Finish doc

README.md

+VARNA API is a Python interface for [VARNA](http://varna.lri.fr/index.php), a Java lightweight component and applet for drawing the RNA secondary structure.
+VARNA allows users to produce drawing in a non-iteractive way via command line.
+However, the command line might be massive and complicate in some use cases.
+VARNA API aims to simplify such process.
+
+__NOTE__: The VARNA API is 0-indexed unlike VARNA, which is 1-indexed.
+
+## Example
+
+The command below highlights region 11-21 and adds a non-canonical base pair at position (14,20)
+on secondary structure `((((((.((((((........)))))).((((((.......))))))..))))))`.
+```bash
+java -cp VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "                                                       " -structureDBN "((((((.((((((........)))))).((((((.......))))))..))))))" -o example.png -algorithm radiate -auxBPs "(14,20):color=#FF00FF,thickness=1.0,edge5=s,edge3=wc,stericity=cis" -highlightRegion "11-21:radius=15.0,fill=#9999FF,outline=#3333FF"
+```
+
+The equivalence in python is
+```python
+from varnaapi import VARNA
+v = VARNA(structure="((((((.((((((........)))))).((((((.......))))))..))))))")
+v.add_highlight_region(10,20)
+v.add_aux_BP(13, 19, edge5="s", color="#FF00FF")
+v.savefig("example.png")
+```
+## Installation
+```
+python3 -m pip install varnaapi
+```
+
+## Usage
+Here, we show the basic usage of varnaapi. Please refer the [API](https://htyao.gitlab.io/varna-api/varna) page for more details.
+The first thing after importing `varnaapi` is to setup the location of VARNA used.
+The default is `VARNAv3-93.jar` in the current folder.
+```python
+import varnaapi
+varnaapi.set_VARNA(path_to_VARNA)
+```
+Each drawing in VARNA is an object called `VARNA` created from given secondary structure or/and RNA sequence.
+```python
+ss = "((((((.((((((........)))))).((((((.......))))))..))))))"
+v = varnaapi.VARNA(structure=ss)
+```
+Then we can add operations on drawing by calling object functions, such as `VARNA.set_algorithm()` to choose a drawing algorithm, `VARNA.add_highlight_region()` to highlight a region etc. 
+```python
+v.set_algorithm('line')
+v.add_highlight_region(0, 5, radius=20)
+```
+Finally, we can draw the secondary structure
+```python
+v.savefig(path_to_store)
+```
+
+## Credits
+Please kindly cite VARNA [supporting manuscript](https://doi.org/10.1093/bioinformatics/btp250) if you use VARNA API in your research.
+Download [bibtex](https://gitlab.inria.fr/amibio/varna-api/-/blob/master/varna.bib) format.
+```
+Darty, K., Denise, A., & Ponty, Y. (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25(15), 1974.
+```

