merge of SIFTs Branch

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

diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java
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+++ b/src/jalview/api/SiftsClientI.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.HashSet;
+
+public interface SiftsClientI
+{
+  /**
+   * Get the DB Accession Id for the SIFTs Entry
+   * 
+   * @return
+   */
+  public String getDbAccessionId();
+
+  /**
+   * Get DB Coordinate system for the SIFTs Entry
+   * 
+   * @return
+   */
+  public String getDbCoordSys();
+
+  /**
+   * Get DB Evidence for the SIFTs Entry
+   * 
+   * @return
+   */
+  public String getDbEvidence();
+
+  /**
+   * Get DB Source for the SIFTs Entry
+   * 
+   * @return
+   */
+  public String getDbSource();
+
+  /**
+   * Get DB version for the SIFTs Entry
+   * 
+   * @return
+   */
+  public String getDbVersion();
+
+  /**
+   * Get Number of Entities available in the SIFTs Entry
+   * 
+   * @return
+   */
+  public int getEntityCount();
+
+  /**
+   * Get a unique Entity by its Id
+   * 
+   * @param id
+   *          ID of the entity to fetch
+   * @return Entity
+   * @throws Exception
+   */
+  public Entity getEntityById(String id) throws SiftsException;
+
+  /**
+   * Get all accession Ids available in the current SIFTs entry
+   * 
+   * @return a unique set of discovered accession strings
+   */
+  public HashSet<String> getAllMappingAccession();
+
+  /**
+   * Check if the accessionId is available in current SIFTs Entry
+   * 
+   * @param accessionId
+   * @return
+   */
+  public boolean isFoundInSiftsEntry(String accessionId);
+
+  /**
+   * Get the standard DB referenced by the SIFTs Entry
+   * 
+   * @return
+   */
+  public String[] getEntryDBs();
+
+  /**
+   * 
+   * @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
+   * 
+   * @param entityId
+   *          Id of the target entity in the SIFTs entry
+   * @param seq
+   *          SequenceI
+   * @return generated mapping
+   * @throws Exception
+   */
+  public int[][] getGreedyMapping(String entityId, SequenceI seq,
+          java.io.PrintStream os) throws SiftsException;
+}
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