JAL-2041 add ID,clinical_significance to feature attributes (for export)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fa135f8..42a1201 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
+
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -69,7 +71,6 @@ public class AlignmentUtils
 
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
   private static final String ID = "ID";
-  private static final String CLINICAL_SIGNIFICANCE = "clinical_significance";
 
   /**
    * A data model to hold the 'normal' base value at a position, and an optional
@@ -1927,10 +1928,11 @@ public class AlignmentUtils
     if (trans != null && !trans.equals(residue))
     {
       String desc = residue + "->" + trans;
-      // set score to 0f so 'graduated colour' option is offered!
+      // set score to 0f so 'graduated colour' option is offered! JAL-2060
       SequenceFeature sf = new SequenceFeature(
               SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
               peptidePos, 0f, null);
+      StringBuilder attributes = new StringBuilder(32);
       String id = (String) var.variant.getValue(ID);
       if (id != null)
       {
@@ -1939,6 +1941,7 @@ public class AlignmentUtils
           id = id.substring(SEQUENCE_VARIANT.length());
         }
         sf.setValue(ID, id);
+        attributes.append(ID).append("=").append(id);
         // TODO handle other species variants
         StringBuilder link = new StringBuilder(32);
         try
@@ -1957,8 +1960,14 @@ public class AlignmentUtils
       if (clinSig != null)
       {
         sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
+        attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
+                .append(clinSig);
       }
       peptide.addSequenceFeature(sf);
+      if (attributes.length() > 0)
+      {
+        sf.setAttributes(attributes.toString());
+      }
       return true;
     }
     return false;

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 4c9aa05..f2eb8ac 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -39,6 +39,10 @@ public class SequenceFeature
   // private key for Phase designed not to conflict with real GFF data
   private static final String PHASE = "!Phase";
 
+  /*
+   * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
+   * name1=value1;name2=value2,value3;...etc
+   */
   private static final String ATTRIBUTES = "ATTRIBUTES";
 
   public int begin;

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8469355..2d76d6b 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -23,6 +23,7 @@ package jalview.io;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.io.gff.GffConstants;
 import jalview.util.DBRefUtils;
 import jalview.util.UrlLink;
 
@@ -175,7 +176,8 @@ public class SequenceAnnotationReport
         {
           sb.append("; (").append(status).append(")");
         }
-        String clinSig = (String) feature.getValue("clinical_significance");
+        String clinSig = (String) feature
+                .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
         if (clinSig != null)
         {
           sb.append("; ").append(clinSig);

diff --git a/src/jalview/io/gff/GffConstants.java b/src/jalview/io/gff/GffConstants.java
new file mode 100644 (file)
index 0000000..545c6e3
--- /dev/null
+++ b/src/jalview/io/gff/GffConstants.java
@@ -0,0 +1,23 @@
+package jalview.io.gff;
+
+/**
+ * A class to hold constants shared by creators and consumers of GFF or feature
+ * data
+ */
+public class GffConstants
+{
+  // SequenceOntology terms are to be found in SequenceOntologyI
+
+  /*
+   * clinical_significance may be an attribute of 
+   * sequence_variant data from Ensembl
+   */
+  public static final String CLINICAL_SIGNIFICANCE = "clinical_significance";
+
+  /*
+   * not instantiable
+   */
+  private GffConstants()
+  {
+  }
+}

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index d811bef..860d979 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1971,6 +1971,7 @@ public class AlignmentUtilsTests
     assertEquals("K->E", sf.getDescription());
     assertEquals("var1.125A>G", sf.getValue("ID"));
     assertNull(sf.getValue("clinical_significance"));
+    assertEquals("ID=var1.125A>G", sf.getAttributes());
     assertEquals(1, sf.links.size());
     // link to variation is urlencoded
     assertEquals(
@@ -1982,6 +1983,7 @@ public class AlignmentUtilsTests
     assertEquals("K->Q", sf.getDescription());
     assertEquals("var2", sf.getValue("ID"));
     assertEquals("Dodgy", sf.getValue("clinical_significance"));
+    assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
             "K->Q var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
@@ -1992,6 +1994,7 @@ public class AlignmentUtilsTests
     assertEquals("K->N", sf.getDescription());
     assertEquals("var4", sf.getValue("ID"));
     assertEquals("Benign", sf.getValue("clinical_significance"));
+    assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
             "K->N var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
@@ -2002,6 +2005,7 @@ public class AlignmentUtilsTests
     assertEquals("P->H", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
+    assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
             "P->H var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
@@ -2013,6 +2017,7 @@ public class AlignmentUtilsTests
     assertEquals("P->R", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
+    assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
             "P->R var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",