docs/index.md

-Hello!
+VARNA API is a Python interface for [VARNA](http://varna.lri.fr/index.php), a Java lightweight component and applet for drawing the RNA secondary structure.
+VARNA allows users to produce drawing in a non-iteractive way via command line.
+However, the command line might be massive and complicate in some use cases.
+VARNA API aims to simplify such process.
+
+__NOTE__: The VARNA API is 0-indexed unlike VARNA, which is 1-indexed.
+
+## Example
+
+The command below highlights region 11-21 and adds a non-canonical base pair at position (14,20)
+on secondary structure `((((((.((((((........)))))).((((((.......))))))..))))))`.
+```bash
+java -cp VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN "                                                       " -structureDBN "((((((.((((((........)))))).((((((.......))))))..))))))" -o example.png -algorithm radiate -auxBPs "(14,20):color=#FF00FF,thickness=1.0,edge5=s,edge3=wc,stericity=cis" -highlightRegion "11-21:radius=15.0,fill=#9999FF,outline=#3333FF"
+```
+
+The equivalence in python is
+```python
+from varnaapi import VARNA
+v = VARNA(structure="((((((.((((((........)))))).((((((.......))))))..))))))")
+v.add_highlight_region(10,20)
+v.add_aux_BP(13, 19, edge5="s", color="#FF00FF")
+v.savefig("example.png")
+```
+## Installation
+```
+python3 -m pip install varnaapi
+```
+
+## Usage
+Here, we show the basic usage of varnaapi. Please refer the [API](https://htyao.gitlab.io/varna-api/varna) page for more details.
+The first thing after importing `varnaapi` is to setup the location of VARNA used.
+The default is `VARNAv3-93.jar` in the current folder.
+```python
+import varnaapi
+varnaapi.set_VARNA(path_to_VARNA)
+```
+Each drawing in VARNA is an object called `VARNA` created from given secondary structure or/and RNA sequence.
+```python
+ss = "((((((.((((((........)))))).((((((.......))))))..))))))"
+v = varnaapi.VARNA(structure=ss)
+```
+Then we can add operations on drawing by calling object functions, such as `VARNA.set_algorithm()` to choose a drawing algorithm, `VARNA.add_highlight_region()` to highlight a region etc. 
+```python
+v.set_algorithm('line')
+v.add_highlight_region(0, 5, radius=20)
+```
+Finally, we can draw the secondary structure
+```python
+v.savefig(path_to_store)
+```
+
+## Credits
+Please kindly cite VARNA [supporting manuscript](https://doi.org/10.1093/bioinformatics/btp250) if you use VARNA API in your research.
+Download [bibtex](https://gitlab.inria.fr/amibio/varna-api/-/blob/master/varna.bib) format.
+```
+Darty, K., Denise, A., & Ponty, Y. (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25(15), 1974.
+```

docs/varna.bib

+@article{darty2009varna,
+  title={VARNA: Interactive drawing and editing of the RNA secondary structure},
+  author={Darty, K{\'e}vin and Denise, Alain and Ponty, Yann},
+  journal={Bioinformatics},
+  volume={25},
+  number={15},
+  pages={1974},
+  year={2009},
+  publisher={Oxford University Press}
+}

docs/varna.md

-We offer two python classes [VARNA](#varnaapi.VARNA) and [Comparison](#varnaapi.Comparison) corresponding to the classic mode and the comparison mode in VARNA.
+In VARNA API, we offer three Python classes [VARNA](#varnaapi.VARNA), [Comparison](#varnaapi.Comparison), and [Motif](#varnaapi.Motif) for RNA secondary structure visualisation.
+The first two correspond to the classic and the comparison mode in VARNA. The last one is the special case for motif drawing.
+Both [Comparison](#varnaapi.Comparison) and [Motif](#varnaapi.Motif) are inherited classes of [VARNA](#varnaapi.VARNA).
 
 ::: varnaapi
     selection:

mkdocs.yml

 # mkdocs.yml
 
 site_name: VARNA API
+repo_url: "https://gitlab.inria.fr/amibio/varna-api"
+repo_name: "AMIBio/VARNA-API"
 theme:
   # name: "readthedocs"
   name: "material"
 
 nav:
-  - Overview: index.md
-  - API: varnaapi.md
-  - Annotation: annotation.md
-  - VARNA: varna.md
+  - Home: index.md
+  - API:
+    - VARNA Classes: varna.md
+    - Annotation: annotation.md
+    - Miscellaneous: varnaapi.md
 
 plugins:
   - search

setup.py

+#!/usr/bin/env python3
+
+import setuptools
+from distutils.core import setup
+
+def read_version(fpath):
+    with open(fpath) as f:
+        for line in f.readlines():
+            if line.startswith('__version__'):
+                return line.strip().split()[-1][1:-1]
+    raise Exception('Version not found')
+
+
+VERSION = read_version('./varnaapi.py')
+
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+
+CLASSIFIERS = """\
+Development Status :: 5 - Production/Stable
+Intended Audience :: Science/Research
+Intended Audience :: Developers
+License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Programming Language :: Python :: 3
+Programming Language :: Python :: 3 :: Only
+Topic :: Scientific/Engineering
+Operating System :: OS Independent
+"""
+
+setup(name='varnaapi',
+      version=VERSION,
+      description='Python Class for VARNA',
+      long_description=long_description,
+      long_description_content_type="text/markdown",
+      maintainer='Hua-Ting Yao',
+      maintainer_email='hua-ting.yao@polytechnique.edu',
+      author='Hua-Ting Yao',
+      author_email='hua-ting.yao@polytechnique.edu',
+      url='https://gitlab.inria.fr/amibio/varna-api',
+      classifiers=[_f for _f in CLASSIFIERS.split('\n') if _f],
+      py_modules=['varnaapi'],
+      python_requires='>=3'
+      )

varnaapi.py

@@ -2,11 +2,10 @@ import re
 import os
 import abc
 from string import ascii_lowercase, ascii_uppercase
-from typing import Union
 
