1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/pytale/dummy_pytale.py	Wed Jun 09 14:46:02 2010 +0400
     1.3 @@ -0,0 +1,162 @@
     1.4 +#!/usr/bin/python
     1.5 +
     1.6 +import wx
     1.7 +import os.path
     1.8 +import project
     1.9 +
    1.10 +class MainFrame(wx.Frame):
    1.11 +    """ Main application frame.
    1.12 +
    1.13 +    The frame contains:
    1.14 +    1) MenuBar
    1.15 +    2) Resizable panel with ListBox containing sequence names
    1.16 +    3) Panel with RichTextBox containing the alignment itself
    1.17 +    4) StatusBar 
    1.18 +    """
    1.19 +    def __init__(self, parent, title, size=(1000, 600)):
    1.20 +        global settings
    1.21 +        wx.Frame.__init__(self, parent, title=title, size=size)
    1.22 +        self.current_project = None
    1.23 +        self.CreateStatusBar()
    1.24 +        # Draw panels and split the frame
    1.25 +        self.splitter = wx.SplitterWindow(self, -1)
    1.26 +        self.names_panel = SeqNamesPanel(self.splitter)
    1.27 +        self.sequences_panel = SequencesPanel(self.splitter)
    1.28 +        self.splitter.SplitVertically(self.names_panel, self.sequences_panel)
    1.29 +        self.splitter.SetSashGravity(0.0) # do not widen the name panel when resizing
    1.30 +        self.splitter.SetSashPosition(200, redraw=True)
    1.31 +        # Set up the menubar
    1.32 +        self.menubar = MenuBar()
    1.33 +        self.SetMenuBar(self.menubar)
    1.34 +        # Bindings (shouldn't menu bindings be in the menu class?)
    1.35 +        self.Bind(wx.EVT_MENU, self.Open, self.menubar.filemenu.menu_open)
    1.36 +        self.Bind(wx.EVT_MENU, self.Save, self.menubar.filemenu.menu_save)
    1.37 +        self.Bind(wx.EVT_MENU, self.Exit, self.menubar.filemenu.menu_exit)
    1.38 +        # Oh, shit, that's awful!
    1.39 +        self.Bind(wx.EVT_MENU, lambda event: \
    1.40 +                               self.sequences_panel.ColourByIdentity(event, self.current_project), \
    1.41 +                               self.menubar.colourmenu.by_identity)
    1.42 +
    1.43 +    def Exit(self, event):
    1.44 +        self.Close(True)
    1.45 +
    1.46 +    def Open(self, event):
    1.47 +        dialog = wx.FileDialog(self, "Choose a file...", '', '', "*.*", wx.OPEN)
    1.48 +        if dialog.ShowModal() == wx.ID_OK:
    1.49 +            self.filename = dialog.GetFilename()
    1.50 +            self.dirname = dialog.GetDirectory()
    1.51 +            file = open(os.path.join(self.dirname, self.filename))
    1.52 +            # create and display the loaded project (fasta alignment)
    1.53 +            current_project = project.Project()
    1.54 +            current_project.sequences, current_project.alignment = \
    1.55 +                                project.Project.get_from_fasta(file)
    1.56 +            self.names_panel.DisplayNames(current_project)
    1.57 +            self.sequences_panel.DisplayAlignment(current_project)
    1.58 +            self.current_project = current_project
    1.59 +            file.close()
    1.60 +        dialog.Destroy()
    1.61 +
    1.62 +    def Save(self, event):
    1.63 +        pass
    1.64 +
    1.65 +class MenuBar(wx.MenuBar):
    1.66 +        def __init__(self):
    1.67 +            wx.MenuBar.__init__(self)
    1.68 +            self.filemenu = FileMenu()
    1.69 +            self.colourmenu = ColourMenu()
    1.70 +            self.Append(self.filemenu, "&File")
    1.71 +            self.Append(self.colourmenu, "&Colour")
    1.72 +
    1.73 +class FileMenu(wx.Menu):
    1.74 +        def __init__(self):
    1.75 +            wx.Menu.__init__(self)
    1.76 +            self.menu_open = self.Append(wx.ID_OPEN, "&Open", "Open alignment")
    1.77 +            self.menu_save = self.Append(wx.ID_SAVE, "&Save", "Save alignment")
    1.78 +            self.menu_exit = self.Append(wx.ID_EXIT, "E&xit", "Quit the editor")
    1.79 +
    1.80 +class ColourMenu(wx.Menu):
    1.81 +        def __init__(self):
    1.82 +            wx.Menu.__init__(self)
    1.83 +            self.by_identity = self.Append(wx.ID_ANY, "By &Identity", "Colour by identity")
