Updated majority consensus rule

bioclipse · Jun 20, 2012 · 31baf5d · 31baf5d
1 parent 13f4cc8
commit 31baf5d
Show file tree

Hide file tree

Showing 4 changed files with 90 additions and 3 deletions.
diff --git a/plugins/net.bioclipse.ds.common/plugin.xml b/plugins/net.bioclipse.ds.common/plugin.xml
@@ -11,14 +11,20 @@
  <extension
        point="net.bioclipse.decisionsupport">
        <consensus
-             id="net.bioclipse.ds.consensus.majority.emptyinconclusive"
+             id="net.bioclipse.ds.consensus.majority"
              name="Majority Voting"
              class="net.bioclipse.ds.cons.MajorityVote"
+             description="A majority voting algorithm. Empty if no results">
+       </consensus>
+       <consensus
+             id="net.bioclipse.ds.consensus.majority.emptyinconclusive"
+             name="Majority Voting, inconclusive if no results"
+             class="net.bioclipse.ds.cons.MajorityVoteEmptyInconclusive"
              description="A majority voting algorithm. Inconclusive if no results">
        </consensus>
        <consensus
              id="net.bioclipse.ds.consensus.majority.emptynegative"
-             name="Normal Consensus"
+             name="Majority voting, negative if empty"
              class="net.bioclipse.ds.cons.MajorityVoteEmptyNegative"
              description="A majority voting algorithm. Negative if no results">
        </consensus>

diff --git a/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/cons/MajorityVote.java b/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/cons/MajorityVote.java
@@ -19,6 +19,7 @@
  * This implementation follows the following rules:
  * <ol>
  *         <li>if #err > #pos && #err > #neg >> ERROR
+ *         <li>if #pos == #neg == 0 >> EMPTY
  *         <li>if #incon >pos && #incon > #neg >> INCONCLUSIVE
  *         <li>if #pos == #neg >> INCONCLUSIVE
  *         <li>if #pos > #neg >> POSITIVE
@@ -58,6 +59,9 @@ else if (res==ITestResult.INFORMATIVE)
         if (numerr>numneg && numerr>numpos)
             return ITestResult.ERROR;
 
+        if (numneg==numpos && numpos==0)
+            return ITestResult.EMPTY;
+
         else if (numinc > numpos && numinc > numneg)
             return ITestResult.INCONCLUSIVE;
 

diff --git a/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/cons/MajorityVoteEmptyInconclusive.java b/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/cons/MajorityVoteEmptyInconclusive.java
@@ -0,0 +1,77 @@
+/* *****************************************************************************
+< * Copyright (c) 2009 Ola Spjuth.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ *     Ola Spjuth - initial API and implementation
+ ******************************************************************************/
+package net.bioclipse.ds.cons;
+
+import java.util.List;
+
+import net.bioclipse.ds.model.ITestResult;
+
+
+/**
+ * This implementation follows the following rules:
+ * <ol>
+ *         <li>if #err > #pos && #err > #neg >> ERROR
+ *         <li>if #incon >pos && #incon > #neg >> INCONCLUSIVE
+ *         <li>if #pos == #neg >> INCONCLUSIVE
+ *         <li>if #pos > #neg >> POSITIVE
+ *         <li>else >> NEGATIVE
+ * </ol>
+ * 
+ * @author ola
+ *
+ */
+public class MajorityVoteEmptyInconclusive extends AbstractConsensusCalculator{
+
+    public int calculate(List<Integer> classifications){
+
+        if (classifications==null)
+            return ITestResult.ERROR;
+
+        int numpos=0;
+        int numneg=0;
+        int numinc=0;
+        int numerr=0;
+        int numinf=0;
+
+        for (Integer res : classifications){
+            if (res==ITestResult.POSITIVE)
+                numpos++;
+            else if (res==ITestResult.NEGATIVE)
+                numneg++;
+            else if (res==ITestResult.INCONCLUSIVE)
+                numinc++;
+            else if (res==ITestResult.ERROR)
+                numerr++;
+            else if (res==ITestResult.INFORMATIVE)
+                numinf++;
+        }
+
+        //If at least one but more pos than neg:
+        if (numerr>numneg && numerr>numpos)
+            return ITestResult.ERROR;
+
+        else if (numinc > numpos && numinc > numneg)
+            return ITestResult.INCONCLUSIVE;
+
+        else if (numpos==numneg)
+            return ITestResult.INCONCLUSIVE;
+
+        //If at least one but more pos than neg:
+        else if (numpos>numneg)
+            return ITestResult.POSITIVE;
+
+        //In all other cases:
+        else
+            return ITestResult.NEGATIVE;
+
+    }    
+
+}
diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/business/DSBusinessModel.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/business/DSBusinessModel.java
@@ -39,7 +39,7 @@ public class DSBusinessModel {
     private static final Logger logger = Logger.getLogger(DSBusinessModel.class);
 
     private static final String DEFAULT_CONSENSUS_CALCULATOR = 
-                        "net.bioclipse.ds.consensus.majority.emptyinconclusive";
+                        "net.bioclipse.ds.consensus.majority";
 
     volatile List<IDSTest> tests;
     volatile List<Endpoint> endpoints;