X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0f7883eb147c76eac330f339469f8bb75aaf1f6b;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=31aeecc00e544ea8c4697aeadb53983ba00b318e;hpb=2e6deb5d089d95ce34b15828766479b4f7803f5c;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 31aeecc..0f7883e 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -24,6 +24,7 @@ import jalview.analysis.Rna; 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; @@ -53,8 +54,6 @@ public class AlignmentAnnotation private static long counter = 0; - private HiddenMarkovModel hmm; - /** * If true, this annotations is calculated every edit, eg consensus, quality * or conservation graphs @@ -95,79 +94,6 @@ public class AlignmentAnnotation private long invalidrnastruc = -2; /** - * 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 - */ - private void _updateRnaSecStr(CharSequence RNAannot) - { - try - { - bps = Rna.getModeleBP(RNAannot); - _rnasecstr = Rna.getBasePairs(bps); - invalidrnastruc = -1; - } catch (WUSSParseException px) - { - // DEBUG System.out.println(px); - invalidrnastruc = px.getProblemPos(); - } - if (invalidrnastruc > -1) - { - return; - } - Rna.HelixMap(_rnasecstr); - // setRNAStruc(RNAannot); - - 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); - } - - /** * map of positions in the associated annotation */ private Map sequenceMapping; @@ -246,19 +172,6 @@ public class AlignmentAnnotation private boolean isrna; - /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() - */ - @Override - protected void finalize() throws Throwable - { - sequenceRef = null; - groupRef = null; - super.finalize(); - } - public static int getGraphValueFromString(String string) { if (string.equalsIgnoreCase("BAR_GRAPH")) @@ -275,12 +188,6 @@ public class AlignmentAnnotation } } - // JBPNote: what does this do ? - public void ConcenStru(CharSequence RNAannot) throws WUSSParseException - { - bps = Rna.getModeleBP(RNAannot); - } - /** * Creates a new AlignmentAnnotation object. * @@ -301,7 +208,246 @@ public class AlignmentAnnotation this.description = description; this.annotations = annotations; - validateRangeAndDisplay(); + 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 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 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(); + } + // 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); } /** @@ -381,49 +527,25 @@ public class AlignmentAnnotation firstChar = annotations[i].displayCharacter.charAt(0); // check to see if it looks like a sequence or is secondary structure // labelling. - if (annotations[i].secondaryStructure != ' ' - && !hasIcons - && - // Uncomment to only catch case where - // displayCharacter==secondary - // Structure - // to correctly redisplay SS annotation imported from Stockholm, - // exported to JalviewXML and read back in again. - // && - // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure - firstChar != ' ' - && firstChar != '$' - && firstChar != 0xCE - && firstChar != '(' - && firstChar != '[' - && firstChar != '>' - && firstChar != '{' - && firstChar != 'A' - && firstChar != 'B' - && firstChar != 'C' - && firstChar != 'D' - && firstChar != 'E' - && firstChar != 'F' - && firstChar != 'G' - && firstChar != 'H' - && firstChar != 'I' - && firstChar != 'J' - && firstChar != 'K' - && firstChar != 'L' - && firstChar != 'M' - && firstChar != 'N' - && firstChar != 'O' - && firstChar != 'P' - && firstChar != 'Q' - && firstChar != 'R' - && firstChar != 'S' - && firstChar != 'T' - && firstChar != 'U' - && firstChar != 'V' - && firstChar != 'W' - && firstChar != 'X' - && firstChar != 'Y' - && firstChar != 'Z' + if (annotations[i].secondaryStructure != ' ' && !hasIcons && + // Uncomment to only catch case where + // displayCharacter==secondary + // Structure + // to correctly redisplay SS annotation imported from Stockholm, + // exported to JalviewXML and read back in again. + // && + // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure + firstChar != ' ' && firstChar != '$' && firstChar != 0xCE + && firstChar != '(' && firstChar != '[' && firstChar != '>' + && firstChar != '{' && firstChar != 'A' && firstChar != 'B' + && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' + && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' + && firstChar != 'I' && firstChar != 'J' && firstChar != 'K' + && firstChar != 'L' && firstChar != 'M' && firstChar != 'N' + && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q' + && firstChar != 'R' && firstChar != 'S' && firstChar != 'T' + && firstChar != 'U' && firstChar != 'V' && firstChar != 'W' + && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z' && firstChar != '-' && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { @@ -514,12 +636,17 @@ public class AlignmentAnnotation { return ((index + offset < 0) || (index + offset) >= max || annotations[index + offset] == null - || (annotations[index + offset].secondaryStructure <= ' ') ? ' ' - : annotations[index + offset].displayCharacter == null - || annotations[index + offset].displayCharacter - .length() == 0 ? annotations[index + offset].secondaryStructure - : annotations[index + offset].displayCharacter - .charAt(0)); + || (annotations[index + offset].secondaryStructure <= ' ') + ? ' ' + : annotations[index + offset].displayCharacter == null + || annotations[index + + offset].displayCharacter + .length() == 0 + ? annotations[index + + offset].secondaryStructure + : annotations[index + + offset].displayCharacter + .charAt(0)); } @Override @@ -530,10 +657,15 @@ public class AlignmentAnnotation for (int i = offset; i < mx; i++) { - string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' ' - : (annotations[i].displayCharacter == null - || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure - : annotations[i].displayCharacter.charAt(0)); + string[i] = (annotations[i] == null + || (annotations[i].secondaryStructure <= 32)) + ? ' ' + : (annotations[i].displayCharacter == null + || annotations[i].displayCharacter + .length() == 0 + ? annotations[i].secondaryStructure + : annotations[i].displayCharacter + .charAt(0)); } return new String(string); } @@ -558,38 +690,6 @@ public class AlignmentAnnotation } /** - * 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 * appropriately, sets null labels to the empty string if appropriate. */ @@ -670,113 +770,6 @@ public class AlignmentAnnotation } /** - * 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 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 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) * and prune any existing sequenceMapping to just those columns. * @@ -809,8 +802,8 @@ public class AlignmentAnnotation Annotation[] temp = new Annotation[endRes - startRes + 1]; if (startRes < annotations.length) { - System.arraycopy(annotations, startRes, temp, 0, endRes - startRes - + 1); + System.arraycopy(annotations, startRes, temp, 0, + endRes - startRes + 1); } if (sequenceRef != null) { @@ -1030,8 +1023,8 @@ public class AlignmentAnnotation { if (i + 1 < iSize) { - System.arraycopy(annotations, i + 1, annotations, i, iSize - i - - 1); + System.arraycopy(annotations, i + 1, annotations, i, + iSize - i - 1); } iSize--; } @@ -1063,14 +1056,16 @@ public class AlignmentAnnotation { if (sequenceRef != null) { - boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI - .getDatasetSequence() == null; + boolean rIsDs = sequenceRef.getDatasetSequence() == null, + tIsDs = sequenceI.getDatasetSequence() == null; if (sequenceRef != sequenceI - && (rIsDs && !tIsDs && sequenceRef != sequenceI - .getDatasetSequence()) - && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI) - && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI - .getDatasetSequence()) + && (rIsDs && !tIsDs + && sequenceRef != sequenceI.getDatasetSequence()) + && (!rIsDs && tIsDs + && sequenceRef.getDatasetSequence() != sequenceI) + && (!rIsDs && !tIsDs + && sequenceRef.getDatasetSequence() != sequenceI + .getDatasetSequence()) && !sequenceRef.equals(sequenceI)) { // if sequenceRef isn't intersecting with sequenceI @@ -1132,36 +1127,6 @@ public class AlignmentAnnotation 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; - } - hidden.makeVisibleAnnotation(this); - } - public void setPadGaps(boolean padgaps, char gapchar) { this.padGaps = padgaps; @@ -1220,7 +1185,7 @@ public class AlignmentAnnotation /** * machine readable ID string indicating what generated this annotation */ - protected String calcId = ""; + private String calcId = ""; /** * properties associated with the calcId @@ -1265,8 +1230,10 @@ public class AlignmentAnnotation throw new Error( "liftOver currently not implemented for transfer of annotation between different types of seqeunce"); } - boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq - .getTo() == sq.getDatasetSequence()) : false; + boolean mapIsTo = (sp2sq != null) + ? (sp2sq.getTo() == sq + || sp2sq.getTo() == sq.getDatasetSequence()) + : false; // TODO build a better annotation element map and get rid of annotations[] Map mapForsq = new HashMap<>(); @@ -1276,9 +1243,9 @@ public class AlignmentAnnotation { for (Entry ie : sequenceMapping.entrySet()) { - Integer mpos = Integer.valueOf(mapIsTo ? sp2sq - .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie - .getKey())); + Integer mpos = Integer + .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey()) + : sp2sq.getPosition(ie.getKey())); if (mpos >= sq.getStart() && mpos <= sq.getEnd()) { mapForsq.put(mpos, ie.getValue()); @@ -1465,8 +1432,8 @@ public class AlignmentAnnotation * 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 closer = String + .valueOf(Rna.getMatchingClosingParenthesis(symbol)); String opener = String.valueOf(symbol); int count = 0; for (int j = col + 1; j < column; j++) @@ -1507,22 +1474,176 @@ public class AlignmentAnnotation } /** - * Returns the HMM associated with this annotation. + * delete any columns in alignmentAnnotation that are hidden (including + * sequence associated annotation). * - * @return + * @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 */ - public HiddenMarkovModel getHMM() + private void removeHiddenAnnotation(int start, int end, + HiddenColumns hiddenColumns) + { + // mangle the alignmentAnnotation annotation array + ArrayList annels = new ArrayList<>(); + Annotation[] els = null; + + int w = 0; + + Iterator 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 findAnnotations( + Iterable list, SequenceI seq, String calcId, + String label) { - return hmm; + List 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; } /** - * Sets the HMM associated with this annotation. + * Answer true if any annotation matches the calcId passed in (if not null). * - * @param hmm + * @param list + * annotation to search + * @param calcId + * @return */ - public void setHMM(HiddenMarkovModel hmm) + public static boolean hasAnnotation(List list, + String calcId) + { + + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : list) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + public static Iterable findAnnotation( + List list, String calcId) { - this.hmm = hmm; + List 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; } }