fixed confusing naming and finished parsing

Author: benjaminbeer256

python/composite.py

@@ -1,102 +1,84 @@
-import numpy as np
 import csv
 import xml.dom.minidom as dom
 import argparse
 import math
 import parseComposite
 
-class Composite:    
+# Objected to store bare-bones composite data, can be used with plot_composite function
+class SimpleComposite:    
     def __init__(self, xmin=None, xmax=None, sense=[], anti=[], id=""):
         self.xmin = xmin
         self.xmax = xmax
         self.sense = sense
         self.anti = anti
         self.id = id
-    
-    def __str__(self):
-        return "Sense: " + str(self.sense) + "\nAnti: " + str(self.anti) + "\nXMin: " + str(self.xmin) + "\nXMax: " + str(self.xmax) + "\nID:" + str(self.id)
 
-class CompositeGroup:
+# Object to store composite data with options for plotting, similar to a settings row
+class Composite:
     def __init__(self, scale=1, color=None, secondary_color=None, i=None, opacity=None, smoothing=None, bp_shift=None, hide_sense=False, hide_anti=False, baseline=0, name=None):
+        # Sets default values
+        self.scale = scale if scale is not None else 1
+        self.color = color if color is not None else "#0000FF"
+        self.secondary_color = secondary_color if secondary_color is not None else color
+        self.baseline = baseline if baseline is not None else 0
         self.xmin = 0
         self.xmax = 0
         self.sense = []
         self.anti = []
-        self.scale = scale
-        self.color = color
-        self.secondary_color = secondary_color if secondary_color is not None else color
         self.opacity = opacity
         self.smoothing = smoothing
         self.bp_shift = bp_shift
         self.hide_anti = hide_anti
-        self.baseline = baseline
         self.hide_sense = hide_sense
-        self.individual_composites = {}
-        self.files_loaded = len(self.individual_composites)
+        self.individual_files = {}
+        self.files_loaded = len(self.individual_files)
         self.name = name
-    
-    def loadComposite(self,composite: Composite):
+    # Adds a simple composite to the 'row'
+    def load_simple_composite(self,composite: SimpleComposite):
         # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain
         self.xmin = min(composite.xmin, self.xmin)
         self.xmax = max(composite.xmax, self.xmax)
-        if len(self.individual_composites) == 0:
+        if len(self.individual_files) == 0:
             self.sense = [0] * (composite.xmax - composite.xmin + 1)
             self.anti = [0] * (composite.xmax - composite.xmin + 1)
         else:
-            xmin = min([int(self.individual_composites[c].xmin) for c in self.individual_composites])
-            xmax = max([int(self.individual_composites[c].xmax) for c in self.individual_composites])
+            xmin = min([int(self.individual_files[c].xmin) for c in self.individual_files])
+            xmax = max([int(self.individual_files[c].xmax) for c in self.individual_files])
             prefix = [0] * (xmin - self.xmin)
             suffix = [0] * (self.xmax - xmax)
             self.sense = prefix + self.sense + suffix
             self.anti = prefix + self.anti + suffix
-
         # Update sense and anti arrays
         j = composite.xmin - self.xmin
         while j <= composite.xmax - composite.xmin:
             idx = composite.xmin - self.xmin + j
             self.sense[idx] += composite.sense[j]
             self.anti[idx] += composite.anti[j]
             j += 1
-
-        self.individual_composites[composite.id] = composite
-
-    def loadCompositeDict(self,compositeDict: dict):
+        self.individual_files[composite.id] = composite
+    # Loads dictionary from parse_multiple_composites
+    def load_composite_dict(self,compositeDict: dict):
         for composite in compositeDict:
             # If no files, initialize sense and anti arrays; otherwise, pad sense and anti arrays to new xdomain
             self.xmin = min(composite.xmin, self.xmin)
             self.xmax = max(composite.xmax, self.xmax)
-            if len(self.individual_composites) == 0:
+            if len(self.individual_files) == 0:
                 self.sense = [0] * (composite.xmax - composite.xmin + 1)
                 self.anti = [0] * (composite.xmax - composite.xmin + 1)
             else:
-                xmin = min([c.xmin for c in self.individual_composites])
-                xmax = max([c.xmax for c in self.individual_composites])
+                xmin = min([c.xmin for c in self.individual_files])
+                xmax = max([c.xmax for c in self.individual_files])
                 prefix = [0] * (xmin - self.xmin)
                 suffix = [0] * (self.xmax - xmax)
                 self.sense = prefix + self.sense + suffix
                 self.anti = prefix + self.anti + suffix
-
             # Update sense and anti arrays
             j = composite.xmin - self.xmin
             while j <= composite.xmax - composite.xmin:
                 idx = composite.xmin - self.xmin + j
                 self.sense[idx] += composite.sense[j]
                 self.anti[idx] += composite.anti[j]
                 j += 1
-
-            self.individual_composites[composite.id] = composite
-
+            self.individual_files[composite.id] = composite
     def __str__(self):
-        return str(self.individual_composites)
-
-def main():
-    c = parseComposite.parseComposite("sample_composites/sample_1.out")
-    compositeGroup = CompositeGroup()
-    compositeGroup.loadComposite(c)
-    c2 = parseComposite.parseComposite("sample_composites/sample2.out.txt")
-    compositeGroup.loadComposite(c2)
-    print(compositeGroup)
-
-
-if __name__ == "__main__":
-    main()
+        return str(self.individual_files)