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more test for isDuplication() and isSpecation() added (phyloXML encoded
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
protein
/
Protein.java
diff --git
a/forester/java/src/org/forester/protein/Protein.java
b/forester/java/src/org/forester/protein/Protein.java
index
a4512df
..
eccc7d7
100644
(file)
--- a/
forester/java/src/org/forester/protein/Protein.java
+++ b/
forester/java/src/org/forester/protein/Protein.java
@@
-22,7
+22,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
package org.forester.protein;
@@
-38,15
+38,15
@@
public interface 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
* 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).
* 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
*/
* @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 String getAccession();
@@
-58,15
+58,17
@@
public interface Protein {
public Domain getProteinDomain( final int index );
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();
- 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 ProteinId getProteinId();
public int getLength();
public Species getSpecies();
+
+ public List<Domain> getDomainsSortedByPosition();
}
\ No newline at end of file
}
\ No newline at end of file