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 97eacab..fa867cd 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -21,45 +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.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ContactMatrix;
 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.javascript.json.JSON;
-import jalview.structure.StructureImportSettings;
-import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.jmol.adapter.readers.simple.JSONReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * @author JimP
  * 
@@ -188,7 +177,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     try
     {
       File tmpFile = File.createTempFile(id, ".cif");
-      Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
+      Console.debug("Retrieving structure file for " + id + " from "
+              + alphaFoldCif);
       UrlDownloadClient.download(alphaFoldCif, tmpFile);
 
       // may not need this check ?
@@ -207,54 +197,85 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                 "exception.no_pdb_records_for_chain", new String[]
                 { id, ((chain == null) ? "' '" : chain) }));
       }
+      retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
 
-      // 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);
+    } catch (Exception ex) // Problem parsing PDB file
+    {
+      stopQuery();
+      throw (ex);
+    }
+    return pdbAlignment;
+  }
 
-      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() + "");
+  /**
+   * 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);
 
-      try {
-        UrlDownloadClient.download(paeURL, pae);        
-      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+    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);
-      }
-
-    } catch (Exception ex) // Problem parsing PDB file
+    } catch (Exception pae_ex)
     {
-      stopQuery();
-      throw (ex);
+      Console.debug("Couldn't download PAE", pae_ex);
     }
-    return pdbAlignment;
+
   }
 
-  private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
-          File pae) throws Exception
+  /**
+   * 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
   {
-    FileInputStream pae_input = new FileInputStream(pae);
 
-    List<Object> pae_obj = (List<Object>) Platform
-            .parseJSON(pae_input);
+    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),
+            (Map<String, Object>) pae_obj.get(0));
 
-    pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+    pdbAlignment.getSequenceAt(0)
+            .addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
     return true;
   }