Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatase...

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblFile.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
deleted file mode 100644 (file)
index 8a32c13..0000000
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ /dev/null
@@ -1,203 +0,0 @@
-/*
- * 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.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.ws.dbsources.Uniprot;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.io.Reader;
-import java.util.Vector;
-
-import org.exolab.castor.mapping.Mapping;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Data model for entries returned from an EMBL query, as marshalled by a Castor
- * binding file
- * 
- * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
- * 
- * @see embl_mapping.xml
- */
-public class EmblFile
-{
-  Vector<EmblEntry> entries;
-
-  Vector<EmblError> errors;
-
-  String text;
-
-  /**
-   * @return the entries
-   */
-  public Vector<EmblEntry> getEntries()
-  {
-    return entries;
-  }
-
-  /**
-   * @param entries
-   *          the entries to set
-   */
-  public void setEntries(Vector<EmblEntry> entries)
-  {
-    this.entries = entries;
-  }
-
-  /**
-   * @return the errors
-   */
-  public Vector<EmblError> getErrors()
-  {
-    return errors;
-  }
-
-  /**
-   * @param errors
-   *          the errors to set
-   */
-  public void setErrors(Vector<EmblError> errors)
-  {
-    this.errors = errors;
-  }
-
-  /**
-   * Parse an EmblXML file into an EmblFile object
-   * 
-   * @param file
-   * @return parsed EmblXML or null if exceptions were raised
-   */
-  public static EmblFile getEmblFile(File file)
-  {
-    if (file == null)
-    {
-      return null;
-    }
-    try
-    {
-      return EmblFile.getEmblFile(new FileReader(file));
-    } catch (Exception e)
-    {
-      System.err.println("Exception whilst reading EMBLfile from " + file);
-      e.printStackTrace(System.err);
-    }
-    return null;
-  }
-
-  public static EmblFile getEmblFile(Reader file)
-  {
-    EmblFile record = new EmblFile();
-    try
-    {
-      // 1. Load the mapping information from the file
-      Mapping map = new Mapping(record.getClass().getClassLoader());
-
-      java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
-      map.loadMapping(url);
-
-      // 2. Unmarshal the data
-      Unmarshaller unmar = new Unmarshaller(record);
-      try
-      {
-        // uncomment to DEBUG EMBLFile reading
-        if (jalview.bin.Cache
-                .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
-                .equalsIgnoreCase("DEBUG"))
-        {
-          unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
-        }
-      } catch (Exception e)
-      {
-      }
-      unmar.setIgnoreExtraElements(true);
-      unmar.setIgnoreExtraAttributes(true);
-      unmar.setMapping(map);
-      unmar.setLogWriter(new PrintWriter(System.out));
-      record = (EmblFile) unmar.unmarshal(file);
-
-      canonicaliseDbRefs(record);
-    } catch (Exception e)
-    {
-      e.printStackTrace(System.err);
-      record = null;
-    }
-
-    return record;
-  }
-
-  /**
-   * Change blank version to "0" in any DBRefEntry, to ensure consistent
-   * comparison with other DBRefEntry in Jalview
-   * 
-   * @param record
-   * @see Uniprot#getDbVersion
-   */
-  static void canonicaliseDbRefs(EmblFile record)
-  {
-    if (record.getEntries() == null)
-    {
-      return;
-    }
-    for (EmblEntry entry : record.getEntries())
-    {
-      if (entry.getDbRefs() != null)
-      {
-        for (DBRefEntry dbref : entry.getDbRefs())
-        {
-          if ("".equals(dbref.getVersion()))
-          {
-            dbref.setVersion("0");
-          }
-        }
-      }
-
-      if (entry.getFeatures() != null)
-      {
-        for (EmblFeature feature : entry.getFeatures())
-        {
-          if (feature.getDbRefs() != null)
-          {
-            for (DBRefEntry dbref : feature.getDbRefs())
-            {
-              if ("".equals(dbref.getVersion()))
-              {
-                dbref.setVersion("0");
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-
-  public String getText()
-  {
-    return text;
-  }
-
-  public void setText(String text)
-  {
-    this.text = text;
-  }
-}