import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
-import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
/** Array of annotations placed in the current coordinate system */
public Annotation[] annotations;
- public ArrayList<SimpleBP> bps = null;
+ public List<SimpleBP> bps = null;
/**
* RNA secondary structure contact positions
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
- * @param RNAannot
+ * @param rnaAnnotation
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
try
{
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- bps = Rna.GetModeleBP(RNAannot);
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
{
return;
}
- Rna.HelixMap(_rnasecstr);
- // setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
*/
private Map<Integer, Annotation> sequenceMapping;
- /** DOCUMENT ME!! */
+ /**
+ * lower range for quantitative data
+ */
public float graphMin;
- /** DOCUMENT ME!! */
+ /**
+ * Upper range for quantitative data
+ */
public float graphMax;
/**
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
sequenceRef = null;
}
}
- // JBPNote: what does this do ?
- public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
- {
- bps = Rna.GetModeleBP(RNAannot);
- }
-
/**
* Creates a new AlignmentAnnotation object.
*
this(0, annotations.length);
}
- public AnnotCharSequence(int start, int end)
+ AnnotCharSequence(int start, int end)
{
offset = start;
max = end;
if (annotations == null)
{
visible = false; // try to prevent renderer from displaying.
+ invalidrnastruc = -1;
return; // this is a non-annotation row annotation - ie a sequence score.
}
@Override
public String toString()
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
}
+ /**
+ * When positional annotation and a sequence reference is present, clears and
+ * resizes the annotations array to the current alignment width, and adds
+ * annotation according to aligned positions of the sequenceRef given by
+ * sequenceMapping.
+ */
public void adjustForAlignment()
{
if (sequenceRef == null)
}
/**
- * Associate this annotion with the aligned residues of a particular sequence.
- * sequenceMapping will be updated in the following way: null sequenceI -
- * existing mapping will be discarded but annotations left in mapped
- * positions. valid sequenceI not equal to current sequenceRef: mapping is
- * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+ * Associate this annotation with the aligned residues of a particular
+ * sequence. sequenceMapping will be updated in the following way: null
+ * sequenceI - existing mapping will be discarded but annotations left in
+ * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+ * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
* parameter to specify correspondence between current and new sequenceRef
*
* @param sequenceI
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- ColumnSelection colSel)
+ HiddenColumns hidden)
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
- colSel.makeVisibleAnnotation(this);
+ hidden.makeVisibleAnnotation(this);
}
public void setPadGaps(boolean padgaps, char gapchar)
* @note caller should add the remapped annotation to newref if they have not
* already
*/
- public void remap(SequenceI newref, int[][] mapping, int from, int to,
- int idxoffset)
+ public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
+ int from, int to, int idxoffset)
{
if (mapping != null)
{
Map<Integer, Annotation> old = sequenceMapping;
Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
int index = -1;
- for (int mp[] : mapping)
+ for (int mp[] : mapping.values())
{
if (index++ < 0)
{
this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
}
+ /**
+ * Returns the match for the last unmatched opening RNA helix pair symbol
+ * preceding the given column, or '(' if nothing found to match.
+ *
+ * @param column
+ * @return
+ */
+ public String getDefaultRnaHelixSymbol(int column)
+ {
+ String result = "(";
+ if (annotations == null)
+ {
+ return result;
+ }
+
+ /*
+ * for each preceding column, if it contains an open bracket,
+ * count whether it is still unmatched at column, if so return its pair
+ * (likely faster than the fancy alternative using stacks)
+ */
+ for (int col = column - 1; col >= 0; col--)
+ {
+ Annotation annotation = annotations[col];
+ if (annotation == null)
+ {
+ continue;
+ }
+ String displayed = annotation.displayCharacter;
+ if (displayed == null || displayed.length() != 1)
+ {
+ continue;
+ }
+ char symbol = displayed.charAt(0);
+ if (!Rna.isOpeningParenthesis(symbol))
+ {
+ continue;
+ }
+
+ /*
+ * found an opening bracket symbol
+ * count (closing-opening) symbols of this type that follow it,
+ * up to and excluding the target column; if the count is less
+ * than 1, the opening bracket is unmatched, so return its match
+ */
+ String closer = String.valueOf(Rna
+ .getMatchingClosingParenthesis(symbol));
+ String opener = String.valueOf(symbol);
+ int count = 0;
+ for (int j = col + 1; j < column; j++)
+ {
+ if (annotations[j] != null)
+ {
+ String s = annotations[j].displayCharacter;
+ if (closer.equals(s))
+ {
+ count++;
+ }
+ else if (opener.equals(s))
+ {
+ count--;
+ }
+ }
+ }
+ if (count < 1)
+ {
+ return closer;
+ }
+ }
+ return result;
+ }
+
protected static synchronized long nextId()
{
return counter++;
}
+
+ /**
+ *
+ * @return true for rows that have a range of values in their annotation set
+ */
+ public boolean isQuantitative()
+ {
+ return graphMin < graphMax;
+ }
}
git://source.jalview.org / jalview.git / blobdiff