Documentation.

2 files changed, 14 insertions, 8 deletions

diff --git a/GenoFusion/utils/dna_utils.py b/GenoFusion/utils/dna_utils.py
index 8e2285c..c519e80 100644
--- a/GenoFusion/utils/dna_utils.py
+++ b/GenoFusion/utils/dna_utils.py
@@ -1,3 +1,16 @@
+"""
+This module provides utility functions for DNA sequence analysis.
+
+Functions:
+- calculate_nucleotide_composition(sequence): Calculates the count of each nucleotide (A, T, G, C) in the given DNA sequence.
+- calculate_nucleotide_percentage(sequence): Calculates the percentage of each nucleotide (A, T, G, C) in the given DNA sequence.
+- calculate_gc_content(sequence): Calculates the GC content (percentage of G and C nucleotides) in the given DNA sequence.
+- reverse_sequence(sequence): Reverses the given DNA sequence.
+- complement_sequence(sequence): Generates the complement sequence of the given DNA sequence.
+- reverse_complement_sequence(sequence): Generates the reverse complement sequence of the given DNA sequence.
+- get_sequence_properties(sequence): Returns a dictionary containing various properties of the given DNA sequence, including length, nucleotide composition, nucleotide percentage, GC content, reverse sequence, complement sequence, and reverse complement sequence.
+"""
+
 def calculate_nucleotide_composition(sequence):
     sequence = sequence.upper()
     composition = {
diff --git a/SequenceViewer/app/sequence_tools.py b/SequenceViewer/app/sequence_tools.py
index e44625d..1fcd5a8 100644
--- a/SequenceViewer/app/sequence_tools.py
+++ b/SequenceViewer/app/sequence_tools.py
@@ -23,7 +23,6 @@ def is_nicking(enzyme):
     """Check if an enzyme is a nicking endonuclease."""
     return "Nicking" in enzyme.__class__.__name__
 
-# Group enzymes based on properties
 enzyme_groups = {
     "All Commercial": CommOnly,
     "Nonredundant Commercial": CommOnly,  # This should be updated with a proper list if available
@@ -38,7 +37,6 @@ enzyme_groups = {
     "Nicking Endonucleases": [enzyme for enzyme in AllEnzymes if is_nicking(enzyme)]
 }
 
-# Define colors for enzyme highlighting
 colors = [
     "red", "green", "blue", "yellow", "orange", "purple", "cyan", "magenta", "lime", "pink",
     "teal", "lavender", "brown", "beige", "maroon", "mint", "olive", "coral", "navy", "grey"
@@ -47,13 +45,11 @@ colors = [
 enzyme_colors = {}
 
 def get_color_for_enzyme(enzyme_name):
-    """Assign a random color to each enzyme for highlighting."""
     if enzyme_name not in enzyme_colors:
         enzyme_colors[enzyme_name] = random.choice(colors)
     return enzyme_colors[enzyme_name]
 
 def get_enzyme_sites(sequence, enzymes):
-    """Find enzyme recognition sites in a given DNA sequence."""
     enzyme_sites = []
     for enzyme in enzymes:
         for site in enzyme.search(sequence):
@@ -62,16 +58,14 @@ def get_enzyme_sites(sequence, enzymes):
     return enzyme_sites
 
 def translate_sequence(nucleotide_sequence):
-    """Translate a nucleotide sequence into a protein sequence."""
     sequence = Seq(nucleotide_sequence)
     return str(sequence.translate())
 
 def find_enzyme_sites(sequence_str, selected_group):
-    """Highlight enzyme recognition sites in a DNA sequence."""
     if selected_group in enzyme_groups:
         enzymes = enzyme_groups[selected_group]
     else:
-        enzymes = AllEnzymes  # Default to all enzymes if group not found
+        enzymes = AllEnzymes
 
     enzyme_sites = get_enzyme_sites(Seq(sequence_str), enzymes)
     highlighted_sequence = ""
@@ -87,7 +81,6 @@ def find_enzyme_sites(sequence_str, selected_group):
     return highlighted_sequence, enzyme_sites
 
 def get_sequence_properties(sequence_str):
-    """Calculate basic properties of a DNA sequence."""
     sequence = Seq(sequence_str)
     gc_content = (sequence.count("G") + sequence.count("C")) / len(sequence) * 100
     return {