
         AutoRedraw      =   -1  'True
         BackColor       =   &H00FFFFFF&
         Height          =   4695
         Left            =   120
         ScaleHeight     =   309
         ScaleMode       =   3  'Pixel
         ScaleWidth      =   333
         TabIndex        =   54
         Top             =   240
         Width           =   5055
         Begin VB.Line Line9 
            BorderStyle     =   3  'Dot
            X1              =   336
            X2              =   -8
            Y1              =   160
            Y2              =   160
         End
         Begin VB.Line Line10 
            BorderStyle     =   3  'Dot
            X1              =   168
            X2              =   168
            Y1              =   0
            Y2              =   312
         End
         Begin VB.Label Label13 
            Alignment       =   1  'Right Justify
            BackStyle       =   0  'Transparent
            Caption         =   "C+G"
            BeginProperty Font 
               Name            =   "Lucida Console"
               Size            =   8.25
               Charset         =   0
               Weight          =   400
               Underline       =   0   'False
               Italic          =   0   'False
               Strikethrough   =   0   'False
            EndProperty
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   4440
            TabIndex        =   56
            Top             =   4440
            Width           =   495
         End
         Begin VB.Label Label14 
            BackStyle       =   0  'Transparent
            Caption         =   "Kappa IC"
            BeginProperty Font 
               Name            =   "Lucida Console"
               Size            =   8.25
               Charset         =   0
               Weight          =   400
               Underline       =   0   'False
               Italic          =   0   'False
               Strikethrough   =   0   'False
            EndProperty
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   120
            TabIndex        =   55
            Top             =   0
            Width           =   1455
         End
      End
   End
   Begin VB.Frame Frame4 
      Caption         =   "Gene promoters"
      Height          =   11535
      Left            =   14640
      TabIndex        =   50
      Top             =   2040
      Width           =   2775
      Begin VB.CheckBox Save_values_HTML 
         Caption         =   "Save measurements as HTML"
         Height          =   255
         Left            =   120
         TabIndex        =   110
         Top             =   3720
         Width           =   2535
      End
      Begin VB.Frame Frame9 
         Caption         =   "Large-scale test"
         Height          =   1095
         Left            =   120
         TabIndex        =   91
         Top             =   960
         Width           =   2535
         Begin VB.CommandButton Stop_p_test 
            Caption         =   "Stop"
            Height          =   255
            Left            =   1320
            TabIndex        =   94
            Top             =   600
            Width           =   1095
         End
         Begin VB.CommandButton Kappa_for_promotor_list 
            Caption         =   "Test promoters"
            Height          =   495
            Left            =   120
            TabIndex        =   93
            Top             =   360
            Width           =   1095
         End
         Begin VB.CommandButton Pause_p_test 
            Caption         =   "Pause"
            Height          =   255
            Left            =   1320
            TabIndex        =   92
            Top             =   360
            Width           =   1095
         End
      End
      Begin VB.Frame Frame8 
         Caption         =   "Selective experiments"
         Height          =   1455
         Left            =   120
         TabIndex        =   87
         Top             =   2160
         Width           =   2535
         Begin VB.CommandButton gene_search 
            Caption         =   "Search"
            Height          =   375
            Left            =   120
            TabIndex        =   90
            Top             =   360
            Width           =   855
         End
         Begin VB.TextBox gene_search_txt 
            Height          =   285
            Left            =   1080
            TabIndex        =   89
            Text            =   "gene name"
            Top             =   360
            Width           =   1335
         End
         Begin VB.CommandButton Search_gene_lis 
            Caption         =   "Load, search and generate"
            Height          =   375
            Left            =   120
            TabIndex        =   88
            Top             =   840
            Width           =   2295
         End
      End
      Begin VB.CommandButton Promotor 
         Caption         =   "Open promoter file"
         Height          =   495
         Left            =   120
         TabIndex        =   52
         Top             =   360
         Width           =   2535
      End
      Begin VB.ListBox List_promotori 
         Height          =   7275
         Left            =   120
         TabIndex        =   51
         Top             =   4080
         Width           =   2535
      End
   End
   Begin VB.Frame Colors_CHART 
      Caption         =   "Pattern KappaIC/C+G - colors"
      Height          =   1695
      Left            =   14640
      TabIndex        =   43
      Top             =   240
      Width           =   2775
      Begin VB.PictureBox Col_pic3 
         BackColor       =   &H00FFFFFF&
         Height          =   255
         Left            =   1560
         ScaleHeight     =   195
         ScaleWidth      =   1035
         TabIndex        =   49
         Top             =   1200
         Width           =   1095
      End
      Begin VB.CommandButton Col_3 
         Caption         =   "BackGround"
         Height          =   255
         Left            =   120
         TabIndex        =   48
         Top             =   1200
         Width           =   1335
      End
      Begin VB.PictureBox Col_pic2 
         BackColor       =   &H000000FF&
         Height          =   255
         Left            =   1560
         ScaleHeight     =   195
         ScaleWidth      =   1035
         TabIndex        =   47
         Top             =   840
         Width           =   1095
      End
      Begin VB.PictureBox Col_pic1 
         BackColor       =   &H00C00000&
         Height          =   255
         Left            =   1560
         ScaleHeight     =   195
         ScaleWidth      =   1035
         TabIndex        =   46
         Top             =   480
         Width           =   1095
      End
      Begin VB.CommandButton Col_2 
         Caption         =   "to color"
         Height          =   255
         Left            =   120
         TabIndex        =   45
         Top             =   840
         Width           =   1335
      End
      Begin VB.CommandButton Col_1 
         Caption         =   "From color"
         Height          =   255
         Left            =   120
         TabIndex        =   44
         Top             =   480
         Width           =   1335
      End
   End
   Begin MSComDlg.CommonDialog dlgBrowse 
      Left            =   14760
      Top             =   360
      _ExtentX        =   847
      _ExtentY        =   847
      _Version        =   393216
   End
   Begin VB.Frame Frame3 
      Caption         =   "Signals"
      Height          =   1455
      Left            =   11520
      TabIndex        =   24
      Top             =   2040
      Width           =   3015
      Begin VB.PictureBox CG_color_line 
         BackColor       =   &H000000FF&
         Height          =   135
         Left            =   120
         ScaleHeight     =   75
         ScaleWidth      =   195
         TabIndex        =   75
         Top             =   1080
         Width           =   255
      End
      Begin VB.PictureBox DI_color_line 
         BackColor       =   &H00FF0000&
         Height          =   135
         Left            =   120
         ScaleHeight     =   75
         ScaleWidth      =   195
         TabIndex        =   74
         Top             =   840
         Width           =   255
      End
      Begin VB.PictureBox Kappa_color_line 
         BackColor       =   &H00000000&
         Height          =   135
         Left            =   120
         ScaleHeight     =   75
         ScaleWidth      =   195
         TabIndex        =   73
         Top             =   600
         Width           =   255
      End
      Begin VB.PictureBox TM_color_line 
         BackColor       =   &H00C00000&
         Height          =   135
         Left            =   120
         ScaleHeight     =   75
         ScaleWidth      =   195
         TabIndex        =   72
         Top             =   360
         Width           =   255
      End
      Begin VB.CheckBox PROC4 
         Caption         =   "C+G RESULTS"
         Height          =   375
         Left            =   480
         TabIndex        =   28
         Top             =   960
         Value           =   1  'Checked
         Width           =   1815
      End
      Begin VB.CheckBox PROC3 
         Caption         =   "DINUCLEOTIDE  RESULTS"
         Height          =   375
         Left            =   480
         TabIndex        =   27
         Top             =   720
         Value           =   1  'Checked
         Width           =   2415
      End
      Begin VB.CheckBox PROC2 
         Caption         =   "KAPPA RESULTS"
         Height          =   375
         Left            =   480
         TabIndex        =   26
         Top             =   480
         Value           =   1  'Checked
         Width           =   1815
      End
      Begin VB.CheckBox PROC1 
         Caption         =   "TM RESULTS"
         Height          =   375
         Left            =   480
         TabIndex        =   25
         Top             =   240
         Value           =   1  'Checked
         Width           =   1815
      End
   End
   Begin VB.PictureBox graf_TM 
      AutoRedraw      =   -1  'True
      BackColor       =   &H00FFFFFF&
      Height          =   4695
      Left            =   9360
      ScaleHeight     =   309
      ScaleMode       =   3  'Pixel
      ScaleWidth      =   333
      TabIndex        =   16
      Top             =   8880
      Width           =   5055
      Begin VB.Line Line8 
         BorderStyle     =   3  'Dot
         X1              =   336
         X2              =   -8
         Y1              =   152
         Y2              =   152
      End
      Begin VB.Line Line3 
         BorderStyle     =   3  'Dot
         X1              =   168
         X2              =   168
         Y1              =   0
         Y2              =   312
      End
      Begin VB.Label Label10 
         BackStyle       =   0  'Transparent
         Caption         =   "Kappa IC"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   120
         TabIndex        =   18
         Top             =   0
         Width           =   735
      End
      Begin VB.Label Label9 
         BackStyle       =   0  'Transparent
         Caption         =   "TM"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   4440
         TabIndex        =   17
         Top             =   4320
         Width           =   495
      End
   End
   Begin VB.PictureBox graf_DI 
