From 0ad68271736bf34febfa87b2525c03345500d54c Mon Sep 17 00:00:00 2001 From: James Procter Date: Tue, 29 Aug 2023 18:27:38 +0100 Subject: [PATCH] JAL-4124 Dataset holds list of MatrixType instances, MapOnAMatrixType allows multiple instances of a MatrixType to be specified across alignment views --- schemas/vamsas.xsd | 323 +++++++++++++------- src/jalview/project/Jalview2XML.java | 256 +++++++++------- src/jalview/xml/binding/jalview/AlcodonFrame.java | 13 +- src/jalview/xml/binding/jalview/Annotation.java | 12 +- .../binding/jalview/AnnotationColourScheme.java | 2 +- .../xml/binding/jalview/AnnotationElement.java | 2 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 2 +- src/jalview/xml/binding/jalview/DoubleVector.java | 2 +- src/jalview/xml/binding/jalview/Feature.java | 2 +- .../xml/binding/jalview/FeatureMatcher.java | 2 +- .../xml/binding/jalview/FeatureMatcherSet.java | 2 +- src/jalview/xml/binding/jalview/FilterBy.java | 2 +- src/jalview/xml/binding/jalview/JalviewModel.java | 2 +- .../xml/binding/jalview/JalviewUserColours.java | 2 +- src/jalview/xml/binding/jalview/MapListType.java | 5 +- .../xml/binding/jalview/MapOnAMatrixType.java | 6 +- src/jalview/xml/binding/jalview/Mapping.java | 11 +- src/jalview/xml/binding/jalview/MatrixType.java | 37 +-- src/jalview/xml/binding/jalview/NoValueColour.java | 2 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 14 +- src/jalview/xml/binding/jalview/PcaDataType.java | 2 +- src/jalview/xml/binding/jalview/Pdbentry.java | 2 +- src/jalview/xml/binding/jalview/Property.java | 2 +- src/jalview/xml/binding/jalview/Sequence.java | 2 +- src/jalview/xml/binding/jalview/SequenceSet.java | 2 +- src/jalview/xml/binding/jalview/SequenceType.java | 2 +- src/jalview/xml/binding/jalview/ThresholdType.java | 2 +- src/jalview/xml/binding/jalview/VAMSAS.java | 2 +- .../binding/jalview/WebServiceParameterSet.java | 2 +- src/jalview/xml/binding/jalview/package-info.java | 2 +- 30 files changed, 431 insertions(+), 288 deletions(-) diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index c4a5d3e..38152fd 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -24,57 +24,83 @@ Note this also generates code for included schemas --> + - - + + - - developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes + + developed after mapRangeType from + http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - This effectively represents a java.util.MapList object + This effectively represents a java.util.MapList + object - + - a region from start to end inclusive + a region from start to end inclusive + - - + + - - + + - a region from start to end inclusive + a region from start to end inclusive + - - + + - + - + - number of dictionary symbol widths involved in each - mapped position on this sequence (for example, 3 for a dna sequence exon - region that is being mapped to a protein sequence). This is optional, - since the unit can be usually be inferred from the dictionary type of - each sequence involved in the mapping. + number of dictionary symbol widths involved in + each + mapped position on this sequence (for example, 3 for a dna + sequence exon + region that is being mapped to a protein sequence). + This is optional, + since the unit can be usually be inferred from the + dictionary type of + each sequence involved in the mapping. + - + - number of dictionary symbol widths involved in each - mapped position on this sequence (for example, 3 for a dna sequence exon - region that is being mapped to a protein sequence). This is optional, - since the unit can be usually be inferred from the dictionary type of - each sequence involved in the mapping. + number of dictionary symbol widths involved in + each + mapped position on this sequence (for example, 3 for a dna + sequence exon + region that is being mapped to a protein sequence). + This is optional, + since the unit can be usually be inferred from the + dictionary type of + each sequence involved in the mapping. + @@ -82,74 +108,94 @@ - Represent the jalview.datamodel.Mapping object - it also provides - a way of storing sequences that are mapped 'to' without adding them - to the sequence set (which will mean they are then added to the alignment too). + Represent the jalview.datamodel.Mapping object - + it also provides + a way of storing sequences that are mapped 'to' + without adding them + to the sequence set (which will mean they are + then added to the alignment too). - + - The sequence whose dataset sequence is to be referenced here + The sequence whose dataset sequence is to + be referenced here + - + - Biotype of the mapping e.g. CdsToPeptide + Biotype of the mapping e.g. CdsToPeptide + - + - + - specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. - Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). + specifies a series of aligned codons from an + associated DNA sequence alignment that when translated + correspond to columns of a peptide alignment. + Element may have + either all pos1,2,3 