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[jalview.git] / forester / java / src / org / forester / surfacing / DomainLengthsTable.java

diff --git a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
index 9a9e0a7..2b291eb 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
@@ -33,7 +33,6 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -42,30 +41,15 @@ import org.forester.util.ForesterUtil;
 
 public class DomainLengthsTable {
 
-    private final static DecimalFormat       DF = new DecimalFormat( "#.0" );
-    final SortedMap<DomainId, DomainLengths> _domain_lengths;
-    final List<Species>                      _species;
+    private final static DecimalFormat     DF = new DecimalFormat( "#.0" );
+    final SortedMap<String, DomainLengths> _domain_lengths;
+    final List<Species>                    _species;
 
     public DomainLengthsTable() {
-        _domain_lengths = new TreeMap<DomainId, DomainLengths>();
+        _domain_lengths = new TreeMap<String, DomainLengths>();
         _species = new ArrayList<Species>();
     }
 
-    private void addDomainLengths( final DomainLengths domain_lengths ) {
-        if ( getDomainLengths().containsKey( domain_lengths.getDomainId() ) ) {
-            throw new IllegalArgumentException( "domain lengths for [" + domain_lengths.getDomainId()
-                    + "] already added" );
-        }
-        getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
-    }
-
-    private void addLength( final DomainId domain_id, final Species species, final int domain_length ) {
-        if ( !getDomainLengths().containsKey( domain_id ) ) {
-            addDomainLengths( new DomainLengths( domain_id ) );
-        }
-        getDomainLengths().get( domain_id ).addLength( species, domain_length );
-    }
-
     public void addLengths( final List<Protein> protein_list ) {
         for( final Protein protein : protein_list ) {
             final Species species = protein.getSpecies();
@@ -87,7 +71,7 @@ public class DomainLengthsTable {
         return stats;
     }
 
-    public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final DomainId domain_id ) {
+    public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final String domain_id ) {
         return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
     }
 
@@ -143,11 +127,7 @@ public class DomainLengthsTable {
         return sb;
     }
 
-    private SortedMap<DomainId, DomainLengths> getDomainLengths() {
-        return _domain_lengths;
-    }
-
-    public DomainLengths getDomainLengths( final DomainId domain_id ) {
+    public DomainLengths getDomainLengths( final String domain_id ) {
         return getDomainLengths().get( domain_id );
     }
 
@@ -159,11 +139,30 @@ public class DomainLengthsTable {
         return list;
     }
 
-    public DescriptiveStatistics getLengthStatistic( final DomainId domain_id, final Species species ) {
+    public DescriptiveStatistics getLengthStatistic( final String domain_id, final Species species ) {
         return getDomainLengths( domain_id ).getLengthStatistic( species );
     }
 
     public List<Species> getSpecies() {
         return _species;
     }
+
+    private void addDomainLengths( final DomainLengths domain_lengths ) {
+        if ( getDomainLengths().containsKey( domain_lengths.getDomainId() ) ) {
+            throw new IllegalArgumentException( "domain lengths for [" + domain_lengths.getDomainId()
+                                                + "] already added" );
+        }
+        getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
+    }
+
+    private void addLength( final String domain_id, final Species species, final int domain_length ) {
+        if ( !getDomainLengths().containsKey( domain_id ) ) {
+            addDomainLengths( new DomainLengths( domain_id ) );
+        }
+        getDomainLengths().get( domain_id ).addLength( species, domain_length );
+    }
+
+    private SortedMap<String, DomainLengths> getDomainLengths() {
+        return _domain_lengths;
+    }
 }