JAL-4034 change to jalview property name

[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 a93f233..e3687bd 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -28,7 +28,9 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
@@ -82,7 +84,7 @@ 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;
   }
@@ -122,6 +124,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
+    return getSequenceRecords(queries, null);
+  }
+
+  public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+          throws Exception
+  {
     AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
@@ -143,12 +151,16 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       return null;
     }
     String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+    if (retrievalUrl != null)
+    {
+      alphaFoldCif = retrievalUrl;
+    }
 
     try
     {
       File tmpFile = File.createTempFile(id, ".cif");
       UrlDownloadClient.download(alphaFoldCif, tmpFile);
-      
+
       // may not need this check ?
       file = tmpFile.getAbsolutePath();
       if (file == null)
@@ -156,8 +168,8 @@ 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)
       {
@@ -175,7 +187,9 @@ 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
@@ -185,8 +199,9 @@ 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?
@@ -238,6 +253,23 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                     dbVersion, (chid == null ? id : id + chid));
             // dbentry.setMap()
             pdbcs.addDBRef(dbentry);
+            // update any feature groups
+            List<SequenceFeature> allsf = pdbcs.getFeatures()
+                    .getAllFeatures();
+            List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+            if (allsf != null && allsf.size() > 0)
+            {
+              for (SequenceFeature f : allsf)
+              {
+                if (file.equals(f.getFeatureGroup()))
+                {
+                  f = new SequenceFeature(f, f.type, f.begin, f.end, id,
+                          f.score);
+                }
+                newsf.add(f);
+              }
+              pdbcs.setSequenceFeatures(newsf);
+            }
           }
         }
         else
@@ -310,4 +342,5 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   {
     return new PDBFeatureSettings();
   }
+
 }