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From tm...@apache.org
Subject svn commit: r1611035 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
Date Wed, 16 Jul 2014 14:52:12 GMT
Author: tmill
Date: Wed Jul 16 14:52:11 2014
New Revision: 1611035

URL: http://svn.apache.org/r1611035
Log:
CTAKES-82: Added backwards compatible constructor to base temporal relations.class.

Modified:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java?rev=1611035&r1=1611034&r2=1611035&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
Wed Jul 16 14:52:11 2014
@@ -44,49 +44,59 @@ import com.google.common.collect.Sets;
 import com.lexicalscope.jewel.cli.Option;
 
 public abstract class EvaluationOfTemporalRelations_ImplBase extends
-		Evaluation_ImplBase<AnnotationStatistics<String>> {
+Evaluation_ImplBase<AnnotationStatistics<String>> {
 
-	  static interface TempRelOptions extends Evaluation_ImplBase.Options{
-		  @Option
-		  public boolean getTest();
-		  
-		  @Option
-		  public boolean getPrintFormattedRelations();
-		  
-		  @Option
-		  public boolean getBaseline();
-	    
-	    @Option
-	    public boolean getClosure();
-	    
-	    @Option
-	    public boolean getClassificationOnly();
-	    
-	  }
-	  
-	  protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
-	  protected static float DEFAULT_DOWNSAMPLE = 1.0f;
-	  protected static double DEFAULT_SVM_C = 1.0;
-	  protected static double DEFAULT_SVM_G = 1.0;
-	  protected static double DEFAULT_TK = 0.5;
-	  protected static double DEFAULT_LAMBDA = 0.5;
-	  
-	  protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "linear",
-	  		  DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
-
-	  
-	  protected ParameterSettings params = null;
-	  protected boolean printRelations = false;
-
-	  public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
-			File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
-			File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors,
boolean printRelations, ParameterSettings params) {
-		super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
-				treebankDirectory, coreferenceDirectory);
-		this.params = params;
-		this.printRelations = printRelations;
-		this.printErrors =  printErrors;
-	}
+  static interface TempRelOptions extends Evaluation_ImplBase.Options{
+    @Option
+    public boolean getTest();
+
+    @Option
+    public boolean getPrintFormattedRelations();
+
+    @Option
+    public boolean getBaseline();
+
+    @Option
+    public boolean getClosure();
+
+    @Option
+    public boolean getClassificationOnly();
+
+  }
+
+  protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+  protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+  protected static double DEFAULT_SVM_C = 1.0;
+  protected static double DEFAULT_SVM_G = 1.0;
+  protected static double DEFAULT_TK = 0.5;
+  protected static double DEFAULT_LAMBDA = 0.5;
+
+  protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "linear",
+      DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+
+
+  protected ParameterSettings params = null;
+  protected boolean printRelations = false;
+
+  public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+      File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+      File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors,
boolean printRelations, ParameterSettings params) {
+    super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+        treebankDirectory, coreferenceDirectory);
+    this.params = params;
+    this.printRelations = printRelations;
+    this.printErrors =  printErrors;
+  }
+
+  public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+      File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+      File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations,
ParameterSettings params) {
+    super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+        treebankDirectory);
+    this.params = params;
+    this.printRelations = printRelations;
+    this.printErrors =  printErrors;
+  }
 
   public static class PreserveEventEventRelations extends JCasAnnotator_ImplBase {
     public static final String PARAM_GOLD_VIEW = "GoldView";
@@ -97,15 +107,15 @@ public abstract class EvaluationOfTempor
     @Override
     public void process(JCas jCas) throws AnalysisEngineProcessException {
       for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(jCas, BinaryTextRelation.class))){
-          RelationArgument arg1 = relation.getArg1();
-          RelationArgument arg2 = relation.getArg2();
-          if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof
EventMention){
-            // these are the kind we keep.
-            continue;
-          }
-          arg1.removeFromIndexes();
-          arg2.removeFromIndexes();
-          relation.removeFromIndexes();
+        RelationArgument arg1 = relation.getArg1();
+        RelationArgument arg2 = relation.getArg2();
+        if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof
EventMention){
+          // these are the kind we keep.
+          continue;
+        }
+        arg1.removeFromIndexes();
+        arg2.removeFromIndexes();
+        relation.removeFromIndexes();
       }
     }   
   }
@@ -115,46 +125,46 @@ public abstract class EvaluationOfTempor
 