attributes specified, or none at all + (indicating a gapped column with no translated peptide). - - - + + + - + - + - a Mapping entry and an associated protein sequence + a Mapping entry and an associated protein + sequence - + - internal jalview id for the dnasq for this mapping. + internal jalview id for the dnasq for this + mapping. - + - + @@ -158,39 +204,49 @@ - + - - - - - - + + + + + + - true for gene locus mapping, source=species, version=assembly, accession=chromosome + true for gene locus mapping, source=species, + version=assembly, accession=chromosome - + - true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot) + true for the representative accession for + databases where multiple accessions map to the same entry + (eg. Uniprot) - + - dataset sequence id for this sequence. Will be created as union of sequences. + dataset sequence id for this sequence. Will be + created as union of sequences. - + Biotype of the sequence (if known) @@ -216,13 +272,16 @@ - + - + - - + + - - height in pixels for the graph if this is a graph-type annotation. + + + height in pixels for the graph if this is a + graph-type annotation. + + + - + - - is an autocalculated annotation row - - - is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores - - Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system. + + + is an autocalculated annotation row + + + + + + is to be shown below the alignment - introduced + in Jalview 2.8 for visualizing T-COFFEE alignment scores + + + + + + Optional string identifier used to group sets of + annotation produced by a particular calculation. Values are opaque + strings but have semantic meaning to Jalview's renderer, data + importer and calculation system. + + - + - - - + + + - - + + - - + + + + Matrices referred to by this set of sequences. + + + - - + + - reference to set where jalview will gather the dataset sequences for all sequences in the set. + reference to set where jalview will gather the + dataset sequences for all sequences in the set. @@ -284,36 +380,47 @@ - - + + - + - + - - + + - - + + - - + + + + Represents matrix data imported to Jalview, and the + results of any derived calculations (independent of a particular + view + on the matrix). + + serialised representation of matrix as one or - more sets of comma separated values + more sets of comma separated values + - - - mapping from the matrix row and column positions to - associated reference frame - - @@ -354,6 +454,11 @@ + + Defines a mapping from the local frame to a matrix + and its associated data specified by MatrixType + + @@ -367,10 +472,10 @@ - + - + reference to the matrix type this Map refers to @@ -382,6 +487,6 @@ - - + + diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index b9e1f46..f8be544 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -91,12 +91,15 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ContactListI; import jalview.datamodel.ContactMatrix; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.FloatContactMatrix; import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; import jalview.datamodel.GroupSet; +import jalview.datamodel.GroupSetI; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; @@ -199,6 +202,7 @@ import jalview.xml.binding.jalview.JalviewUserColours.Colour; import jalview.xml.binding.jalview.MapListType; import jalview.xml.binding.jalview.MapListType.MapListFrom; import jalview.xml.binding.jalview.MapListType.MapListTo; +import jalview.xml.binding.jalview.MapOnAMatrixType; import jalview.xml.binding.jalview.Mapping; import jalview.xml.binding.jalview.MatrixType; import jalview.xml.binding.jalview.NoValueColour; @@ -2432,39 +2436,47 @@ public class Jalview2XML { String cmId = contactMatrices.get(cm); MatrixType xmlmat=null; - if (cmId==null) + + // first create an xml ref for the matrix data, if none exist + if (cmId == null) { -xmlmat = new MatrixType(); - xmlmat.setType(cm.getType()); - xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); - xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); - // consider using an opaque to/from -> allow instance to control - // its representation ? - xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); - if (cm.hasGroups()) - { - for (BitSet gp : cm.getGroups()) + xmlmat = new MatrixType(); + xmlmat.setType(cm.getType()); + xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); + xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); + // consider using an opaque to/from -> allow instance to control + // its representation ? + xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); + if (cm.hasGroups()) { - xmlmat.getGroups().add(stringifyBitset(gp)); + for (BitSet gp : cm.getGroups()) + { + xmlmat.getGroups().add(stringifyBitset(gp)); + } } - } - if (cm.hasTree()) - { - // provenance object for tree ? - xmlmat.getNewick().add(cm.getNewick()); - xmlmat.setTreeMethod(cm.getTreeMethod()); - } - if (cm.hasCutHeight()) - { - xmlmat.setCutHeight(cm.getCutHeight()); - } - xmlmat.setId(makeHashCode(cm, cm.get)); + if (cm.hasTree()) + { + // provenance object for tree ? + xmlmat.getNewick().add(cm.getNewick()); + xmlmat.setTreeMethod(cm.getTreeMethod()); + } + if (cm.hasCutHeight()) + { + xmlmat.setCutHeight(cm.getCutHeight()); + } + xmlmat.setId(cmId = makeHashCode(cm, null)); + contactMatrices.put(cm, cmId); + contactMatrixRefs.put(cmId, cm); root.getMatrices().add(xmlmat); } - else { - - } - // set/get properties + + // now store mapping + + MapOnAMatrixType xmlmatmapping = new MapOnAMatrixType(); + xmlmatmapping.setMatrix(cmId); + + // Pretty much all matrices currently managed in this way are + // mappableContactMatrixI implementations - but check anyway if (cm instanceof MappableContactMatrixI) { jalview.util.MapList mlst = ((MappableContactMatrixI) cm) @@ -2490,14 +2502,13 @@ xmlmat = new MatrixType(); // mp.addMapListTo(mto); mp.getMapListTo().add(mto); } - mp.setMapFromUnit( - BigInteger.valueOf(mlst.getFromRatio())); + mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio())); mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio())); - xmlmat.setMapping(mp); + xmlmatmapping.setMapping(mp); } } // and add to model - an.getContactmatrix().add(xmlmat); + an.getContactmatrix().add(xmlmatmapping); } private String stringifyBitset(BitSet gp) @@ -3521,6 +3532,14 @@ xmlmat = new MatrixType(); } // //////////////////////////////// + // LOAD MATRICES (IF ANY) + + if (vamsasSet.getMatrices()!=null && vamsasSet.getMatrices().size()>0) + { + importMatrixData(vamsasSet.getMatrices()); + } + + // //////////////////////////////// // LOAD SEQUENCES List hiddenSeqs = null; @@ -4052,80 +4071,10 @@ xmlmat = new MatrixType(); if (annotation.getContactmatrix() != null && annotation.getContactmatrix().size() > 0) { - for (MatrixType xmlmat : annotation.getContactmatrix()) + for (MapOnAMatrixType xmlmat : annotation.getContactmatrix()) { - if (PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType())) - { - if (!xmlmat.getRows().equals(xmlmat.getCols())) - { - Console.error("Can't handle non square PAE Matrices"); - } - else - { - float[][] elements = ContactMatrix - .fromFloatStringToContacts(xmlmat.getElements(), - xmlmat.getCols().intValue(), - xmlmat.getRows().intValue()); - jalview.util.MapList mapping = null; - if (xmlmat.getMapping() != null) - { - MapListType m = xmlmat.getMapping(); - // Mapping m = dr.getMapping(); - int fr[] = new int[m.getMapListFrom().size() * 2]; - Iterator from = m.getMapListFrom() - .iterator();// enumerateMapListFrom(); - for (int _i = 0; from.hasNext(); _i += 2) - { - MapListFrom mf = from.next(); - fr[_i] = mf.getStart(); - fr[_i + 1] = mf.getEnd(); - } - int fto[] = new int[m.getMapListTo().size() * 2]; - Iterator to = m.getMapListTo().iterator();// enumerateMapListTo(); - for (int _i = 0; to.hasNext(); _i += 2) - { - MapListTo mf = to.next(); - fto[_i] = mf.getStart(); - fto[_i + 1] = mf.getEnd(); - } - - mapping = new jalview.util.MapList(fr, fto, - m.getMapFromUnit().intValue(), - m.getMapToUnit().intValue()); - } - List newgroups = new ArrayList(); - if (xmlmat.getGroups().size() > 0) - { - for (String sgroup : xmlmat.getGroups()) - { - newgroups.add(deStringifyBitset(sgroup)); - } - } - String nwk = xmlmat.getNewick().size() > 0 - ? xmlmat.getNewick().get(0) - : null; - if (xmlmat.getNewick().size() > 1) - { - Console.log.info( - "Ignoring additional clusterings for contact matrix"); - } - String treeMethod = xmlmat.getTreeMethod(); - double thresh = xmlmat.getCutHeight() != null - ? xmlmat.getCutHeight() - : 0; - GroupSet grpset = new GroupSet(); - grpset.restoreGroups(newgroups, treeMethod, nwk, thresh); - PAEContactMatrix newpae = new PAEContactMatrix( - jaa.sequenceRef, mapping, elements, grpset); - jaa.sequenceRef.addContactListFor(jaa, newpae); - } - } - else - { - Console.error("Ignoring CONTACT_MAP annotation with type " - + xmlmat.getType()); - } - } + restoreMatrixFor(jaa.sequenceRef, jaa, xmlmat); + } } } @@ -4355,6 +4304,103 @@ xmlmat = new MatrixType(); return af; } + private void importMatrixData(List xmlmatrices) + { + for (MatrixType xmlmat:xmlmatrices) + { + if (!PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType())) + { + Console.error("Ignoring matrix '"+xmlmat.getId()+"' of type '"+xmlmat.getType()); + continue; + } + + if (!xmlmat.getRows().equals(xmlmat.getCols())) + { + Console.error("Can't handle non square matrices"); + continue; + } + + float[][] elements = ContactMatrix + .fromFloatStringToContacts(xmlmat.getElements(), + xmlmat.getCols().intValue(), + xmlmat.getRows().intValue()); + + List newgroups = new ArrayList(); + if (xmlmat.getGroups().size() > 0) + { + for (String sgroup : xmlmat.getGroups()) + { + newgroups.add(deStringifyBitset(sgroup)); + } + } + String nwk = xmlmat.getNewick().size() > 0 + ? xmlmat.getNewick().get(0) + : null; + if (xmlmat.getNewick().size() > 1) + { + Console.log.info( + "Ignoring additional clusterings for contact matrix"); + } + String treeMethod = xmlmat.getTreeMethod(); + double