Merge branch 'features/JAL-3375vcfValidation' into

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 6b82671..5a55b5b 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -23,6 +23,8 @@ package jalview.io;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -68,11 +70,11 @@ public class SequenceAnnotationReport
     @Override
     public int compare(DBRefEntry ref1, DBRefEntry ref2)
     {
-      if (ref1.isChromosome())
+      if (ref1 instanceof GeneLociI)
       {
         return -1;
       }
-      if (ref2.isChromosome())
+      if (ref2 instanceof GeneLociI)
       {
         return 1;
       }
@@ -125,19 +127,33 @@ public class SequenceAnnotationReport
    * Append text for the list of features to the tooltip
    * 
    * @param sb
-   * @param rpos
+   * @param residuePos
    * @param features
    * @param minmax
    */
-  public void appendFeatures(final StringBuilder sb, int rpos,
+  public void appendFeatures(final StringBuilder sb, int residuePos,
           List<SequenceFeature> features, FeatureRendererModel fr)
   {
-    if (features != null)
+    for (SequenceFeature feature : features)
     {
-      for (SequenceFeature feature : features)
-      {
-        appendFeature(sb, rpos, fr, feature);
-      }
+      appendFeature(sb, residuePos, fr, feature, null);
+    }
+  }
+
+  /**
+   * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
+   * 
+   * @param sb
+   * @param residuePos
+   * @param mf
+   * @param fr
+   */
+  public void appendFeatures(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr)
+  {
+    for (SequenceFeature feature : mf.features)
+    {
+      appendFeature(sb, residuePos, fr, feature, mf);
     }
   }
 
@@ -150,7 +166,8 @@ public class SequenceAnnotationReport
    * @param feature
    */
   void appendFeature(final StringBuilder sb, int rpos,
-          FeatureRendererModel fr, SequenceFeature feature)
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf)
   {
     if (feature.isContactFeature())
     {
@@ -219,6 +236,15 @@ public class SequenceAnnotationReport
           }
         }
       }
+
+      if (mf != null)
+      {
+        String variants = mf.findProteinVariants(feature);
+        if (!variants.isEmpty())
+        {
+          sb.append(" ").append(variants);
+        }
+      }
     }
   }
 
@@ -373,7 +399,7 @@ public class SequenceAnnotationReport
               .getNonPositionalFeatures())
       {
         int sz = -sb.length();
-        appendFeature(sb, 0, fr, sf);
+        appendFeature(sb, 0, fr, sf, null);
         sz += sb.length();
         maxWidth = Math.max(maxWidth, sz);
       }