X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7858822483796789e3f310acae6dd5aeee7876f7;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=9c3af271926de7b81ec0ebdfee51d7ca3084bc81;hpb=bc85369667c2665d81631e96f0701038f04f9bb3;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 9c3af27..7858822 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -25,10 +25,12 @@ 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.Map; import java.util.Map.Entry; @@ -79,7 +81,7 @@ public class AlignmentAnnotation /** Array of annotations placed in the current coordinate system */ public Annotation[] annotations; - public ArrayList bps = null; + public List bps = null; /** * RNA secondary structure contact positions @@ -96,14 +98,13 @@ public class AlignmentAnnotation * 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) { @@ -114,8 +115,6 @@ public class AlignmentAnnotation { return; } - Rna.HelixMap(_rnasecstr); - // setRNAStruc(RNAannot); if (_rnasecstr != null && _rnasecstr.length > 0) { @@ -166,14 +165,76 @@ public class AlignmentAnnotation } /** + * 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 sequenceMapping; - /** DOCUMENT ME!! */ + /** + * lower range for quantitative data + */ public float graphMin; - /** DOCUMENT ME!! */ + /** + * Upper range for quantitative data + */ public float graphMax; /** @@ -240,18 +301,6 @@ public class AlignmentAnnotation private boolean isrna; - /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() - */ - protected void finalize() throws Throwable - { - sequenceRef = null; - groupRef = null; - super.finalize(); - } - public static int getGraphValueFromString(String string) { if (string.equalsIgnoreCase("BAR_GRAPH")) @@ -268,12 +317,6 @@ public class AlignmentAnnotation } } - // JBPNote: what does this do ? - public void ConcenStru(CharSequence RNAannot) throws WUSSParseException - { - bps = Rna.GetModeleBP(RNAannot); - } - /** * Creates a new AlignmentAnnotation object. * @@ -298,6 +341,245 @@ 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. + } + + /** + * 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); + } + + /** * Checks if annotation labels represent secondary structures * */ @@ -310,6 +592,7 @@ public class AlignmentAnnotation char firstChar = 0; for (int i = 0; i < annotations.length; i++) { + // DEBUG System.out.println(i + ": " + annotations[i]); if (annotations[i] == null) { continue; @@ -317,12 +600,15 @@ public class AlignmentAnnotation 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 == '(' @@ -333,10 +619,12 @@ public class AlignmentAnnotation || 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' @@ -374,49 +662,25 @@ 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) { @@ -484,7 +748,7 @@ public class AlignmentAnnotation this(0, annotations.length); } - public AnnotCharSequence(int start, int end) + AnnotCharSequence(int start, int end) { offset = start; max = end; @@ -507,12 +771,17 @@ 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 @@ -523,10 +792,15 @@ 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); } @@ -551,38 +825,6 @@ 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. */ @@ -592,180 +834,74 @@ public class AlignmentAnnotation 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. } int graphType = graph; float min = graphMin; - float max = graphMax; - boolean drawValues = true; - _linecolour = null; - if (min == max) - { - min = 999999999; - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] == null) - { - continue; - } - - if (drawValues && annotations[i].displayCharacter != null - && annotations[i].displayCharacter.length() > 1) - { - drawValues = false; - } - - if (annotations[i].value > max) - { - max = annotations[i].value; - } - - if (annotations[i].value < min) - { - min = annotations[i].value; - } - if (_linecolour == null && annotations[i].colour != null) - { - _linecolour = annotations[i].colour; - } - } - // ensure zero is origin for min/max ranges on only one side of zero - if (min > 0) - { - min = 0; - } - else - { - if (max < 0) - { - max = 0; - } - } - } - - graphMin = min; - graphMax = max; - - areLabelsSecondaryStructure(); - - if (!drawValues && graphType != NO_GRAPH) - { - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] != null) - { - annotations[i].displayCharacter = ""; - } - } - } - } - - /** - * 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) + float max = graphMax; + boolean drawValues = true; + _linecolour = null; + if (min == max) { - this.annotations = new Annotation[ann.length]; - for (int i = 0; i < ann.length; i++) + min = 999999999; + for (int i = 0; i < annotations.length; i++) { - if (ann[i] != null) + if (annotations[i] == null) { - annotations[i] = new Annotation(ann[i]); - if (_linecolour != null) - { - _linecolour = annotations[i].colour; - } + continue; } - } - } - 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()) + + if (drawValues && annotations[i].displayCharacter != null + && annotations[i].displayCharacter.length() > 1) { - // 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]); - } - } - } + drawValues = false; } + + if (annotations[i].value > max) + { + max = annotations[i].value; + } + + if (annotations[i].value < min) + { + min = annotations[i].value; + } + if (_linecolour == null && annotations[i].colour != null) + { + _linecolour = annotations[i].colour; + } + } + // ensure zero is origin for min/max ranges on only one side of zero + if (min > 0) + { + min = 0; } else { - this.sequenceMapping = null; + if (max < 0) + { + max = 0; + } } } - // TODO: check if we need to do this: JAL-952 - // if (this.isrna=annotation.isrna) + + graphMin = min; + graphMax = max; + + areLabelsSecondaryStructure(); + + if (!drawValues && graphType != NO_GRAPH) { - // _rnasecstr=new SequenceFeature[annotation._rnasecstr]; + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + annotations[i].displayCharacter = ""; + } + } } - validateRangeAndDisplay(); // construct hashcodes, etc. } /** @@ -801,8 +937,8 @@ 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) { @@ -811,7 +947,7 @@ public class AlignmentAnnotation int epos = sequenceRef.findPosition(endRes); if (sequenceMapping != null) { - Map newmapping = new HashMap(); + Map newmapping = new HashMap<>(); Iterator e = sequenceMapping.keySet().iterator(); while (e.hasNext()) { @@ -861,6 +997,10 @@ public class AlignmentAnnotation @Override public String toString() { + if (annotations == null) + { + return ""; + } StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) @@ -920,6 +1060,7 @@ public class AlignmentAnnotation * @param seqRef * @param startRes * @param alreadyMapped + * - annotation are at aligned columns */ public void createSequenceMapping(SequenceI seqRef, int startRes, boolean alreadyMapped) @@ -934,7 +1075,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new HashMap(); + sequenceMapping = new HashMap<>(); int seqPos; @@ -951,16 +1092,26 @@ public class AlignmentAnnotation seqPos = i + startRes; } - sequenceMapping.put(new Integer(seqPos), annotations[i]); + sequenceMapping.put(Integer.valueOf(seqPos), annotations[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 || sequenceMapping == null - || annotations == null) + if (sequenceRef == null) + { + return; + } + + if (annotations == null) { return; } @@ -976,18 +1127,20 @@ public class AlignmentAnnotation int position; Annotation[] temp = new Annotation[aSize]; Integer index; - - for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) + if (sequenceMapping != null) { - index = new Integer(a); - if (sequenceMapping.containsKey(index)) + for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) { - position = sequenceRef.findIndex(a) - 1; + index = Integer.valueOf(a); + Annotation annot = sequenceMapping.get(index); + if (annot != null) + { + position = sequenceRef.findIndex(a) - 1; - temp[position] = sequenceMapping.get(index); + temp[position] = annot; + } } } - annotations = temp; } @@ -1006,8 +1159,8 @@ 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--; } @@ -1024,11 +1177,11 @@ public class AlignmentAnnotation } /** - * 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 @@ -1039,14 +1192,16 @@ 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 @@ -1108,36 +1263,6 @@ 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, - ColumnSelection colSel) - { - this(alignmentAnnotation); - if (annotations == null) - { - return; - } - colSel.makeVisibleAnnotation(this); - } - public void setPadGaps(boolean padgaps, char gapchar) { this.padGaps = padgaps; @@ -1196,12 +1321,12 @@ public class AlignmentAnnotation /** * machine readable ID string indicating what generated this annotation */ - protected String calcId = ""; + private String calcId = ""; /** * properties associated with the calcId */ - protected Map properties = new HashMap(); + protected Map properties = new HashMap<>(); /** * base colour for line graphs. If null, will be set automatically by @@ -1241,20 +1366,22 @@ 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(); + Map mapForsq = new HashMap<>(); if (sequenceMapping != null) { if (sp2sq != null) { 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()); @@ -1292,15 +1419,15 @@ public class AlignmentAnnotation * @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 mapping, + int from, int to, int idxoffset) { if (mapping != null) { Map old = sequenceMapping; - Map remap = new HashMap(); + Map remap = new HashMap<>(); int index = -1; - for (int mp[] : mapping) + for (int mp[] : mapping.values()) { if (index++ < 0) { @@ -1356,7 +1483,7 @@ public class AlignmentAnnotation { if (properties == null) { - properties = new HashMap(); + properties = new HashMap<>(); } properties.put(property, value); } @@ -1397,8 +1524,263 @@ public class AlignmentAnnotation 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; + } + + /** + * 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 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) + { + 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; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param list + * annotation to search + * @param calcId + * @return + */ + 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) + { + 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; + } + }