From: James Procter Date: Wed, 22 Feb 2023 22:02:20 +0000 (+0000) Subject: JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset... X-Git-Tag: Release_2_11_3_0~18^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests. --- diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index cd05e5f..e7cb580 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -36,22 +36,28 @@ - - + + - + - - - - - + + + + additional @@ -110,8 +116,9 @@ - + Flag @@ -140,8 +147,9 @@ - + Flag @@ -172,8 +180,9 @@ - + Flag @@ -200,8 +209,8 @@ - + An @@ -228,66 +237,109 @@ - - + + - Reference to a viewer showing RNA structure - for this sequence. Schema supports one viewer showing multiple - annotations for multiple sequences, though currently only one - annotation for one sequence (gapped or trimmed) is used + + Reference to a viewer showing + RNA structure for this sequence. + Schema supports one viewer + showing multiple annotations for + multiple sequences, though + currently only one annotation + for one sequence (gapped or + trimmed) is used - - - + + - id attribute of Annotation in - vamsasModel for - the secondary structure annotation shown - in the viewer + + id attribute + of + Annotation + in + vamsasModel + for the + secondary + structure + annotation + shown in the + viewer - + - if true the RNA structure is shown with gaps, if false without + + if true the + RNA + structure is + shown with + gaps, if + false + without - + - name of the project jar entry that holds - the VARNA viewer state for the structure + + name of the + project jar + entry that + holds the + VARNA viewer + state for + the + structure - - - + + + - An id unique to the RNA viewer panel + + An id unique to the RNA + viewer panel - + - horizontal position of split pane divider + + horizontal position of + split pane divider - + - Index of the selected structure in the - viewer panel + + Index of the selected + structure in the viewer + panel diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 333a4e4..5fd2bab 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -216,6 +216,9 @@ + + @@ -308,4 +311,14 @@ + + + + + + + + + + diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java index f6ccc6a..5849374 100644 --- a/src/jalview/datamodel/ContactMapHolder.java +++ b/src/jalview/datamodel/ContactMapHolder.java @@ -66,6 +66,14 @@ public class ContactMapHolder implements ContactMapHolderI public void addContactListFor(AlignmentAnnotation annotation, ContactMatrixI cm) { + // update annotation with data from contact map + annotation.graphMin = cm.getMin(); + annotation.graphMax = cm.getMax(); + annotation.editable = false; + annotation.graph = AlignmentAnnotation.CONTACT_MAP; + annotation.calcId = cm.getType(); + annotation.label = cm.getAnnotLabel(); + annotation.description = cm.getAnnotDescr(); contactmaps.put(annotation.annotationId, cm); } } diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java index b4f7c07..f2e207c 100644 --- a/src/jalview/datamodel/ContactMatrix.java +++ b/src/jalview/datamodel/ContactMatrix.java @@ -1,7 +1,12 @@ package jalview.datamodel; +import java.math.BigInteger; import java.util.ArrayList; import java.util.List; +import java.util.Spliterator; +import java.util.StringTokenizer; + +import jalview.bin.Console; public abstract class ContactMatrix implements ContactMatrixI { @@ -166,4 +171,53 @@ public abstract class ContactMatrix implements ContactMatrixI { return "Contact Matrix"; } + + public static String contactToFloatString(ContactMatrixI cm) + { + StringBuilder sb = new StringBuilder(); + for (int c=0;c0) { + sb.append('\t'); + } + sb.append(cl.getContactAt(h)); + } + } + } + return sb.toString(); + } + + public static float[][] fromFloatStringToContacts(String values, int cols, + int rows) + { + float[][] vals = new float[cols][rows]; + StringTokenizer tabsep = new StringTokenizer(values,""+'\t'); + int c=0,r=0; + + while (tabsep.hasMoreTokens()) + { + double elem = Double.valueOf(tabsep.nextToken()); + vals[c][r++]=(float) elem; + if (r>=vals[c].length) + { + r=0; + c++; + } + if (c>=vals.length) + { + + break; + } + } + if (tabsep.hasMoreElements()) + { + Console.warn("Ignoring additional elements for Float string to contact matrix parsing."); + } + + return vals; + } } diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java index d9afc7f..2367414 100644 --- a/src/jalview/datamodel/ContactMatrixI.java +++ b/src/jalview/datamodel/ContactMatrixI.java @@ -23,4 +23,7 @@ public interface ContactMatrixI */ String getType(); + int getWidth(); + int