+__version__ = '0.1.0'
 
-
-VARNA_PATH="VARNAv3-93.jar"
+_VARNA_PATH="VARNAv3-93.jar"
 HEX = re.compile('^#(?:[0-9a-fA-F]{3}){1,2}$')
 BORDER = re.compile('^\d+x\d+$')
 
@@ -37,10 +36,12 @@ OPTIONS = ['autoHelices', 'autoInteriorLoops', 'autoTerminalLoops', 'drawBackbon
 | drawBackbone      | Backbone drawing                                                                                                                              | True    |
 | drawBases         | Displays the outline of a nucleotide base                                                                                                     | True    |
 | drawNC            | Displays non-canonical base-pairs                                                                                                             | True    |
-| drawTertiary      | Display of `non-planar` base-pairs, _i.e._ pseudoknots                                                                                        | False   |
+| drawTertiary      | Display of `non-planar` base-pairs, _i.e._ pseudoknots [^1]                                                                                   | False   |
 | fillBases         | Fill bases                                                                                                                                    | True    |
 | flat              | In `radiate` drawing mode, redraws the whole structure, aligning to a  baseline the base featured on the exterior loops (aka "dangling ends") | False   |
 
+[^1]: Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms.
+
 """
 
 NUMERIC_PARAMS = ['bpIncrement', 'periodNum', 'resolution', 'rotation', 'spaceBetweenBases', 'zoom']
@@ -79,11 +80,16 @@ PARENTHESES_SYSTEMS = [
 PARENTHESES_OPENING = [c1 for c1, c2 in PARENTHESES_SYSTEMS]
 PARENTHESES_CLOSING = {c2: c1 for c1, c2 in PARENTHESES_SYSTEMS}
 
+def set_VARNA(path):
+    """Set VARNA location
+    """
+    global _VARNA_PATH
+    _VARNA_PATH = path
 
 class BasesStyle:
     """Defines a custom base-style, to be applied later to a set of bases.
     A BasesStyle style contains colors used for different components of a base.
-    See [\_\_init\_\_][varnaapi.BasesStyle.\_\_init\_\_] for more details.
+    See [\_\_init\_\_][varnaapi.BasesStyle.__init__] for more details.
 
     __See Also:__ [VARNA.add_bases_style][varnaapi.VARNA.add_bases_style]
     """
@@ -105,7 +111,7 @@ class BasesStyle:
 
     def update(self, fill=None, outline=None, label=None, number=None):
         """Update component colors.
-        Same rule as [\_\_init\_\_][varnaapi.BasesStyle.\_\_init\_\_]
+        Same rule as [\_\_init\_\_][varnaapi.BasesStyle.__init__]
         """
         if fill is None and outline is None and label is None and number is None:
             raise Exception("At least one should not be None")
@@ -267,7 +273,7 @@ def _parse_vienna(ss):
 
 class VARNA:
     def __init__(self, seq:str=None, structure=None):
-        """Classis VARNA drawing mode. Constructor from given RNA sequence or/and secondary structure.
+        """Classic VARNA drawing mode. Constructor from given RNA sequence or/and secondary structure.
         If sequence and structure have different size, the larger one is used
         and ` `s or `.`s will be added to sequence or structure to complement.
 
@@ -535,7 +541,7 @@ class VARNA:
         """
         Return command to run VARNA
         """
-        cmd = "java -cp {} fr.orsay.lri.varna.applications.VARNAcmd".format(VARNA_PATH)
+        cmd = "java -cp {} fr.orsay.lri.varna.applications.VARNAcmd".format(_VARNA_PATH)
 
         cmd += self._gen_input_cmd()