Merge branch 'bug/JAL-2034contextchange' into develop

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 76ad093..8c29ca5 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -52,6 +52,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   boolean colourText = false;
 
   /**
+   * True if the group is defined as a group on the alignment, false if it is
+   * just a selection.
+   */
+  boolean isDefined = false;
+
+  /**
    * after Olivier's non-conserved only character display
    */
   boolean showNonconserved = false;
@@ -59,7 +65,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private List<SequenceI> sequences = new ArrayList<SequenceI>();
+  private List<SequenceI> sequences = new ArrayList<>();
 
   /**
    * representative sequence for this group (if any)
@@ -161,7 +167,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this();
     if (seqsel != null)
     {
-      sequences = new ArrayList<SequenceI>();
+      sequences = new ArrayList<>();
       sequences.addAll(seqsel.sequences);
       if (seqsel.groupName != null)
       {
@@ -311,7 +317,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     else
     {
-      List<SequenceI> allSequences = new ArrayList<SequenceI>();
+      List<SequenceI> allSequences = new ArrayList<>();
       for (SequenceI seq : sequences)
       {
         allSequences.add(seq);
@@ -1015,7 +1021,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new ArrayList<SequenceI>();
+    sgroup.sequences = new ArrayList<>();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
       if (map == null || map.containsKey(insect[s]))
@@ -1242,7 +1248,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     // TODO add in other methods like 'getAlignmentAnnotation(String label),
     // etc'
-    ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
     synchronized (sequences)
     {
       for (SequenceI seq : sequences)
@@ -1274,7 +1280,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {
       return aa;
@@ -1293,7 +1299,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
       if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
@@ -1343,9 +1349,28 @@ public class SequenceGroup implements AnnotatedCollectionI
   private AnnotatedCollectionI context;
 
   /**
+   * Sets the alignment or group context for this group, and whether it is
+   * defined as a group
+   * 
+   * @param ctx
+   *          the context for the group
+   * @param defined
+   *          whether the group is defined on the alignment or is just a
+   *          selection
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
+   */
+  public void setContext(AnnotatedCollectionI ctx, boolean defined)
+  {
+    setContext(ctx);
+    this.isDefined = defined;
+  }
+
+  /**
    * Sets the alignment or group context for this group
    * 
    * @param ctx
+   *          the context for the group
    * @throws IllegalArgumentException
    *           if setting the context would result in a circular reference chain
    */
@@ -1375,6 +1400,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     return context;
   }
 
+  public boolean isDefined()
+  {
+    return isDefined;
+  }
+
   public void setColourScheme(ColourSchemeI scheme)
   {
     if (cs == null)