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JAL-3368 'web' colour parsing reinstated (for now)
[jalview.git]
/
src
/
jalview
/
api
/
SiftsClientI.java
diff --git
a/src/jalview/api/SiftsClientI.java
b/src/jalview/api/SiftsClientI.java
index
35cb57f
..
367a0de
100644
(file)
--- a/
src/jalview/api/SiftsClientI.java
+++ b/
src/jalview/api/SiftsClientI.java
@@
-26,8
+26,11
@@
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;
import java.util.HashSet;
+// JBPComment: this isn't a top-level Jalview API - should be in its own package api
+
public interface SiftsClientI
{
/**
public interface SiftsClientI
{
/**
@@
-45,13
+48,6
@@
public interface SiftsClientI
public String getDbCoordSys();
/**
public String getDbCoordSys();
/**
- * Get DB Evidence for the SIFTs Entry
- *
- * @return
- */
- public String getDbEvidence();
-
- /**
* Get DB Source for the SIFTs Entry
*
* @return
* Get DB Source for the SIFTs Entry
*
* @return
@@
-95,14
+91,7
@@
public interface SiftsClientI
* @param accessionId
* @return
*/
* @param accessionId
* @return
*/
- public boolean isFoundInSiftsEntry(String accessionId);
-
- /**
- * Get the standard DB referenced by the SIFTs Entry
- *
- * @return
- */
- public String[] getEntryDBs();
+ public boolean isAccessionMatched(String accessionId);
/**
*
/**
*
@@
-111,7
+100,7
@@
public interface SiftsClientI
* @return Sequence<->Structure mapping as int[][]
* @throws SiftsException
*/
* @return Sequence<->Structure mapping as int[][]
* @throws SiftsException
*/
- public StringBuffer getMappingOutput(MappingOutputPojo mop)
+ public StringBuilder getMappingOutput(MappingOutputPojo mop)
throws SiftsException;
/**
throws SiftsException;
/**
@@
-127,7
+116,7
@@
public interface SiftsClientI
*/
public StructureMapping getSiftsStructureMapping(SequenceI seq,
String pdbFile, String chain) 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
*
/**
* Get residue by residue mapping for a given Sequence and SIFTs entity
*
@@
-138,6
+127,6
@@
public interface SiftsClientI
* @return generated mapping
* @throws Exception
*/
* @return generated mapping
* @throws Exception
*/
- public int[][] getGreedyMapping(String entityId, SequenceI seq,
- java.io.PrintStream os) throws SiftsException;
+ public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+ SequenceI seq, java.io.PrintStream os) throws SiftsException;
}
\ No newline at end of file
}
\ No newline at end of file