X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;fp=src%2Fjalview%2Fio%2FFeaturesFile.java;h=9a4dc0e023ee79e8ee79b2c37324d855bb8e6dd0;hb=3b3c59cfa50e942d2fa5b367b7117cade9459ce7;hp=a69788b8bdb1f627822d39ca62ede0cf18b484e1;hpb=be03fb892bd2f0ffde22bbc5e9ada5aba6752231;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a69788b..9a4dc0e 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -36,7 +36,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.Desktop;
-import jalview.io.gff.GffHelperBase;
 import jalview.io.gff.GffHelperFactory;
 import jalview.io.gff.GffHelperI;
 import jalview.schemes.FeatureColour;
@@ -75,6 +74,12 @@ import java.util.TreeMap;
  */
 public class FeaturesFile extends AlignFile implements FeaturesSourceI
 {
+  /*
+   * map-valued attributes are prefixed with this for output to GFF3;
+   * the prefix is removed if found on reading
+   */
+  public static final String MAP_ATTRIBUTE_PREFIX = "jvmap_";
+
   private static final String TAB_REGEX = "\\t";
 
   private static final String STARTGROUP = "STARTGROUP";
@@ -1126,12 +1131,112 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     String phase = sf.getPhase();
     out.append(phase == null ? "." : phase);
 
-    // miscellaneous key-values (GFF column 9)
-    String attributes = sf.getAttributes();
-    if (attributes != null)
+    if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
+    {
+      Map<String, Object> map = sf.otherDetails;
+      formatAttributes(out, map);
+    }
+  }
+
+  /**
+   * A helper method that outputs attributes stored in the map as
+   * semicolon-delimited values e.g.
+   * 
+   * <pre>
+   * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
+   * </pre>
+   * 
+   * A map-valued attribute is formatted as a comma-delimited list within braces,
+   * for example
+   * 
+   * <pre>
+   * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
+   * </pre>
+   * 
+   * The {@code jvmap_} prefix designates a values map and is removed if the value
+   * is parsed when read in. (The GFF3 specification allows 'semi-structured data'
+   * to be represented provided the attribute name begins with a lower case
+   * letter.)
+   * 
+   * @param sb
+   * @param map
+   * @see http://gmod.org/wiki/GFF3#GFF3_Format
+   */
+  void formatAttributes(StringBuilder sb, Map<String, Object> map)
+  {
+    sb.append(TAB);
+    boolean first = true;
+    for (String key : map.keySet())
+    {
+      if (SequenceFeature.STRAND.equals(key)
+              || SequenceFeature.PHASE.equals(key))
+      {
+        /*
+         * values stashed in map but output to their own columns
+         */
+        continue;
+      }
+      {
+        if (!first)
+        {
+          sb.append(";");
+        }
+      }
+      first = false;
+      Object value = map.get(key);
+      if (value instanceof Map<?, ?>)
+      {
+        formatMapAttribute(sb, key, (Map<?, ?>) value);
+      }
+      else
+      {
+        String formatted = StringUtils.urlEncode(value.toString(),
+                GffHelperI.GFF_ENCODABLE);
+        sb.append(key).append("=").append(formatted);
+      }
+    }
+  }
+
+  /**
+   * Formats the map entries as
+   * 
+   * <pre>
+   * jvmap_key={key1=value1,key2=value2,...}
+   * </pre>
+   * 
+   * and appends this to the string buffer
+   * 
+   * @param sb
+   * @param key
+   * @param map
+   */
+  private void formatMapAttribute(StringBuilder sb, String key,
+          Map<?, ?> map)
+  {
+    if (map == null || map.isEmpty())
+    {
+      return;
+    }
+
+    /*
+     * AbstractMap.toString would be a shortcut here, but more reliable
+     * to code the required format in case toString changes in future
+     */
+    sb.append(MAP_ATTRIBUTE_PREFIX).append(key).append("={");
+    boolean first = true;
+    for (Entry<?, ?> entry : map.entrySet())
     {
-      out.append(TAB).append(attributes);
+      if (!first)
+      {
+        sb.append(",");
+      }
+      first = false;
+      sb.append(entry.getKey().toString()).append("=");
+      String formatted = StringUtils.urlEncode(entry.getValue().toString(),
+              GffHelperI.GFF_ENCODABLE);
+      sb.append(formatted);
     }
+    sb.append("}");
   }
 
   /**
@@ -1139,11 +1244,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * format)
    * 
    * @param alignedRegions
-   *          a list of "Align fromStart toStart fromCount"
+   *                         a list of "Align fromStart toStart fromCount"
    * @param mapIsFromCdna
-   *          if true, 'from' is dna, else 'from' is protein
+   *                         if true, 'from' is dna, else 'from' is protein
    * @param strand
-   *          either 1 (forward) or -1 (reverse)
+   *                         either 1 (forward) or -1 (reverse)
    * @return
    * @throws IOException
    */
@@ -1279,38 +1384,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   }
 
   /**
-   * Process the 'column 9' data of the GFF file. This is less formally defined,
-   * and its interpretation will vary depending on the tool that has generated
-   * it.
-   * 
-   * @param attributes
-   * @param sf
-   */
-  protected void processGffColumnNine(String attributes, SequenceFeature sf)
-  {
-    sf.setAttributes(attributes);
-
-    /*
-     * Parse attributes in column 9 and add them to the sequence feature's 
-     * 'otherData' table; use Note as a best proxy for description
-     */
-    char nameValueSeparator = gffVersion == 3 ? '=' : ' ';
-    // TODO check we don't break GFF2 values which include commas here
-    Map<String, List<String>> nameValues = GffHelperBase
-            .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
-    for (Entry<String, List<String>> attr : nameValues.entrySet())
-    {
-      String values = StringUtils.listToDelimitedString(attr.getValue(),
-              "; ");
-      sf.setValue(attr.getKey(), values);
-      if (NOTE.equals(attr.getKey()))
-      {
-        sf.setDescription(values);
-      }
-    }
-  }
-
-  /**
    * After encountering ##fasta in a GFF3 file, process the remainder of the
    * file as FAST sequence data. Any placeholder sequences created during
    * feature parsing are updated with the actual sequences.