From 6dc45733ae695efaad3f3a627534c9e3039c29b8 Mon Sep 17 00:00:00 2001 From: tva Date: Wed, 5 Jun 2019 14:14:25 +0100 Subject: [PATCH] JAL-3285 add unmerged code to AlignmentAnnotation --- src/jalview/datamodel/AlignmentAnnotation.java | 413 ++++++++++-------------- 1 file changed, 172 insertions(+), 241 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 7858822..6ac5da8 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -341,245 +341,6 @@ 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. - } - - /** - * 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 * */ @@ -823,6 +584,38 @@ public class AlignmentAnnotation } 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 @@ -903,6 +696,113 @@ 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) @@ -1262,6 +1162,37 @@ 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; + } + makeVisibleAnnotation(hidden); + } + public void setPadGaps(boolean padgaps, char gapchar) { @@ -1321,7 +1252,7 @@ public class AlignmentAnnotation /** * machine readable ID string indicating what generated this annotation */ - private String calcId = ""; + protected String calcId = ""; /** * properties associated with the calcId @@ -1722,7 +1653,7 @@ public class AlignmentAnnotation Iterable list, SequenceI seq, String calcId, String label) { - List aa = new ArrayList<>(); + ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : list) { if ((calcId == null || (ann.getCalcId() != null -- 1.7.10.2