X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEmblFlatFile.java;h=33701f6934c991f3918174c268523b544d9073bf;hb=0b7d63e48815f1f80b24049ce272d2e0241e07f2;hp=759fa28302f46557330586541aee5cd557c581b4;hpb=fe3cd724aecdeb06a130a502ce3a967ad643f458;p=jalview.git

diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
index 759fa28..33701f6 100644
--- a/src/jalview/io/EmblFlatFile.java
+++ b/src/jalview/io/EmblFlatFile.java
@@ -1,22 +1,30 @@
+/*
+ * 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.io;
 
 import java.io.IOException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.DnaUtils;
-import jalview.util.MappingUtils;
+import jalview.util.DBRefUtils;
 
 /**
  * A class that provides selective parsing of the EMBL flatfile format.
@@ -37,49 +45,18 @@ import jalview.util.MappingUtils;
  * @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 AlignFile // FileParse
+public class EmblFlatFile extends EMBLLikeFlatFile
 {
-  private static final String WHITESPACE = "\\s+";
-
-  private String sourceDb;
-  
-  /*
-   * values parsed from the EMBL flatfile record
-   */
-  private String accession; // from ID (first token)
-
-  private String version; // from ID (second token)
-
-  private int length = 128; // from ID (7th token), with usable default
-
-  private List<DBRefEntry> dbrefs; // from DR and also CDS /db_xref qualifiers
-
-  private String sequenceString; // from SQ lines
-
-  private String translation; // from CDS feature /translation
-
-  private String cdsLocation; // CDS /location raw value
-
-  private int codonStart = 1; // from CDS /codon_start
-
-  private String proteinName; // from CDS /product
-
-  private String proteinId; // from CDS /protein_id
-
-  private Map<String, String> cdsProps; // CDS other qualifiers e.g. 'note'
-
   /**
-   * Constructor
+   * 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(false, fp); // don't parse immediately
-    this.sourceDb = sourceId;
-    dbrefs = new ArrayList<>();
-    cdsProps = new Hashtable<>();
+    super(fp, sourceId);
   }
 
   /**
@@ -88,6 +65,7 @@ public class EmblFlatFile extends AlignFile // FileParse
    * 
    * @throws IOException
    */
+  @Override
   public void parse() throws IOException
   {
     String line = nextLine();
@@ -95,26 +73,30 @@ public class EmblFlatFile extends AlignFile // FileParse
     {
       if (line.startsWith("ID"))
       {
-        line = processID(line);
+        line = parseID(line);
+      }
+      else if (line.startsWith("DE"))
+      {
+        line = parseDE(line);
       }
       else if (line.startsWith("DR"))
       {
-        line = processDR(line);
+        line = parseDR(line);
       }
       else if (line.startsWith("SQ"))
       {
-        line = processSQ();
+        line = parseSequence();
       }
       else if (line.startsWith("FT"))
       {
-        line = processFT(line);
+        line = parseFeature(line.substring(2));
       }
       else
       {
         line = nextLine();
       }
     }
-    assembleSequence();
+    buildSequence();
   }
 
   /**
@@ -124,7 +106,7 @@ public class EmblFlatFile extends AlignFile // FileParse
    * @param line
    * @throws IOException
    */
-  String processID(String line) throws IOException
+  String parseID(String line) throws IOException
   {
     String[] tokens = line.substring(2).split(";");
 
@@ -162,7 +144,7 @@ public class EmblFlatFile extends AlignFile // FileParse
         this.length = Integer.valueOf(bits[0]);
       } catch (NumberFormatException e)
       {
-        Cache.log.error("bad length read in flatfile, line: " + line);
+        Console.error("bad length read in flatfile, line: " + line);
       }
     }
 
@@ -170,286 +152,78 @@ public class EmblFlatFile extends AlignFile // FileParse
   }
 
   /**
-   * Processes one DR line and saves as a DBRefEntry cross-reference. Returns
-   * the line following the line processed.
+   * 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 processDR(String line) throws IOException
+  String parseDE(String line) throws IOException
   {
-    String[] tokens = line.substring(2).split(";");
-    if (tokens.length > 1)
+    String desc = line.substring(2).trim();
+    if (desc.endsWith("."))
     {
-      String db = tokens[0].trim();
-      String acc = tokens[1].trim();
-      if (acc.endsWith("."))
-      {
-        acc = acc.substring(0, acc.length() - 1);
-      }
-      this.dbrefs.add(new DBRefEntry(db, "0", acc));
+      desc = desc.substring(0, desc.length() - 1);
     }
+    this.description = desc;
 
