JAL-1919 basic support for importing and viewing mmCIF files - mapping support not...

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 7d5ae2e..81a7e5d 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -281,6 +281,10 @@ public class SiftsClient implements SiftsClientI
    */
   public static File downloadSiftsFile(String pdbId) throws SiftsException
   {
+    if (pdbId.contains(".cif"))
+    {
+      pdbId = pdbId.replace(".cif", "");
+    }
     String siftFile = pdbId + ".xml.gz";
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
     String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory()
@@ -622,6 +626,58 @@ public class SiftsClient implements SiftsClientI
   }
 
   /**
+   * 
+   * @param chainId
+   *          Target chain to populate mapping of its atom positions.
+   * @param mapping
+   *          Two dimension array of residue index versus atom position
+   * @throws IllegalArgumentException
+   *           Thrown if chainId or mapping is null
+   */
+  void populateAtomPositions(String chainId,
+          HashMap<Integer, int[]> mapping) throws IllegalArgumentException
+  {
+    PDBChain chain = pdb.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);
+      }
+    }
+  }
+
+  /**
+   * 
+   * @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
+   */
+  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;
+  }
+
+  /**
    * Checks if the residue instance is marked 'Not_observed' or not
    * 
    * @param residue
@@ -705,57 +761,7 @@ public class SiftsClient implements SiftsClientI
     }
   }
 
-  /**
-   * 
-   * @param chainId
-   *          Target chain to populate mapping of its atom positions.
-   * @param mapping
-   *          Two dimension array of residue index versus atom position
-   * @throws IllegalArgumentException
-   *           Thrown if chainId or mapping is null
-   */
-  void populateAtomPositions(String chainId, HashMap<Integer, int[]> mapping)
-          throws IllegalArgumentException
-  {
-    PDBChain chain = pdb.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);
-      }
-    }
-  }
 
-  /**
-   * 
-   * @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
-   */
-  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;
-  }
 
   @Override
   public Entity getEntityById(String id) throws SiftsException