From 5d5099b75d2653cedf49bb98308dcb94202ed16e Mon Sep 17 00:00:00 2001 From: James Procter Date: Fri, 17 Mar 2023 17:32:40 +0000 Subject: [PATCH] JAL-4134 store/restore Newick tree for PAE annotation row --- schemas/jalview.xsd | 2 + src/jalview/gui/AlignFrame.java | 46 +++-- src/jalview/gui/AnnotationLabels.java | 2 +- src/jalview/gui/TreeCanvas.java | 6 +- src/jalview/gui/TreePanel.java | 22 +- src/jalview/project/Jalview2XML.java | 33 ++- .../ws/datamodel/alphafold/PAEContactMatrix.java | 3 +- src/jalview/xml/binding/embl/EntrySetType.java | 2 +- src/jalview/xml/binding/embl/EntryType.java | 2 +- src/jalview/xml/binding/embl/ObjectFactory.java | 2 +- src/jalview/xml/binding/embl/ROOT.java | 2 +- src/jalview/xml/binding/embl/XrefType.java | 2 +- src/jalview/xml/binding/jalview/AlcodonFrame.java | 2 +- src/jalview/xml/binding/jalview/Annotation.java | 2 +- .../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 | 210 +++++++++++++------- .../xml/binding/jalview/JalviewUserColours.java | 2 +- src/jalview/xml/binding/jalview/MapListType.java | 2 +- src/jalview/xml/binding/jalview/Mapping.java | 2 +- src/jalview/xml/binding/jalview/MatrixType.java | 2 +- src/jalview/xml/binding/jalview/NoValueColour.java | 2 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 2 +- src/jalview/xml/binding/jalview/PcaDataType.java | 2 +- src/jalview/xml/binding/jalview/Pdbentry.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 +- src/jalview/xml/binding/uniprot/CitationType.java | 2 +- src/jalview/xml/binding/uniprot/CofactorType.java | 2 +- src/jalview/xml/binding/uniprot/CommentType.java | 2 +- .../xml/binding/uniprot/ConsortiumType.java | 2 +- .../xml/binding/uniprot/DbReferenceType.java | 2 +- src/jalview/xml/binding/uniprot/Entry.java | 2 +- src/jalview/xml/binding/uniprot/EventType.java | 2 +- src/jalview/xml/binding/uniprot/EvidenceType.java | 2 +- .../xml/binding/uniprot/EvidencedStringType.java | 2 +- src/jalview/xml/binding/uniprot/FeatureType.java | 2 +- .../xml/binding/uniprot/GeneLocationType.java | 2 +- src/jalview/xml/binding/uniprot/GeneNameType.java | 2 +- src/jalview/xml/binding/uniprot/GeneType.java | 2 +- .../xml/binding/uniprot/ImportedFromType.java | 2 +- .../xml/binding/uniprot/InteractantType.java | 2 +- src/jalview/xml/binding/uniprot/IsoformType.java | 2 +- src/jalview/xml/binding/uniprot/KeywordType.java | 2 +- src/jalview/xml/binding/uniprot/LocationType.java | 2 +- src/jalview/xml/binding/uniprot/MoleculeType.java | 2 +- src/jalview/xml/binding/uniprot/NameListType.java | 2 +- src/jalview/xml/binding/uniprot/ObjectFactory.java | 2 +- .../xml/binding/uniprot/OrganismNameType.java | 2 +- src/jalview/xml/binding/uniprot/OrganismType.java | 2 +- src/jalview/xml/binding/uniprot/PersonType.java | 2 +- .../binding/uniprot/PhysiologicalReactionType.java | 2 +- src/jalview/xml/binding/uniprot/PositionType.java | 2 +- src/jalview/xml/binding/uniprot/PropertyType.java | 2 +- .../xml/binding/uniprot/ProteinExistenceType.java | 2 +- src/jalview/xml/binding/uniprot/ProteinType.java | 2 +- src/jalview/xml/binding/uniprot/ReactionType.java | 2 +- src/jalview/xml/binding/uniprot/ReferenceType.java | 2 +- src/jalview/xml/binding/uniprot/SequenceType.java | 2 +- .../xml/binding/uniprot/SourceDataType.java | 2 +- src/jalview/xml/binding/uniprot/SourceType.java | 2 +- src/jalview/xml/binding/uniprot/StatusType.java | 2 +- .../binding/uniprot/SubcellularLocationType.java | 2 +- src/jalview/xml/binding/uniprot/Uniprot.java | 2 +- src/jalview/xml/binding/uniprot/package-info.java | 2 +- test/jalview/project/Jalview2xmlTests.java | 1 + 77 files changed, 290 insertions(+), 171 deletions(-) diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index 7a18d59..adaa3ee 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -554,6 +554,8 @@ + Set for trees associated with columns of an alignment, sequence or annotation row + Refers to annotation row the tree is provided by diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 82ec1d2..92a18ec 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4189,34 +4189,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { int x = 4, y = 5; int w = 400, h = 500; + try { NewickFile fin = new NewickFile( - new FileParse(cm.getNewickString(), DataSourceType.PASTE)); - fin.parse(); - if (fin.getTree() == null) - { - return; - } + new FileParse(cm.getNewick(), DataSourceType.PASTE)); String title = "PAE Matrix Tree for " + cm.getReferenceSeq().getDisplayId(false); - TreePanel tp = new TreePanel(alignPanel, fin, aa, title); - - tp.setSize(w, h); - - if (x > 0 && y > 0) - { - tp.setLocation(x, y); - } - Desktop.addInternalFrame(tp, title, w, h); + showColumnWiseTree(fin, aa, title, w,h, x,y); } catch (Throwable xx) { Console.error("Unexpected exception showing tree for contact matrix", xx); } + } + public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle, + int w, int h, int x, int y) + { + try + { + nf.parse(); + if (nf.getTree() == null) + { + return null; + } + TreePanel tp = new TreePanel(alignPanel, nf, aa, title); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + Desktop.addInternalFrame(tp, title, w, h); + return tp; + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + return null; } + private boolean buildingMenu = false; /** diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 0ccd6c2..d1a40e5 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -428,7 +428,7 @@ public class AnnotationLabels extends JPanel { final PAEContactMatrix cm = (PAEContactMatrix) av .getContactMatrix(aa[selectedRow]); - if (cm.getNewickString()!