JAL-3855 ALPHAFOLD database source based on the PDB retriever

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
new file mode 100644 (file)
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+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -0,0 +1,281 @@
+
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+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.ws.utils.UrlDownloadClient;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * @author JimP
+ * 
+ */
+public class EBIAlfaFold extends EbiFileRetrievedProxy
+{
+  private static final String SEPARATOR = "|";
+
+  private static final String COLON = ":";
+
+  private static final int PDB_ID_LENGTH = 4;
+
+  public EBIAlfaFold()
+  {
+    super();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+   */
+  @Override
+  public String getAccessionSeparator()
+  {
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+   */
+  @Override
+  public Regex getAccessionValidator()
+  {
+    return new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource()
+   */
+  @Override
+  public String getDbSource()
+  {
+    return "ALPHAFOLD";
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbVersion()
+   */
+  @Override
+  public String getDbVersion()
+  {
+    return "1";
+  }
+  public static String getAlphaFoldCifDownloadUrl(String id)
+  {
+    return "https://alphafold.ebi.ac.uk/files/"+id+"-model_v1.cif";
+  }
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+   */
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    AlignmentI pdbAlignment = null;
+    String chain = null;
+    String id = null;
+    if (queries.indexOf(COLON) > -1)
+    {
+      chain = queries.substring(queries.indexOf(COLON) + 1);
+      id = queries.substring(0, queries.indexOf(COLON));
+    }
+    else
+    {
+      id = queries;
+    }
+
+    if (!isValidReference(id))
+    {
+      System.err.println("(AFClient) Ignoring invalid pdb query: '" + id + "'");
+      stopQuery();
+      return null;
+    }
+    String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+    
+    try {
+      File tmpFile = File.createTempFile(id,"cif");
+      UrlDownloadClient.download(alphaFoldCif, tmpFile);
+      file = tmpFile.getAbsolutePath();
+      if (file == null)
+      {
+      return null;
+    }
+      // todo get rid of Type and use FileFormatI instead?
+      FileFormatI fileFormat = FileFormat.MMCif;
+      pdbAlignment = new FormatAdapter().readFile(tmpFile, DataSourceType.FILE,
+              fileFormat);
+      if (pdbAlignment != null)
+      {
+        List<SequenceI> toremove = new ArrayList<SequenceI>();
+        for (SequenceI pdbcs : pdbAlignment.getSequences())
+        {
+          String chid = null;
+          // Mapping map=null;
+          for (PDBEntry pid : pdbcs.getAllPDBEntries())
+          {
+            if (pid.getFile() == file)
+            {
+              chid = pid.getChainCode();
+
+            }
+          }
+          if (chain == null || (chid != null && (chid.equals(chain)
+                  || chid.trim().equals(chain.trim())
+                  || (chain.trim().length() == 0 && chid.equals("_")))))
+          {
+            // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+            // TODO: suggest simplify naming to 1qip|A as default name defined
+            pdbcs.setName(id
+                    + SEPARATOR + pdbcs.getName());
+            // Might need to add more metadata to the PDBEntry object
+            // like below
+            /*
+             * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+             * entry.setId(id); if (entry.getProperty() == null)
+             * entry.setProperty(new Hashtable());
+             * entry.getProperty().put("chains", pdbchain.id + "=" +
+             * sq.getStart() + "-" + sq.getEnd());
+             * sq.getDatasetSequence().addPDBId(entry);
+             */
+            // Add PDB DB Refs
+            // We make a DBRefEtntry because we have obtained the PDB file from
+            // a
+            // verifiable source
+            // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+            // information
+            DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+                    getDbVersion(), (chid == null ? id : id + chid));
+            // dbentry.setMap()
+            pdbcs.addDBRef(dbentry);
+          }
+          else
+          {
+            // mark this sequence to be removed from the alignment
+            // - since it's not from the right chain
+            toremove.add(pdbcs);
+          }
+        }
+        // now remove marked sequences
+        for (SequenceI pdbcs : toremove)
+        {
+          pdbAlignment.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation() != null)
+          {
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+            {
+              pdbAlignment.deleteAnnotation(aa);
+            }
+          }
+        }
+      }
+
+      if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
+      {
+        throw new Exception(MessageManager.formatMessage(
+                "exception.no_pdb_records_for_chain", new String[]
+                { id, ((chain == null) ? "' '" : chain) }));
+      }
+
+    } catch (Exception ex) // Problem parsing PDB file
+    {
+      stopQuery();
+      throw (ex);
+    }
+    return pdbAlignment;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+   */
+  @Override
+  public boolean isValidReference(String accession)
+  {
+    Regex r = getAccessionValidator();
+    return r.search(accession.trim());
+  }
+
+  /**
+   * human glyoxalase
+   */
+  @Override
+  public String getTestQuery()
+  {
+    return "1QIP";
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "PDB"; // getDbSource();
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
+}