thresh = xmlmat.getCutHeight() != null + ? xmlmat.getCutHeight() + : 0; + GroupSet grpset = new GroupSet(); + grpset.restoreGroups(newgroups, treeMethod, nwk, thresh); + + FloatContactMatrix newcm = new FloatContactMatrix(elements, grpset); + contactMatrixRefs.put(xmlmat.getId(), newcm); + Console.trace("Restored base contact matrix "+xmlmat.getId()); + } + } + + private void restoreMatrixFor(SequenceI sequenceRef, + AlignmentAnnotation jaa, MapOnAMatrixType xmlmatmapping) + { + MatrixType xmlmat; + + // locate matrix data in project XML and import + ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix()); + if (cm == null) + { + Console.error("Cannot restore mapping to matrix " + + xmlmatmapping.getMatrix() + " - not found in project."); + } + + // restore mapping data to matrix data + jalview.util.MapList mapping = null; + if (xmlmatmapping.getMapping() != null) + { + MapListType m = xmlmatmapping.getMapping(); + // Mapping m = dr.getMapping(); + int fr[] = new int[m.getMapListFrom().size() * 2]; + Iterator from = m.getMapListFrom().iterator();// enumerateMapListFrom(); + for (int _i = 0; from.hasNext(); _i += 2) + { + MapListFrom mf = from.next(); + fr[_i] = mf.getStart(); + fr[_i + 1] = mf.getEnd(); + } + int fto[] = new int[m.getMapListTo().size() * 2]; + Iterator to = m.getMapListTo().iterator();// enumerateMapListTo(); + for (int _i = 0; to.hasNext(); _i += 2) + { + MapListTo mf = to.next(); + fto[_i] = mf.getStart(); + fto[_i + 1] = mf.getEnd(); + } + + mapping = new jalview.util.MapList(fr, fto, + m.getMapFromUnit().intValue(), m.getMapToUnit().intValue()); + } + PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef, mapping, + cm); + + jaa.sequenceRef.addContactListFor(jaa, newpae); + + return; + } + /** * Load Overview window, restoring colours, 'show hidden regions' flag, title * and geometry as saved diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 77ea749..9d356a0 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -163,7 +163,8 @@ public class AlcodonFrame { /** * - * a Mapping entry and an associated protein sequence + * a Mapping entry and an associated protein + * sequence * * * @return @@ -216,8 +217,12 @@ public class AlcodonFrame { /** * - * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. - * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). + * specifies a series of aligned codons from an + * associated DNA sequence alignment that when translated + * correspond to columns of a peptide alignment. + * Element may have + * either all pos1,2,3 attributes specified, or none at all + * (indicating a gapped column with no translated peptide). * * *

Java class for anonymous complex type. diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 8a5d9b2..dc485c5 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -42,7 +42,7 @@ import javax.xml.bind.annotation.XmlType; * </complexContent> * </complexType> * </element> - * <element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/> + * <element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0"/> * <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/> * </sequence> * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> @@ -86,7 +86,7 @@ public class Annotation { protected String label; protected String description; protected Annotation.ThresholdLine thresholdLine; - protected List contactmatrix; + protected List contactmatrix; protected List property; @XmlAttribute(name = "graph", required = true) protected boolean graph; @@ -242,13 +242,13 @@ public class Annotation { * *

* Objects of the following type(s) are allowed in the list - * {@link MatrixType } + * {@link MapOnAMatrixType } * * */ - public List getContactmatrix() { + public List getContactmatrix() { if (contactmatrix == null) { - contactmatrix = new ArrayList(); + contactmatrix = new ArrayList(); } return this.contactmatrix; } diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index a9f545d..5bfa180 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index 912be73..cdb697e 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index cb0fe86..c96d6fa 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index 83a2476..12dd58d 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 5902d10..70c35dc 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 9d28efa..b560eb9 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index 6499485..cb6375a 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index f2b113f..3982b52 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 9241fdd..2b4b89e 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 481a7b7..703178c 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 498e6e2..ac05ff5 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -21,7 +21,8 @@ import javax.xml.bind.annotation.XmlType; /** * - * This effectively represents a java.util.MapList object + * This effectively represents a java.util.MapList + * object * * *