=null && cm.getNewickString().length()>0) + if (cm.getNewick()!=null && cm.getNewick().length()>0) { item = new JMenuItem("Show Matrix"); item.addActionListener(new ActionListener() diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 354feac..97ca391 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -295,7 +295,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, // Colour selected leaves differently boolean isSelected = false; - if (tp.getColumnWise()) + if (tp.isColumnWise()) { isSelected = isColumnForNodeSelected(node); } @@ -822,7 +822,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { Vector leaves = tree.findLeaves(highlightNode); - if (tp.getColumnWise()) { + if (tp.isColumnWise()) { markColumnsFor(getAssociatedPanels(), leaves, Color.red); } else { for (int i = 0; i < leaves.size(); i++) @@ -1000,7 +1000,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - if (!tp.getColumnWise()) { + if (!tp.isColumnWise()) { createSeqGroupFor(aps, l, col); } else { markColumnsFor(aps,l,col); diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 6a07a4e..30e4305 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -135,18 +135,23 @@ public class TreePanel extends GTreePanel public TreePanel(AlignmentPanel alignPanel, NewickFile fin, AlignmentAnnotation aa, String title) { - this(alignPanel, fin, title, null); + super(); columnWise=true; assocAnnotation = aa; - - + this.setFrameIcon(null); + this.treeTitle = title; + initTreePanel(alignPanel, null, null, fin, null); } + boolean columnWise=false; AlignmentAnnotation assocAnnotation=null; - public boolean getColumnWise() + public boolean isColumnWise() { return columnWise; } + public AlignmentAnnotation getAssocAnnotation() { + return assocAnnotation; + } public AlignmentI getAlignment() { @@ -167,6 +172,15 @@ public class TreePanel extends GTreePanel this.treeType = type; this.scoreModelName = modelName; + if (columnWise) + { + bootstrapMenu.setVisible(false); + placeholdersMenu.setSelected(false); + placeholdersMenu.setVisible(false); + fitToWindow.setSelected(false); + sortAssocViews.setVisible(false); + } + treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 36c87ce..efcc7ff 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1325,6 +1325,13 @@ public class Jalview2XML tree.setLinkToAllViews( tp.getTreeCanvas().isApplyToAllViews()); + // columnWiseTree + if (tp.isColumnWise()) + { + tree.setColumnWise(true); + String annId = tp.getAssocAnnotation().annotationId; + tree.setColumnReference(annId); + } // jms.addTree(tree); object.getTree().add(tree); } @@ -4385,10 +4392,28 @@ public class Jalview2XML TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.showNewickTree(new NewickFile(tree.getNewick()), - tree.getTitle(), safeInt(tree.getWidth()), - safeInt(tree.getHeight()), safeInt(tree.getXpos()), - safeInt(tree.getYpos())); + if (tree.isColumnWise()) + { + AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree + .getColumnReference()); + if (aa == null) + { + Console.warn( + "Null alignment annotation when restoring columnwise tree"); + } + tp = af.showColumnWiseTree(new NewickFile(tree.getNewick()), aa, + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); + + } + else + { + tp = af.showNewickTree(new NewickFile(tree.getNewick()), + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); + } if (tree.getId() != null) { // perhaps bind the tree id to something ? diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index 3ce1c83..a5ce9a0 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -262,7 +262,8 @@ public class PAEContactMatrix implements ContactMatrixI return groups!=null; } String newick=null; - public String getNewickString() + @Override + public String getNewick() { return newick; } diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index 5e1b3ea..0479a34 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: 2023.03.09 at 07:45:03 AM GMT +// Generated on: 2023.03.17 at 05:31:45 PM GMT // diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java index 84a1ab3..6336ef1 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: 2023.03.09 at 07:45:03 AM GMT +// Generated on: 2023.03.17 at 05:31:45 PM GMT // diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java index 234c721..e1a917a 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: 2023.03.09 at 07:45:03 AM GMT +// Generated on: 2023.03.17 at 05:31:45 PM GMT // diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java index 76cb42d..958cdbc 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: 2023.03.09 at 07:45:03 AM GMT +// Generated on: 2023.03.17 at 05:31:45 PM GMT // diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java index 56a9539..244d0fe 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: 2023.03.09 at 07:45:03 AM GMT +// Generated on: 2023.03.17 at 05:31:45 PM GMT // diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index cdc21a5..2a40e11 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index ba54d37..8d99141 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index ccd6222..27e0cc6 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index 72a3e73..c5f75e0 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index