      AutoRedraw      =   -1  'True
      BackColor       =   &H00FFFFFF&
      Height          =   4695
      Left            =   9360
      ScaleHeight     =   309
      ScaleMode       =   3  'Pixel
      ScaleWidth      =   333
      TabIndex        =   13
      Top             =   4080
      Width           =   5055
      Begin VB.Line Line6 
         BorderStyle     =   3  'Dot
         X1              =   336
         X2              =   -8
         Y1              =   160
         Y2              =   160
      End
      Begin VB.Line Line2 
         BorderStyle     =   3  'Dot
         X1              =   168
         X2              =   168
         Y1              =   0
         Y2              =   312
      End
      Begin VB.Label DINUCLEO 
         BackStyle       =   0  'Transparent
         Caption         =   "CG"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   4440
         TabIndex        =   15
         Top             =   4320
         Width           =   495
      End
      Begin VB.Label Label7 
         BackStyle       =   0  'Transparent
         Caption         =   "Kappa IC"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   120
         TabIndex        =   14
         Top             =   0
         Width           =   735
      End
   End
   Begin VB.PictureBox graf_IC_CG 
      AutoRedraw      =   -1  'True
      BackColor       =   &H00FFFFFF&
      Height          =   4695
      Left            =   4200
      ScaleHeight     =   309
      ScaleMode       =   3  'Pixel
      ScaleWidth      =   333
      TabIndex        =   10
      Top             =   8880
      Width           =   5055
      Begin VB.Line Line7 
         BorderStyle     =   3  'Dot
         X1              =   336
         X2              =   0
         Y1              =   152
         Y2              =   152
      End
      Begin VB.Line Line4 
         BorderStyle     =   3  'Dot
         X1              =   168
         X2              =   168
         Y1              =   0
         Y2              =   312
      End
      Begin VB.Label Label6 
         BackStyle       =   0  'Transparent
         Caption         =   "Kappa IC"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   120
         TabIndex        =   12
         Top             =   0
         Width           =   735
      End
      Begin VB.Label Label5 
         BackStyle       =   0  'Transparent
         Caption         =   "C+G%"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   4440
         TabIndex        =   11
         Top             =   4320
         Width           =   495
      End
   End
   Begin VB.PictureBox graf_point 
      AutoRedraw      =   -1  'True
      BackColor       =   &H00FFFFFF&
      Height          =   4695
      Left            =   4200
      ScaleHeight     =   309
      ScaleMode       =   3  'Pixel
      ScaleWidth      =   333
      TabIndex        =   7
      Top             =   4080
      Width           =   5055
      Begin VB.CommandButton pattern_show_more 
         Caption         =   "^"
         Height          =   255
         Left            =   4560
         TabIndex        =   99
         Top             =   120
         Width           =   255
      End
      Begin VB.Frame Pattern_data_window 
         BorderStyle     =   0  'None
         Caption         =   "Frame10"
         Height          =   3015
         Left            =   240
         TabIndex        =   98
         Top             =   480
         Visible         =   0   'False
         Width           =   4575
         Begin VB.CheckBox circle_on_window 
            Caption         =   "Show circle on point"
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   240
            TabIndex        =   109
            Top             =   600
            Value           =   1  'Checked
            Width           =   1935
         End
         Begin VB.CheckBox F_point 
            Caption         =   "Follow point on pattern"
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   240
            TabIndex        =   106
            Top             =   240
            Value           =   1  'Checked
            Width           =   1935
         End
         Begin VB.CommandButton hide_pattern_show_more 
            Caption         =   "x"
            Height          =   255
            Left            =   4200
            TabIndex        =   105
            Top             =   120
            Width           =   255
         End
         Begin VB.CommandButton Show_numbers 
            Caption         =   "&Show Pattern Data"
            Height          =   615
            Left            =   240
            TabIndex        =   104
            Top             =   2160
            Width           =   4095
         End
         Begin VB.TextBox CG_mean_txt 
            BackColor       =   &H0080C0FF&
            Height          =   285
            Left            =   2040
            TabIndex        =   102
            Text            =   "0"
            Top             =   1440
            Width           =   735
         End
         Begin VB.TextBox KIC_mean_txt 
            BackColor       =   &H00FFC0C0&
            Height          =   285
            Left            =   2040
            TabIndex        =   100
            Text            =   "0"
            Top             =   1080
            Width           =   735
         End
         Begin VB.Label ACGV 
            BackStyle       =   0  'Transparent
            Caption         =   "Average C+G values:"
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   480
            TabIndex        =   103
            Top             =   1440
            Width           =   1575
         End
         Begin VB.Label AKIC 
            BackColor       =   &H00FFFFFF&
            BackStyle       =   0  'Transparent
            Caption         =   "Average Kappa IC values:"
            ForeColor       =   &H00404040&
            Height          =   255
            Left            =   120
            TabIndex        =   101
            Top             =   1080
            Width           =   1935
         End
         Begin VB.Shape Shape1 
            BorderColor     =   &H00808080&
            Height          =   3015
            Left            =   0
            Top             =   0
            Width           =   4575
         End
      End
      Begin VB.Label KIC_VAL_T 
         AutoSize        =   -1  'True
         BackStyle       =   0  'Transparent
         Caption         =   "50"
         Height          =   195
         Left            =   120
         TabIndex        =   108
         Top             =   2040
         Width           =   180
      End
      Begin VB.Label CG_VAL_T 
         AutoSize        =   -1  'True
         BackStyle       =   0  'Transparent
         Caption         =   "50"
         Height          =   195
         Left            =   2640
         TabIndex        =   107
         Top             =   0
         Width           =   180
      End
      Begin VB.Shape pos_in_pattern 
         BorderColor     =   &H00000000&
         BorderWidth     =   2
         Height          =   255
         Left            =   5280
         Shape           =   3  'Circle
         Top             =   0
         Width           =   255
      End
      Begin VB.Shape Focus_Shape 
         BorderColor     =   &H0000FF00&
         BorderWidth     =   2
         Height          =   135
         Left            =   5040
         Top             =   0
         Width           =   135
      End
      Begin VB.Line Line5 
         BorderStyle     =   3  'Dot
         X1              =   336
         X2              =   0
         Y1              =   160
         Y2              =   160
      End
      Begin VB.Line Line1 
         BorderStyle     =   3  'Dot
         X1              =   168
         X2              =   168
         Y1              =   0
         Y2              =   312
      End
      Begin VB.Label Label4 
         BackStyle       =   0  'Transparent
         Caption         =   "C+G%"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   4440
         TabIndex        =   9
         Top             =   4320
         Width           =   495
      End
      Begin VB.Label Label3 
         BackStyle       =   0  'Transparent
         Caption         =   "Kappa IC"
         ForeColor       =   &H00404040&
         Height          =   255
         Left            =   120
         TabIndex        =   8
         Top             =   0
         Width           =   735
      End
   End
   Begin VB.Frame Frame2 
      Caption         =   "Results"
      Height          =   4695
      Index           =   0
      Left            =   240
      TabIndex        =   3
      Top             =   8880
      Width           =   3855
      Begin VB.TextBox Rezultate_txt 
         Height          =   3135
         Left            =   240
         MultiLine       =   -1  'True
         ScrollBars      =   2  'Vertical
         TabIndex        =   42
         Top             =   1320
         Width           =   3495
      End
      Begin VB.CommandButton Procesare 
         Caption         =   "Start sequence analisys"
         Height          =   375
         Left            =   240
         TabIndex        =   22
         Top             =   360
         Width           =   3375
      End
      Begin VB.CommandButton Stop_procesare 
         Caption         =   "Stop"
         Height          =   375
         Left            =   240
         TabIndex        =   21
         Top             =   840
         Width           =   3375
      End
   End
   Begin VB.Frame Frame1 
      Caption         =   "Parameters"
      Height          =   4695
      Left            =   240
      TabIndex        =   2
      Top             =   4080
      Width           =   3855
      Begin VB.CommandButton Tools 
         Caption         =   "T"
         Height          =   375
         Left            =   240
         TabIndex        =   95
         ToolTipText     =   "Tools for sequence manipulation"
         Top             =   3840
         Width           =   375
      End
      Begin VB.CheckBox Save_Result 
         Caption         =   "Save results as images (BMP)"
         Height          =   255
         Left            =   240
         TabIndex        =   86
         Top             =   4320
         Value           =   1  'Checked
         Width           =   2535
      End
      Begin VB.TextBox mot33 
         ForeColor       =   &H00C00000&
         Height          =   285
         Left            =   3480
         TabIndex        =   83
         Text            =   "0"
         Top             =   3360
         Width           =   255
      End
      Begin VB.TextBox mot22 
         ForeColor       =   &H0000C000&
         Height          =   285
         Left            =   3480
         TabIndex        =   82
         Text            =   "0"
         Top             =   3000
         Width           =   255
      End
      Begin VB.TextBox mot11 
         ForeColor       =   &H000000FF&
         Height          =   285
         Left            =   3480
         TabIndex        =   81
         Text            =   "0"
         Top             =   2640
         Width           =   255
      End
      Begin VB.TextBox mot3 
         ForeColor       =   &H00C00000&
         Height          =   285
         Left            =   3120
         TabIndex        =   80
         Text            =   "0"
         Top             =   3360
         Width           =   255
      End
      Begin VB.TextBox mot2 
         ForeColor       =   &H0000C000&
         Height          =   285
         Left            =   3120
         TabIndex        =   79
         Text            =   "0"
         Top             =   3000
         Width           =   255
      End
      Begin VB.TextBox mot1 
         ForeColor       =   &H000000FF&
         Height          =   285
         Left            =   3120
         TabIndex        =   78
         Text            =   "0"
         Top             =   2640
         Width           =   255
      End
      Begin VB.CheckBox PPDOG 
         Caption         =   "Print promoter data on graph"
         Height          =   255
         Left            =   240
         TabIndex        =   77
         Top             =   2160
         Width           =   2415
      End
      Begin VB.CheckBox SecSenzitiv 
         Caption         =   "Calculate the promoter nucleotide frequency"
         Height          =   375
         Left            =   240
         TabIndex        =   76
         Top             =   1800
         Value           =   1  'Checked
         Width           =   3495
      End
      Begin VB.CommandButton Filtru3 
         Caption         =   "L"
         Height          =   375
         Left            =   1200
         TabIndex        =   38
         ToolTipText     =   "Make the sequence lowercase"
         Top             =   3840
         Width           =   375
      End
      Begin VB.CommandButton Filtru2 
         Caption         =   "U"
         Height          =   375
         Left            =   1680
         TabIndex        =   37
         ToolTipText     =   "Make the sequence uppercase"
         Top             =   3840
         Width           =   375
      End
      Begin VB.CommandButton Filtru1 
         Caption         =   "C"
         Height          =   375
         Left            =   2160
         TabIndex        =   36
         ToolTipText     =   "Delete line feed and carriage return from the sequence"
         Top             =   3840
         Width           =   375
      End
      Begin VB.CheckBox Check1 
         Caption         =   "DELETE RESULTS"
         Height          =   375
         Left            =   2640
         TabIndex        =   35
         Top             =   3840
         Value           =   1  'Checked
         Width           =   1095
      End
      Begin VB.TextBox TATA 
         ForeColor       =   &H000000FF&
         Height          =   285
         Left            =   1080
         TabIndex        =   34
         Text            =   "TATA"
         Top             =   2640
         Width           =   1935
      End
      Begin VB.TextBox ATAAA 
         ForeColor       =   &H00C00000&
         Height          =   285
         Left            =   1080
         TabIndex        =   33
         Text            =   "AATAAA"
         Top             =   3360
         Width           =   1935
      End
      Begin VB.TextBox ATG 
         ForeColor       =   &H0000C000&
         Height          =   285
         Left            =   1080
         TabIndex        =   32
         Text            =   "ATG"
         Top             =   3000
         Width           =   1935
      End
      Begin VB.CommandButton Filtru4 
         Caption         =   "G"
         Height          =   375
         Left            =   720
         TabIndex        =   31
         ToolTipText     =   "Generate random sequence"
         Top             =   3840
         Width           =   375
      End
      Begin VB.TextBox Step_Window 
         Height          =   285
         Left            =   2160
         TabIndex        =   29
         Text            =   "1"
         Top             =   840
         Width           =   615
      End
      Begin VB.ComboBox DubleN 
         Height          =   315
         Left            =   2160
         TabIndex        =   19
         Text            =   "CG"
         Top             =   1440
         Width           =   615
      End
      Begin VB.TextBox Lungime_fereastra 
         Height          =   285
         Left            =   2160
         TabIndex        =   4
         Text            =   "30"
         Top             =   480
         Width           =   615
      End
      Begin VB.Line Line18 
         X1              =   3600
         X2              =   3480
         Y1              =   2520
         Y2              =   2400
      End
      Begin VB.Line Line17 
         X1              =   3240
         X2              =   3360
         Y1              =   2520
         Y2              =   2400
      End
      Begin VB.Line Line16 
         X1              =   3600
         X2              =   3480
         Y1              =   2280
         Y2              =   2400
      End
      Begin VB.Line Line15 
         X1              =   3480
         X2              =   3720
         Y1              =   2400
         Y2              =   2400
      End
      Begin VB.Line Line14 
         X1              =   3240
         X2              =   3360
         Y1              =   2280
         Y2              =   2400
      End
      Begin VB.Line Line13 
         X1              =   3120
         X2              =   3360
         Y1              =   2400
         Y2              =   2400
      End
      Begin VB.Label Label2 
         Caption         =   "Motif 1:"
         Height          =   255
         Left            =   240
         TabIndex        =   41
         Top             =   2640
         Width           =   855
      End
      Begin VB.Label Label11 
         Caption         =   "Motif 2:"
         Height          =   255
         Left            =   240
         TabIndex        =   40
         Top             =   3000
         Width           =   855
      End
      Begin VB.Label Label12 
         Caption         =   "Motif 3:"
         Height          =   255
         Left            =   240
         TabIndex        =   39
         Top             =   3360
         Width           =   855
      End
      Begin VB.Label Label8 
         Alignment       =   1  'Right Justify
         Caption         =   "Window step:"
         Height          =   255
         Left            =   960
         TabIndex        =   30
         Top             =   840
         Width           =   1095
      End
      Begin VB.Label Label28 
         Alignment       =   1  'Right Justify
         Caption         =   "Dinucleotide:"
         BeginProperty Font 
            Name            =   "Arial"
            Size            =   9.75
            Charset         =   238
            Weight          =   400
            Underline       =   0   'False
            Italic          =   0   'False
            Strikethrough   =   0   'False
         EndProperty
         Height          =   375
         Left            =   480
         TabIndex        =   20
         Top             =   1440
         Width           =   1575
      End
      Begin VB.Label Label1 
         Alignment       =   1  'Right Justify
         Caption         =   "Sliding window length:"
         Height          =   255
         Left            =   120
         TabIndex        =   5
         Top             =   480
         Width           =   1935
      End
   End
   Begin VB.PictureBox Picture1 
      AutoRedraw      =   -1  'True
      BackColor       =   &H00FFFFFF&
      Height          =   1575
      Left            =   240
      ScaleHeight     =   101
      ScaleMode       =   3  'Pixel
      ScaleWidth      =   949
      TabIndex        =   1
      Top             =   360
      Width           =   14295
      Begin VB.Shape Window_Shape 
         BorderColor     =   &H00808080&
         Height          =   1335
         Left            =   0
         Top             =   120
         Visible         =   0   'False
         Width           =   15
      End
      Begin VB.Label Status_sus 
         AutoSize        =   -1  'True
         BackStyle       =   0  'Transparent
         Caption         =   "Processing: 100%"
         BeginProperty Font 
            Name            =   "Arial"
            Size            =   24
            Charset         =   238
            Weight          =   400
            Underline       =   0   'False
            Italic          =   0   'False
            Strikethrough   =   0   'False
         EndProperty
         ForeColor       =   &H00404040&
         Height          =   555
         Left            =   5640
         TabIndex        =   6
         Top             =   480
         Visible         =   0   'False
         Width           =   3840
      End
   End
   Begin VB.TextBox secventata 
      Height          =   1815
      Left            =   240
      MultiLine       =   -1  'True
      ScrollBars      =   2  'Vertical
      TabIndex        =   0
      Top             =   2160
      Width           =   11175
   End
   Begin VB.Image Image1 
      Height          =   720
      Left            =   -7800
      Picture         =   "CG.frx":1D6BF
      Top             =   13680
      Width           =   25290
   End
   Begin VB.Label Label17 
      Caption         =   "Sequence name :"
      Height          =   255
      Left            =   240
      TabIndex        =   71
      Top             =   1920
      Width           =   1335
   End
   Begin VB.Label seq_name_from_file 
      Caption         =   "DNA sequence name ..."
      Height          =   255
      Left            =   1560
      TabIndex        =   70
      Top             =   1920
      Width           =   9975
   End
   Begin VB.Image graf_point_I 
      Height          =   135
      Left            =   11040
      Top             =   120
      Visible         =   0   'False
      Width           =   255
   End
   Begin VB.Label info 
      Caption         =   "Overall results ..."
      Height          =   255
      Left            =   240
      TabIndex        =   23
      Top             =   120
      Width           =   8895
   End
End
Attribute VB_Name = "PromKappa"
Attribute VB_GlobalNameSpace = False
Attribute VB_Creatable = False
Attribute VB_PredeclaredId = True
Attribute VB_Exposed = False
'   ________________________________                          ____________________
'  /            PromKappa           \________________________/       v2.00        |
' |                                                                               |
' |            Name:  PromKappa V3.0                                              |
' |        Category:  Open source software                                        |
' |          Author:  Paul A. Gagniuc                                             |
' |            Book:  Algorithms in Bioinformatics: Theory and Implementation     |
' |           Email:  paul_gagniuc@acad.ro                                        |
' |  ____________________________________________________________________________ |
' |                                                                               |
' |    Date Created:  September 2013                                              |
' |          Update:  July 2021                                                   |
' |       Tested On:  WinXP, WinVista, Win7, Win8, Win10                          |
' |             Use:  Analysis of gene promoters                                  |
' |                                                                               |
' |                  _____________________________                                |
' |_________________/                             \_______________________________|
'

