X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FBasicBinaryDomainCombination.java;h=b5844a188c80272217d9ff344319aa3656fb856d;hb=df8e9950662eaab9427f6873dcd0072f0d28f690;hp=9436ce9e1cafa96131253dcbfae8a1eded576c7f;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java index 9436ce9..b5844a1 100644 --- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java @@ -6,7 +6,7 @@ // 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 @@ -16,48 +16,55 @@ // 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; +import java.util.HashMap; +import java.util.Map; + +import org.forester.protein.BasicDomain; +import org.forester.protein.BinaryDomainCombination; import org.forester.util.ForesterUtil; public class BasicBinaryDomainCombination implements BinaryDomainCombination { - DomainId _id_0; - DomainId _id_1; + final static boolean VERBOSE = false; + final private static Map DC_POOL = new HashMap(); + final private static Map S_POOL = new HashMap(); + short _id0; + short _id1; BasicBinaryDomainCombination() { - _id_0 = null; - _id_1 = null; + _id0 = -1; + _id1 = -1; } - public BasicBinaryDomainCombination( final DomainId id_0, final DomainId 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" ); } - if ( id_0.compareTo( id_1 ) < 0 ) { - _id_0 = id_0; - _id_1 = 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 = id_1; - _id_1 = id_0; + _id0 = BasicDomain.obtainIdAsShort( id1 ); + _id1 = BasicDomain.obtainIdAsShort( id0 ); } } - public BasicBinaryDomainCombination( final String id_0, final String id_1 ) { - this( new DomainId( id_0 ), new DomainId( id_1 ) ); - } - @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() + "]" ); @@ -75,7 +82,7 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { } @Override - public boolean equals( final Object o ) { + final public boolean equals( final Object o ) { if ( this == o ) { return true; } @@ -87,27 +94,40 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { + o.getClass() + "]" ); } else { - return ( getId0().equals( ( ( BinaryDomainCombination ) o ).getId0() ) ) - && ( getId1().equals( ( ( BinaryDomainCombination ) o ).getId1() ) ); + return ( getId0Code() == ( ( BinaryDomainCombination ) o ).getId0Code() ) + && ( getId1Code() == ( ( BinaryDomainCombination ) o ).getId1Code() ); } } - public DomainId getId0() { - return _id_0; + @Override + final public String getId0() { + return BasicDomain.obtainIdFromShort( _id0 ); } - public DomainId getId1() { - return _id_1; + @Override + final public short getId0Code() { + return _id0; } @Override - public int hashCode() { - return getId0().hashCode() + ( 19 * getId1().hashCode() ); + final public String getId1() { + return BasicDomain.obtainIdFromShort( _id1 ); } - public StringBuffer toGraphDescribingLanguage( final OutputFormat format, - final String node_attribute, - final String edge_attribute ) { + @Override + final public short getId1Code() { + return _id1; + } + + @Override + final public int hashCode() { + return calcCode( _id0, _id1 ); + } + + @Override + final public StringBuffer toGraphDescribingLanguage( final OutputFormat format, + final String node_attribute, + final String edge_attribute ) { final StringBuffer sb = new StringBuffer(); switch ( format ) { case DOT: @@ -149,15 +169,19 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { } @Override - public String toString() { - final StringBuffer sb = new StringBuffer(); - sb.append( getId0() ); - sb.append( BinaryDomainCombination.SEPARATOR ); - sb.append( getId1() ); - 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 + "]" ); } @@ -165,6 +189,31 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { 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; } }