getHeight(); + } diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java index 0773e12..731948b 100644 --- a/src/jalview/datamodel/SeqDistanceContactMatrix.java +++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java @@ -106,4 +106,16 @@ public class SeqDistanceContactMatrix implements ContactMatrixI { return SEQUENCE_DISTANCE; } + + @Override + public int getWidth() + { + return width; + } + + @Override + public int getHeight() + { + return width; + } } diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java index de02939..e1ef021 100644 --- a/src/jalview/io/PContactPredictionFile.java +++ b/src/jalview/io/PContactPredictionFile.java @@ -114,6 +114,19 @@ public class PContactPredictionFile extends AlignFile { return CONTACT_PREDICTION; } + @Override + public int getHeight() + { + // TODO Auto-generated method stub + // return maximum contact height + return 0; + }@Override + public int getWidth() + { + // TODO Auto-generated method stub + // return total number of residues with contacts + return 0; + } }; models.add(cm); } @@ -133,6 +146,8 @@ public class PContactPredictionFile extends AlignFile cm.addContact(left, right, (float) strength); } } + // TODO COMPLETE + throw(new Error("Not Implemented yet.")); } @Override diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 8d2efe0..2b1b687 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -89,6 +89,8 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; @@ -148,6 +150,7 @@ import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -192,6 +195,7 @@ import jalview.xml.binding.jalview.JalviewUserColours.Colour; import jalview.xml.binding.jalview.MapListType.MapListFrom; import jalview.xml.binding.jalview.MapListType.MapListTo; import jalview.xml.binding.jalview.Mapping; +import jalview.xml.binding.jalview.MatrixType; import jalview.xml.binding.jalview.NoValueColour; import jalview.xml.binding.jalview.ObjectFactory; import jalview.xml.binding.jalview.PcaDataType; @@ -2289,6 +2293,22 @@ public class Jalview2XML line.setColour(annotation.getThreshold().colour.getRGB()); an.setThresholdLine(line); } + if (annotation.graph==AlignmentAnnotation.CONTACT_MAP) + { + if (annotation.sequenceRef.getContactMaps()!=null) + { + ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation); + if (cm!=null) + { + MatrixType xmlmat = new MatrixType(); + xmlmat.setType(cm.getType()); + xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); + xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); + xmlmat.setValue(ContactMatrix.contactToFloatString(cm)); + an.getContactmatrix().add(xmlmat); + } + } + } } else { @@ -3902,6 +3922,40 @@ public class Jalview2XML jaa.setProperty(prop.getName(), prop.getValue()); } } + if (jaa.graph == AlignmentAnnotation.CONTACT_MAP) + { + if (annotation.getContactmatrix() != null + && annotation.getContactmatrix().size() > 0) + { + for (MatrixType 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.getValue(), + xmlmat.getCols().intValue(), + xmlmat.getRows().intValue()); + + PAEContactMatrix newpae = new PAEContactMatrix( + jaa.sequenceRef, elements); + jaa.sequenceRef.addContactListFor(jaa, newpae); + } + } + else + { + Console.error("Ignoring CONTACT_MAP annotation with type " + + xmlmat.getType()); + } + } + } + } + if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index 58a4a83..92d27a0 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -78,6 +78,7 @@ public class PAEContactMatrix implements ContactMatrixI } } maxrow=matrix.length; + elements = matrix; } @@ -167,7 +168,7 @@ public class PAEContactMatrix implements ContactMatrixI @Override public int getContactHeight() { - return maxcol - 1; + return maxcol-1; } @Override @@ -224,4 +225,14 @@ public class PAEContactMatrix implements ContactMatrixI { return PAEMATRIX; } + @Override + public int getWidth() + { + return length; + } + @Override + public int getHeight() + { + return length; + } } diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index 7c061d7..492bfab 100644 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.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: 2023.01.31 at 04:07:09 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java index 2791f66..5faed76 100644 --- a/src/jalview/xml/binding/embl/EntryType.java +++ b/src/jalview/xml/binding/embl/EntryType.