final Domain d2 ) {
final int m1 = ( d1.getTo() + d1.getFrom() );
final int m2 = ( d2.getTo() + d2.getFrom() );
- return m1 < m2 ? -1 : m1 > m2 ? 1 : d1
- .getDomainId().getId()
- .compareTo( d2.getDomainId().getId() );
+ return m1 < m2 ? -1
+ : m1 > m2 ? 1
+ : d1.getDomainId()
+ .compareTo( d2
+ .getDomainId() );
}
};
* If in_nc_order is set to true, this returns true only and only if
* the order in List 'domains' and this protein (as determined by the start positions
* of the domains of this proteins, _not_ by their index) are the same
- * (interspersing, 'other', domains in this are ignored).
+ * (interspersing, 'other', domains in this are ignored).
* If in_nc_order is set to false, this returns true only and only if
* this contains all domains listed in 'domains' (order and count do not matter).
- *
+ *
* @param domains a list of domain ids in a certain order.
* @param in_nc_order to consider order
* @return
*/
- public boolean contains( final List<DomainId> query_domain_ids, final boolean in_nc_order ) {
+ public boolean contains( final List<String> query_domain_ids, final boolean in_nc_order ) {
if ( !in_nc_order ) {
- for( final DomainId query_domain_id : query_domain_ids ) {
+ for( final String query_domain_id : query_domain_ids ) {
if ( !getProteinDomainIds().contains( query_domain_id ) ) {
return false;
}
}
else {
int current_start_position = -1;
- I: for( final DomainId query_domain_id : query_domain_ids ) {
+ I: for( final String query_domain_id : query_domain_ids ) {
if ( getProteinDomainIds().contains( query_domain_id ) ) {
final List<Domain> found_domains = getProteinDomains( query_domain_id );
final SortedSet<Integer> ordered_start_positions = new TreeSet<Integer>();
}
@Override
- public int getProteinDomainCount( final DomainId domain_id ) {
+ public int getProteinDomainCount( final String domain_id ) {
return getProteinDomains( domain_id ).size();
}
}
@Override
- public List<Domain> getProteinDomains( final DomainId domain_id ) {
+ public List<Domain> getProteinDomains( final String domain_id ) {
final List<Domain> domains = new ArrayList<Domain>();
for( final Domain domain : getProteinDomains() ) {
if ( domain.getDomainId().equals( domain_id ) ) {
_name = name;
}
- public String toDomainArchitectureString( final String separator ) {
+ @Override
+ public final String toDomainArchitectureString( final String separator, final double ie_cutoff ) {
final StringBuilder sb = new StringBuilder();
boolean first = true;
for( final Domain d : getDomainsSortedByPosition() ) {
- if ( first ) {
- first = false;
- }
- else {
- sb.append( separator );
+ if ( ( ie_cutoff <= -1 ) || ( d.getPerDomainEvalue() <= ie_cutoff ) ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( separator );
+ }
+ sb.append( d.getDomainId() );
}
- sb.append( d.getDomainId().getId() );
}
return sb.toString();
}
+ public final String toDomainArchitectureString( final String separator ) {
+ return toDomainArchitectureString( separator, -1 );
+ }
+
public String toDomainArchitectureString( final String separator,
final int repeats_limit,
final String repeat_separator ) {
String prev_id = "";
int counter = 1;
for( final Domain d : getDomainsSortedByPosition() ) {
- final String id = d.getDomainId().getId();
+ final String id = d.getDomainId();
if ( prev_id.equals( id ) ) {
counter++;
}
@Override
public String toString() {
- return toDomainArchitectureString( "~" );
+ return toDomainArchitectureString( "--", 1 );
}
- private List<DomainId> getProteinDomainIds() {
- final List<DomainId> ids = new ArrayList<DomainId>( getProteinDomains().size() );
+ private List<String> getProteinDomainIds() {
+ final List<String> ids = new ArrayList<String>( getProteinDomains().size() );
for( final Domain domain : getProteinDomains() ) {
ids.add( domain.getDomainId() );
}