From 82a7e45f51504522b531484eabb8d40793c8dc84 Mon Sep 17 00:00:00 2001
From: Luke Slater <tinmachin3@gmail.com>
Date: Tue, 30 Aug 2022 20:29:48 +0100
Subject: [PATCH] remove some unnecessary functions, additional parallelisation

---
 klarigi/src/main/groovy/klarigi/App.groovy    |  1 +
 klarigi/src/main/groovy/klarigi/Scorer.groovy | 22 +++++--------------
 .../src/main/groovy/klarigi/StepDown.groovy   | 12 +++++++---
 3 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/klarigi/src/main/groovy/klarigi/App.groovy b/klarigi/src/main/groovy/klarigi/App.groovy
index a458ee6..d3a9c8b 100644
--- a/klarigi/src/main/groovy/klarigi/App.groovy
+++ b/klarigi/src/main/groovy/klarigi/App.groovy
@@ -218,6 +218,7 @@ class App {
         println "Could not handle the --group-file: ${e.toString()}"
         System.exit(1)
       }
+      if(o['verbose']) { println "[...] Loaded ${o['group'].size()} groups from ${o['group-file']}. Ignoring any --group argument." }
     } else if(o['group'] =~ ';') {
       o['group'] = o['group'].tokenize(';')
     } else if(o['group']) {
diff --git a/klarigi/src/main/groovy/klarigi/Scorer.groovy b/klarigi/src/main/groovy/klarigi/Scorer.groovy
index 96cbf41..d0df2be 100644
--- a/klarigi/src/main/groovy/klarigi/Scorer.groovy
+++ b/klarigi/src/main/groovy/klarigi/Scorer.groovy
@@ -187,22 +187,7 @@ public class Scorer {
       }
     }
   }
-/*
-  private def findRelevantClasses(relevant, c) {
-		/*if(relevant.contains(c)) { return; }
-    relevant << c
-
-		def ce = ontoHelper.dataFactory.getOWLClass(IRI.create(c))
-		ontoHelper.reasoner.getSuperClasses(ce, false).each { n ->
-			n.getEntities().each { sc ->
-				def strc = sc.getIRI().toString()
-				findRelevantClasses(relevant, strc)
-			}
-		
-
-    relevant += scMap[c]
-  }
-*/
+
   def scoreClasses(cid, classes) {
     scoreClasses(cid, classes, false)
   }
@@ -232,7 +217,10 @@ public class Scorer {
 
   def scoreAllClasses(cid, returnAll) {
     // No point running expensive unique here since we check in processClass whether we already have it
-    def relevant = data.allAssociations.collect { scMap[it] }.flatten()
+    def relevant
+    GParsPool.withPool(o['threads']) { p ->
+      relevant = data.allAssociations.collectParallel { scMap[it] }.flatten()
+    }
 
     def explainers = new ConcurrentHashMap()
     GParsPool.withPool(o['threads']) { p ->
diff --git a/klarigi/src/main/groovy/klarigi/StepDown.groovy b/klarigi/src/main/groovy/klarigi/StepDown.groovy
index 3fa2d78..6dec28d 100644
--- a/klarigi/src/main/groovy/klarigi/StepDown.groovy
+++ b/klarigi/src/main/groovy/klarigi/StepDown.groovy
@@ -14,9 +14,13 @@ public class StepDown {
     def stepDown = { e, icCutoff, powerCutoff, totalInclusionCutoff ->
       while(totalCoverage <= (totalInclusionCutoff*100)) {
 
-        def ef = candidates.findAll {
+        
+        def ef
+        GParsPool.withPool(threads) { p ->
+        ef = candidates.findAllParallel {
           it.nIc >= icCutoff && it.nPower >= powerCutoff
         } 
+        }
 
         totalCoverage = CalculateOI(c, cid, data, ef, threads, false)
 
@@ -52,12 +56,14 @@ public class StepDown {
   static def CalculateOI(c, cid, data, candidates, threads, total) {
     def contributingEf = candidates
     if(!total) {
-      contributingEf = contributingEf.findAll { it.nInclusion <= c.MAX_INCLUSION && it.nExclusion <= c.MAX_EXCLUSION && it.nPower <= c.MAX_R_SCORE }
+      GParsPool.withPool(threads) { p ->
+      contributingEf = contributingEf.findAllParallel { it.nInclusion <= c.MAX_INCLUSION && it.nExclusion <= c.MAX_EXCLUSION && it.nPower <= c.MAX_R_SCORE }
+      }
     }
     
     def covered = new AtomicInteger(0)
     GParsPool.withPool(threads) { p ->
-      data.groupings[cid].each { ee ->
+      data.groupings[cid].eachParallel { ee ->
         if(contributingEf.any { it.incEnts.containsKey(ee) }) {
           covered.getAndIncrement()
         }