Dim numar As Variant
Dim oprire As Boolean
Dim pascupas As Variant
Dim Pause_all_tests As Boolean

Private Sub circle_on_window_Click()
    If pos_in_pattern.Visible = False Then
        pos_in_pattern.Visible = True
    Else
        pos_in_pattern.Visible = False
    End If
End Sub

Private Sub DubleN_LostFocus()
    DINUCLEO.Caption = DubleN.Text
End Sub

Private Sub Erase_Center_patt_Click()
    Center_patt.Cls
End Sub

Private Sub Erase_MasterGraph_Click()
    MasterGraph.Cls
End Sub

Private Sub F_point_Click()
    If F_point.Value = 0 Then
        Line1.X1 = graf_point.ScaleWidth / 2
        Line1.X2 = graf_point.ScaleWidth / 2
        
        Line5.Y1 = graf_point.ScaleHeight / 2
        Line5.Y2 = graf_point.ScaleHeight / 2
        
        CG_VAL_T.Left = Line1.X1 + 5
        KIC_VAL_T.Top = Line5.Y1 + 5
    
    End If
End Sub

Private Sub Filtru1_Click()
    secventata.Text = Replace(secventata.Text, Chr(10), "")
    secventata.Text = Replace(secventata.Text, Chr(13), "")
End Sub

Private Sub Filtru2_Click()
    secventata.Text = UCase(secventata.Text)
End Sub

Private Sub Filtru3_Click()
    secventata.Text = LCase(secventata.Text)
End Sub

Private Sub Filtru4_Click()

    Dim ans As String
    
    ans = InputBox("Enter the number of nucleotides (DNA sequence length)", "Random DNA sequence generator", 10000)
    
    If ans = "" Then
        MsgBox "Random DNA sequence has not been generated"
    Else
        secventata.Text = GENEREAZA_NUCLEOTIDE(ans, "ADN")
    End If

End Sub

Private Sub Form_Load()
    pascupas = 0
    dlgBrowse.InitDir = App.Path 'GetPrimaryDrive
    dlgBrowse.Filter = "(All files)|*.*|"
    dlgBrowse.Flags = cdlOFNHideReadOnly + cdlOFNLongNames + cdlOFNPathMustExist + cdlOFNFileMustExist
    
    aq = 0
    numar = 0
    
    total_val_x = 0 ' valori totale per set de promotori
    total_val_y = 0
    
    Filtru1_Click
    
    DubleN.AddItem "AT"
    DubleN.AddItem "AC"
    DubleN.AddItem "AG"
    DubleN.AddItem "AA"
    
    DubleN.AddItem "CA"
    DubleN.AddItem "CT"
    DubleN.AddItem "CG"
    DubleN.AddItem "CC"
    
    DubleN.AddItem "GT"
    DubleN.AddItem "GA"
    DubleN.AddItem "GC"
    DubleN.AddItem "GG"
    
    DubleN.AddItem "TC"
    DubleN.AddItem "TG"
    DubleN.AddItem "TA"
    DubleN.AddItem "TT"
    
    Pause_all_tests = False
    
    html = "<HTML><HEAD>" & vbCrLf
    html = html & "<script type='text/javascript'>" & vbCrLf
    html = html & "window.onload=function(){" & vbCrLf
    html = html & "var tfrow = document.getElementById('tfhover').rows.length;" & vbCrLf
    html = html & "var tbRow=[];" & vbCrLf
    html = html & "for (var i=1;i<tfrow;i++) {" & vbCrLf
    html = html & "tbRow[i]=document.getElementById('tfhover').rows[i];" & vbCrLf
    html = html & "tbRow[i].onmouseover = function(){" & vbCrLf
    html = html & "this.style.backgroundColor = '#ffffff';" & vbCrLf
    html = html & "};" & vbCrLf
    html = html & "tbRow[i].onmouseout = function() {" & vbCrLf
    html = html & "this.style.backgroundColor = '#d4e3e5';" & vbCrLf
    html = html & "};" & vbCrLf
    html = html & "}" & vbCrLf
    html = html & "};" & vbCrLf
    html = html & "</script>" & vbCrLf
    
