JAL-2136 New Phyre2 branch + attempt to resynced with develop

[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 6d961c0..53a2b8c 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -21,7 +21,7 @@
 package jalview.ws.sifts;
 
 import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.DBRefEntryI;
 import jalview.api.SiftsClientI;
@@ -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;
@@ -76,9 +77,19 @@ import MCview.PDBChain;
 
 public class SiftsClient implements SiftsClientI
 {
+  /*
+   * for use in mocking out file fetch for tests only
+   * - reset to null after testing!
+   */
+  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;
 
@@ -88,10 +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";
@@ -144,10 +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);
   }
@@ -189,6 +196,14 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
+    /*
+     * return mocked file if it has been set
+     */
+    if (mockSiftsFile != null)
+    {
+      return mockSiftsFile;
+    }
+
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
             + pdbId.toLowerCase() + ".xml.gz";
     File siftsFile = new File(siftsFileName);
@@ -518,7 +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());
@@ -563,18 +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
@@ -587,19 +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)
@@ -622,6 +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.
@@ -636,7 +657,7 @@ public class SiftsClient implements SiftsClientI
   {
     try
     {
-      PDBChain chain = pdb.findChain(chainId);
+      PDBChain chain = structureFile.findChain(chainId);
 
       if (chain == null || mapping == null)
       {
@@ -945,7 +966,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuilder getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputModel mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -988,8 +1009,7 @@ public class SiftsClient implements SiftsClientI
     output.append(String.valueOf(pdbEnd));
     output.append(NEWLINE).append(NEWLINE);
 
-    PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
-            .getInstance().forName(ScoreModels.PAM250);
+    ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
     int matchedSeqCount = 0;
     for (int j = 0; j < nochunks; j++)
     {
@@ -1103,4 +1123,10 @@ public class SiftsClient implements SiftsClientI
     return siftsEntry.getDbVersion();
   }
 
+  public static void setMockSiftsFile(File file)
+  {
+    mockSiftsFile = file;
+  }
+
+
 }