package jalview.api;
import jalview.datamodel.SequenceI;
-import jalview.structure.StructureMapping;
-import jalview.ws.sifts.MappingOutputPojo;
+import jalview.structure.StructureMappingClient.StructureMappingException;
import jalview.ws.sifts.SiftsException;
import jalview.xml.binding.sifts.Entry.Entity;
*/
public boolean isAccessionMatched(String accessionId);
- /**
- *
- * @param mop
- * MappingOutputPojo
- * @return Sequence<->Structure mapping as int[][]
- * @throws SiftsException
- */
- public StringBuffer getMappingOutput(MappingOutputPojo mop)
- throws SiftsException;
- /**
- *
- * @param seq
- * sequence to generate mapping against the structure
- * @param pdbFile
- * PDB file for the mapping
- * @param chain
- * the chain of the entry to use for mapping
- * @return StructureMapping
- * @throws SiftsException
- */
- public StructureMapping getSiftsStructureMapping(SequenceI seq,
- String pdbFile, String chain) throws SiftsException;
/**
* Get residue by residue mapping for a given Sequence and SIFTs entity
* @throws Exception
*/
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
- SequenceI seq, java.io.PrintStream os) throws SiftsException;
+ SequenceI seq, java.io.PrintStream os) throws SiftsException,
+ StructureMappingException;
}
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