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'
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;
{
return;
}
- hidden.makeVisibleAnnotation(this);
+ makeVisibleAnnotation(hidden);
}
public void setPadGaps(boolean padgaps, char gapchar)
/**
* 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);
}
return graphMin < graphMax;
}
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+ }
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ if (hiddenColumns.hasHiddenColumns())
+ {
+ removeHiddenAnnotation(start, end, hiddenColumns);
+ }
+ else
+ {
+ restrict(start, end);
+ }
+ }
+ }
+
+ /**
+ * The actual implementation of deleting hidden annotation columns
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ private void removeHiddenAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ // mangle the alignmentAnnotation annotation array
+ ArrayList<Annotation[]> annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+ end + 1, false);
+
+ int copylength;
+ int annotationLength;
+ while (blocks.hasNext())
+ {
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ if (annotationLength + block[0] <= annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ copylength = annotations.length - block[0];
+ }
+ }
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(annotations, block[0], els, 0, copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, annotations, w, chnk.length);
+ w += chnk.length;
+ }
+ }
+ }
+
public static Iterable<AlignmentAnnotation> findAnnotations(
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
}
for (AlignmentAnnotation a : list)
{
- if (calcId.equals(a.getCalcId()))
+
+ if (a.getCalcId() == calcId || (a.getCalcId() != null
+ && calcId != null && a.getCalcId().equals(calcId)))
{
aa.add(a);
}
}
return aa;
}
+
}
git://source.jalview.org / jalview.git / blobdiff