X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainLengthsTable.java;h=2b291eb6e296dab5665210a95ce1d15e632bd23c;hb=876ced97014fafe54ff51dcc17da8bf25913fec7;hp=4b6ca22e0ca9adfb00929fc32c346325519be0ff;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
index 4b6ca22..2b291eb 100644
--- a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2010 Christian M. Zmasek
 // Copyright (C) 2008-2010 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,13 +16,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
 
@@ -32,36 +32,24 @@ import java.util.List;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
+import org.forester.protein.Domain;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 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();
@@ -83,7 +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();
     }
 
@@ -139,11 +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 );
     }
 
@@ -155,11 +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;
+    }
 }