X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=fc4ee46b5439fe587c5135d464c02f03185e27eb;hb=cf02a7088e2835fa4764d034e662f4319073c8a9;hp=3cba683f2342a16272322b8fbe3a53922a20824f;hpb=3ab582bfeeab1563bedf60e97994e63e672d2e31;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 3cba683..fc4ee46 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -38,6 +38,8 @@ public class PDBEntry
 
   private static final int PDB_ID_LENGTH = 4;
 
+  private static final String FAKED_ID = "faked_pdbid";
+
   private String file;
 
   private String type;
@@ -46,7 +48,39 @@ public class PDBEntry
 
   public enum Type
   {
-    PDB, MMCIF, FILE;
+    // TODO is FILE needed; if not is this enum needed, or can we
+    // use FileFormatI for PDB, MMCIF?
+    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+
+    /*
+     * file extension for cached structure file; must be one that
+     * is recognised by Chimera 'open' command
+     * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+     */
+    String ext;
+
+    /*
+     * format specifier used in dbfetch request
+     * @see http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb
+     */
+    String format;
+
+    private Type(String fmt, String ex)
+    {
+      format = fmt;
+      ext = ex;
+    }
+
+    public String getFormat()
+    {
+      return format;
+    }
+
+    public String getExtension()
+    {
+      return ext;
+    }
+
     /**
      * case insensitive matching for Type enum
      * 
@@ -77,7 +111,6 @@ public class PDBEntry
     }
   }
 
-
   /**
    * Answers true if obj is a PDBEntry with the same id and chain code (both
    * ignoring case), file, type and properties
@@ -121,17 +154,6 @@ public class PDBEntry
   {
   }
 
-  /**
-   * Constructor given file path and PDB id.
-   * 
-   * @param filePath
-   */
-  // public PDBEntry(String filePath, String pdbId)
-  // {
-  // this.file = filePath;
-  // this.id = pdbId;
-  // }
-
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
@@ -144,7 +166,8 @@ public class PDBEntry
    * @param entryType
    * @param filePath
    */
-  void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+  void init(String pdbId, String chain, PDBEntry.Type entryType,
+          String filePath)
   {
     this.id = pdbId;
     this.type = entryType == null ? null : entryType.toString();
@@ -179,8 +202,8 @@ public class PDBEntry
   {
     if (!DBRefSource.PDB.equals(dbr.getSource()))
     {
-      throw new IllegalArgumentException("Invalid source: "
-              + dbr.getSource());
+      throw new IllegalArgumentException(
+              "Invalid source: " + dbr.getSource());
     }
 
     String pdbId = dbr.getAccessionId();
@@ -363,21 +386,40 @@ public class PDBEntry
       return false; // shouldn't happen
     }
 
-    /*
-     * id has to match (ignoring case)
-     */
-    if (!getId().equalsIgnoreCase(newId))
-    {
-      return false;
-    }
+    boolean idMatches = getId().equalsIgnoreCase(newId);
 
     /*
      * Don't update if associated with different structure files
      */
     String newFile = newEntry.getFile();
-    if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+    if (newFile != null && getFile() != null)
     {
-      return false;
+      if (!newFile.equals(getFile()))
+      {
+        return false;
+      }
+      else
+      {
+        // files match.
+        if (!idMatches)
+        {
+          // this shouldn't happen, but could do if the id from the
+          // file is not the same as the id from the authority that provided
+          // the file
+          if (!newEntry.fakedPDBId())
+          {
+            return false;
+          } // otherwise we can update
+        }
+      }
+    }
+    else
+    {
+      // one has data, one doesn't ..
+      if (!idMatches)
+      {
+        return false;
+      } // otherwise maybe can update
     }
 
     /*
@@ -432,6 +474,11 @@ public class PDBEntry
        */
       String key = newProps.nextElement();
       Object value = newEntry.getProperty(key);
+      if (FAKED_ID.equals(key))
+      {
+        // we never update the fake ID property
+        continue;
+      }
       if (!value.equals(getProperty(key)))
       {
         setProperty(key, value);
@@ -439,4 +486,111 @@ public class PDBEntry
     }
     return true;
   }
+  
+  /**
+   * set when Jalview has manufactured the ID using a local filename
+   * @return
+   */
+  public boolean fakedPDBId()
+  {
+    if (_hasProperty(FAKED_ID))
+    {
+      return true;
+    }
+    return false;
+  }
+  public void setFakedPDBId(boolean faked)
+  {
+    if (faked)
+    {
+      setProperty(FAKED_ID, Boolean.TRUE);
+    }
+    else 
+    {
+      if (properties!=null) {
+        properties.remove(FAKED_ID);
+      }
+    }
+  }
+
+  private boolean _hasProperty(final String key)
+  {
+    return (properties != null && properties.containsKey(key));
+  }
+
+  private static final String RETRIEVE_FROM = "RETRIEVE_FROM";
+
+  private static final String PROVIDER = "PROVIDER";
+
+  private static final String MODELPAGE = "PROVIDERPAGE";
+
+  /**
+   * Permanent URI for retrieving the original structure data
+   * 
+   * @param urlStr
+   */
+  public void setRetrievalUrl(String urlStr)
+  {
+    setProperty(RETRIEVE_FROM, urlStr);
+  }
+
+  public boolean hasRetrievalUrl()
+  {
+    return _hasProperty(RETRIEVE_FROM);
+  }
+
+  /**
+   * get the Permanent URI for retrieving the original structure data
+   */
+  public String getRetrievalUrl()
+  {
+    return (String) getProperty(RETRIEVE_FROM);
+  }
+
+  /**
+   * Data provider name - from 3D Beacons
+   * 
+   * @param provider
+   */
+  public void setProvider(String provider)
+  {
+    setProperty(PROVIDER, provider);
+  }
+
+  /**
+   * Get Data provider name - from 3D Beacons
+   * 
+   */
+  public String getProvider()
+  {
+    return (String) getProperty(PROVIDER);
+  }
+
+  /**
+   * Permanent URI for retrieving the original structure data
+   * 
+   * @param urlStr
+   */
+  public void setProviderPage(String urlStr)
+  {
+    setProperty(MODELPAGE, urlStr);
+  }
+
+  /**
+   * get the Permanent URI for retrieving the original structure data
+   */
+  public String getProviderPage()
+  {
+    return (String) getProperty(MODELPAGE);
+  }
+
+  public boolean hasProviderPage()
+  {
+    return _hasProperty(MODELPAGE);
+  }
+
+  public boolean hasProvider()
+  {
+    return _hasProperty(PROVIDER);
+  }
 }