JAL-3855 refactor the pAE retrieval code so it can be called via structureselectionma...

[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 e3687bd..fa867cd 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -21,33 +21,34 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import com.stevesoft.pat.Regex;
+
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrixI;
 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;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
-import jalview.structure.StructureImportSettings;
-import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
+import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * @author JimP
  * 
@@ -60,6 +61,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
   private static final int PDB_ID_LENGTH = 4;
 
+  private static String AF_VERSION = "2";
+
   public EBIAlfaFold()
   {
     super();
@@ -111,9 +114,24 @@ 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, String vnum)
+  {
+    if (vnum == null || vnum.length() == 0)
+    {
+      vnum = AF_VERSION;
+    }
+    return "https://alphafold.ebi.ac.uk/files/" + id
+            + "-predicted_aligned_error_v" + vnum + ".json";
   }
 
   /*
@@ -146,11 +164,11 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     if (!isValidReference(id))
     {
       System.err.println(
-              "(AFClient) Ignoring invalid pdb query: '" + id + "'");
+              "(AFClient) Ignoring invalid alphafold query: '" + id + "'");
       stopQuery();
       return null;
     }
-    String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+    String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION);
     if (retrievalUrl != null)
     {
       alphaFoldCif = retrievalUrl;
@@ -159,6 +177,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     try
     {
       File tmpFile = File.createTempFile(id, ".cif");
+      Console.debug("Retrieving structure file for " + id + " from "
+              + alphaFoldCif);
       UrlDownloadClient.download(alphaFoldCif, tmpFile);
 
       // may not need this check ?
@@ -177,6 +197,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                 "exception.no_pdb_records_for_chain", new String[]
                 { id, ((chain == null) ? "' '" : chain) }));
       }
+      retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
 
     } catch (Exception ex) // Problem parsing PDB file
     {
@@ -187,6 +208,78 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   /**
+   * get an alphafold pAE for the given id, and add it to sequence 0 in
+   * pdbAlignment (assuming it came from structurefile parser).
+   * 
+   * @param id
+   * @param pdbAlignment
+   * @param retrievalUrl
+   *          - URL of .mmcif from EBI-AlphaFold - will be used to generate the
+   *          pAE URL automatically
+   * @throws Exception
+   */
+  public static void retrieve_AlphaFold_pAE(String id,
+          AlignmentI pdbAlignment, String retrievalUrl) throws Exception
+  {
+    // 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, 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");
+    }
+    Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+            + "");
+
+    try
+    {
+      UrlDownloadClient.download(paeURL, pae);
+      FileInputStream pae_input = new FileInputStream(pae);
+
+      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+      {
+        Console.warn("Couln't import contact matrix from " + paeURL
+                + " (stored in " + pae.toString() + ")");
+      }
+    } catch (Exception pae_ex)
+    {
+      Console.debug("Couldn't download PAE", pae_ex);
+    }
+
+  }
+
+  /**
+   * parses the given pAE matrix and adds it to sequence 0 in the given
+   * alignment
+   * 
+   * @param pdbAlignment
+   * @param pae_input
+   * @return true if there was a pAE matrix added
+   * @throws Exception
+   */
+  public static boolean importPaeJSONAsContactMatrix(
+          AlignmentI pdbAlignment, InputStream pae_input) throws Exception
+  {
+
+    List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
+    if (pae_obj == null)
+    {
+      return false;
+    }
+    ContactMatrixI matrix = new PAEContactMatrix(
+            pdbAlignment.getSequenceAt(0),
+            (Map<String, Object>) pae_obj.get(0));
+
+    pdbAlignment.getSequenceAt(0)
+            .addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+    return true;
+  }
+
+  /**
    * general purpose structure importer - designed to yield alignment useful for
    * transfer of annotation to associated sequences
    * 
@@ -313,13 +406,13 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public String getTestQuery()
   {
-    return "1QIP";
+    return "AF-O15552-F1";
   }
 
   @Override
   public String getDbName()
   {
-    return "PDB"; // getDbSource();
+    return "ALPHAFOLD"; // getDbSource();
   }
 
   @Override