Java class for mapListType complex type. diff --git a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java index 91ac690..d94f60e 100644 --- a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java +++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -17,6 +17,10 @@ import javax.xml.bind.annotation.XmlType; /** + * Defines a mapping from the local frame to a matrix + * and its associated data specified by MatrixType + * + * *

Java class for MapOnAMatrixType complex type. * *

The following schema fragment specifies the expected content contained within this class. diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index a3ce15f..c7b1386 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -18,9 +18,12 @@ import javax.xml.bind.annotation.XmlType; /** * - * Represent the jalview.datamodel.Mapping object - it also provides - * a way of storing sequences that are mapped 'to' without adding them - * to the sequence set (which will mean they are then added to the alignment too). + * Represent the jalview.datamodel.Mapping object - + * it also provides + * a way of storing sequences that are mapped 'to' + * without adding them + * to the sequence set (which will mean they are + * then added to the alignment too). * * *

Java class for anonymous complex type. diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java index 973456e..aac0c43 100644 --- a/src/jalview/xml/binding/jalview/MatrixType.java +++ b/src/jalview/xml/binding/jalview/MatrixType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -19,6 +19,12 @@ import javax.xml.bind.annotation.XmlType; /** + * Represents matrix data imported to Jalview, and the + * results of any derived calculations (independent of a particular + * view + * on the matrix). + * + * *

Java class for MatrixType complex type. * *

The following schema fragment specifies the expected content contained within this class. @@ -32,7 +38,6 @@ import javax.xml.bind.annotation.XmlType; * <element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/> * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/> * <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/> - * <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/> * </sequence> * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /> @@ -52,8 +57,7 @@ import javax.xml.bind.annotation.XmlType; "elements", "groups", "newick", - "property", - "mapping" + "property" }) public class MatrixType { @@ -62,7 +66,6 @@ public class MatrixType { protected List groups; protected List newick; protected List property; - protected MapListType mapping; @XmlAttribute(name = "type", required = true) protected String type; @XmlAttribute(name = "rows", required = true) @@ -188,30 +191,6 @@ public class MatrixType { } /** - * Gets the value of the mapping property. - * - * @return - * possible object is - * {@link MapListType } - * - */ - public MapListType getMapping() { - return mapping; - } - - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is - * {@link MapListType } - * - */ - public void setMapping(MapListType value) { - this.mapping = value; - } - - /** * Gets the value of the type property. * * @return diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 3bede57..f626036 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 4cb7753..bb6c7be 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @@ -275,11 +275,11 @@ public class ObjectFactory { } /** - * Create an instance of {@link MatrixType } + * Create an instance of {@link MapOnAMatrixType } * */ - public MatrixType createMatrixType() { - return new MatrixType(); + public MapOnAMatrixType createMapOnAMatrixType() { + return new MapOnAMatrixType(); } /** @@ -299,11 +299,11 @@ public class ObjectFactory { } /** - * Create an instance of {@link MapOnAMatrixType } + * Create an instance of {@link MatrixType } * */ - public MapOnAMatrixType createMapOnAMatrixType() { - return new MapOnAMatrixType(); + public MatrixType createMatrixType() { + return new MatrixType(); } /** diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index b7e2881..e4952bd 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 19c44fb..5c7a219 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java index d171a73..095d48b 100644 --- a/src/jalview/xml/binding/jalview/Property.java +++ b/src/jalview/xml/binding/jalview/Property.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index 98390ef..a9ed23d 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index 8322ca7..78df533 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index ca7e899..3d3e616 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index 42cf56a..0a9aa13 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index 84fe566..a56f957 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 0c61ab1..d067e81 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index d2c51bc..817f533 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.07.18 at 05:07:54 PM BST +// Generated on: 2023.08.28 at 01:52:46 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) -- 1.7.10.2