X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=53a2b8c9c20a3ff8fa1c1f75223c2b7a3693f59e;hb=c51dbe7933683b64548f5353e67561d2b5e377f7;hp=847377d5f0c9f78d0e886856ddfe5320e8d74a32;hpb=76c239505d13a123cc83621623aaca16e47ddb12;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 847377d..53a2b8c 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -31,6 +31,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.structures.models.MappingOutputModel;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
@@ -82,9 +83,13 @@ public class SiftsClient implements SiftsClientI
    */
   private static File mockSiftsFile;
 
+  private static final int UNASSIGNED = StructureMapping.UNASSIGNED; // -1
+
+  private static final int PDB_RES_POS = StructureMapping.PDB_RES_NUM_INDEX; // 0
+
   private Entry siftsEntry;
 
-  private StructureFile pdb;
+  private StructureFile structureFile;
 
   private String pdbId;
 
@@ -94,10 +99,6 @@ public class SiftsClient implements SiftsClientI
 
   private static final int BUFFER_SIZE = 4096;
 
-  public static final int UNASSIGNED = -1;
-
-  private static final int PDB_RES_POS = 0;
-
   private static final int PDB_ATOM_POS = 1;
 
   private static final String NOT_OBSERVED = "Not_Observed";
@@ -150,10 +151,10 @@ public class SiftsClient implements SiftsClientI
    * @param pdbId
    * @throws SiftsException
    */
-  public SiftsClient(StructureFile pdb) throws SiftsException
+  public SiftsClient(StructureFile structureFile) throws SiftsException
   {
-    this.pdb = pdb;
-    this.pdbId = pdb.getId();
+    this.structureFile = structureFile;
+    this.pdbId = structureFile.getId();
     File siftsFile = getSiftsFile(pdbId);
     siftsEntry = parseSIFTs(siftsFile);
   }
@@ -532,7 +533,7 @@ public class SiftsClient implements SiftsClientI
 
     if (os != null)
     {
-      MappingOutputPojo mop = new MappingOutputPojo();
+      MappingOutputModel mop = new MappingOutputModel();
       mop.setSeqStart(seqStart);
       mop.setSeqEnd(seqEnd);
       mop.setSeqName(seq.getName());
@@ -577,18 +578,8 @@ public class SiftsClient implements SiftsClientI
                   .equalsIgnoreCase(seqCoordSys.getName())
                   && isAccessionMatched(cRefDb.getDbAccessionId()))
           {
-            String resNumIndexString = cRefDb.getDbResNum()
-                    .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
-                    : cRefDb.getDbResNum();
-            try
-            {
-              currSeqIndex = Integer.valueOf(resNumIndexString);
-            } catch (NumberFormatException nfe)
-            {
-              currSeqIndex = Integer.valueOf(resNumIndexString
-                      .split("[a-zA-Z]")[0]);
-              continue;
-            }
+            currSeqIndex = getLeadingIntegerValue(
+                    cRefDb.getDbResNum(), UNASSIGNED);
             if (pdbRefDb != null)
             {
               break;// exit loop if pdb and uniprot are already found
@@ -601,19 +592,11 @@ public class SiftsClient implements SiftsClientI
         }
         if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
         {
-          int resNum;
-          try
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
-                    .getDbResNum());
-          } catch (NumberFormatException nfe)
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
-                    .getDbResNum().split("[a-zA-Z]")[0]);
-            continue;
-          }
+
+          int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
+                  residue.getDbResNum(), UNASSIGNED)
+                  : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+                          UNASSIGNED);
 
           if (isResidueObserved(residue)
                   || seqCoordSys == CoordinateSys.UNIPROT)
@@ -636,6 +619,30 @@ public class SiftsClient implements SiftsClientI
   }
 
   /**
+   * Get the leading integer part of a string that begins with an integer.
+   * 
+   * @param input
+   *          - the string input to process
+   * @param failValue
+   *          - value returned if unsuccessful
+   * @return
+   */
+  static int getLeadingIntegerValue(String input, int failValue)
+  {
+    if (input == null)
+    {
+      return failValue;
+    }
+    String[] parts = input.split("(?=\\D)(?<=\\d)");
+    if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+    {
+      return Integer.valueOf(parts[0]);
+    }
+    return failValue;
+  }
+
+
+  /**
    * 
    * @param chainId
    *          Target chain to populate mapping of its atom positions.
@@ -650,7 +657,7 @@ public class SiftsClient implements SiftsClientI
   {
     try
     {
-      PDBChain chain = pdb.findChain(chainId);
+      PDBChain chain = structureFile.findChain(chainId);
 
       if (chain == null || mapping == null)
       {
@@ -959,7 +966,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuilder getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputModel mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -1121,4 +1128,5 @@ public class SiftsClient implements SiftsClientI
     mockSiftsFile = file;
   }
 
+
 }