*/
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
+ *
+ * @param rnaAnnotation
+ */
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
+ {
+ try
+ {
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
+ {
+ // DEBUG System.out.println(px);
+ invalidrnastruc = px.getProblemPos();
+ }
+ if (invalidrnastruc > -1)
+ {
+ return;
+ }
+
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ isrna = true;
+ showAllColLabels = true;
+ scaleColLabel = true;
+ _markRnaHelices();
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
+ }
+
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
+
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
+ }
+
+ /**
+ * 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
*/
}
else if (string.equalsIgnoreCase("LINE_GRAPH"))
{
- return LINE_GRAPH;
- }
- else
- {
- return NO_GRAPH;
- }
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * short label shown under sequence labels
- * @param description
- * text displayed on mouseover
- * @param annotations
- * set of positional annotation elements
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations)
- {
- setAnnotationId();
- // always editable?
- editable = true;
- this.label = label;
- this.description = description;
- this.annotations = annotations;
-
- validateRangeAndDisplay();
- }
-
- /**
- * Copy constructor creates a new independent annotation row with the same
- * associated sequenceRef
- *
- * @param annotation
- */
- public AlignmentAnnotation(AlignmentAnnotation annotation)
- {
- setAnnotationId();
- this.label = new String(annotation.label);
- if (annotation.description != null)
- {
- this.description = new String(annotation.description);
- }
- this.graphMin = annotation.graphMin;
- this.graphMax = annotation.graphMax;
- this.graph = annotation.graph;
- this.graphHeight = annotation.graphHeight;
- this.graphGroup = annotation.graphGroup;
- this.groupRef = annotation.groupRef;
- this.editable = annotation.editable;
- this.autoCalculated = annotation.autoCalculated;
- this.hasIcons = annotation.hasIcons;
- this.hasText = annotation.hasText;
- this.height = annotation.height;
- this.label = annotation.label;
- this.padGaps = annotation.padGaps;
- this.visible = annotation.visible;
- this.centreColLabels = annotation.centreColLabels;
- this.scaleColLabel = annotation.scaleColLabel;
- this.showAllColLabels = annotation.showAllColLabels;
- this.calcId = annotation.calcId;
- if (annotation.properties != null)
- {
- properties = new HashMap<>();
- for (Map.Entry<String, String> val : annotation.properties.entrySet())
- {
- properties.put(val.getKey(), val.getValue());
- }
- }
- if (this.hasScore = annotation.hasScore)
- {
- this.score = annotation.score;
- }
- if (annotation.threshold != null)
- {
- threshold = new GraphLine(annotation.threshold);
- }
- Annotation[] ann = annotation.annotations;
- if (annotation.annotations != null)
- {
- this.annotations = new Annotation[ann.length];
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] != null)
- {
- annotations[i] = new Annotation(ann[i]);
- if (_linecolour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- }
- }
- if (annotation.sequenceRef != null)
- {
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
- {
- Integer p = null;
- sequenceMapping = new HashMap<>();
- Iterator<Integer> pos = annotation.sequenceMapping.keySet()
- .iterator();
- while (pos.hasNext())
- {
- // could optimise this!
- p = pos.next();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
- if (ann != null)
- {
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] == a)
- {
- sequenceMapping.put(p, annotations[i]);
- }
- }
- }
- }
- }
- else
- {
- this.sequenceMapping = null;
- }
- }
- // TODO: check if we need to do this: JAL-952
- // if (this.isrna=annotation.isrna)
- {
- // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
- }
- validateRangeAndDisplay(); // construct hashcodes, etc.
- }
-
- /**
- * copy constructor with edit based on the hidden columns marked in colSel
- *
- * @param alignmentAnnotation
- * @param colSel
- */
- public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- HiddenColumns hidden)
- {
- this(alignmentAnnotation);
- if (annotations == null)
- {
- return;
- }
- makeVisibleAnnotation(hidden);
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * DOCUMENT ME!
- * @param description
- * DOCUMENT ME!
- * @param annotations
- * DOCUMENT ME!
- * @param min
- * DOCUMENT ME!
- * @param max
- * DOCUMENT ME!
- * @param winLength
- * DOCUMENT ME!
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max, int graphType)
- {
- setAnnotationId();
- // graphs are not editable
- editable = graphType == 0;
-
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
- graphMin = min;
- graphMax = max;
- validateRangeAndDisplay();
- }
-
- /**
- * Score only annotation
- *
- * @param label
- * @param description
- * @param score
- */
- public AlignmentAnnotation(String label, String description, double score)
- {
- this(label, description, null);
- setScore(score);
- }
-
- /**
- * Updates the _rnasecstr field Determines the positions that base pair and
- * the positions of helices based on secondary structure from a Stockholm file
- *
- * @param rnaAnnotation
- */
- private void _updateRnaSecStr(CharSequence rnaAnnotation)
- {
- try
- {
- _rnasecstr = Rna.getHelixMap(rnaAnnotation);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
- {
- // DEBUG System.out.println(px);
- invalidrnastruc = px.getProblemPos();
- }
- if (invalidrnastruc > -1)
- {
- return;
- }
-
- if (_rnasecstr != null && _rnasecstr.length > 0)
- {
- // show all the RNA secondary structure annotation symbols.
