JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template...

[jalview.git] / src / jalview / api / SiftsClientI.java

diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java
index c795f3f..3497c3f 100644 (file)
--- a/src/jalview/api/SiftsClientI.java
+++ b/src/jalview/api/SiftsClientI.java
@@ -21,8 +21,7 @@
 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;
 
@@ -93,29 +92,7 @@ public interface SiftsClientI
    */
   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
@@ -128,5 +105,6 @@ public interface SiftsClientI
    * @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;
 }
\ No newline at end of file