JAL-3127 use AlignViewportI.addGroup() to add group and propagate to complement view...

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

diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java
index 13223af..367a0de 100644 (file)
--- a/src/jalview/api/SiftsClientI.java
+++ b/src/jalview/api/SiftsClientI.java
@@ -22,10 +22,15 @@ package jalview.api;
 
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureMapping;
+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
 {
   /**
@@ -43,13 +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
@@ -78,7 +76,7 @@ public interface SiftsClientI
    * @return Entity
    * @throws Exception
    */
-  public Entity getEntityById(String id) throws Exception;
+  public Entity getEntityById(String id) throws SiftsException;
 
   /**
    * Get all accession Ids available in the current SIFTs entry
@@ -93,37 +91,17 @@ public interface SiftsClientI
    * @param accessionId
    * @return
    */
-  public boolean isFoundInSiftsEntry(String accessionId);
+  public boolean isAccessionMatched(String accessionId);
 
   /**
-   * Get the standard DB referenced by the SIFTs Entry
    * 
-   * @return
+   * @param mop
+   *          MappingOutputPojo
+   * @return Sequence<->Structure mapping as int[][]
+   * @throws SiftsException
    */
-  public String[] getEntryDBs();
-
-  /**
-   * Get the SIFTs Entry details
-   */
-  public void getEntryDetails();
-
-  /**
-   * 
-   * @param seq1
-   *          Sequence to map
-   * @param seq2
-   *          Structure Sequence
-   * @param seqID1
-   *          sequence id
-   * @param seqID2
-   *          structure sequence id
-   * @param seqType
-   *          type of sequence for the mapping (pep or protein)
-   * @param nochunks
-   * @return sequence->structure mapping as int [][]
-   */
-  public StringBuffer getMappingOutput(String seq1, String seq2,
-          String seqID1, String seqID2, String seqType, int nochunks);
+  public StringBuilder getMappingOutput(MappingOutputPojo mop)
+          throws SiftsException;
 
   /**
    * 
@@ -134,10 +112,11 @@ public interface SiftsClientI
    * @param chain
    *          the chain of the entry to use for mapping
    * @return StructureMapping
+   * @throws SiftsException
    */
-  public StructureMapping getSiftsStructureMapping(SequenceI seq, String pdbFile,
-          String chain);
-  
+  public StructureMapping getSiftsStructureMapping(SequenceI seq,
+          String pdbFile, String chain) throws SiftsException;
+
   /**
    * Get residue by residue mapping for a given Sequence and SIFTs entity
    * 
@@ -148,6 +127,6 @@ public interface SiftsClientI
    * @return generated mapping
    * @throws Exception
    */
-  public int[][] getGreedyMapping(String entityId, SequenceI seq,
-          java.io.PrintStream os) throws Exception;
+  public HashMap<Integer, int[]> getGreedyMapping(String entityId,
+          SequenceI seq, java.io.PrintStream os) throws SiftsException;
 }
\ No newline at end of file