    html = html & "<style type='text/css'>" & vbCrLf
    html = html & "table.tftable {font-size:12px;color:#333333;width:100%;border-width: 1px;border-color: #729ea5;border-collapse: collapse;}" & vbCrLf
    html = html & "table.tftable th {font-size:12px;background-color:#acc8cc;border-width: 1px;padding: 8px;border-style: solid;border-color: #729ea5;text-align:left;}" & vbCrLf
    html = html & "table.tftable tr {background-color:#d4e3e5;}" & vbCrLf
    html = html & "table.tftable td {font-size:12px;border-width: 1px;padding: 8px;border-style: solid;border-color: #729ea5;}" & vbCrLf
    html = html & "</style>" & vbCrLf
    
    html = html & "</HEAD>" & vbCrLf
    html = html & "<BODY bgcolor='#454545'>" & vbCrLf
    
    html = html & "<table id='tfhover' class='tftable' border='1'>" & vbCrLf
    html = html & "<tr>" & vbCrLf
    html = html & "<th>" & "Gene name" & "</th>" & vbCrLf
    html = html & "<th>" & "Average KIC values" & "</th>" & vbCrLf
    html = html & "<th>" & "Average C+G values" & "</th>" & vbCrLf
    html = html & "<th>" & "Pattern surface (%)" & "</th>" & vbCrLf
    html = html & "<th>" & "AT/CG Equilibrium (-90,0,90)" & "</th>" & vbCrLf
    html = html & "<th>" & "Angle 360°" & "</th>" & vbCrLf
    html = html & "<th>" & "Angle 180" & "</th>" & vbCrLf
    html = html & "<th>" & "Y max limit" & "</th>" & vbCrLf
    html = html & "<th>" & "Y min limit" & "</th>" & vbCrLf
    html = html & "<th>" & "X min limit" & "</th>" & vbCrLf
    html = html & "<th>" & "X max limit" & "</th>" & vbCrLf
    html = html & "<th>" & "Pattern height" & "</th>" & vbCrLf
    html = html & "<th>" & "Pattern width" & "</th>" & vbCrLf
    html = html & "</tr>" & vbCrLf

End Sub

Private Sub Form_Unload(Cancel As Integer)
    Unload Pattern_Numbers
    Unload Search_gene_names
    Unload Me
End Sub

Private Sub gene_search_Click()
pro_no = List_promotori.ListCount

For i = 0 To pro_no

    If List_promotori.List(i) <> "" Then

        If InStr(UCase(List_promotori.List(i)), UCase(gene_search_txt.Text)) <> 0 Then
        
        a = List_promotori.ItemData(i)
        MsgBox "Item found in row no " & i
        
            List_promotori.Enabled = False

            secventata.Text = Split(List_promotori.List(i), "|")(1)
            seq_name_from_file.Caption = Split(List_promotori.List(i), "|")(0)
            Procesare_Click

            List_promotori.Enabled = True
        
        
        
        Exit Sub
        End If
        

    End If


Next i


MsgBox "Gene promoter not found !"
End Sub

Private Sub graf_point_Click()
    Line1.X1 = graf_point.ScaleWidth / 2
    Line1.X2 = graf_point.ScaleWidth / 2
    
    Line5.Y1 = graf_point.ScaleHeight / 2
    Line5.Y2 = graf_point.ScaleHeight / 2
    
    Pattern_data_window.Visible = False
    
    CG_VAL_T.Left = Line1.X1 + 5
    KIC_VAL_T.Top = Line5.Y1 + 5
End Sub

Private Sub Graph1_show_Click()
    MRP.Visible = True
End Sub

Private Sub Graph2_show_Click()
    MRP.Visible = False
End Sub

Private Sub hide_pattern_show_more_Click()
    Pattern_data_window.Visible = False
End Sub

Private Sub pattern_show_more_Click()
    If Pattern_data_window.Visible = False Then
        Pattern_data_window.Visible = True
    Else
        Pattern_data_window.Visible = False
    End If
End Sub

Private Sub Pause_p_test_Click()
    If Pause_all_tests = True Then
        Pause_all_tests = False
    Else
        Pause_all_tests = True
    End If
End Sub

Private Sub Picture1_MouseMove(Button As Integer, Shift As Integer, X As Single, Y As Single)

    Dim ax() As String
    Dim ay() As String
    
    Window_Shape.Visible = True
    'On Error Resume Next
    q = (Len(secventata.Text) / Picture1.ScaleWidth) * X
    
    secventata.SetFocus
    secventata.SelStart = q
    secventata.SelLength = Lungime_fereastra.Text
    
    secventaADN = secventata.SelText
    
    If Len(secventata.Text) < 3 Then Exit Sub
    
    Window_Shape.Width = (Picture1.ScaleWidth / Len(secventata.Text)) * Len(secventaADN)
    Window_Shape.Left = X
    
    If Len(secventaADN) >= Val(Lungime_fereastra.Text) Then
    
    
        If SecSenzitiv.Value = 0 Then
        
            pos_in_pattern.Visible = False
            'Here we read the values in real time, directly from the sliding window sequence
            For i = 1 To Val(Lungime_fereastra.Text)
                nucleotida = LCase(Mid(secventaADN, i, 1))
                If nucleotida = "a" Then a = a + 1
                If nucleotida = "t" Then t = t + 1
                If nucleotida = "g" Then G = G + 1
                If nucleotida = "c" Then c = c + 1
            Next i
            
            Toltal_CG_Procent = Round((100 / (c + G + t + a)) * (c + G), 2)
            
            Focus_Shape.Width = (graf_point.ScaleWidth / Val(Lungime_fereastra.Text))
            Focus_Shape.Height = 3
            Focus_Shape.Left = ((graf_point.ScaleWidth / 100) * Toltal_CG_Procent)
            ICSDNA = IC(secventaADN)
            Focus_Shape.Top = graf_point.ScaleHeight - ((graf_point.ScaleHeight / 100) * ICSDNA) - 1
            
            CG_VAL_T.Caption = Round(Toltal_CG_Procent, 2)
            KIC_VAL_T.Caption = Val(ICSDNA)
        
        Else
        
        
            If circle_on_window.Value = 1 Then
                pos_in_pattern.Visible = True
            End If
            
            'Here we read the values from the global array ax() and ay(). This approach is equivalent to the above method.
            ax() = Split(Sir_CG_regression, ",")
            ay() = Split(Sir_IC_regression, ",")
        
            If Round(q) > UBound(ax) - 1 Then Exit Sub
            
                Focus_Shape.Width = 2
                Focus_Shape.Height = 2
                Focus_Shape.Left = (graf_point.ScaleWidth / 100) * Val(ax(Round(q)))
                Focus_Shape.Top = graf_point.ScaleHeight - ((graf_point.ScaleHeight / 100) * Val(ay(Round(q))))
                'graf_point.Circle (Focus_Shape.Left, Focus_Shape.Top), 2, vbRed
                
                pos_in_pattern.Left = Focus_Shape.Left - (pos_in_pattern.Width / 2)
                pos_in_pattern.Top = Focus_Shape.Top - (pos_in_pattern.Height / 2)
                
                CG_VAL_T.Caption = Round(Val(ax(Round(q))), 2)
                KIC_VAL_T.Caption = Val(ay(Round(q)))
        End If
    
        If F_point.Value = 1 Then
            Line1.X1 = Focus_Shape.Left
            Line1.X2 = Line1.X1
            Line5.Y1 = Focus_Shape.Top
            Line5.Y2 = Line5.Y1
            
            CG_VAL_T.Left = Line1.X1 + 5
            KIC_VAL_T.Top = Line5.Y1 + 5
        End If
    
    End If
    
    info.Caption = "Sliding window starts at ~ : " & Int(q) & "b and ends at " & _
    Int(q + Val(Lungime_fereastra.Text)) & "b" & vbCrLf
End Sub

Private Sub Picture2_MouseMove(Button As Integer, Shift As Integer, X As Single, Y As Single)
    q = (Len(secventata.Text) / Picture1.ScaleWidth) * X
    secventata.SetFocus
    secventata.SelStart = q
    secventata.SelLength = Lungime_fereastra.Text
End Sub


Function call_sub_Procesare_Click()
    Procesare_Click
End Function



Private Sub Procesare_Click()
    Dim punct As Long
    
    oprire = False
    Window_Shape.Visible = False
    
    Sir_IC_regression = ""
    Sir_CG_regression = ""
    
