inprogress

diff --git a/forester/java/src/org/forester/protein/DomainId.java b/forester/java/src/org/forester/protein/DomainId.java
deleted file mode 100644 (file)
index 8802283..0000000
--- a/forester/java/src/org/forester/protein/DomainId.java
+++ /dev/null
@@ -1,122 +0,0 @@
-// $Id:
-//
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.protein;
-
-import org.forester.util.ForesterUtil;
-
-public class DomainId implements Comparable<DomainId> {
-
-    final private String _id;
-
-    //  private List<GoId>   _go_ids;
-    private DomainId( final String id ) {
-        if ( ForesterUtil.isEmpty( id ) ) {
-            throw new IllegalArgumentException( "attempt to create domain id from empty or null string" );
-        }
-        _id = id.trim();
-        if ( _id.indexOf( ' ' ) > -1 ) {
-            throw new IllegalArgumentException( "attempt to create domain id from string containing one ore more spaces ["
-                    + _id + "]" );
-        }
-        else if ( _id.indexOf( BinaryDomainCombination.SEPARATOR ) > -1 ) {
-            throw new IllegalArgumentException( "attempt to create domain id from string containing the separator character ["
-                    + BinaryDomainCombination.SEPARATOR + "] for domain combinations [" + _id + "]" );
-        }
-        ///////////////////////////// //      setGoIds( null );
-    }
-
-    //  public void addGoId( final GoId go_id ) {
-    //       if ( getGoIds() == null ) {
-    //           setGoIds( new ArrayList<GoId>() );
-    //      }
-    //      getGoIds().add( go_id );
-    //  }
-    @Override
-    public int compareTo( final DomainId domain_id ) {
-        if ( this == domain_id ) {
-            return 0;
-        }
-        return getId().toLowerCase().compareTo( domain_id.getId().toLowerCase() );
-    }
-
-    @Override
-    public boolean equals( final Object o ) {
-        if ( this == o ) {
-            return true;
-        }
-        else if ( o == null ) {
-            throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to null" );
-        }
-        else if ( o.getClass() != this.getClass() ) {
-            throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
-                    + o.getClass() + "]" );
-        }
-        else {
-            return getId().equals( ( ( DomainId ) o ).getId() );
-        }
-    }
-
-    // public GoId getGoId( final int i ) {
-    //     return getGoIds().get( i );
-    //}
-    // Note.
-    // The fact that equals and compareTo do not behave the same in cases where ids only differ by their case
-    // is not ideal. From Sun regarding Interface SortedSet<E>:
-    // "Note that the ordering maintained by a sorted set (whether or not an explicit comparator is provided)
-    // must be consistent with equals if the sorted set is to correctly implement the Set interface.
-    // (See the Comparable interface or Comparator interface for a precise definition of consistent 
-    // with equals.) This is so because the Set interface is defined in terms of the equals  operation,
-    // but a sorted set performs all element comparisons using its compareTo (or compare) method, 
-    // so two elements that are deemed equal by this method are, from the standpoint of the sorted set,
-    // equal. The behavior of a sorted set is well-defined even if its ordering is inconsistent with equals; 
-    // it just fails to obey the general contract of the Set interface."
-    // public List<GoId> getGoIds() {
-    //     return _go_ids;
-    // }
-    private String getId() {
-        return _id;
-    }
-
-    // public int getNumberOfGoIds() {
-    //     if ( getGoIds() == null ) {
-    //         return 0;
-    //     }
-    //     return getGoIds().size();
-    // }
-    @Override
-    public int hashCode() {
-        return getId().hashCode();
-    }
-
-    // private void setGoIds( final List<GoId> go_ids ) {
-    //     _go_ids = go_ids;
-    // }
-    @Override
-    public String toString() {
-        return getId();
-    }
-}