X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;fp=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;h=e3687bdb037306d2bb6a814c615f9a1720d96f43;hb=9949854f4c2dc75980f15acdee69594ca6b22631;hp=0000000000000000000000000000000000000000;hpb=cfba86992cd64bb0df6105bbf5dfc076ba8a93b2;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
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+
+/*
+ * 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.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.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()
+  {
+    Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    validator.setIgnoreCase(true);
+    return validator;
+  }
+
+  /*
+   * (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
+  {
+    return getSequenceRecords(queries, null);
+  }
+
+  public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+          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);
+    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)
+      {
+        return null;
+      }
+
+      pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
+              id, chain, getDbSource(), getDbVersion());
+
+      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;
+  }
+
+  /**
+   * general purpose structure importer - designed to yield alignment useful for
+   * transfer of annotation to associated sequences
+   * 
+   * @param alphaFoldCif
+   * @param tmpFile
+   * @param id
+   * @param chain
+   * @param dbSource
+   * @param dbVersion
+   * @return
+   * @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?
+    FileFormatI fileFormat = FileFormat.MMCif;
+    AlignmentI 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
+          if (dbSource != null)
+          {
+            DBRefEntry dbentry = new DBRefEntry(dbSource,
+
+                    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
+        {
+          // 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);
+          }
+        }
+      }
+    }
+    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();
+  }
+
+}