X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainLengths.java;h=6d39b6119393915f27543091df994cf287253c75;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=7e628ce782b24337a78daef641bf9ffe5dbd7000;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainLengths.java b/forester/java/src/org/forester/surfacing/DomainLengths.java
index 7e628ce..6d39b61 100644
--- a/forester/java/src/org/forester/surfacing/DomainLengths.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengths.java
@@ -31,17 +31,16 @@ import java.util.List;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 
 public class DomainLengths {
 
-    final DomainId                                  _domain_id;
+    final String                                    _domain_id;
     final SortedMap<Species, DescriptiveStatistics> _length_statistics;
 
-    public DomainLengths( final DomainId domain_id ) {
+    public DomainLengths( final String domain_id ) {
         _domain_id = domain_id;
         _length_statistics = new TreeMap<Species, DescriptiveStatistics>();
     }
@@ -53,18 +52,11 @@ public class DomainLengths {
         getLengthStatistic( species ).addValue( domain_length );
     }
 
-    private void addLengthStatistics( final Species species, final DescriptiveStatistics length_statistic ) {
-        if ( getLengthStatistics().containsKey( species ) ) {
-            throw new IllegalArgumentException( "length statistics for [" + species.getSpeciesId() + "] already added" );
-        }
-        getLengthStatistics().put( species, length_statistic );
-    }
-
     /**
      * Returns descriptive statistics based on the arithmetic means
-     * for each species.  
-     * 
-     * 
+     * for each species.
+     *
+     *
      * @return
      */
     public DescriptiveStatistics calculateMeanBasedStatistics() {
@@ -76,10 +68,10 @@ public class DomainLengths {
     }
 
     /**
-     * 
+     *
      * Note. This is not technically a Z-score since the distribution
      * of means is unknown (and not normal).
-     * 
+     *
      * @param species
      * @return
      */
@@ -91,7 +83,7 @@ public class DomainLengths {
         return ( species_mean - population_mean ) / population_sd;
     }
 
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _domain_id;
     }
 
@@ -99,10 +91,6 @@ public class DomainLengths {
         return getLengthStatistics().get( species );
     }
 
-    private SortedMap<Species, DescriptiveStatistics> getLengthStatistics() {
-        return _length_statistics;
-    }
-
     public List<DescriptiveStatistics> getLengthStatisticsList() {
         final List<DescriptiveStatistics> list = new ArrayList<DescriptiveStatistics>();
         for( final DescriptiveStatistics stats : _length_statistics.values() ) {
@@ -142,4 +130,15 @@ public class DomainLengths {
     public boolean isHasLengthStatistic( final Species species ) {
         return getLengthStatistics().containsKey( species );
     }
+
+    private void addLengthStatistics( final Species species, final DescriptiveStatistics length_statistic ) {
+        if ( getLengthStatistics().containsKey( species ) ) {
+            throw new IllegalArgumentException( "length statistics for [" + species.getSpeciesId() + "] already added" );
+        }
+        getLengthStatistics().put( species, length_statistic );
+    }
+
+    private SortedMap<Species, DescriptiveStatistics> getLengthStatistics() {
+        return _length_statistics;
+    }
 }