merge develop

[jalview.git] / src / jalview / structure / StructureMappingClient.java

diff --git a/src/jalview/structure/StructureMappingClient.java b/src/jalview/structure/StructureMappingClient.java
new file mode 100644 (file)
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+++ b/src/jalview/structure/StructureMappingClient.java
@@ -0,0 +1,113 @@
+package jalview.structure;
+
+import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
+import jalview.structures.models.MappingOutputModel;
+
+import java.util.Collection;
+import java.util.Map;
+
+import MCview.Atom;
+import MCview.PDBChain;
+
+public abstract class StructureMappingClient
+{
+
+  protected StructureFile structureFile;
+
+  public static final int UNASSIGNED = -1;
+
+  private static final int PDB_RES_POS = 0;
+
+  private static final int PDB_ATOM_POS = 1;
+
+  public void populateAtomPositions(String chainId,
+          Map<Integer, int[]> mapping)
+ throws IllegalArgumentException,
+          StructureMappingException
+  {
+    try
+    {
+      PDBChain chain = structureFile.findChain(chainId);
+
+      if (chain == null || mapping == null)
+      {
+        throw new IllegalArgumentException(
+                "Chain id or mapping must not be null.");
+      }
+      for (int[] map : mapping.values())
+      {
+        if (map[PDB_RES_POS] != UNASSIGNED)
+        {
+          map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+        }
+      }
+    } catch (Exception e)
+    {
+      throw new StructureMappingException(
+              "Structure mapping exception occured.");
+    }
+  }
+
+  /**
+   * 
+   * @param residueIndex
+   *          The residue index used for the search
+   * @param atoms
+   *          A collection of Atom to search
+   * @return atom position for the given residue index
+   */
+  public int getAtomIndex(int residueIndex, Collection<Atom> atoms)
+  {
+    if (atoms == null)
+    {
+      throw new IllegalArgumentException(
+              "atoms collection must not be null!");
+    }
+    for (Atom atom : atoms)
+    {
+      if (atom.resNumber == residueIndex)
+      {
+        return atom.atomIndex;
+      }
+    }
+    return UNASSIGNED;
+  }
+
+  public class StructureMappingException extends Exception
+  {
+
+    private static final long serialVersionUID = 1L;
+
+    public StructureMappingException(String message)
+    {
+      super(message);
+    }
+  }
+
+  /**
+   * 
+   * @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 Exception
+   */
+  public abstract StructureMapping getStructureMapping(SequenceI seq,
+          String pdbFile, String chain) throws Exception,
+          StructureMappingException;
+
+  /**
+   * 
+   * @param mop
+   *          MappingOutputPojo
+   * @return Sequence<->Structure mapping as int[][]
+   * @throws StructureMappingException
+   */
+  public abstract StringBuffer getMappingOutput(MappingOutputModel mp)
+          throws StructureMappingException;
+
+}