+
+ /**
+ * set flag indicating if logo should be normalised when rendered
+ *
+ * @param norm
+ */
+ public void setNormaliseSequenceLogo(boolean norm)
+ {
+ normaliseSequenceLogo = norm;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ @Override
+ /**
+ * returns a new array with all annotation involving this group
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ // TODO add in other methods like 'getAlignmentAnnotation(String label),
+ // etc'
+ ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
+ {
+ for (AlignmentAnnotation al : aa)
+ {
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
+ }
+ }
+ }
+ if (consensus != null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation != null)
+ {
+ annot.add(conservation);
+ }
+ }
+ return annot.toArray(new AlignmentAnnotation[0]);
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+ }
+
+ /**
+ * Answer true if any annotation matches the calcId passed in (if not null).
+ *
+ * @param calcId
+ * @return
+ */
+ public boolean hasAnnotation(String calcId)
+ {
+ return AlignmentAnnotation
+ .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
+ }
+
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
+ public void clear()
+ {
+ synchronized (sequences)
+ {
+ int before = sequences.size();
+ sequences.clear();
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+ sequences.size());
+ }
+ }
+
+ /**
+ * 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
+ */
+ public void setContext(AnnotatedCollectionI ctx)
+ {
+ AnnotatedCollectionI ref = ctx;
+ while (ref != null)
+ {
+ if (ref == this || ref.getContext() == ctx)
+ {
+ throw new IllegalArgumentException(
+ "Circular reference in SequenceGroup.context");
+ }
+ ref = ref.getContext();
+ }
+ this.context = ctx;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return context;
+ }
+
+ public boolean isDefined()
+ {
+ return isDefined;
+ }
+
+ public void setColourScheme(ColourSchemeI scheme)
+ {
+ if (cs == null)
+ {
+ cs = new ResidueShader();
+ }
+ cs.setColourScheme(scheme);
+ }
+
+ public void setGroupColourScheme(ResidueShaderI scheme)
+ {
+ cs = scheme;
+ }
+
+ public ColourSchemeI getColourScheme()
+ {
+ return cs == null ? null : cs.getColourScheme();
+ }
+
+ public ResidueShaderI getGroupColourScheme()
+ {
+ return cs;
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ if (context != null)
+ {
+ return context.isNucleotide();
+ }
+ return false;
+ }
+
+ /**
+ * @param seq
+ * @return true if seq is a member of the group
+ */
+
+ public boolean contains(SequenceI seq1)
+ {
+ return sequences.contains(seq1);
+ }
+
+ /**
+ * @param seq
+ * @param apos
+ * @return true if startRes<=apos and endRes>=apos and seq is in the group
+ */
+ public boolean contains(SequenceI seq, int apos)
+ {
+ return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+ }