import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
}
/**
+ * Get the RNA Secondary Structure SequenceFeature Array if present
+ */
+ public SequenceFeature[] getRnaSecondaryStructure()
+ {
+ return this._rnasecstr;
+ }
+
+ /**
+ * Check the RNA Secondary Structure is equivalent to one in given
+ * AlignmentAnnotation param
+ */
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
+ {
+ return rnaSecondaryStructureEquivalent(that, true);
+ }
+
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+ {
+ SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
+ SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
+ if (thisSfArray == null || thatSfArray == null)
+ {
+ return thisSfArray == null && thatSfArray == null;
+ }
+ if (thisSfArray.length != thatSfArray.length)
+ {
+ return false;
+ }
+ Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
+ // like this
+ for (int i=0; i < thisSfArray.length; i++) {
+ SequenceFeature thisSf = thisSfArray[i];
+ SequenceFeature thatSf = thatSfArray[i];
+ if (compareType) {
+ if (thisSf.getType() == null || thatSf.getType() == null) {
+ if (thisSf.getType() == null && thatSf.getType() == null) {
+ continue;
+ } else {
+ return false;
+ }
+ }
+ if (! thisSf.getType().equals(thatSf.getType())) {
+ return false;
+ }
+ }
+ if (!(thisSf.getBegin() == thatSf.getBegin()
+ && thisSf.getEnd() == thatSf.getEnd()))
+ {
+ return false;
+ }
+ }
+ return true;
+
+ }
+
+ /**
* map of positions in the associated annotation
*/
private Map<Integer, Annotation> sequenceMapping;
char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
+ // DEBUG System.out.println(i + ": " + annotations[i]);
if (annotations[i] == null)
{
continue;
if (annotations[i].secondaryStructure == 'H'
|| annotations[i].secondaryStructure == 'E')
{
+ // DEBUG System.out.println( "/H|E/ '" +
+ // annotations[i].secondaryStructure + "'");
hasIcons |= true;
}
else
// Check for RNA secondary structure
{
- // System.out.println(annotations[i].secondaryStructure);
+ // DEBUG System.out.println( "/else/ '" +
+ // annotations[i].secondaryStructure + "'");
// TODO: 2.8.2 should this ss symbol validation check be a function in
// RNA/ResidueProperties ?
if (annotations[i].secondaryStructure == '('
|| annotations[i].secondaryStructure == 'B'
|| annotations[i].secondaryStructure == 'C'
|| annotations[i].secondaryStructure == 'D'
- || annotations[i].secondaryStructure == 'E'
+ // || annotations[i].secondaryStructure == 'E' // ambiguous on
+ // its own -- already checked above
|| annotations[i].secondaryStructure == 'F'
|| annotations[i].secondaryStructure == 'G'
- || annotations[i].secondaryStructure == 'H'
+ // || annotations[i].secondaryStructure == 'H' // ambiguous on
+ // its own -- already checked above
|| annotations[i].secondaryStructure == 'I'
|| annotations[i].secondaryStructure == 'J'
|| annotations[i].secondaryStructure == 'K'
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
- && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '(' && firstChar != '[' && firstChar != '<'
&& firstChar != '{' && firstChar != 'A' && firstChar != 'B'
&& firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
&& firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
}
}
+ public static Iterable<AlignmentAnnotation> findAnnotations(
+ Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
+ String label)
+ {
+
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+ for (AlignmentAnnotation ann : list)
+ {
+ if ((calcId == null || (ann.getCalcId() != null
+ && ann.getCalcId().equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null
+ && ann.sequenceRef == seq))
+ && (label == null
+ || (ann.label != null && ann.label.equals(label))))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
+ /**
+ * Answer true if any annotation matches the calcId passed in (if not null).
+ *
+ * @param list
+ * annotation to search
+ * @param calcId
+ * @return
+ */
+ public static boolean hasAnnotation(List<AlignmentAnnotation> list,
+ String calcId)
+ {
+
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : list)
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public static Iterable<AlignmentAnnotation> findAnnotation(
+ List<AlignmentAnnotation> list, String calcId)
+ {
+
+ List<AlignmentAnnotation> aa = new ArrayList<>();
+ if (calcId == null)
+ {
+ return aa;
+ }
+ for (AlignmentAnnotation a : list)
+ {
+
+ if (a.getCalcId() == calcId || (a.getCalcId() != null
+ && calcId != null && a.getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
}