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JAL-2079 use new service to retrieve Rfam Seed alignment
[jalview.git]
/
src
/
jalview
/
api
/
SiftsClientI.java
diff --git
a/src/jalview/api/SiftsClientI.java
b/src/jalview/api/SiftsClientI.java
index
8a246e1
..
e2fac14
100644
(file)
--- a/
src/jalview/api/SiftsClientI.java
+++ b/
src/jalview/api/SiftsClientI.java
@@
-26,6
+26,7
@@
import jalview.ws.sifts.MappingOutputPojo;
import jalview.ws.sifts.SiftsException;
import jalview.xml.binding.sifts.Entry.Entity;
import jalview.ws.sifts.SiftsException;
import jalview.xml.binding.sifts.Entry.Entity;
+import java.util.HashMap;
import java.util.HashSet;
public interface SiftsClientI
import java.util.HashSet;
public interface SiftsClientI
@@
-95,7
+96,7
@@
public interface SiftsClientI
* @param accessionId
* @return
*/
* @param accessionId
* @return
*/
- public boolean isFoundInSiftsEntry(String accessionId);
+ public boolean isAccessionMatched(String accessionId);
/**
* Get the standard DB referenced by the SIFTs Entry
/**
* Get the standard DB referenced by the SIFTs Entry
@@
-109,8
+110,10
@@
public interface SiftsClientI
* @param mop
* MappingOutputPojo
* @return Sequence<->Structure mapping as int[][]
* @param mop
* MappingOutputPojo
* @return Sequence<->Structure mapping as int[][]
+ * @throws SiftsException
*/
*/
- public StringBuffer getMappingOutput(MappingOutputPojo mop);
+ public StringBuffer getMappingOutput(MappingOutputPojo mop)
+ throws SiftsException;
/**
*
/**
*
@@
-136,6
+139,7
@@
public interface SiftsClientI
* @return generated mapping
* @throws Exception
*/
* @return generated mapping
* @throws Exception
*/
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq,
java.io.PrintStream os) throws SiftsException;
}
\ No newline at end of file
java.io.PrintStream os) throws SiftsException;
}
\ No newline at end of file