*/
package jalview.datamodel;
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
/**
* DOCUMENT ME!
*
*/
private long invalidrnastruc = -2;
+ private double bitScore;
+
+ private double eValue;
+
/**
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
}
/**
+ * 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;
// annotations[i].secondaryStructure + "'");
// TODO: 2.8.2 should this ss symbol validation check be a function in
// RNA/ResidueProperties ?
+ // allow for DSSP extended code:
+ // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
+ // GHITEBS as well as C and X (for missing?)
if (annotations[i].secondaryStructure == '('
|| annotations[i].secondaryStructure == '['
|| annotations[i].secondaryStructure == '<'
|| annotations[i].secondaryStructure == '{'
|| annotations[i].secondaryStructure == 'A'
- || annotations[i].secondaryStructure == 'B'
- || annotations[i].secondaryStructure == 'C'
+ // || 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 == 'I'
+ // || annotations[i].secondaryStructure == 'G'
+ // || 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].secondaryStructure == 'L'
|| annotations[i].secondaryStructure == 'P'
|| annotations[i].secondaryStructure == 'Q'
|| annotations[i].secondaryStructure == 'R'
- || annotations[i].secondaryStructure == 'S'
- || annotations[i].secondaryStructure == 'T'
+ // || annotations[i].secondaryStructure == 'S'
+ // || annotations[i].secondaryStructure == 'T'
|| annotations[i].secondaryStructure == 'U'
|| annotations[i].secondaryStructure == 'V'
|| annotations[i].secondaryStructure == 'W'
- || annotations[i].secondaryStructure == 'X'
+ // || annotations[i].secondaryStructure == 'X'
|| annotations[i].secondaryStructure == 'Y'
|| annotations[i].secondaryStructure == 'Z')
{
: annotations[index + offset].displayCharacter == null
|| annotations[index
+ offset].displayCharacter
- .length() == 0
- ? annotations[index
- + offset].secondaryStructure
- : annotations[index
- + offset].displayCharacter
- .charAt(0));
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
}
return null;
}
-
+
/**
* Creates a new AlignmentAnnotation object.
*
}
}
}
-
+
/**
* Copy constructor creates a new independent annotation row with the same
* associated sequenceRef
public AlignmentAnnotation(AlignmentAnnotation annotation)
{
setAnnotationId();
+ updateAlignmentAnnotationFrom(annotation);
+ }
+
+ /**
+ * copy attributes and annotation from an existing annotation (used by copy
+ * constructor). This method does not update the unique annotationId
+ *
+ * @param annotation
+ */
+ public void updateAlignmentAnnotationFrom(AlignmentAnnotation annotation)
+ {
this.label = new String(annotation.label);
if (annotation.description != null)
{
this.scaleColLabel = annotation.scaleColLabel;
this.showAllColLabels = annotation.showAllColLabels;
this.calcId = annotation.calcId;
+ this.bitScore = annotation.bitScore;
+ this.eValue = annotation.eValue;
+
if (annotation.properties != null)
{
properties = new HashMap<>();
* @param seqRef
* @param startRes
* @param alreadyMapped
+ * - annotation are at aligned columns
*/
public void createSequenceMapping(SequenceI seqRef, int startRes,
boolean alreadyMapped)
seqPos = i + startRes;
}
- sequenceMapping.put(new Integer(seqPos), annotations[i]);
+ sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
}
}
{
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
- index = new Integer(a);
+ index = Integer.valueOf(a);
Annotation annot = sequenceMapping.get(index);
if (annot != null)
{
{
return hasScore || !Double.isNaN(score);
}
-
+
/**
* Score only annotation
*
makeVisibleAnnotation(hidden);
}
+
public void setPadGaps(boolean padgaps, char gapchar)
{
this.padGaps = padgaps;
{
if (seqname && this.sequenceRef != null)
{
- int i = description.toLowerCase().indexOf("<html>");
+ int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
if (i > -1)
{
// move the html tag to before the sequence reference.
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
-
ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
public static Iterable<AlignmentAnnotation> findAnnotation(
List<AlignmentAnnotation> list, String calcId)
{
-
List<AlignmentAnnotation> aa = new ArrayList<>();
if (calcId == null)
{
}
return aa;
}
+
+ public double getBitScore()
+ {
+ return bitScore;
+ }
+
+ public void setBitScore(double bitScore)
+ {
+ this.bitScore = bitScore;
+ }
+
+ public double getEValue()
+ {
+ return eValue;
+ }
+
+ public void setEValue(double eValue)
+ {
+ this.eValue = eValue;
+ }
+
+ public static AlignmentAnnotation findFirstAnnotation(
+ Iterable<AlignmentAnnotation> alignmentAnnotation, String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+
+ for (AlignmentAnnotation annot : alignmentAnnotation)
+ {
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff