Initial merge: Dash sequence viewer

.gitignore

@@ -1,5 +1,6 @@
 # See https://help.github.com/ignore-files/ for more about ignoring files.
 
+
 # dependencies
 /node_modules
 

assets/sequence-viewer-style.css

@@ -0,0 +1,85 @@
+@import url('https://fonts.googleapis.com/css?family=Open+Sans');
+
+#seq-view-body {
+    position: absolute;
+    overflow: auto;
+    top: 0px;
+    left: 0px;
+    bottom: 0px; 
+    width: 100%;
+    height: 100%;
+    background-color: #F3F6FA; 
+    font-family: 'Open Sans'; 
+}
+::-webkit-scrollbar{
+    width: 0px;
+    height: 0px;
+}
+#seq-view-header {
+    width: calc(100% - 40px);
+    height: auto;
+    margin: 0px;
+    font-size: 60px;
+    margin-bottom: 20px; 
+    background: #C8D4E3;
+    color: #636efa;
+    font-family: 'Open Sans';
+    font-variant: all-small-caps;
+}
+
+.inputSearchSeq {
+    font-size: 14px;
+    width: 100px;
+    padding:5px;
+    border-radius:3px;
+    border: solid 1px grey;
+    margin-left: 10px;
+}
+#seq-view-fasta-upload{
+    width: 400px;
+    margin: 20px;
+    padding: 10px;
+}
+#sequence-viewer-container{
+    width: 400px;
+    display: inline-block;
+    vertical-align: top;
+    border: solid 1px #636efa;
+    border-radius: 5px;
+    padding: 10px;
+    margin:20px;
+    overflow:scroll;
+}
+
+#seq-view-controls-container {
+    width:150px;
+    display: inline-block;
+    vertical-align: top; 
+    height:auto;
+    margin: 20px; 
+    border: solid 1px #636efa; 
+    border-radius: 5px;
+    padding: 10px;
+    padding-top:30px;
+}
+
+#seq-view-sel-slider-container {
+    width: 100px;
+    padding: 10px;
+    border: solid 1px #636efa; 
+    border-radius: 5px;
+    margin: 10px;
+    margin-top:30px;
+}
+
+#seq-view-info-container {
+    width: 400px;
+    height: 500px;
+    border: solid 1px #636efa; 
+    overflow:scroll;
+    margin: 20px;
+    vertical-align: top; 
+    border-radius: 5px;
+    padding: 20px;
+    display: inline-block;
+}

config.py

@@ -1,12 +1,14 @@
 import os
+
 # Replace with the name of your Dash app
 # This will end up being part of the URL of your deployed app,
 # so it can't contain any spaces, capitalizations, or special characters
 #
 # This name MUST match the name that you specified in the
 # Dash App Manager
 DASH_APP_NAME = 'dash-bio'
- # Set to 'private' if you want to add a login screen to your app
+# Set to 'private' if you want to add a login screen to your app
+
 # You can choose who can view the app in your list of files
 # at <your-plotly-server>/organize.
 # Set to 'public' if you want your app to be accessible to
@@ -15,7 +17,8 @@
 # Set to 'secret' if you want to add a login screen, but allow it
 # to be bypassed by using a secret "share_key" parameter.
 DASH_APP_PRIVACY = 'public'
- # Dash On-Premise is configured with either "Path based routing"
+
+# Dash On-Premise is configured with either "Path based routing"
 # or "Domain based routing"
 # Ask your server administrator which version was set up.
 # If a separate subdomain was created,
@@ -30,21 +33,24 @@
  # Fill in with your Plotly On-Premise username
 os.environ['PLOTLY_USERNAME'] = 'shammamah'
  # Fill in with your Plotly On-Premise API key
-# See <your-plotly-server>/settings/api to generate a key
+
+ # See <your-plotly-server>/settings/api to generate a key
 # If you have already created a key and saved it on your own machine
 # (from the Plotly-Python library instructions at https://plot.ly/python/getting-started)
 # then you can view that key in your ~/.plotly/.config file
 # or inside a Python session with these commands:
 # import plotly
 # print(plotly.tools.get_config_file())
 os.environ['PLOTLY_API_KEY'] = 'your-plotly-api-key'
+
  # Fill in with your Plotly On-Premise domain
 os.environ['PLOTLY_DOMAIN'] = 'https://your-plotly-domain.com'
 os.environ['PLOTLY_API_DOMAIN'] = os.environ['PLOTLY_DOMAIN']
  # Fill in with the domain of your Dash subdomain.
 # This matches the domain of the Dash App Manager
 PLOTLY_DASH_DOMAIN='https://your-dash-manager-plotly-domain.com'
  # Keep as True if your SSL certificates are valid.
+
 # If you are just trialing Plotly On-Premise with self signed certificates,
 # then you can set this to False. Note that self-signed certificates are not
 # safe for production.