    Rezultate_txt.Text = ""
    
    mot1.Text = "0"
    mot11.Text = "0"
    mot2.Text = "0"
    mot22.Text = "0"
    mot3.Text = "0"
    mot33.Text = "0"
    
    
    Last_x_lim_min = 0
    Last_x_lim_max = 0
    
    Last_y_lim_min = 0
    Last_y_lim_max = 0
    
    If Check1.Value = 1 Then
        Picture1.Cls
        graf_point.Cls
        graf_DI.Cls
        graf_IC_CG.Cls
        graf_TM.Cls
    End If
    
    Status_sus.Visible = True
    '-----------------------------------------------------------------
    lungimeADN = Len(secventata.Text)
    
    secventaADN = Replace(secventata.Text, vbCrLf, "")
    Fereastra = Val(Lungime_fereastra.Text)
    
    For i = 1 To lungimeADN
        nucleotida = LCase(Mid(secventaADN, i, 1))
        If nucleotida = "a" Then a = a + 1
        If nucleotida = "t" Then t = t + 1
        If nucleotida = "g" Then G = G + 1
        If nucleotida = "c" Then c = c + 1
        Next i
        
        Toltal_CG_Procent = (100 / (c + G + t + a)) * (c + G)
        
        Rezultate_txt.Text = Rezultate_txt.Text & vbCrLf & "CG = " & Toltal_CG_Procent & " %" & vbCrLf & vbCrLf & _
        "A = " & Int((100 / (c + G + t + a)) * a) & " %" & vbCrLf & _
        "T = " & Int((100 / (c + G + t + a)) * t) & " %" & vbCrLf & _
        "C = " & Int((100 / (c + G + t + a)) * c) & " %" & vbCrLf & _
        "G= " & Int((100 / (c + G + t + a)) * G) & " %" & vbCrLf
        '-----------------------------------------------------------------
        
        For i = 1 To lungimeADN - Fereastra Step Val(Step_Window.Text)
        
        Motifs_pos = Val(Picture1.ScaleWidth) / Val(lungimeADN)
        
        a = 0
        t = 0
        c = 0
        G = 0
        
        Status_sus.Caption = "Processing: " & Int((100 / (lungimeADN - Fereastra)) * i) & " %"
        
        
        For j = 1 To Fereastra
        
            nucleotida = LCase(Mid(secventaADN, i + j - 1, 1))
            
            If nucleotida = "a" Then a = a + 1
            If nucleotida = "t" Then t = t + 1
            If nucleotida = "g" Then G = G + 1
            If nucleotida = "c" Then c = c + 1
            
            
            fereastra_continut = fereastra_continut & nucleotida
        
        Next j
        
        If oprire = True Then Exit Sub
        DoEvents
        
        If SecSenzitiv.Value = 1 Then
        Fereastra_CG_Procent = (Toltal_CG_Procent / (c + G + t + a)) * (c + G)
        Else
        Fereastra_CG_Procent = (100 / (c + G + t + a)) * (c + G)
        End If
        
        
        
        Sir_Proportii = Sir_Proportii & Fereastra_CG_Procent & ","
        Sir_CG_regression = Sir_CG_regression & Fereastra_CG_Procent & ","
        
        If PROC1.Value = 1 Then
        formula_primer_PCR = Int(81.5 + 16.6 * (Log(0.05) / Log(10)) + 0.41 * (Fereastra_CG_Procent) - 675 / Len(fereastra_continut))
        Sir_TM = Sir_TM & formula_primer_PCR & ","
        End If
        
        If PROC2.Value = 1 Then
        Fereastra_Kappa = IC(fereastra_continut)
        Sir_IC = Sir_IC & Fereastra_Kappa & ","
        Sir_IC_regression = Sir_IC_regression & Fereastra_Kappa & ","
        End If
        
        If PROC3.Value = 1 Then
        Fereastra_CG_Content = Dinucleotide_Content(fereastra_continut)
        Sir_DI = Sir_DI & Fereastra_CG_Content & ","
        End If
        
        
        fereastra_continut_strand2 = strand2(fereastra_continut)
        
        
        If Mid(UCase(fereastra_continut), 1, Len(TATA.Text)) = TATA.Text Then
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 30), vbRed
        Picture1.Line (mi, 30)-(mi + 5, 30), vbRed
        Picture1.Line (mi + 5, 30)-(mi + 2, 27), vbRed
        Picture1.Line (mi + 5, 30)-(mi + 2, 33), vbRed
        
        mot1.Text = Val(mot1.Text) + 1
        
        End If
        
        If Mid(UCase(fereastra_continut_strand2), 1, Len(TATA.Text)) = TATA.Text Then ' STRAND 2
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 30), vbRed
        Picture1.Line (mi, 30)-(mi - 5, 30), vbRed
        Picture1.Line (mi - 5, 30)-(mi - 2, 27), vbRed
        Picture1.Line (mi - 5, 30)-(mi - 2, 33), vbRed
        
        mot11.Text = Val(mot11.Text) + 1
        
        End If
        
        If Mid(UCase(fereastra_continut), 1, Len(ATG.Text)) = ATG.Text Then
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 20), &HC000&
        Picture1.Line (mi, 20)-(mi + 5, 20), &HC000&
        Picture1.Line (mi + 5, 20)-(mi + 2, 17), &HC000&
        Picture1.Line (mi + 5, 20)-(mi + 2, 23), &HC000&
        
        mot2.Text = Val(mot2.Text) + 1
        
        End If
        
        If Mid(UCase(fereastra_continut_strand2), 1, Len(ATG.Text)) = ATG.Text Then ' STRAND 2
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 20), &HC000&
        Picture1.Line (mi, 20)-(mi - 5, 20), &HC000&
        Picture1.Line (mi - 5, 20)-(mi - 2, 17), &HC000&
        Picture1.Line (mi - 5, 20)-(mi - 2, 23), &HC000&
        
        mot22.Text = Val(mot22.Text) + 1
        
        End If
        
        If Mid(UCase(fereastra_continut), 1, Len(ATAAA.Text)) = ATAAA.Text Then
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 10), vbBlue
        Picture1.Line (mi, 10)-(mi + 5, 10), vbBlue
        Picture1.Line (mi + 5, 10)-(mi + 2, 7), vbBlue
        Picture1.Line (mi + 5, 10)-(mi + 2, 13), vbBlue
        
        mot3.Text = Val(mot3.Text) + 1
        
        End If
        
        If Mid(UCase(fereastra_continut_strand2), 1, Len(ATAAA.Text)) = ATAAA.Text Then ' STRAND 2
        mi = Val(Motifs_pos) * i
        Picture1.Line (mi, 0)-(mi, 10), vbBlue
        Picture1.Line (mi, 10)-(mi - 5, 10), vbBlue
        Picture1.Line (mi - 5, 10)-(mi - 2, 7), vbBlue
        Picture1.Line (mi - 5, 10)-(mi - 2, 13), vbBlue
        
        mot33.Text = Val(mot33.Text) + 1
        
        End If
        
        fereastra_continut = ""
    
    Next i
    
    If PROC1.Value = 1 Then Call Deseneaza_TM(lungimeADN, Sir_TM)
    If PROC2.Value = 1 Then Call Deseneaza_grafic_IC(lungimeADN, Sir_IC)
    If PROC3.Value = 1 Then Call Deseneaza_DI(lungimeADN, Sir_DI)
    If PROC4.Value = 1 Then Call Deseneaza_grafic(lungimeADN, Sir_Proportii)
    
    
    Dim aa() As String ' C+G procentage array
    Dim bb() As String ' Kappa IC array
    Dim cc() As String ' Dinucleotide content array
    Dim tt() As String ' TM array
    
    aa() = Split(Sir_Proportii, ",")
    bb() = Split(Sir_IC, ",")
    cc() = Split(Sir_DI, ",")
    tt() = Split(Sir_TM, ",")
    
    Xa = graf_point.ScaleWidth / 100
    Yb = graf_point.ScaleHeight / 100
    Xc = graf_DI.ScaleWidth / 100 'dinucleotide
    