-    return nextLine();
-  }
-
-  /**
-   * Reads and saves the sequence, read from the lines following the SQ line.
-   * Whitespace and position counters are discarded. Returns the next line
-   * following the sequence data (the next line that doesn't start with
-   * whitespace).
-   * 
-   * @throws IOException
-   */
-  String processSQ() throws IOException
-  {
-    StringBuilder sb = new StringBuilder(this.length);
-    String line = nextLine();
-    while (line != null && line.startsWith(" "))
+    /*
+     * pass over any additional DE lines
+     */
+    while ((line = nextLine()) != null)
     {
-      line = line.trim();
-      String[] blocks = line.split(WHITESPACE);
-
-      /*
-       * omit the last block (position counter) on each line
-       */
-      for (int i = 0; i < blocks.length - 1; i++)
+      if (!line.startsWith("DE"))
       {
-        sb.append(blocks[i]);
+        break;
       }
-      line = nextLine();
     }
-    this.sequenceString = sb.toString();
 
     return line;
   }
 
   /**
-   * Processes an FT line. If it declares a feature type of interest (currently,
-   * only CDS is processed), processes all of the associated lines (feature
-   * qualifiers), and returns the next line after that, otherwise simply returns
-   * the next line.
+   * Processes one DR line and saves as a DBRefEntry cross-reference. Returns
+   * the line following the line processed.
    * 
    * @param line
-   * @return
    * @throws IOException
    */
-  String processFT(String line) throws IOException
+  String parseDR(String line) throws IOException
   {
-    String[] tokens = line.split(WHITESPACE);
-    if (tokens.length < 3 || !"CDS".equals(tokens[1]))
-    {
-      return nextLine();
-    }
-
-    this.cdsLocation = tokens[2];
-
-    while ((line = nextLine()) != null)
+    String[] tokens = line.substring(2).split(";");
+    if (tokens.length > 1)
     {
-      if (!line.startsWith("FT    ")) // 4 spaces
-      {
-        // e.g. start of next feature "FT source..."
-        break;
-      }
-
       /*
-       * extract qualifier, e.g. FT    /protein_id="CAA37824.1"
+       * ensure UniProtKB/Swiss-Prot converted to UNIPROT
        */
-      int slashPos = line.indexOf('/');
-      if (slashPos == -1)
-      {
-        Cache.log.error("Unexpected EMBL line ignored: " + line);
-        continue;
-      }
-      int eqPos = line.indexOf('=', slashPos + 1);
-      if (eqPos == -1)
-      {
-        Cache.log.error("Unexpected EMBL line ignored: " + line);
-        continue;
-      }
-      String qualifier = line.substring(slashPos + 1, eqPos);
-      String value = line.substring(eqPos + 1);
-      if (value.startsWith("\"") && value.endsWith("\""))
-      {
-        value = value.substring(1, value.length() - 1);
-      }
-
-      if ("protein_id".equals(qualifier))
-      {
-        proteinId = value;
-      }
-      else if ("codon_start".equals(qualifier))
-      {
-        try
-        {
-          codonStart = Integer.parseInt(value.trim());
-        } catch (NumberFormatException e)
-        {
-          Cache.log.error("Invalid codon_start in XML for " + this.accession
-                  + ": " + e.getMessage());
-        }
-      }
-      else if ("product".equals(qualifier))
-      {
-        // sometimes name is returned e.g. for V00488
-        proteinName = value;
-      }
-      else if ("translation".equals(qualifier))
-      {
-        line = readTranslation(value);
-      }
-      else if (!"".equals(value))
-      {
-        // throw anything else into the additional properties hash
-        cdsProps.put(qualifier, value);
-      }
-    }
-    
-    return line;
-  }
-
-  /**
-   * Reads and saves the CDS translation from one or more lines of the file, and
-   * returns the next line after that
-   * 
-   * @param value
-   *          the first line of the translation (likely quoted)
-   * @return
-   * @throws IOException
-   */
-  String readTranslation(String value) throws IOException
-  {
-    StringBuilder sb = new StringBuilder(this.length / 3 + 1);
-    sb.append(value.replace("\"", ""));
-
-    String line;
-    while ((line = nextLine()) != null)
-    {
-      if (!line.startsWith("FT    "))
-      {
-        break; // reached next feature or other input line
-      }
-      String[] tokens = line.split(WHITESPACE);
-      if (tokens.length < 2)
-      {
-        Cache.log.error("Ignoring bad EMBL line: " + line);
-        break;
-      }
-      if (tokens[1].startsWith("/"))
+      String db = tokens[0].trim();
+      db = DBRefUtils.getCanonicalName(db);
+      String acc = tokens[1].trim();
+      if (acc.endsWith("."))
       {
-        break; // next feature qualifier
+        acc = acc.substring(0, acc.length() - 1);
       }
-      sb.append(tokens[1].replace("\"", ""));
-    }
-
-    return sb.toString();
-  }
-
-  /**
-   * Processes the parsed CDS feature data to
-   * <ul>
-   * <li>add a CDS feature to the sequence for each CDS start-end range</li>
-   * <li>create a protein product sequence for the translation</li>
-   * <li>create a cross-reference to protein with mapping from dna</li>
-   * <li>add any CDS dbrefs to the sequence and to the protein product</li> 
-   * </ul>
-   * @param SequenceI dna
-   */
-  void processCDS(SequenceI dna)
-  {
-    /*
-     * parse location into a list of [start, end, start, end] positions
-     */
-    int[] exons = getCdsRanges(this.accession, this.cdsLocation);
-    int exonNumber = 0;
-    
-    for (int xint = 0; exons != null
-            && xint < exons.length - 1; xint += 2)
-    {
-      int exonStart = exons[xint];
-      int exonEnd = exons[xint + 1];
-      int begin = Math.min(exonStart, exonEnd);
-      int end = Math.max(exonStart, exonEnd);
-      exonNumber++;
-      String desc = String.format("Exon %d for protein EMBLCDS:%s",
-              exonNumber, proteinId);
-
-      SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end, this.sourceDb);
-      if (!cdsProps.isEmpty())
+      String version = "0";
+      if (tokens.length > 2)
       {
-        for (Entry<String, String> val : cdsProps.entrySet())
+        String secondaryId = tokens[2].trim();
+        if (!secondaryId.isEmpty())
         {
-          sf.setValue(val.getKey(), val.getValue());
+          // todo: is this right? secondary id is not a version number
+          // version = secondaryId;
         }
       }
-
-      sf.setEnaLocation(this.cdsLocation);
-      boolean forwardStrand = exonStart <= exonEnd;
-      sf.setStrand(forwardStrand ? "+" : "-");
-      sf.setPhase(String.valueOf(codonStart - 1));
-      sf.setValue(FeatureProperties.EXONPOS, exonNumber);
-      sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
-
-      dna.addSequenceFeature(sf);
+      this.dbrefs.add(new DBRefEntry(db, version, acc));
     }
-  }
 
