From 25ae256a88bf092f45a78b649a48f41e6fd5d70b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 26 Aug 2008 09:10:53 +0000
Subject: [PATCH] pdb xrefs added as dbrefs and as PDB file links

---
 src/jalview/ws/dbsources/Uniprot.java |  540 ++++++++++++++++-----------------
 1 file changed, 270 insertions(+), 270 deletions(-)

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 65141f8..f29a555 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,270 +1,270 @@
-/**
- * 
- */
-package jalview.ws.dbsources;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.exolab.castor.xml.Unmarshaller;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * @author JimP
- * 
- */
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
-{
-  public Uniprot() {
-    super();
-    addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
-    addDbSourceProperty(DBRefSource.PROTSEQDB);
-//    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  public String getAccessionSeparator()
-  {
-    return null; // ";";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  public Regex getAccessionValidator()
-  {
-    return null;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
-  public String getDbSource()
-  {
-    return DBRefSource.UNIPROT;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  public String getDbVersion()
-  {
-    return "0"; // we really don't know what version we're on.
-  }
-
-  private EBIFetchClient ebi = null;
-
-  public Vector getUniprotEntries(File file)
-  {
-    UniprotFile uni = new UniprotFile();
-    try
-    {
-      // 1. Load the mapping information from the file
-      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
-      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
-      map.loadMapping(url);
-
-      // 2. Unmarshal the data
-      Unmarshaller unmar = new Unmarshaller(uni);
-      unmar.setIgnoreExtraElements(true);
-      unmar.setMapping(map);
-
-      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
-    }
-    catch (Exception e)
-    {
-      System.out.println("Error getUniprotEntries() " + e);
-    }
-
-    return uni.getUniprotEntries();
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  public AlignmentI getSequenceRecords(String queries) throws Exception
-  {
-    startQuery();
-    try
-    {
-      Alignment al=null;
-      ebi = new EBIFetchClient();
-      StringBuffer result=new StringBuffer();
-      // uniprotxml parameter required since december 2007
-      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
-      Vector entries = getUniprotEntries(file);
-
-      if (entries != null)
-      {
-        // First, make the new sequences
-        Enumeration en = entries.elements();
-        while (en.hasMoreElements())
-        {
-          UniprotEntry entry = (UniprotEntry) en.nextElement();
-
-          StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
-          Enumeration en2 = entry.getAccession().elements();
-          while (en2.hasMoreElements())
-          {
-            name.append("|");
-            name.append(en2.nextElement());
-          }
-          en2 = entry.getName().elements();
-          while (en2.hasMoreElements())
-          {
-            name.append("|");
-            name.append(en2.nextElement());
-          }
-
-          if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
-          {
-              for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)
-              {
-                name.append(" " + entry.getProtein().getName().elementAt(nm));
-              }
-          }
-
-          result.append(name + "\n"
-                  + entry.getUniprotSequence().getContent() + "\n");
-
-        }
-
-        // Then read in the features and apply them to the dataset
-        al = parseResult(result.toString());
-        if (al!=null)
-        {
-          // Decorate the alignment with database entries.
-          addUniprotXrefs(al, entries);
-        } else {
-          results = result;
-        }
-      }
-      stopQuery();
-      return al;
-    } catch (Exception e)
-    {
-      stopQuery();
-      throw(e);
-    }
-  }
-
-  /**
-   * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
-   * 
-   * @param al -
-   *          a sequence of n sequences
-   * @param entries
-   *          a seuqence of n uniprot entries to be analysed.
-   */
-  public void addUniprotXrefs(Alignment al, Vector entries)
-  {
-    for (int i = 0; i < entries.size(); i++)
-    {
-      UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
-      Enumeration e = entry.getDbReference().elements();
-      Vector onlyPdbEntries = new Vector();
-      Vector dbxrefs = new Vector();
-      while (e.hasMoreElements())
-      {
-        PDBEntry pdb = (PDBEntry) e.nextElement();
-        if (!pdb.getType().equals("PDB"))
-        {
-          DBRefEntry dbr = new DBRefEntry();
-          dbr.setSource(pdb.getType());
-          dbr.setAccessionId(pdb.getId());
-          dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
-          dbxrefs.addElement(dbr);
-          continue;
-        }
-
-        onlyPdbEntries.addElement(pdb);
-      }
-      SequenceI sq = al.getSequenceAt(i);
-      while (sq.getDatasetSequence()!=null)
-      {
-        sq = sq.getDatasetSequence();
-      }
-
-      Enumeration en2 = entry.getAccession().elements();
-      while (en2.hasMoreElements())
-      {
-        // we always add as uniprot if we retrieved from uniprot or uniprot name
-        sq.addDBRef(
-                new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
-                        .toString()));
-      }
-      en2 = dbxrefs.elements();
-      while (en2.hasMoreElements())
-      {
-     // we always add as uniprot if we retrieved from uniprot or uniprot name
-        sq.addDBRef((DBRefEntry) en2.nextElement());
-                    
-      }
-      sq.setPDBId(onlyPdbEntries);
-      if (entry.getFeature() != null)
-      {
-        e = entry.getFeature().elements();
-        while (e.hasMoreElements())
-        {
-          SequenceFeature sf = (SequenceFeature) e.nextElement();
-          sf.setFeatureGroup("Uniprot");
-          sq.addSequenceFeature(sf);
-        }
-      }
-    }
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    return true;
-  }
-  /**
-   * return LDHA_CHICK uniprot entry
-   */
-  public String getTestQuery()
-  {
-    return "P00340";
-  }
-  public String getDbName()
-  {
-    return "Uniprot"; // getDbSource();
-  }
-}
+/**
+ * 
+ */
+package jalview.ws.dbsources;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.UniprotEntry;
+import jalview.datamodel.UniprotFile;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+/**
+ * @author JimP
+ * 
+ */
+public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
+{
+  public Uniprot() {
+    super();
+    addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
+    addDbSourceProperty(DBRefSource.PROTSEQDB);
+//    addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+   */
+  public String getAccessionSeparator()
+  {
+    return null; // ";";
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+   */
+  public Regex getAccessionValidator()
+  {
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource()
+   */
+  public String getDbSource()
+  {
+    return DBRefSource.UNIPROT;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbVersion()
+   */
+  public String getDbVersion()
+  {
+    return "0"; // we really don't know what version we're on.