    1.84 +
    1.85 +class SeqNamesPanel(wx.Panel):
    1.86 +    def __init__(self, parent):
    1.87 +        wx.Panel.__init__(self, parent)
    1.88 +        global settings
    1.89 +        self.settings = settings
    1.90 +        self.box = wx.BoxSizer(wx.VERTICAL)
    1.91 +        self.text = wx.TextCtrl(self, style=wx.TE_MULTILINE | wx.TE_READONLY | wx.TE_DONTWRAP)
    1.92 +        self.text.SetFont(self.settings.font)
    1.93 +        self.box.Add(self.text, 1, wx.EXPAND)
    1.94 +        self.SetSizer(self.box)
    1.95 +        self.SetAutoLayout(1)
    1.96 +
    1.97 +    def DisplayNames(self, current_project):
    1.98 +        names = map(lambda seq: seq.name, current_project.sequences)
    1.99 +        for name in names:
   1.100 +            self.text.AppendText(name + '\n')
   1.101 +
   1.102 +class SequencesPanel(wx.Panel):
   1.103 +    def __init__(self, parent):
   1.104 +        wx.Panel.__init__(self, parent)
   1.105 +        global settings
   1.106 +        self.settings = settings
   1.107 +        self.lines = [] # to know which sequence resides in particular line
   1.108 +        self.box = wx.BoxSizer(wx.VERTICAL)
   1.109 +        self.text = wx.TextCtrl(self, style=wx.TE_MULTILINE | wx.TE_READONLY | wx.TE_DONTWRAP)
   1.110 +        self.text.SetFont(self.settings.font)
   1.111 +        self.box.Add(self.text, 1, wx.EXPAND)
   1.112 +        self.SetSizer(self.box)
   1.113 +        self.SetAutoLayout(1)
   1.114 +
   1.115 +    def DisplayAlignment(self, current_project):
   1.116 +        for aligned_seq in current_project.alignment:
   1.117 +            seq_string = ''
   1.118 +            for monomer in current_project.alignment[aligned_seq]:
   1.119 +                if monomer is not None:
   1.120 +                    seq_string += monomer.code
   1.121 +                else:
   1.122 +                    seq_string += '-'
   1.123 +            seq_string += '\n'
   1.124 +            self.lines.append(aligned_seq)
   1.125 +            self.text.AppendText(seq_string)
   1.126 +
   1.127 +    def ColourByIdentity(self, event, current_project):
   1.128 +        # Looks awful but works. Fine for now.
   1.129 +        if not hasattr(current_project, 'identity_percentages'):
   1.130 +            current_project.calc_identity()
   1.131 +            print 'calculation done'
   1.132 +        thresholds = {1:0.9, 2:0.7, 3:0.5, 0:0.0}
   1.133 +        prj_len = len(current_project)
   1.134 +        for line in range(len(self.lines)):
   1.135 +            for column in range(prj_len):
   1.136 +                position = current_project.identity_percentages[self.lines[line]][column]
   1.137 +                for threshold in [0, 3, 2, 1]:
   1.138 +                    if position > thresholds[threshold]:
   1.139 +                        conser = threshold
   1.140 +                if position is None:
   1.141 +                    continue
   1.142 +                start = self.text.XYToPosition(column, line)
   1.143 +                end = self.text.XYToPosition(column+1, line)
   1.144 +                self.text.SetStyle(start, end, self.settings.conservation_styles[conser])
   1.145 +        print 'colouring done'
   1.146 +                
   1.147 +
   1.148 +class Settings(object):
   1.149 +    def __init__(self):
   1.150 +        self.font = wx.Font(pointSize=10, family=wx.FONTFAMILY_MODERN, \
   1.151 +                            style=wx.FONTSTYLE_NORMAL, weight=wx.FONTWEIGHT_NORMAL)
   1.152 +        self.conservation_styles = {
   1.153 +            1: wx.TextAttr(colText=wx.Colour(255, 255, 255), colBack=wx.Colour(0, 0, 0)),
   1.154 +            2: wx.TextAttr(colBack=wx.Colour(150, 150, 150)),
   1.155 +            3: wx.TextAttr(colBack=wx.Colour(200, 200, 200)),
   1.156 +            0: wx.TextAttr()
   1.157 +        }
   1.158 +
   1.159 +if __name__ == "__main__":
   1.160 +    app = wx.App(False)
   1.161 +    settings = Settings()
   1.162 +    frame = MainFrame(None, 'Python Alignment Editor')
   1.163 +    frame.Show(True)
   1.164 +    app.MainLoop()
   1.165 +