// 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;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.forester.protein.BasicDomain;
import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
import org.forester.util.ForesterUtil;
public class BasicBinaryDomainCombination implements BinaryDomainCombination {
- String _id_0;
- String _id_1;
+ final static boolean VERBOSE = false;
+ final private static Map<Integer, BasicBinaryDomainCombination> DC_POOL = new HashMap<Integer, BasicBinaryDomainCombination>();
+ final private static Map<Integer, String> S_POOL = new HashMap<Integer, String>();
+ short _id0;
+ short _id1;
- //DomainId _id_0;
- //DomainId _id_1;
BasicBinaryDomainCombination() {
- _id_0 = null;
- _id_1 = null;
+ _id0 = -1;
+ _id1 = -1;
}
- public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
- if ( ( id_0 == null ) || ( id_1 == null ) ) {
+ private BasicBinaryDomainCombination( final String id0, final String id1 ) {
+ if ( ( id0 == null ) || ( id1 == null ) ) {
throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
}
- final String my_id_0 = id_0.trim();
- final String my_id_1 = id_1.trim();
- if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) {
- _id_0 = my_id_0;
- _id_1 = my_id_1;
+ if ( ( id0.indexOf( SEPARATOR ) != -1 ) || ( id1.indexOf( SEPARATOR ) != -1 ) ) {
+ throw new IllegalArgumentException( "ill formatted domain id: " + id0 + ", " + id1 );
+ }
+ if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
+ _id0 = BasicDomain.obtainIdAsShort( id0 );
+ _id1 = BasicDomain.obtainIdAsShort( id1 );
}
else {
- _id_0 = my_id_1;
- _id_1 = my_id_0;
+ _id0 = BasicDomain.obtainIdAsShort( id1 );
+ _id1 = BasicDomain.obtainIdAsShort( id0 );
}
}
- public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
- this( id_0.getId(), id_1.getId() );
- }
-
@Override
- public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
+ final public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
if ( binary_domain_combination.getClass() != this.getClass() ) {
throw new IllegalArgumentException( "attempt to compare [" + binary_domain_combination.getClass() + "] to "
+ "[" + this.getClass() + "]" );
}
@Override
- public boolean equals( final Object o ) {
+ final public boolean equals( final Object o ) {
if ( this == o ) {
return true;
}
+ o.getClass() + "]" );
}
else {
- return ( getId0().equals( ( ( BinaryDomainCombination ) o ).getId0() ) )
- && ( getId1().equals( ( ( BinaryDomainCombination ) o ).getId1() ) );
+ return ( getId0Code() == ( ( BinaryDomainCombination ) o ).getId0Code() )
+ && ( getId1Code() == ( ( BinaryDomainCombination ) o ).getId1Code() );
}
}
@Override
- public DomainId getId0() {
- return new DomainId( _id_0 );
+ final public String getId0() {
+ return BasicDomain.obtainIdFromShort( _id0 );
+ }
+
+ @Override
+ final public short getId0Code() {
+ return _id0;
+ }
+
+ @Override
+ final public String getId1() {
+ return BasicDomain.obtainIdFromShort( _id1 );
}
@Override
- public DomainId getId1() {
- return new DomainId( _id_1 );
+ final public short getId1Code() {
+ return _id1;
}
@Override
- public int hashCode() {
- // return getId0().hashCode() + ( 19 * getId1().hashCode() );
- return ( _id_0 + _id_1 ).hashCode();
+ final public int hashCode() {
+ return calcCode( _id0, _id1 );
}
@Override
- public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
- final String node_attribute,
- final String edge_attribute ) {
+ final public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
+ final String node_attribute,
+ final String edge_attribute ) {
final StringBuffer sb = new StringBuffer();
switch ( format ) {
case DOT:
}
@Override
- public String toString() {
- final StringBuffer sb = new StringBuffer();
- sb.append( _id_0 );
- sb.append( BinaryDomainCombination.SEPARATOR );
- sb.append( _id_1 );
- return sb.toString();
+ final public String toString() {
+ final int code = calcCode( _id0, _id1 );
+ if ( S_POOL.containsKey( code ) ) {
+ return S_POOL.get( code );
+ }
+ else {
+ final String s = getId0() + SEPARATOR + getId1();
+ S_POOL.put( code, s );
+ return s;
+ }
}
- public static BinaryDomainCombination createInstance( final String ids ) {
+ public static BinaryDomainCombination obtainInstance( final String ids ) {
if ( ids.indexOf( BinaryDomainCombination.SEPARATOR ) < 1 ) {
throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
}
if ( ids_ary.length != 2 ) {
throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
}
- return new BasicBinaryDomainCombination( ids_ary[ 0 ], ids_ary[ 1 ] );
+ return BasicBinaryDomainCombination.obtainInstance( ids_ary[ 0 ], ids_ary[ 1 ] );
+ }
+
+ public static BasicBinaryDomainCombination obtainInstance( final String id0, final String id1 ) {
+ int code;
+ if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
+ code = calcCode( BasicDomain.obtainIdAsShort( id0 ), BasicDomain.obtainIdAsShort( id1 ) );
+ }
+ else {
+ code = calcCode( BasicDomain.obtainIdAsShort( id1 ), BasicDomain.obtainIdAsShort( id0 ) );
+ }
+ if ( DC_POOL.containsKey( code ) ) {
+ return DC_POOL.get( code );
+ }
+ else {
+ final BasicBinaryDomainCombination dc = new BasicBinaryDomainCombination( id0, id1 );
+ DC_POOL.put( code, dc );
+ if ( VERBOSE && ( ( DC_POOL.size() % 100 ) == 0 ) ) {
+ System.out.println( " dc pool size: " + DC_POOL.size() );
+ }
+ return dc;
+ }
+ }
+
+ final static int calcCode( final int id0, final int id1 ) {
+ return ( id0 * ( Short.MAX_VALUE + 1 ) ) + id1;
}
}
git://source.jalview.org / jalview.git / blobdiff