Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalv...

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 6b82671..66db038 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,8 +21,11 @@
 package jalview.io;
 
 import jalview.api.FeatureColourI;
+import jalview.datamodel.AlignmentAnnotation;
 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 +71,11 @@ 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 +128,33 @@ 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 +167,8 @@ 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 +237,15 @@ public class SequenceAnnotationReport
           }
         }
       }
+
+      if (mf != null)
+      {
+        String variants = mf.findProteinVariants(feature);
+        if (!variants.isEmpty())
+        {
+          sb.append(" ").append(variants);
+        }
+      }
     }
   }
 
@@ -353,12 +380,27 @@ public class SequenceAnnotationReport
       sb.append("<br>").append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
+
     SequenceI ds = sequence;
     while (ds.getDatasetSequence() != null)
     {
       ds = ds.getDatasetSequence();
     }
 
+    /*
+     * add any annotation scores
+     */
+    AlignmentAnnotation[] anns = ds.getAnnotation();
+    for (int i = 0; anns != null && i < anns.length; i++)
+    {
+      AlignmentAnnotation aa = anns[i];
+      if (aa != null && aa.hasScore() && aa.sequenceRef != null)
+      {
+        sb.append("<br>").append(aa.label).append(": ")
+                .append(aa.getScore());
+      }
+    }
+
     if (showDbRefs)
     {
       maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
@@ -373,12 +415,29 @@ 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);
       }
     }
+
+
+    if (sequence.getAnnotation("Search Scores") != null)
+    {
+      sb.append("<br>");
+      String eValue = " E-Value: "
+              + sequence.getAnnotation("Search Scores")[0].getEValue();
+      String bitScore = " Bit Score: "
+              + sequence.getAnnotation("Search Scores")[0].getBitScore();
+      sb.append(eValue);
+      sb.append("<br>");
+      sb.append(bitScore);
+      maxWidth = Math.max(maxWidth, eValue.length());
+      maxWidth = Math.max(maxWidth, bitScore.length());
+    }
+    sb.append("<br>");
     sb.append("</i>");
+
     return maxWidth;
   }