    For i = 1 To UBound(aa()) - 1
        
        mean_aa = mean_aa + Val(aa(i))
        mean_bb = mean_bb + Val(bb(i))
        'mean_cc = mean_cc + Val(cc(i)) 'dinucleotide
        'mean_tt = mean_tt + Val(tt(i))
            
        If PROC4.Value = 1 And PROC2.Value = 1 Then
        
        punct = graf_point.Point(aa(i) * Xa, graf_point.ScaleHeight - (bb(i) * Yb))
            
        If punct = Col_pic3.BackColor Or punct = Empty Then punct = Col_pic1.BackColor
        punct = BlendColors(punct, Col_pic2.BackColor, 0.9)
            
        If SecSenzitiv.Value = 1 Then
            BAR_WITH = Xa
        Else
            BAR_WITH = (graf_point.ScaleWidth / Val(Lungime_fereastra.Text)) - 1
        End If
            
        graf_point.Line (aa(i) * Xa, graf_point.ScaleHeight - (bb(i) * Yb))-((aa(i) * Xa) + (BAR_WITH), graf_point.ScaleHeight - (bb(i) * Yb)), punct
            
        '----------------
        'calculate the minimum and maximum limits of the pattern on both axes
        
        Lim_x_min = aa(i) * Xa
        Lim_x_max = (aa(i) * Xa) + (BAR_WITH)
            
            
         If Last_x_lim_min = "0" Then Last_x_lim_min = Lim_x_min
            
         If Lim_x_min < Last_x_lim_min Then
            Last_x_lim_min = Lim_x_min
         End If
         
         If Lim_x_max > Last_x_lim_max Then
            Last_x_lim_max = Lim_x_max
         End If
         
         
        Lim_y_min = graf_point.ScaleHeight - (bb(i) * Yb)
        Lim_y_max = graf_point.ScaleHeight - (bb(i) * Yb)
         
         If Last_y_lim_min = "0" Then Last_y_lim_min = Lim_y_min
            
         If Lim_y_min < Last_y_lim_min Then
            Last_y_lim_min = Lim_y_min
         End If
         
         If Lim_y_max > Last_y_lim_max Then
            Last_y_lim_max = Lim_y_max
         End If
            
        '----------------
            End If
                    
            If PROC4.Value = 1 And PROC2.Value = 1 Then
                If aa(i) > bb(i) Then
                    aaa = aaa + 1
                    graf_IC_CG.Line (aa(i) * Xa, graf_IC_CG.ScaleHeight - (bb(i) * Yb))-((aa(i) * Xa) + (BAR_WITH), graf_IC_CG.ScaleHeight - (bb(i) * Yb)), BlendColorsRGB(55, 0, 0, 22, 0, 0, vbRed)
                Else
                    aaa = aaa - 1
                    graf_IC_CG.Line (aa(i) * Xa, graf_IC_CG.ScaleHeight - (bb(i) * Yb))-((aa(i) * Xa) + (BAR_WITH), graf_IC_CG.ScaleHeight - (bb(i) * Yb)), vbBlue
                End If
            End If
                    
            If PROC3.Value = 1 And PROC2.Value = 1 Then
                graf_DI.Line (cc(i) * Xc, graf_DI.ScaleHeight - (bb(i) * Yb))-((cc(i) * Xc) + (BAR_WITH), graf_DI.ScaleHeight - (bb(i) * Yb)), vbRed
            End If
                
            If PROC1.Value = 1 And PROC2.Value = 1 Then graf_TM.Line (tt(i) * Xa, graf_TM.ScaleHeight - (bb(i) * Yb))-((tt(i) * Xa) + (BAR_WITH), graf_TM.ScaleHeight - (bb(i) * Yb)), vbRed
               
    Next i
    
    mean_aa = mean_aa / UBound(aa())
    mean_bb = mean_bb / UBound(bb())
    
    graf_point.Circle (mean_aa * Xa, graf_point.ScaleHeight - (mean_bb * Yb)), 6, vbBlack
    
    
    KIC_mean_txt.Text = Round((100 / graf_point.ScaleWidth) * (mean_bb * Yb), 2) ' mean Kappa IC
    CG_mean_txt.Text = Round((100 / graf_point.ScaleWidth) * (mean_aa * Xa), 2) ' mean C+G
    '---------------------------------------------------------------------------
    total_val_x = total_val_x + Val(mean_aa * Xa)
    total_val_y = total_val_y + Val(Center_patt.ScaleHeight - (mean_bb * Yb))
    '---------------------------------------------------------------------------
    If Option1.Value = True Then
        punct = Center_patt.Point(mean_aa * Xa, Center_patt.ScaleHeight - (mean_bb * Yb))
        If punct = Col_pic3.BackColor Or punct = Empty Then punct = Col_pic1.BackColor
        punct = BlendColors(punct, Col_pic2.BackColor, 0.9)
        Center_patt.PSet (mean_aa * Xa, Center_patt.ScaleHeight - (mean_bb * Yb)), punct
    End If
    
    If Option2.Value = True Then
        punct = Center_patt.Point(mean_aa * Xa, Center_patt.ScaleHeight - (mean_bb * Yb))
        If punct = Col_pic3.BackColor Or punct = Empty Then punct = Col_pic1.BackColor
        punct = BlendColors(punct, Col_pic2.BackColor, 0.9)
        Center_patt.Circle (mean_aa * Xa, Center_patt.ScaleHeight - (mean_bb * Yb)), 1, punct
        'KIC_mean_txt.Text = total_val_x '(100 / mean_bb) * Yb ' mean Kappa IC
        'CG_mean_txt = total_val_y '(100 / mean_aa) * Xa ' mean C+G
    End If
    
    On Error Resume Next
    If PROC4.Value = 1 And PROC2.Value = 1 Then
        Rezultate_txt.Text = Rezultate_txt.Text & vbCrLf & "Intersections Kappa IC with C+G content (IC_CG):" & aaa & " times " & vbCrLf & "DNA length:" & lungimeADN & "b " & vbCrLf
        Rezultate_txt.Text = Rezultate_txt.Text & vbCrLf & "(IC_CG / L_DNA) = " & (lungimeADN / aaa)
    End If
    
    Status_sus.Visible = False
    
    If PPDOG.Value = 1 Then
        graf_point.ForeColor = vbRed
        graf_point.FontSize = 10
        graf_point.CurrentX = 30
        graf_point.CurrentY = 10
        graf_point.Print seq_name_from_file.Caption
    
        graf_IC_CG.ForeColor = vbRed
        graf_IC_CG.FontSize = 10
        graf_IC_CG.CurrentX = 30
        graf_IC_CG.CurrentY = 10
        graf_IC_CG.Print seq_name_from_file.Caption
    End If
    
    If Save_Result.Value = 1 Then
    
        gene_name_for_file = Split(seq_name_from_file.Caption, ")")(1)
        gene_name_for_file = Split(gene_name_for_file, ";")(0)
        gene_name_for_file = Replace(gene_name_for_file, "'", "-")
        gene_name_for_file = Replace(gene_name_for_file, ":", "-")
    
        numar = numar + 1
        graf_point_I.Picture = graf_point.Image
        'tmp_name = App.Path & "\chart\" & numar & "-" & Replace(Time, ":", "-") & ".bmp"
        tmp_name = App.Path & "\chart\" & gene_name_for_file & "-[" & numar & "].bmp"
        SavePicture graf_point_I.Picture, tmp_name
        
        
        numar = numar + 1
        graf_point_I.Picture = graf_IC_CG.Image
        tmp_name = App.Path & "\chart_comp\" & gene_name_for_file & "-[" & numar & "].bmp"
        SavePicture graf_point_I.Picture, tmp_name
        
    End If
    
    Window_Shape.Visible = True
End Sub


Function Deseneaza_grafic(ByVal lungime As Variant, ByVal sir As Variant)
Dim a() As String

a() = Split(sir, ",")

X = Picture1.ScaleWidth / UBound(a())
    
