X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainLengths.java;h=6d39b6119393915f27543091df994cf287253c75;hb=cb49ee5684c6907b3161db82ff9aea72961b8548;hp=0e96aca3a8212c8c17f660802cabf32a8e75e64c;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainLengths.java b/forester/java/src/org/forester/surfacing/DomainLengths.java
index 0e96aca..6d39b61 100644
--- a/forester/java/src/org/forester/surfacing/DomainLengths.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengths.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
@@ -31,15 +31,16 @@ import java.util.List;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
+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>();
     }
@@ -51,18 +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() {
@@ -74,10 +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
      */
@@ -89,7 +83,7 @@ public class DomainLengths {
         return ( species_mean - population_mean ) / population_sd;
     }
 
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _domain_id;
     }
 
@@ -97,10 +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() ) {
@@ -140,4 +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;
+    }
 }