+  }
+
+  private EBIFetchClient ebi = null;
+
+  public Vector getUniprotEntries(File file)
+  {
+    UniprotFile uni = new UniprotFile();
+    try
+    {
+      // 1. Load the mapping information from the file
+      org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
+      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+      map.loadMapping(url);
+
+      // 2. Unmarshal the data
+      Unmarshaller unmar = new Unmarshaller(uni);
+      unmar.setIgnoreExtraElements(true);
+      unmar.setMapping(map);
+
+      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+    }
+    catch (Exception e)
+    {
+      System.out.println("Error getUniprotEntries() " + e);
+    }
+
+    return uni.getUniprotEntries();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+   */
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    startQuery();
+    try
+    {
+      Alignment al=null;
+      ebi = new EBIFetchClient();
+      StringBuffer result=new StringBuffer();
+      // uniprotxml parameter required since december 2007
+      File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
+      Vector entries = getUniprotEntries(file);
+
+      if (entries != null)
+      {
+        // First, make the new sequences
+        Enumeration en = entries.elements();
+        while (en.hasMoreElements())
+        {
+          UniprotEntry entry = (UniprotEntry) en.nextElement();
+
+          StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
+          Enumeration en2 = entry.getAccession().elements();
+          while (en2.hasMoreElements())
+          {
+            name.append("|");
+            name.append(en2.nextElement());
+          }
+          en2 = entry.getName().elements();
+          while (en2.hasMoreElements())
+          {
+            name.append("|");
+            name.append(en2.nextElement());
+          }
+
+          if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
+          {
+              for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)
+              {
+                name.append(" " + entry.getProtein().getName().elementAt(nm));
+              }
+          }
+
+          result.append(name + "\n"
+                  + entry.getUniprotSequence().getContent() + "\n");
+
+        }
+
+        // Then read in the features and apply them to the dataset
+        al = parseResult(result.toString());
+        if (al!=null)
+        {
+          // Decorate the alignment with database entries.
+          addUniprotXrefs(al, entries);
+        } else {
+          results = result;
+        }
+      }
+      stopQuery();
+      return al;
+    } catch (Exception e)
+    {
+      stopQuery();
+      throw(e);
+    }
+  }
+
+  /**
+   * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
+   * 
+   * @param al -
+   *          a sequence of n sequences
+   * @param entries
+   *          a seuqence of n uniprot entries to be analysed.
+   */
+  public void addUniprotXrefs(Alignment al, Vector entries)
+  {
+    for (int i = 0; i < entries.size(); i++)
+    {
+      UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
+      Enumeration e = entry.getDbReference().elements();
+      Vector onlyPdbEntries = new Vector();
+      Vector dbxrefs = new Vector();
+      while (e.hasMoreElements())
+      {
+        PDBEntry pdb = (PDBEntry) e.nextElement();
+        DBRefEntry dbr = new DBRefEntry();
+        dbr.setSource(pdb.getType());
+        dbr.setAccessionId(pdb.getId());
+        dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
+        dbxrefs.addElement(dbr);
+        if (!pdb.getType().equals("PDB"))
+        {
+          continue;
+        }
+        
+        onlyPdbEntries.addElement(pdb);
+      }
+      SequenceI sq = al.getSequenceAt(i);
+      while (sq.getDatasetSequence()!=null)
+      {
+        sq = sq.getDatasetSequence();
+      }
+
+      Enumeration en2 = entry.getAccession().elements();
+      while (en2.hasMoreElements())
+      {
+        // we always add as uniprot if we retrieved from uniprot or uniprot name
+        sq.addDBRef(
+                new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
+                        .toString()));
+      }
+      en2 = dbxrefs.elements();
+      while (en2.hasMoreElements())
+      {
+     // we always add as uniprot if we retrieved from uniprot or uniprot name
+        sq.addDBRef((DBRefEntry) en2.nextElement());
+                    
+      }
+      sq.setPDBId(onlyPdbEntries);
+      if (entry.getFeature() != null)
+      {
+        e = entry.getFeature().elements();
+        while (e.hasMoreElements())
+        {
+          SequenceFeature sf = (SequenceFeature) e.nextElement();
+          sf.setFeatureGroup("Uniprot");
+          sq.addSequenceFeature(sf);
+        }
+      }
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+   */
+  public boolean isValidReference(String accession)
+  {
+    return true;
+  }
+  /**
+   * return LDHA_CHICK uniprot entry
+   */
+  public String getTestQuery()
+  {
+    return "P00340";
+  }
+  public String getDbName()
+  {
+    return "Uniprot"; // getDbSource();
+  }
+}
-- 
1.7.10.2