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: 2023.01.31 at 04:07:09 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java index 3e9d660..5d805e2 100644 --- a/src/jalview/xml/binding/embl/ObjectFactory.java +++ b/src/jalview/xml/binding/embl/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: 2023.01.31 at 04:07:09 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java index 6b8b2ea..a4a56ac 100644 --- a/src/jalview/xml/binding/embl/ROOT.java +++ b/src/jalview/xml/binding/embl/ROOT.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: 2023.01.31 at 04:07:09 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java index 4aa7e5e..9d68a83 100644 --- a/src/jalview/xml/binding/embl/XrefType.java +++ b/src/jalview/xml/binding/embl/XrefType.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: 2023.01.31 at 04:07:09 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index bee5c06..63a8c00 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 8c07465..0dd0c99 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // @@ -42,6 +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="property" maxOccurs="unbounded" minOccurs="0"> * <complexType> * <complexContent> @@ -83,6 +84,7 @@ import javax.xml.bind.annotation.XmlType; "label", "description", "thresholdLine", + "contactmatrix", "property" }) @XmlRootElement(name = "Annotation") @@ -93,6 +95,7 @@ public class Annotation { protected String label; protected String description; protected Annotation.ThresholdLine thresholdLine; + protected List contactmatrix; protected List property; @XmlAttribute(name = "graph", required = true) protected boolean graph; @@ -231,6 +234,35 @@ public class Annotation { } /** + * Gets the value of the contactmatrix property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the contactmatrix property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getContactmatrix().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link MatrixType } + * + * + */ + public List getContactmatrix() { + if (contactmatrix == null) { + contactmatrix = new ArrayList(); + } + return this.contactmatrix; + } + + /** * Gets the value of the property property. * *

diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 522d9c6..17d55ce 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index 99d82a7..40fdc11 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index 77c6bb7..9bcdde4 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index f1dad96..c4cc54a 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index dac24c4..d1491a0 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 8a30d89..5368a64 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index a902a83..7a2a052 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index a95d432..57a5796 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 2de1eba..518d8ff 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 21abacb..a1994be 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 99c5b4b..e6f0b6f 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index e898ca2..3b8ba23 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 0eb5a86..54c1d75 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 8b38877..367ed50 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // @@ -275,6 +275,14 @@ public class ObjectFactory { } /** + * Create an instance of {@link MatrixType } + * + */ + public MatrixType createMatrixType() { + return new MatrixType(); + } + + /** * Create an instance of {@link Annotation.Property } * */ diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index b261199..a98326a 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index fd2e336..3e686fb 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index 6a199a2..59c7d39 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index ed2c120..075d82b 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index cb7fa05..bc9649b 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index 49c2dd2..3d8b492 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index d697534..b12aa27 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 1935391..64b7c35 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index 338e645..56339f7 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: 2023.01.31 at 04:07:08 PM GMT +// Generated on: 2023.02.22 at 05:27:55 PM GMT // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java index b07b8e2..c4a231a 100644 --- a/src/jalview/xml/binding/uniprot/CitationType.java +++ b/src/jalview/xml/binding/uniprot/CitationType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java index 7dc9df3..0a99cff 100644 --- a/src/jalview/xml/binding/uniprot/CofactorType.java +++ b/src/jalview/xml/binding/uniprot/CofactorType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java