c304ff8..9be9876 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index 2a8d1eb..6546be9 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 09701ba..a124e62 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 2e41fe0..61e66ce 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index faf4182..24190b8 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index e4ea645..3a9428c 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 0bf4211..22b2533 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // @@ -260,6 +260,8 @@ import javax.xml.datatype.XMLGregorianCalendar; * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * </restriction> @@ -310,8 +312,8 @@ import javax.xml.datatype.XMLGregorianCalendar; * </element> * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> * <attGroup ref="{www.jalview.org}SimilarityParams"/> + * <attGroup ref="{www.jalview.org}swingwindow"/> * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> @@ -3124,8 +3126,8 @@ public class JalviewModel { * </element> * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> * <attGroup ref="{www.jalview.org}SimilarityParams"/> + * <attGroup ref="{www.jalview.org}swingwindow"/> * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> @@ -3180,14 +3182,6 @@ public class JalviewModel { protected Boolean showLabels; @XmlAttribute(name = "linkToAllViews") protected Boolean linkToAllViews; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; @XmlAttribute(name = "includeGaps") protected Boolean includeGaps; @XmlAttribute(name = "matchGaps") @@ -3196,6 +3190,14 @@ public class JalviewModel { protected Boolean includeGappedColumns; @XmlAttribute(name = "denominateByShortestLength") protected Boolean denominateByShortestLength; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; /** * Gets the value of the sequencePoint property. @@ -3544,195 +3546,195 @@ public class JalviewModel { } /** - * Gets the value of the width property. + * Gets the value of the includeGaps property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getWidth() { - return width; + public Boolean isIncludeGaps() { + return includeGaps; } /** - * Sets the value of the width property. + * Sets the value of the includeGaps property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setWidth(Integer value) { - this.width = value; + public void setIncludeGaps(Boolean value) { + this.includeGaps = value; } /** - * Gets the value of the height property. + * Gets the value of the matchGaps property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getHeight() { - return height; + public Boolean isMatchGaps() { + return matchGaps; } /** - * Sets the value of the height property. + * Sets the value of the matchGaps property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setHeight(Integer value) { - this.height = value; + public void setMatchGaps(Boolean value) { + this.matchGaps = value; } /** - * Gets the value of the xpos property. + * Gets the value of the includeGappedColumns property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getXpos() { - return xpos; + public Boolean isIncludeGappedColumns() { + return includeGappedColumns; } /** - * Sets the value of the xpos property. + * Sets the value of the includeGappedColumns property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setXpos(Integer value) { - this.xpos = value; + public void setIncludeGappedColumns(Boolean value) { + this.includeGappedColumns = value; } /** - * Gets the value of the ypos property. + * Gets the value of the denominateByShortestLength property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getYpos() { - return ypos; + public Boolean isDenominateByShortestLength() { + return denominateByShortestLength; } /** - * Sets the value of the ypos property. + * Sets the value of the denominateByShortestLength property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setYpos(Integer value) { - this.ypos = value; + public void setDenominateByShortestLength(Boolean value) { + this.denominateByShortestLength = value; } /** - * Gets the value of the includeGaps property. + * Gets the value of the width property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isIncludeGaps() { - return includeGaps; + public Integer getWidth() { + return width; } /** - * Sets the value of the includeGaps property. + * Sets the value of the width property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setIncludeGaps(Boolean value) { - this.includeGaps = value; + public void setWidth(Integer value) { + this.width = value; } /** - * Gets the value of the matchGaps property. + * Gets the value of the height property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isMatchGaps() { - return matchGaps; + public Integer getHeight() { + return height; } /** - * Sets the value of the matchGaps property. + * Sets the value of the height property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setMatchGaps(Boolean value) { - this.matchGaps = value; + public void setHeight(Integer value) { + this.height = value; } /** - * Gets the value of the includeGappedColumns property. + * Gets the value of the xpos property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isIncludeGappedColumns() { - return includeGappedColumns; + public Integer getXpos() { + return xpos; } /** - * Sets the value of the includeGappedColumns property. + * Sets the value of the xpos