-  /**
-   * Constructs and saves the sequence from parsed components
-   */
-  void assembleSequence()
-  {
-    String name = this.accession;
-    if (this.sourceDb != null)
-    {
-      name = this.sourceDb + "|" + name;
-    }
-    SequenceI seq = new Sequence(name, this.sequenceString);
-    for (DBRefEntry dbref : this.dbrefs)
-    {
-      seq.addDBRef(dbref);
-    }
-    
-    processCDS(seq);
-    seq.deriveSequence();
-    
-    addSequence(seq);
+    return nextLine();
   }
 
-  /**
-   * Output (print) is not implemented for EMBL flat file format
-   */
   @Override
-  public String print(SequenceI[] seqs, boolean jvsuffix)
+  protected boolean isFeatureContinuationLine(String line)
   {
-    return null;
-  }
-
-  /**
-   * Returns the CDS location as a single array of [start, end, start, end...]
-   * positions. If on the reverse strand, these will be in descending order.
-   * 
-   * @param accession
-   * @param location
-   * @return
-   */
-  protected int[] getCdsRanges(String accession, String location)
-  {
-    if (location == null)
-    {
-      return new int[] {};
-    }
-
-    try
-    {
-      List<int[]> ranges = DnaUtils.parseLocation(location);
-      return MappingUtils.listToArray(ranges);
-    } catch (ParseException e)
-    {
-      Cache.log.warn(
-              String.format("Not parsing inexact CDS location %s in ENA %s",
-                      location, accession));
-      return new int[] {};
-    }
+    return line.startsWith("FT    "); // 4 spaces
   }
 }