JAL-3855 update EBI Alphafold barcoded URL generation to v2.cif/json URLs

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index bbb1f8b..97eacab 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -72,6 +72,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
   private static final int PDB_ID_LENGTH = 4;
 
+  private static String AF_VERSION = "2";
+
   public EBIAlfaFold()
   {
     super();
@@ -96,7 +98,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public Regex getAccessionValidator()
   {
-    Regex validator =  new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
     validator.setIgnoreCase(true);
     return validator;
   }
@@ -123,15 +125,24 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return "1";
   }
 
-  public static String getAlphaFoldCifDownloadUrl(String id)
+  public static String getAlphaFoldCifDownloadUrl(String id, String vnum)
   {
-    return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
+    if (vnum == null || vnum.length() == 0)
+    {
+      vnum = AF_VERSION;
+    }
+    return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v" + vnum
+            + ".cif";
   }
 
-  public static String getAlphaFoldPaeDownloadUrl(String id)
+  public static String getAlphaFoldPaeDownloadUrl(String id, String vnum)
   {
+    if (vnum == null || vnum.length() == 0)
+    {
+      vnum = AF_VERSION;
+    }
     return "https://alphafold.ebi.ac.uk/files/" + id
-            + "-predicted_aligned_error_v1.json";
+            + "-predicted_aligned_error_v" + vnum + ".json";
   }
 
   /*
@@ -144,7 +155,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   {
     return getSequenceRecords(queries, null);
   }
-  public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+
+  public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+          throws Exception
   {
     AlignmentI pdbAlignment = null;
     String chain = null;
@@ -166,7 +179,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
-    String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+    String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION);
     if (retrievalUrl != null)
     {
       alphaFoldCif = retrievalUrl;
@@ -177,7 +190,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       File tmpFile = File.createTempFile(id, ".cif");
       Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
       UrlDownloadClient.download(alphaFoldCif, tmpFile);
-      
+
       // may not need this check ?
       file = tmpFile.getAbsolutePath();
       if (file == null)
@@ -185,8 +198,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
         return null;
       }
 
-      pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
-      
+      pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
+              id, chain, getDbSource(), getDbVersion());
 
       if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
@@ -198,9 +211,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       // import PAE as contact matrix - assume this will work if there was a
       // model
       File pae = File.createTempFile(id, "pae_json");
-      String paeURL = getAlphaFoldPaeDownloadUrl(id);
-      
-      if (retrievalUrl!=null) {
+      String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION);
+
+      if (retrievalUrl != null)
+      {
         // manufacture the PAE url from a url like ...-model-vN.cif
         paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
       }
@@ -245,7 +259,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   /**
-   * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+   * general purpose structure importer - designed to yield alignment useful for
+   * transfer of annotation to associated sequences
+   * 
    * @param alphaFoldCif
    * @param tmpFile
    * @param id
@@ -255,8 +271,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
    * @return
    * @throws Exception
    */
-  public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
-          File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+  public static AlignmentI importDownloadedStructureFromUrl(
+          String alphaFoldCif, File tmpFile, String id, String chain,
+          String dbSource, String dbVersion) throws Exception
   {
     String file = tmpFile.getAbsolutePath();
     // todo get rid of Type and use FileFormatI instead?
@@ -309,15 +326,17 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             // dbentry.setMap()
             pdbcs.addDBRef(dbentry);
             // update any feature groups
-            List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+            List<SequenceFeature> allsf = pdbcs.getFeatures()
+                    .getAllFeatures();
             List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
-            if (allsf!=null && allsf.size()>0)
+            if (allsf != null && allsf.size() > 0)
             {
-              for (SequenceFeature f:allsf)
+              for (SequenceFeature f : allsf)
               {
                 if (file.equals(f.getFeatureGroup()))
                 {
-                  f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+                  f = new SequenceFeature(f, f.type, f.begin, f.end, id,
+                          f.score);
                 }
                 newsf.add(f);
               }