     @ConfigurationParameter(name = PARAM_RELATION_VIEW)
     private String relationViewName = CAS.NAME_DEFAULT_SOFA;
-  @Override
-  public void process(JCas jCas) throws AnalysisEngineProcessException {
-    JCas relationView = null;
-    
-    try {
-      relationView = jCas.getView(relationViewName);
-    } catch (CASException e) {
-      e.printStackTrace();
-    }
-    for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
-        relationView,
-        BinaryTextRelation.class))) {
-    	String relationType = relation.getCategory();
-      if (relationType.startsWith("BEFORE")|| relationType.startsWith("BEGINS-ON")|| relationType.startsWith("ENDS-ON"))
{
-//        relation.getArg1().removeFromIndexes();
-//        relation.getArg2().removeFromIndexes();
-//        relation.removeFromIndexes();
-    	  relation.setCategory("RARE");
-      }else if(relationType.startsWith("CONTAINS")|| relationType.startsWith("OVERLAP")){
-    	  relation.setCategory("COMMON");
-      }
-    }
-  }
-  
-  public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
     @Override
     public void process(JCas jCas) throws AnalysisEngineProcessException {
-      for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
-        if(event.getEvent() != null && event.getEvent().getProperties() != null){
-          event.getEvent().getProperties().setContextualAspect("UNK");
-          event.getEvent().getProperties().setContextualModality("UNK");
+      JCas relationView = null;
+
+      try {
+        relationView = jCas.getView(relationViewName);
+      } catch (CASException e) {
+        e.printStackTrace();
+      }
+      for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+          relationView,
+          BinaryTextRelation.class))) {
+        String relationType = relation.getCategory();
+        if (relationType.startsWith("BEFORE")|| relationType.startsWith("BEGINS-ON")|| relationType.startsWith("ENDS-ON"))
{
+          //        relation.getArg1().removeFromIndexes();
+          //        relation.getArg2().removeFromIndexes();
+          //        relation.removeFromIndexes();
+          relation.setCategory("RARE");
+        }else if(relationType.startsWith("CONTAINS")|| relationType.startsWith("OVERLAP")){
+          relation.setCategory("COMMON");
         }
       }
-      for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
-        timex.setTimeClass("UNK");
+    }
+
+    public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
+      @Override
+      public void process(JCas jCas) throws AnalysisEngineProcessException {
+        for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
+          if(event.getEvent() != null && event.getEvent().getProperties() != null){
+            event.getEvent().getProperties().setContextualAspect("UNK");
+            event.getEvent().getProperties().setContextualModality("UNK");
+          }
+        }
+        for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
+          timex.setTimeClass("UNK");
+        }
       }
     }
   }
-}
-  
+
   protected static Collection<BinaryTextRelation> correctArgOrder(
       Collection<BinaryTextRelation> systemRelations,
       Collection<BinaryTextRelation> goldRelations) {
@@ -187,57 +197,57 @@ public abstract class EvaluationOfTempor
     return result;
   }
 
-	  protected static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation>
relations) {
+  protected static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation>
relations) {
+
+    for(BinaryTextRelation binaryTextRelation : relations) {
+
+      Annotation arg1 = binaryTextRelation.getArg1().getArgument();
+      Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+
+      String arg1Type = arg1.getClass().getSimpleName();
+      String arg2Type = arg2.getClass().getSimpleName();
 
-		  for(BinaryTextRelation binaryTextRelation : relations) {
+      int arg1Begin = arg1.getBegin();
+      int arg1End = arg1.getEnd();
+      int arg2Begin = arg2.getBegin();
+      int arg2End = arg2.getEnd();
 
-			  Annotation arg1 = binaryTextRelation.getArg1().getArgument();
-			  Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+      String category = binaryTextRelation.getCategory();
 
-			  String arg1Type = arg1.getClass().getSimpleName();
-			  String arg2Type = arg2.getClass().getSimpleName();
-
-			  int arg1Begin = arg1.getBegin();
-			  int arg1End = arg1.getEnd();
-			  int arg2Begin = arg2.getBegin();
-			  int arg2End = arg2.getEnd();
-
-			  String category = binaryTextRelation.getCategory();
-
-			  System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n", 
-					  fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
-		  }
-	  }
-	  
-	  protected static String formatRelation(BinaryTextRelation relation) {
-		  IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
-		  IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
-		  String arg1Type ="E";
-		  String arg2Type ="T";
-		  if(arg1 instanceof TimeMention) arg1Type = "T";
-		  if(arg2 instanceof EventMention) arg2Type = "E";
-		  String text = arg1.getCAS().getDocumentText();
-		  int begin = Math.min(arg1.getBegin(), arg2.getBegin());
-		  int end = Math.max(arg1.getBegin(), arg2.getBegin());
-		  begin = Math.max(0, begin - 50);
-		  end = Math.min(text.length(), end + 50);
-		  return String.format(
-				  "%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
-				  relation.getCategory(),
-				  arg1.getCoveredText(),
-				  arg1.getTypeID(),
-				  //add extra
-				  arg1.getBegin(),
-				  arg1.getEnd(),
-				  arg1Type,
-				  
-				  arg2.getCoveredText(),
-				  arg2.getTypeID(),
-				  //add extra
-				  arg2.getBegin(),
-				  arg2.getEnd(),
-				  arg2Type,
-				  text.substring(begin, end).replaceAll("[\r\n]", " "));
-	  }
+      System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n", 
+          fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
+    }
+  }
+
+  protected static String formatRelation(BinaryTextRelation relation) {
+    IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
+    IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
+    String arg1Type ="E";
+    String arg2Type ="T";
+    if(arg1 instanceof TimeMention) arg1Type = "T";
+    if(arg2 instanceof EventMention) arg2Type = "E";
+    String text = arg1.getCAS().getDocumentText();
+    int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+    int end = Math.max(arg1.getBegin(), arg2.getBegin());
+    begin = Math.max(0, begin - 50);
+    end = Math.min(text.length(), end + 50);
+    return String.format(
+        "%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
+        relation.getCategory(),
+        arg1.getCoveredText(),
+        arg1.getTypeID(),
+        //add extra
+        arg1.getBegin(),
+        arg1.getEnd(),
+        arg1Type,
+
+        arg2.getCoveredText(),
+        arg2.getTypeID(),
+        //add extra
+        arg2.getBegin(),
+        arg2.getEnd(),
+        arg2Type,
+        text.substring(begin, end).replaceAll("[\r\n]", " "));
+  }
 
 }



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