provide groupings for similarity calculation

klarigi/build.gradle

@@ -88,4 +88,4 @@ jacocoTestReport {
   }
 }
 
-version = '0.0.11'
+version = '0.0.12-SNAPSHOT'

klarigi/src/main/groovy/klarigi/App.groovy

@@ -28,6 +28,7 @@ class App {
       _ longOpt: 'save-ic', 'Save the IC values to the given file', args:1
 
       g longOpt: 'group', 'The group to explain.', args: 1
+      gf longOpt: 'group-file', 'You can pass a file with a list of groups to: one per line. If you do this, the --group argument will be ignored.', args: 1
 
       _ longOpt: 'max-ic', 'Max IC to use in stepdown algorithm. Default: 0.8', args: 1
       _ longOpt: 'min-ic', 'Min IC to use in stepdown algorithm. Default: 0.4', args: 1
@@ -80,36 +81,44 @@ class App {
 
     def k = new Klarigi(o)
     if(!o['similarity-mode']) {
-      if(!o['group'] || (o['group'] && o['group'] == '*')) {
-        def allExplanations = k.explainAllClusters(o['output-scores'], o['power'], threads)
-        allExplanations.each {
-          k.output(it.cluster, it.results, o['output-type'], o['print-members'], o['output'])
+      def allExplanations 
+      if(o['group-file']) {
+        def groups
+        try {
+          groups = new File(o['group-file']).text.split('\n')
+        } catch(e) {
+          println "Could not handle the --group-file: ${e.toString()}"
+          System.exit(1)
         }
 
-        if(o['output-exp-dataframe']) {
-          k.writeDataframe('train', allExplanations)
-        }
-
-        if(o['reclassify']) {
-          k.reclassify(allExplanations, o['output-classification-scores'])
-        }
-        if(o['classify']) {
-          k.classify(o['classify'], allExplanations, o['output-classification-scores'])
-
-          if(o['output-exp-dataframe']) {
-            k.writeDataframe('test', allExplanations)
-          }
-        }
+        allExplanations = k.explainClusters(groups, o['output-scores'], o['power'], threads)
+      } else if(o['group'] && o['group'] != '*') {
+        allExplanations = k.explainClusters([o['group']], o['output-scores'], o['power'], threads)
       } else {
-        def r = k.explainCluster(o['group'], o['power'], o['output-scores'], threads)
-        k.output(o['group'], r, o['output-type'], o['print-members'], o['output'])
+        allExplanations = k.explainAllClusters(o['output-scores'], o['power'], threads)
+      }
 
-        if(o['reclassify'] || o['output-exp-dataframe']) {
-          println "Must explain all groups for --reclassify or --output-exp-dataframe"
+      allExplanations.each {
+        k.output(it.cluster, it.results, o['output-type'], o['print-members'], o['output'])
+      }
+
+      if(o['output-exp-dataframe']) {
+        k.writeDataframe('train', allExplanations)
+      }
+
+      if(o['reclassify']) {
+        k.reclassify(allExplanations, o['output-classification-scores'])
+      }
+      if(o['classify']) {
+        k.classify(o['classify'], allExplanations, o['output-classification-scores'])
+
+        if(o['output-exp-dataframe']) {
+          k.writeDataframe('test', allExplanations)
         }
       }
+
     } else {
-      k.genSim(o['output'])
+      k.genSim(o['output'], o['group'])
     }
   }
 }

klarigi/src/main/groovy/klarigi/InformationContent.groovy

@@ -106,12 +106,13 @@ public class InformationContent {
   }
 
 	// this should really go to a diff class
-  def compareEntities(assoc) {
+  def compareEntities(assoc, groupings, group) {
     def smConfPairwise = new SMconf(SMConstants.FLAG_SIM_PAIRWISE_DAG_NODE_RESNIK_1995, icConf)
     def smConfGroupwise = new SMconf(SMConstants.FLAG_SIM_GROUPWISE_BMA, icConf)
 
     def results = [:]
 		assoc.each { k1, v1 ->
+      if(group && !groupings[group].contains(k1)) { return; }
       if(!results.containsKey(k1)) { results[k1] = [:] }
       assoc.each { k2, v2 ->
         if(k1 == k2) { return; }
@@ -134,7 +135,7 @@ public class InformationContent {
     results
   }
 
-  static def WriteSimilarity(results, groups, toFile) {
+  static def WriteSimilarity(results, toFile) {
     def out = []
 
     results.each { k1, v1 ->

klarigi/src/main/groovy/klarigi/Klarigi.groovy

@@ -179,6 +179,12 @@ public class Klarigi {
     }
   }
 
+  def explainClusters(groups, outputScores, powerMode, threads) {
+    data.groupings.findAll { g, v -> groups.contains(g) }.collect { g, v ->
+      [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads) ]
+    }
+  }
+
   def explainAllClusters(outputScores, powerMode, threads) {
     data.groupings.collect { g, v ->
       [ cluster: g, results: explainCluster(g, powerMode, outputScores, threads) ]
@@ -210,12 +216,12 @@ public class Klarigi {
     }
   }
 
-  def genSim(toFile) {
+  def genSim(toFile, group) {
     if(!icFactory) {
       println "Error: IC class not loaded (--similarity and --ic are not compatible)"
       System.exit(1)
     }
-    def results = icFactory.compareEntities(data.associations)
+    def results = icFactory.compareEntities(data.associations, data.groupings, group)
     InformationContent.WriteSimilarity(results, toFile)
   }