package org.forester.protein;
-import org.forester.go.GoId;
+import java.util.HashMap;
+import java.util.Map;
+
import org.forester.util.ForesterUtil;
public class BasicDomain implements Domain {
- final private DomainId _id;
- final private int _from;
- final private int _to;
- final private short _number;
- final private short _total_count;
- final private double _per_sequence_evalue;
- final private double _per_sequence_score;
- final private double _per_domain_evalue;
- final private double _per_domain_score;
-
- public BasicDomain( final String id_str ) {
- if ( ForesterUtil.isEmpty( id_str ) ) {
+ private static short COUNT = 0;
+ private final static Map<Short, String> ID_TO_STRING = new HashMap<Short, String>();
+ private final static Map<String, Short> STRING_TO_ID = new HashMap<String, Short>();
+ final private int _from;
+ final private short _id;
+ final private short _number;
+ final private double _per_domain_evalue;
+ final private double _per_domain_score;
+ final private int _to;
+ final private short _total_count;
+ final private short _hmm_len;
+ final private short _hmm_from;
+ final private short _hmm_to;
+
+ public BasicDomain( final String id ) {
+ if ( ForesterUtil.isEmpty( id ) ) {
throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
}
- _id = new DomainId( id_str );
+ _id = obtainIdAsShort( id );
_from = -1;
_to = -1;
_number = -1;
_total_count = -1;
- _per_sequence_evalue = -1;
- _per_sequence_score = -1;
_per_domain_evalue = -1;
_per_domain_score = -1;
+ _hmm_len = -1;
+ _hmm_from= -1;
+ _hmm_to= -1;
+
}
- public BasicDomain( final String id_str,
+ public BasicDomain( final String id,
final int from,
final int to,
final short number,
final short total_count,
- final double per_sequence_evalue,
- final double per_sequence_score ) {
- this( id_str, from, to, number, total_count, per_sequence_evalue, per_sequence_score, 0, 0 );
+ final double per_domain_evalue,
+ final double per_domain_score ) {
+ if ( ( from >= to ) || ( from < 0 ) ) {
+ throw new IllegalArgumentException( "attempt to create protein domain from " + from + " to " + to );
+ }
+ if ( ForesterUtil.isEmpty( id ) ) {
+ throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
+ }
+ if ( ( number > total_count ) || ( number < 0 ) ) {
+ throw new IllegalArgumentException( "attempt to create protein domain number " + number + " out of "
+ + total_count );
+ }
+ if ( per_domain_evalue < 0.0 ) {
+ throw new IllegalArgumentException( "attempt to create protein domain with negative E-value" );
+ }
+ _id = obtainIdAsShort( id );
+ _from = from;
+ _to = to;
+ _number = number;
+ _total_count = total_count;
+ _per_domain_evalue = per_domain_evalue;
+ _per_domain_score = per_domain_score;
+ _hmm_len = -1;
+ _hmm_from= -1;
+ _hmm_to= -1;
}
-
- public BasicDomain( final String id_str,
+
+ public BasicDomain( final String id,
final int from,
final int to,
final short number,
final short total_count,
- final double per_sequence_evalue,
- final double per_sequence_score,
final double per_domain_evalue,
- final double per_domain_score ) {
+ final double per_domain_score,
+ final short hmm_len,
+ final short hmm_from,
+ final short hmm_to) {
if ( ( from >= to ) || ( from < 0 ) ) {
throw new IllegalArgumentException( "attempt to create protein domain from " + from + " to " + to );
}
- if ( ForesterUtil.isEmpty( id_str ) ) {
+ if ( ForesterUtil.isEmpty( id ) ) {
throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
}
if ( ( number > total_count ) || ( number < 0 ) ) {
throw new IllegalArgumentException( "attempt to create protein domain number " + number + " out of "
+ total_count );
}
- if ( ( per_sequence_evalue < 0.0 ) || ( per_domain_evalue < 0.0 ) ) {
+ if ( per_domain_evalue < 0.0 ) {
throw new IllegalArgumentException( "attempt to create protein domain with negative E-value" );
}
- _id = new DomainId( id_str );
+ if ( ( hmm_from >= hmm_to ) || ( hmm_from < 0 ) ) {
+ throw new IllegalArgumentException( "attempt to create protein domain matching hmm from " + from + " to " + to );
+ }
+ if ( hmm_len <= 0 ) {
+ throw new IllegalArgumentException( "attempt to create protein domain with zero or negative hmm length" );
+ }
+ _id = obtainIdAsShort( id );
_from = from;
_to = to;
_number = number;
_total_count = total_count;
- _per_sequence_evalue = per_sequence_evalue;
- _per_sequence_score = per_sequence_score;
_per_domain_evalue = per_domain_evalue;
_per_domain_score = per_domain_score;
- }
-
- @Override
- public void addGoId( final GoId go_id ) {
- getDomainId().getGoIds().add( go_id );
+ _hmm_len = hmm_len;
+ _hmm_from= hmm_from;
+ _hmm_to= hmm_to;
}
/**
* Basic domains are compared/sorted based upon their identifiers (case
* insensitive) and their numbers.
- *
+ *
*/
@Override
public int compareTo( final Domain domain ) {
/**
* Basic domains are considered equal if they have the same identifier (case
* sensitive).
- *
+ *
*/
@Override
public boolean equals( final Object o ) {
}
@Override
- public DomainId getDomainId() {
- return _id;
+ public String getDomainId() {
+ return obtainIdFromShort( _id );
}
@Override
}
@Override
- public GoId getGoId( final int i ) {
- return getDomainId().getGoIds().get( i );
+ public int getLength() {
+ return ( 1 + getTo() ) - getFrom();
}
@Override
}
@Override
- public int getNumberOfGoIds() {
- return getDomainId().getGoIds().size();
- }
-
- @Override
public double getPerDomainEvalue() {
return _per_domain_evalue;
}
}
@Override
- public double getPerSequenceEvalue() {
- return _per_sequence_evalue;
+ public int getTo() {
+ return _to;
}
@Override
- public double getPerSequenceScore() {
- return _per_sequence_score;
+ public short getTotalCount() {
+ return _total_count;
}
@Override
- public int getTo() {
- return _to;
+ public final short getHmmLen() {
+ return _hmm_len;
}
@Override
- public short getTotalCount() {
- return _total_count;
+ public final short getHmmFrom() {
+ return _hmm_from;
}
@Override
+ public final short getHmmTo() {
+ return _hmm_to;
+ }
+
+ @Override
public int hashCode() {
- return getDomainId().getId().hashCode();
+ return getDomainId().hashCode();
}
@Override
public String toString() {
- return toStringBuffer().toString();
+ return getDomainId();
}
public StringBuffer toStringBuffer() {
- return new StringBuffer( getDomainId().getId() );
+ return new StringBuffer( getDomainId() );
}
- @Override
- public int getLength() {
- return ( 1 + getTo() ) - getFrom();
+ public final static short obtainIdAsShort( final String id ) {
+ if ( !STRING_TO_ID.containsKey( id ) ) {
+ if ( COUNT >= ( Short.MAX_VALUE - 2 ) ) {
+ throw new RuntimeException( "too many domain ids!" );
+ }
+ ID_TO_STRING.put( COUNT, id );
+ STRING_TO_ID.put( id, COUNT );
+ ++COUNT;
+ }
+ return STRING_TO_ID.get( id );
}
+
+ public final static String obtainIdFromShort( final short id ) {
+ return ID_TO_STRING.get( id );
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff