Add Markov Clustering

app.py

@@ -16,6 +16,7 @@ __author__ = 'Dmitry Ustalov'
 __license__ = 'Apache 2.0'
 
 import csv
+import os
 import re
 import subprocess
 from dataclasses import dataclass
@@ -36,6 +37,7 @@ class Algorithm:
     local_params: Optional[str] = None
     global_name: Optional[str] = None
     global_params: Optional[str] = None
+    mcl_bin: Optional[str] = None
 
     def args_clustering(self) -> List[str]:
         args = [self.name]
@@ -51,6 +53,9 @@ class Algorithm:
         if self.global_params:
             args.extend(['--global-params', self.global_params])
 
+        if self.mcl_bin:
+            args.extend(['--mcl-bin', self.mcl_bin])
+
         return args
 
     def args_graph(self) -> List[str]:
@@ -65,6 +70,11 @@ class Algorithm:
         return args
 
 
+if 'MCL_BIN' in os.environ and os.path.isfile(os.environ['MCL_BIN']) and os.access(os.environ['MCL_BIN'], os.X_OK):
+    mcl: Optional[str] = os.environ['MCL_BIN']
+else:
+    mcl = None
+
 ALGORITHMS: Dict[str, Algorithm] = {
     'Watset[CW_top, CW_top]': Algorithm('watset', None, 'cw', 'mode=top', 'cw', 'mode=top'),
     'Watset[CW_lin, CW_top]': Algorithm('watset', None, 'cw', 'mode=lin', 'cw', 'mode=top'),
@@ -84,6 +94,15 @@ ALGORITHMS: Dict[str, Algorithm] = {
     'MaxMax': Algorithm('maxmax')
 }
 
+if mcl:
+    ALGORITHMS.update({
+        'Watset[CW_top, MCL]': Algorithm('watset', None, 'cw', 'mode=top', 'mcl', 'mcl-bin=' + mcl),
+        'Watset[CW_lin, MCL]': Algorithm('watset', None, 'cw', 'mode=lin', 'mcl', 'mcl-bin=' + mcl),
+        'Watset[CW_log, MCL]': Algorithm('watset', None, 'cw', 'mode=log', 'mcl', 'mcl-bin=' + mcl),
+        'Watset[MCL, MCL]': Algorithm('watset', None, 'mcl', None, 'mcl', 'mcl-bin=' + mcl),
+        'MCL': Algorithm('mcl')
+    })
+
 SENSE = re.compile(r'^(?P<item>\d+)#(?P<sense>\d+)$')
 
 

packages.txt

@@ -1 +1,2 @@
 default-jre
+mcl