JAL-3814 NONEWS property

[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 java.util.HashMap;
 import java.util.HashSet;
 
+// JBPComment: this isn't a top-level Jalview API - should be in its own package api
+
 public interface SiftsClientI
 {
   /**
@@ -45,13 +48,6 @@ public interface SiftsClientI
   public String getDbCoordSys();
 
   /**
-   * Get DB Evidence for the SIFTs Entry
-   * 
-   * @return
-   */
-  public String getDbEvidence();
-
-  /**
    * Get DB Source for the SIFTs Entry
    * 
    * @return
@@ -95,14 +91,7 @@ public interface SiftsClientI
    * @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
    */
-  public StringBuffer getMappingOutput(MappingOutputPojo mop)
+  public StringBuilder getMappingOutput(MappingOutputPojo mop)
           throws SiftsException;
 
   /**
@@ -127,7 +116,7 @@ public interface SiftsClientI
    */
   public StructureMapping getSiftsStructureMapping(SequenceI seq,
           String pdbFile, String chain) throws SiftsException;
-  
+
   /**
    * Get residue by residue mapping for a given Sequence and SIFTs entity
    * 
@@ -138,6 +127,6 @@ public interface SiftsClientI
    * @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