index 8766f7a..34e2a6f 100644 --- a/src/jalview/xml/binding/uniprot/CommentType.java +++ b/src/jalview/xml/binding/uniprot/CommentType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java index e1b1db1..2605fcf 100644 --- a/src/jalview/xml/binding/uniprot/ConsortiumType.java +++ b/src/jalview/xml/binding/uniprot/ConsortiumType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java index 9bfde39..c774562 100644 --- a/src/jalview/xml/binding/uniprot/DbReferenceType.java +++ b/src/jalview/xml/binding/uniprot/DbReferenceType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java index 8ca1da7..7424da7 100644 --- a/src/jalview/xml/binding/uniprot/Entry.java +++ b/src/jalview/xml/binding/uniprot/Entry.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java index 44566fe..88aaf7a 100644 --- a/src/jalview/xml/binding/uniprot/EventType.java +++ b/src/jalview/xml/binding/uniprot/EventType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java index 371a778..e3870ea 100644 --- a/src/jalview/xml/binding/uniprot/EvidenceType.java +++ b/src/jalview/xml/binding/uniprot/EvidenceType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java index def955e..8d8f9d0 100644 --- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java +++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java index 0a6f7fe..e4aa4cc 100644 --- a/src/jalview/xml/binding/uniprot/FeatureType.java +++ b/src/jalview/xml/binding/uniprot/FeatureType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java index 9a04acc..7fdc013 100644 --- a/src/jalview/xml/binding/uniprot/GeneLocationType.java +++ b/src/jalview/xml/binding/uniprot/GeneLocationType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java index 8b69d3d..722c376 100644 --- a/src/jalview/xml/binding/uniprot/GeneNameType.java +++ b/src/jalview/xml/binding/uniprot/GeneNameType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java index 24285cb..f198fed 100644 --- a/src/jalview/xml/binding/uniprot/GeneType.java +++ b/src/jalview/xml/binding/uniprot/GeneType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java index 070e48e..b85f402 100644 --- a/src/jalview/xml/binding/uniprot/ImportedFromType.java +++ b/src/jalview/xml/binding/uniprot/ImportedFromType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java index 9a0e97a..5e636cd 100644 --- a/src/jalview/xml/binding/uniprot/InteractantType.java +++ b/src/jalview/xml/binding/uniprot/InteractantType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java index 33710ef..a782347 100644 --- a/src/jalview/xml/binding/uniprot/IsoformType.java +++ b/src/jalview/xml/binding/uniprot/IsoformType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java index 3f1a75f..a5a2146 100644 --- a/src/jalview/xml/binding/uniprot/KeywordType.java +++ b/src/jalview/xml/binding/uniprot/KeywordType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java index 5d7e7e9..0fd27de 100644 --- a/src/jalview/xml/binding/uniprot/LocationType.java +++ b/src/jalview/xml/binding/uniprot/LocationType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java index b7657f8..57a5a55 100644 --- a/src/jalview/xml/binding/uniprot/MoleculeType.java +++ b/src/jalview/xml/binding/uniprot/MoleculeType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java index c316941..6a79d3a 100644 --- a/src/jalview/xml/binding/uniprot/NameListType.java +++ b/src/jalview/xml/binding/uniprot/NameListType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java index 324ef9f..12151f4 100644 --- a/src/jalview/xml/binding/uniprot/ObjectFactory.java +++ b/src/jalview/xml/binding/uniprot/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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java index 5e82f4f..017e233 100644 --- a/src/jalview/xml/binding/uniprot/OrganismNameType.java +++ b/src/jalview/xml/binding/uniprot/OrganismNameType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java index ca8ad97..6e8fdb2 100644 --- a/src/jalview/xml/binding/uniprot/OrganismType.java +++ b/src/jalview/xml/binding/uniprot/OrganismType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java index 4639054..dfc88ae 100644 --- a/src/jalview/xml/binding/uniprot/PersonType.java +++ b/src/jalview/xml/binding/uniprot/PersonType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java index b01e412..dd09ace 100644 --- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java +++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java index 25d6030..ffec70a 100644 --- a/src/jalview/xml/binding/uniprot/PositionType.java +++ b/src/jalview/xml/binding/uniprot/PositionType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java index b1ab0f3..aa1c388 100644 --- a/src/jalview/xml/binding/uniprot/PropertyType.java +++ b/src/jalview/xml/binding/uniprot/PropertyType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java index 73f4c21..32c8aae 100644 --- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java +++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java index f3d0e80..45309f5 100644 --- a/src/jalview/xml/binding/uniprot/ProteinType.java +++ b/src/jalview/xml/binding/uniprot/ProteinType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java index 0e84d09..8e05607 100644 --- a/src/jalview/xml/binding/uniprot/ReactionType.java +++ b/src/jalview/xml/binding/uniprot/ReactionType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java index afd4647..a277dbb 100644 --- a/src/jalview/xml/binding/uniprot/ReferenceType.java +++ b/src/jalview/xml/binding/uniprot/ReferenceType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java index cddff7f..08b7fe6 100644 --- a/src/jalview/xml/binding/uniprot/SequenceType.java +++ b/src/jalview/xml/binding/uniprot/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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java index f66020c..796b9fd 100644 --- a/src/jalview/xml/binding/uniprot/SourceDataType.java +++ b/src/jalview/xml/binding/uniprot/SourceDataType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java index 012d588..be6f86f 100644 --- a/src/jalview/xml/binding/uniprot/SourceType.java +++ b/src/jalview/xml/binding/uniprot/SourceType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java index 8411265..f0ae4fd 100644 --- a/src/jalview/xml/binding/uniprot/StatusType.java +++ b/src/jalview/xml/binding/uniprot/StatusType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java index 77765a7..657157b 100644 --- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java +++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java index a18d58b..9860147 100644 --- a/src/jalview/xml/binding/uniprot/Uniprot.java +++ b/src/jalview/xml/binding/uniprot/Uniprot.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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java index b8a8636..7c68798 100644 --- a/src/jalview/xml/binding/uniprot/package-info.java +++ b/src/jalview/xml/binding/uniprot/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: 2023.01.31 at 04:07:10 PM GMT +// Generated on: 2023.02.22 at 05:27:56 PM GMT // @javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 6281c29..510b21d 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -55,6 +55,7 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrix; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; @@ -1547,7 +1548,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); AlignmentI al = af.getViewport().getAlignment(); - SequenceI sq = al.getSequenceAt(0); + // PAE matrices are added as reference annotation to the dataset sequence + // at least for now. + SequenceI sq = al.getSequenceAt(0).getDatasetSequence(); int i = sq.getLength(); float[][] paevals = new float[i][i]; for (i = i - 1; i >= 0; i--) @@ -1560,6 +1563,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase } } PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); + String content = ContactMatrix.contactToFloatString(dummyMat); + Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1 + float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength()); + assertEquals(vals[3][4],paevals[3][4]); + AlignmentAnnotation paeCm = sq.addContactList(dummyMat); al.addAnnotation(paeCm); File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", @@ -1570,15 +1578,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); AlignmentI newAl = af.getViewport().getAlignment(); - SequenceI newSeq = newAl.getSequenceAt(0); + SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence(); // check annotation of the expected type exists Assert.assertEquals(newSeq.getAnnotation().length, 1); Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph); // check a contact matrix was recovered Assert.assertEquals(newSeq.getContactMaps().size(), 1); - // and can be found for the annotation - ContactMatrixI restoredMat = al + // and can be found for the annotation on the sequence + ContactMatrixI restoredMat = newSeq .getContactMatrixFor(newSeq.getAnnotation()[0]); Assert.assertNotNull(restoredMat); for (i = sq.getLength() - 1; i >= 0; i--) @@ -1590,6 +1598,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j)); } } + } }