dash_bio/SequenceViewerComponent.py

@@ -0,0 +1,91 @@
+# AUTO GENERATED FILE - DO NOT EDIT
+
+from dash.development.base_component import Component, _explicitize_args
+
+
+class SequenceViewerComponent(Component):
+    """A SequenceViewerComponent component.
+
+
+Keyword arguments:
+- id (string; optional): The ID used to identify this component in Dash callbacks.
+- sequence (string; optional): The amino acid sequence that will be displayed.
+- showLineNumbers (boolean; optional): The option of whether or not to display line numbers.
+- wrapAminoAcids (boolean; optional): The option of whether or not to display the list of amino acids
+as broken up into separate lines of a fixed length set by 
+charsPerLine.
+- charsPerLine (number; optional): The number of amino acids that will display per line.
+- toolbar (boolean; optional): The option of whether or not to display a toolbar at the top
+that allows the user to choose the number of letters per line.
+- search (boolean; optional): The option of whether or not to include a search bar in
+the header. This supports regex.
+- title (string; optional): A string that displays at the top of the component.
+- sequenceMaxHeight (string; optional): The maximum height of the sequence; default "400px".
+- badge (boolean; optional): The option of whether or not to display a badge showing the
+amino acid count at the top of the component beside the title.
+- selection (list; optional): A highlighted section of the sequence; the color of the highlight 
+can also be defined. Takes a list of format [min, max, color] where 
+min is a number that represents the starting index of the selection, 
+max is a number that represents the stopping index of the selection, 
+and color is a string that defines the highlight color.
+Cannot be used at the same time as coverage.
+- coverage (list; optional): A coverage of the entire sequence; each section of the sequence
+can have its own text color, background color, tooltip (on hover),
+and an optional underscore. The props start and end represent the
+beginning and terminating indices of the section in question.
+Cannot be used at the same time as selection.
+- legend (list; optional): A legend corresponding to the color codes above (optionally displayed).
+- coverageClicked (number; optional): Contains the index of the section that was clicked last in 
+the coverage.
+- mouseSelection (optional): A string containing the mouse selection.. mouseSelection has the following type: dict containing keys 'start', 'end', 'selection'.
+Those keys have the following types: 
+  - start (number; optional)
+  - end (number; optional)
+  - selection (string; optional)
+- subpartSelected (list; optional): A string containing all of the highlighted sections when 
+using the search bar.
+
+Available events: """
+    @_explicitize_args
+    def __init__(self, id=Component.UNDEFINED, sequence=Component.UNDEFINED, showLineNumbers=Component.UNDEFINED, wrapAminoAcids=Component.UNDEFINED, charsPerLine=Component.UNDEFINED, toolbar=Component.UNDEFINED, search=Component.UNDEFINED, title=Component.UNDEFINED, sequenceMaxHeight=Component.UNDEFINED, badge=Component.UNDEFINED, selection=Component.UNDEFINED, coverage=Component.UNDEFINED, legend=Component.UNDEFINED, coverageClicked=Component.UNDEFINED, mouseSelection=Component.UNDEFINED, subpartSelected=Component.UNDEFINED, onMouseSelection=Component.UNDEFINED, onSubpartSelected=Component.UNDEFINED, **kwargs):
+        self._prop_names = ['id', 'sequence', 'showLineNumbers', 'wrapAminoAcids', 'charsPerLine', 'toolbar', 'search', 'title', 'sequenceMaxHeight', 'badge', 'selection', 'coverage', 'legend', 'coverageClicked', 'mouseSelection', 'subpartSelected']
+        self._type = 'SequenceViewerComponent'
+        self._namespace = 'dash_bio'
+        self._valid_wildcard_attributes =            []
+        self.available_events = []
+        self.available_properties = ['id', 'sequence', 'showLineNumbers', 'wrapAminoAcids', 'charsPerLine', 'toolbar', 'search', 'title', 'sequenceMaxHeight', 'badge', 'selection', 'coverage', 'legend', 'coverageClicked', 'mouseSelection', 'subpartSelected']
+        self.available_wildcard_properties =            []
+
+        _explicit_args = kwargs.pop('_explicit_args')
+        _locals = locals()
+        _locals.update(kwargs)  # For wildcard attrs
+        args = {k: _locals[k] for k in _explicit_args if k != 'children'}
+
+        for k in []:
+            if k not in args:
+                raise TypeError(
+                    'Required argument `' + k + '` was not specified.')
+        super(SequenceViewerComponent, self).__init__(**args)
+
+    def __repr__(self):
+        if(any(getattr(self, c, None) is not None
+               for c in self._prop_names
+               if c is not self._prop_names[0])
+           or any(getattr(self, c, None) is not None
+                  for c in self.__dict__.keys()
+                  if any(c.startswith(wc_attr)
+                  for wc_attr in self._valid_wildcard_attributes))):
+            props_string = ', '.join([c+'='+repr(getattr(self, c, None))
+                                      for c in self._prop_names
+                                      if getattr(self, c, None) is not None])
+            wilds_string = ', '.join([c+'='+repr(getattr(self, c, None))
+                                      for c in self.__dict__.keys()
+                                      if any([c.startswith(wc_attr)
+                                      for wc_attr in
+                                      self._valid_wildcard_attributes])])
+            return ('SequenceViewerComponent(' + props_string +
+                   (', ' + wilds_string if wilds_string != '' else '') + ')')
+        else:
+            return (
+                'SequenceViewerComponent(' +
+                repr(getattr(self, self._prop_names[0], None)) + ')')

dash_bio/_imports_.py

@@ -1,5 +1,5 @@
-from .ExampleComponent import ExampleComponent
+from .SequenceViewerComponent import SequenceViewerComponent
 
 __all__ = [
-    "ExampleComponent"
+    "SequenceViewerComponent",
 ]