JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index ca2b6d4..f8e70b1 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -472,18 +472,19 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the sequence name, with '/start-end' appended if jvsuffix is true
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public String getDisplayId(boolean jvsuffix)
   {
-    StringBuffer result = new StringBuffer(name);
-    if (jvsuffix)
+    if (!jvsuffix)
     {
-      result.append("/" + start + "-" + end);
+      return name;
     }
+    StringBuilder result = new StringBuilder(name);
+    result.append("/").append(start).append("-").append(end);
 
     return result.toString();
   }
@@ -522,6 +523,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -696,8 +698,8 @@ public class Sequence extends ASequence implements SequenceI
   public void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map)
   {
-    addDBRef(new DBRefEntry(speciesId, assemblyId,
-            DBRefEntry.CHROMOSOME + ":" + chromosomeId, new Mapping(map)));
+    addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+            new Mapping(map)));
   }
 
   /**
@@ -713,41 +715,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (final DBRefEntry ref : refs)
       {
-        if (ref.isChromosome())
+        if (ref instanceof GeneLociI)
         {
-          return new GeneLociI()
-          {
-            @Override
-            public String getSpeciesId()
-            {
-              return ref.getSource();
-            }
-
-            @Override
-            public String getAssemblyId()
-            {
-              // DEV NOTE: DBRefEntry is reused here to hold chromosomal locus
-              // of a gene sequence.
-              // source=species, version=assemblyId, accession=chromosome, map =
-              // positions.
-
-              return ref.getVersion();
-            }
-
-            @Override
-            public String getChromosomeId()
-            {
-              // strip off "chromosome:" prefix to chrId
-              return ref.getAccessionId()
-                      .substring(DBRefEntry.CHROMOSOME.length() + 1);
-            }
-
-            @Override
-            public MapList getMap()
-            {
-              return ref.getMap().getMap();
-            }
-          };
+          return (GeneLociI) ref;
         }
       }
     }
@@ -1445,6 +1415,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO JAL-3980 maintain as sorted list
     if (datasetSequence != null)
     {
       datasetSequence.addDBRef(entry);
@@ -1455,6 +1426,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       dbrefs = new DBModList<>();
     }
+    // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
 
     for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
@@ -1612,7 +1584,7 @@ public class Sequence extends ASequence implements SequenceI
       _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
-  };
+  }
 
   /*
    * (non-Javadoc)
@@ -1829,13 +1801,30 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
+    return getAlignmentAnnotations(calcId, label, null, true);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description)
+  {
+    return getAlignmentAnnotations(calcId, label, description, false);
+  }
+
+  private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description, boolean ignoreDescription)
+  {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        if ((ann.calcId != null && ann.calcId.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
+
         {
           result.add(ann);
         }
@@ -1967,15 +1956,6 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
-    if (datasetSequence != null)
-    {
-      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-              types);
-    }
-    else
-    {
-      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    }
 
     /*
      * if end column is gapped, endPos may be to the right,