this.calcId = annotation.calcId;
if (annotation.properties != null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
for (Map.Entry<String, String> val : annotation.properties.entrySet())
{
properties.put(val.getKey(), val.getValue());
if (annotation.sequenceMapping != null)
{
Integer p = null;
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
Iterator<Integer> pos = annotation.sequenceMapping.keySet()
.iterator();
while (pos.hasNext())
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> newmapping = new HashMap<>();
Iterator<Integer> e = sequenceMapping.keySet().iterator();
while (e.hasNext())
{
{
return;
}
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
int seqPos;
/**
* properties associated with the calcId
*/
- protected Map<String, String> properties = new HashMap<String, String>();
+ protected Map<String, String> properties = new HashMap<>();
/**
* base colour for line graphs. If null, will be set automatically by
: false;
// TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> mapForsq = new HashMap<>();
if (sequenceMapping != null)
{
if (sp2sq != null)
if (mapping != null)
{
Map<Integer, Annotation> old = sequenceMapping;
- Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> remap = new HashMap<>();
int index = -1;
for (int mp[] : mapping.values())
{
{
if (properties == null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
}
properties.put(property, value);
}
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
-
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
if ((calcId == null || (ann.getCalcId() != null
public static Iterable<AlignmentAnnotation> findAnnotation(
List<AlignmentAnnotation> list, String calcId)
{
-
List<AlignmentAnnotation> aa = new ArrayList<>();
if (calcId == null)
{