- isrna = true;
- showAllColLabels = true;
- scaleColLabel = true;
- _markRnaHelices();
+ return LINE_GRAPH;
+ }
+ else
+ {
+ return NO_GRAPH;
}
- // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
}
- private void _markRnaHelices()
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label
+ * short label shown under sequence labels
+ * @param description
+ * text displayed on mouseover
+ * @param annotations
+ * set of positional annotation elements
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations)
{
- int mxval = 0;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < _rnasecstr.length; x++)
- {
-
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- int val = 0;
- try
- {
- val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
- if (mxval < val)
- {
- mxval = val;
- }
- } catch (NumberFormatException q)
- {
- }
- ;
-
- annotations[_rnasecstr[x].getBegin()].value = val;
- annotations[_rnasecstr[x].getEnd()].value = val;
+ setAnnotationId();
+ // always editable?
+ editable = true;
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
- // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
- }
- setScore(mxval);
+ validateRangeAndDisplay();
}
/**
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 ?
+ // 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[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'
: 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.
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param description
+ * DOCUMENT ME!
+ * @param annotations
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ * @param winLength
+ * DOCUMENT ME!
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations, float min, float max, int graphType)
+ {
+ setAnnotationId();
+ // graphs are not editable
+ editable = graphType == 0;
+
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+ graph = graphType;
+ graphMin = min;
+ graphMax = max;
+ validateRangeAndDisplay();
+ }
/**
* checks graphMin and graphMax, secondary structure symbols, sets graphType
}
}
}
+
+ /**
+ * Copy constructor creates a new independent annotation row with the same
+ * associated sequenceRef
+ *
+ * @param annotation
+ */
+ 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.description = new String(annotation.description);
+ }
+ this.graphMin = annotation.graphMin;
+ this.graphMax = annotation.graphMax;
+ this.graph = annotation.graph;
+ this.graphHeight = annotation.graphHeight;
+ this.graphGroup = annotation.graphGroup;
+ this.groupRef = annotation.groupRef;
+ this.editable = annotation.editable;
+ this.autoCalculated = annotation.autoCalculated;
+ this.hasIcons = annotation.hasIcons;
+ this.hasText = annotation.hasText;
+ this.height = annotation.height;
+ this.label = annotation.label;
+ this.padGaps = annotation.padGaps;
+ this.visible = annotation.visible;
+ this.centreColLabels = annotation.centreColLabels;
+ 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<>();
+ for (Map.Entry<String, String> val : annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
+ if (annotation.threshold != null)
+ {
+ threshold = new GraphLine(annotation.threshold);
+ }
+ Annotation[] ann = annotation.annotations;
+ if (annotation.annotations != null)
+ {
+ this.annotations = new Annotation[ann.length];
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] != null)
+ {
+ annotations[i] = new Annotation(ann[i]);
+ if (_linecolour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
+ }
+ }
+ }
+ if (annotation.sequenceRef != null)
+ {
+ this.sequenceRef = annotation.sequenceRef;
+ if (annotation.sequenceMapping != null)
+ {
+ Integer p = null;
+ sequenceMapping = new HashMap<>();
+ Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+ .iterator();
+ while (pos.hasNext())
+ {
+ // could optimise this!
+ p = pos.next();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
+ {
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] == a)
+ {
+ sequenceMapping.put(p, annotations[i]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ this.sequenceMapping = null;
+ }
+ }
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
+ validateRangeAndDisplay(); // construct hashcodes, etc.
+ }
/**
* clip the annotation to the columns given by startRes and endRes (inclusive)
* @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
+ *
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
+ }
+
+ /**
+ * copy constructor with edit based on the hidden columns marked in colSel
+ *
+ * @param alignmentAnnotation
+ * @param colSel
+ */
+ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+ HiddenColumns hidden)
+ {
+ this(alignmentAnnotation);
+ if (annotations == null)
+ {
+ return;
+ }
+ makeVisibleAnnotation(hidden);
+ }
+
public void setPadGaps(boolean padgaps, char gapchar)
{
{
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.
/**
* machine readable ID string indicating what generated this annotation
*/
- private String calcId = "";
+ protected String calcId = "";
/**
* properties associated with the calcId
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
- List<AlignmentAnnotation> aa = new ArrayList<>();
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
if ((calcId == null || (ann.getCalcId() != 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