// 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.protein;
* If in_nc_order is set to true, this should return 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 should return 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> domains, final boolean in_nc_order );
+ public boolean contains( final List<String> domains, final boolean in_nc_order );
public String getAccession();
public Domain getProteinDomain( final int index );
- public int getProteinDomainCount( final DomainId domain_id );
+ public int getProteinDomainCount( final String domain_id );
public List<Domain> getProteinDomains();
- public List<Domain> getProteinDomains( final DomainId domain_id );
+ public List<Domain> getProteinDomains( final String domain_id );
public ProteinId getProteinId();
public int getLength();
public Species getSpecies();
+
+ public List<Domain> getDomainsSortedByPosition();
+
+ public String toDomainArchitectureString( final String separator, final double ie_cutoff );
+
}
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