        For i = 1 To UBound(a()) - 1

            Picture1.Line (i * X, Picture1.ScaleHeight - a(i - 1))-((i + 1) * X, Picture1.ScaleHeight - a(i)), CG_color_line.BackColor
    
        Next i

End Function

Function Deseneaza_DI(ByVal lungime As Variant, ByVal sir As Variant)
Dim a() As String

a() = Split(sir, ",")

X = Picture1.ScaleWidth / UBound(a())
    
        For i = 1 To UBound(a()) - 1

            Picture1.Line (i * X, Picture1.ScaleHeight - a(i - 1))-((i + 1) * X, Picture1.ScaleHeight - a(i)), DI_color_line.BackColor
    
        Next i

End Function

Function Deseneaza_TM(ByVal lungime As Variant, ByVal sir As Variant)
Dim a() As String

a() = Split(sir, ",")

X = Picture1.ScaleWidth / UBound(a())
    
        For i = 1 To UBound(a()) - 1
    
            Picture1.Line (i * X, Picture1.ScaleHeight - a(i - 1))-((i + 1) * X, Picture1.ScaleHeight - a(i)), TM_color_line.BackColor
    
        Next i
    
End Function

Function Deseneaza_grafic_IC(ByVal lungime As Variant, ByVal sir As Variant)
Dim a() As String

a() = Split(sir, ",")

X = Picture1.ScaleWidth / UBound(a())
    
        For i = 1 To UBound(a()) - 1
    
            Picture1.Line (i * X, Picture1.ScaleHeight - a(i - 1))-((i + 1) * X, Picture1.ScaleHeight - a(i)), Kappa_color_line.BackColor
    
        Next i
    
End Function

Private Sub Search_gene_lis_Click()
    Search_gene_names.Show
End Sub

Private Sub Show_numbers_Click()
    Pattern_Numbers.Show
    Pattern_data_window.Visible = False
End Sub

Private Sub Stop_procesare_Click()
    oprire = True
End Sub

Function Dinucleotide_Content(ByVal Window As String) As String

    CG_nr = Split(Window, LCase(DubleN.Text))
    CG_nr_buff = UBound(CG_nr)

    op = CG_nr_buff * 2
    Total_CG = (100 / Len(Window)) * op

    Dinucleotide_Content = Total_CG
    
End Function

Function GENEREAZA_NUCLEOTIDE(ByVal nr As Variant, ByVal tip As String) As String
    '***
    Dim nucleo(1 To 5) As String
    nucleo(1) = "A"
    nucleo(2) = "T"
    nucleo(3) = "G"
    nucleo(4) = "C"
    nucleo(5) = "U"
    
    For n = 1 To nr
    
    If (tip = "ADN") Then
        c = Int(4 * Rnd(4))
        P = P & nucleo(c + 1)
    End If
    
    If (tip = "ARN") Then
        c = Int(4 * Rnd(4))
        If (c + 1 = 2) Then c = 4
        P = P & nucleo(c + 1)
    End If
    
    Next n
    '***
    GENEREAZA_NUCLEOTIDE = P
End Function


Private Sub Promotor_Click()
Dim Msg As String

  On Error Resume Next
  dlgBrowse.ShowOpen
  List_promotori.Clear
  
  Msg = dlgBrowse.FileName

If Msg <> "" Then
  If Err.Number = 0 Then
  
    ff = FreeFile
    Open Msg For Input As #ff
        Do While Not EOF(ff)
           Line Input #ff, inputdata
           
           If UBound(Split(inputdata, ">")) > 0 Then

                If tmp <> "" Then
                
                    If InStr(tmp, "N") <> 0 Then
                        
                    Else
                        List_promotori.AddItem nume_gena & "|" & tmp
                    End If
                
                End If
                
                nume_gena = Replace(inputdata, "|", "-")
                tmp = Empty
           
           Else
           
                 tmp = tmp & UCase(inputdata)
           
           End If
           
        Loop
    Close #ff
    
  End If
  
  Frame4.Caption = "Gene promotors(" & List_promotori.ListCount & ")"
  
End If
End Sub

Private Sub Col_1_Click()
    dlgBrowse.ShowColor
    Col_pic1.BackColor = dlgBrowse.Color
End Sub

Private Sub Col_2_Click()
    dlgBrowse.ShowColor
    Col_pic2.BackColor = dlgBrowse.Color
End Sub

Private Sub Col_3_Click()
    dlgBrowse.ShowColor
    Col_pic3.BackColor = dlgBrowse.Color
    graf_point.BackColor = Col_pic3.BackColor
End Sub

Private Sub List_promotori_Click()
    List_promotori.Enabled = False
    secventata.Text = Split(List_promotori.List(List_promotori.ListIndex), "|")(1)
    seq_name_from_file.Caption = Split(List_promotori.List(List_promotori.ListIndex), "|")(0)
    
    Procesare_Click ' generate pattern
    
    If Save_values_HTML.Value = 1 Then
        Pattern_Numbers.L_R_Click ' measure the pattern
        Pattern_Numbers.Add_data_of_the_pattern_to_mem_Click ' add data to html variable
        Pattern_Numbers.Save_Data_HTML_Click 'and save the values as HTML
    End If
    
    List_promotori.Enabled = True
End Sub


Private Sub Kappa_for_promotor_list_Click()

If List_promotori.ListCount = 0 Then
    MsgBox "Promoter list is empty. Please load the promoter file !"
    Exit Sub
End If

Stop_p_test.Enabled = True
List_promotori.Enabled = False


total_val_x = 0
total_val_y = 0

pro_no = List_promotori.ListCount

For i = pascupas To pro_no

    pascupas = i
    
    If Stop_p_test.Enabled = False Then Exit For
'-------------- pause ---------------------------------------------
1:
    DoEvents
    If Pause_all_tests = True Then GoTo 1
'-------------- pause ---------------------------------------------
    
    If List_promotori.List(i) <> "" Then

        secventata.Text = Split(List_promotori.List(i), "|")(1)
        seq_name_from_file.Caption = Split(List_promotori.List(i), "|")(0)

    End If

    Procesare_Click
    
    Frame4.Caption = "Gene promotors(" & pro_no & "): " & Int((100 / pro_no) * i) & " %"
    DoEvents
    
Next i


x_set = total_val_x / pro_no
y_set = total_val_y / pro_no

If Show_center_PC.Value = 1 Then Center_patt.Circle (x_set, y_set), 6, vbRed
MasterGraph.Circle (x_set, y_set), 6, vbRed
    'KIC_mean_txt.Text = x_set '(100 / mean_bb) * Yb ' mean Kappa IC
    'CG_mean_txt = y_set '(100 / mean_aa) * Xa ' mean C+G

If Save_Result_MP.Value = 1 Then
    numar = numar + 1
    graf_point_I.Picture = Center_patt.Image
    tmp_name = App.Path & "\chart\" & numar & "-" & Replace(Time, ":", "-") & ".bmp"
    SavePicture graf_point_I.Picture, tmp_name
End If

If Save_Result_MR.Value = 1 Then
    numar = numar + 1
    graf_point_I.Picture = MasterGraph.Image
    tmp_name = App.Path & "\chart\" & numar & "-" & Replace(Time, ":", "-") & ".bmp"
    SavePicture graf_point_I.Picture, tmp_name
End If


List_promotori.Enabled = True
End Sub

Private Sub Stop_p_test_Click()
    Stop_p_test.Enabled = False
End Sub

Private Sub TM_color_line_Click()
    dlgBrowse.ShowColor
    TM_color_line.BackColor = dlgBrowse.Color
End Sub

Private Sub Kappa_color_line_Click()
    dlgBrowse.ShowColor
    Kappa_color_line.BackColor = dlgBrowse.Color
End Sub

Private Sub DI_color_line_Click()
    dlgBrowse.ShowColor
    DI_color_line.BackColor = dlgBrowse.Color
End Sub

Private Sub CG_color_line_Click()
    dlgBrowse.ShowColor
    CG_color_line.BackColor = dlgBrowse.Color
End Sub

Private Sub Tools_Click()
    String_tool.Show
End Sub