Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / src / jalview / io / EmblFlatFile.java

diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
new file mode 100644 (file)
index 0000000..75b8981
--- /dev/null
+++ b/src/jalview/io/EmblFlatFile.java
@@ -0,0 +1,209 @@
+package jalview.io;
+
+import java.io.IOException;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.util.DBRefUtils;
+
+/**
+ * A class that provides selective parsing of the EMBL flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ * 
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ * 
+ * For a complete parser, it may be best to adopt that provided in
+ * https://github.com/enasequence/sequencetools/tree/master/src/main/java/uk/ac/ebi/embl/flatfile
+ * (but note this has a dependency on the Apache Commons library)
+ * 
+ * @author gmcarstairs
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
+ */
+public class EmblFlatFile extends EMBLLikeFlatFile
+{
+  /**
+   * Constructor given a data source and the id of the source database
+   * 
+   * @param fp
+   * @param sourceId
+   * @throws IOException
+   */
+  public EmblFlatFile(FileParse fp, String sourceId) throws IOException
+  {
+    super(fp, sourceId);
+  }
+
+  /**
+   * Parses the flatfile, and if successful, saves as an annotated sequence
+   * which may be retrieved by calling {@code getSequence()}
+   * 
+   * @throws IOException
+   */
+  @Override
+  public void parse() throws IOException
+  {
+    String line = nextLine();
+    while (line != null)
+    {
+      if (line.startsWith("ID"))
+      {
+        line = parseID(line);
+      }
+      else if (line.startsWith("DE"))
+      {
+        line = parseDE(line);
+      }
+      else if (line.startsWith("DR"))
+      {
+        line = parseDR(line);
+      }
+      else if (line.startsWith("SQ"))
+      {
+        line = parseSequence();
+      }
+      else if (line.startsWith("FT"))
+      {
+        line = parseFeature(line.substring(2));
+      }
+      else
+      {
+        line = nextLine();
+      }
+    }
+    buildSequence();
+  }
+
+  /**
+   * Extracts and saves the primary accession and version (SV value) from an ID
+   * line, or null if not found. Returns the next line after the one processed.
+   * 
+   * @param line
+   * @throws IOException
+   */
+  String parseID(String line) throws IOException
+  {
+    String[] tokens = line.substring(2).split(";");
+
+    /*
+     * first is primary accession
+     */
+    String token = tokens[0].trim();
+    if (!token.isEmpty())
+    {
+      this.accession = token;
+    }
+
+    /*
+     * second token is 'SV versionNo'
+     */
+    if (tokens.length > 1)
+    {
+      token = tokens[1].trim();
+      if (token.startsWith("SV"))
+      {
+        String[] bits = token.trim().split(WHITESPACE);
+        this.version = bits[bits.length - 1];
+      }
+    }
+
+    /*
+     * seventh token is 'length BP'
+     */
+    if (tokens.length > 6)
+    {
+      token = tokens[6].trim();
+      String[] bits = token.trim().split(WHITESPACE);
+      try
+      {
+        this.length = Integer.valueOf(bits[0]);
+      } catch (NumberFormatException e)
+      {
+        Console.error("bad length read in flatfile, line: " + line);
+      }
+    }
+
+    return nextLine();
+  }
+
+  /**
+   * Reads sequence description from the first DE line found. Any trailing
+   * period is discarded. If there are multiple DE lines, only the first (short
+   * description) is read, the rest are ignored.
+   * 
+   * @param line
+   * @return
+   * @throws IOException
+   */
+  String parseDE(String line) throws IOException
+  {
+    String desc = line.substring(2).trim();
+    if (desc.endsWith("."))
+    {
+      desc = desc.substring(0, desc.length() - 1);
+    }
+    this.description = desc;
+
+    /*
+     * pass over any additional DE lines
+     */
+    while ((line = nextLine()) != null)
+    {
+      if (!line.startsWith("DE"))
+      {
+        break;
+      }
+    }
+
+    return line;
+  }
+
+  /**
+   * Processes one DR line and saves as a DBRefEntry cross-reference. Returns
+   * the line following the line processed.
+   * 
+   * @param line
+   * @throws IOException
+   */
+  String parseDR(String line) throws IOException
+  {
+    String[] tokens = line.substring(2).split(";");
+    if (tokens.length > 1)
+    {
+      /*
+       * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+       */
+      String db = tokens[0].trim();
+      db = DBRefUtils.getCanonicalName(db);
+      String acc = tokens[1].trim();
+      if (acc.endsWith("."))
+      {
+        acc = acc.substring(0, acc.length() - 1);
+      }
+      String version = "0";
+      if (tokens.length > 2)
+      {
+        String secondaryId = tokens[2].trim();
+        if (!secondaryId.isEmpty())
+        {
+          // todo: is this right? secondary id is not a version number
+          // version = secondaryId;
+        }
+      }
+      this.dbrefs.add(new DBRefEntry(db, version, acc));
+    }
+
+    return nextLine();
+  }
+
+  @Override
+  protected boolean isFeatureContinuationLine(String line)
+  {
+    return line.startsWith("FT    "); // 4 spaces
+  }
+}