property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setIncludeGappedColumns(Boolean value) { - this.includeGappedColumns = value; + public void setXpos(Integer value) { + this.xpos = value; } /** - * Gets the value of the denominateByShortestLength property. + * Gets the value of the ypos property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isDenominateByShortestLength() { - return denominateByShortestLength; + public Integer getYpos() { + return ypos; } /** - * Sets the value of the denominateByShortestLength property. + * Sets the value of the ypos property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setDenominateByShortestLength(Boolean value) { - this.denominateByShortestLength = value; + public void setYpos(Integer value) { + this.ypos = value; } @@ -4200,6 +4202,8 @@ public class JalviewModel { * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /> * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> * </restriction> @@ -4238,6 +4242,10 @@ public class JalviewModel { protected Boolean fitToWindow; @XmlAttribute(name = "currentTree") protected Boolean currentTree; + @XmlAttribute(name = "columnWise") + protected Boolean columnWise; + @XmlAttribute(name = "columnReference") + protected String columnReference; @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -4519,6 +4527,58 @@ public class JalviewModel { } /** + * Gets the value of the columnWise property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColumnWise() { + if (columnWise == null) { + return false; + } else { + return columnWise; + } + } + + /** + * Sets the value of the columnWise property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColumnWise(Boolean value) { + this.columnWise = value; + } + + /** + * Gets the value of the columnReference property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getColumnReference() { + return columnReference; + } + + /** + * Sets the value of the columnReference property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setColumnReference(String value) { + this.columnReference = value; + } + + /** * Gets the value of the id property. * * @return diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index c5177ba..b62cf15 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 22242eb..7a86123 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index a147ab4..10d3d5b 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java index fcf9958..d884100 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 935adc5..22b78a5 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 3a2f81b..f034a2a 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index 3d19c58..06aecab 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 544b568..401022a 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index 5851659..d02fd03 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index f96550a..a915d94 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index 62c04c8..fa65d58 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index 304d653..192caf8 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index 0571f85..dd41877 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 21b35d7..d3c2098 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 PM GMT // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index a8e5b9f..2cfefda 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: 2023.03.09 at 07:45:02 AM GMT +// Generated on: 2023.03.17 at 05:31:44 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 15940c7..de12eb2 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java index f2ecd0c..e9244e9 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java index 7ce7ebc..e0692c9 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java index 022099d..71db504 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java index b623d2c..73ccfa8 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java index 74efb7c..21963a8 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java index f8d37c5..0b4d4bd 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java index afe1b60..59c9857 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java index 78ed315..0fa25a6 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java index 0632ac3..f818e2e 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java index 1094851..f2d5638 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java index 6547333..71af71f 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java index 0dbe520..5fa628e 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java index 4c493d5..3d6c308 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java index 038f37f..c9cadc2 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java index b3aa4e8..ea55664 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java index 7f3c265..f6409ee 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java index 38c1665..62e9999 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java index 285b8d3..8b52523 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java index eddabb2..be68867 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java index d18fdcd..e2bb255 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java index 06a0470..bc5c8c5 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java index 80171d4..bb76add 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java index 63ea683..1354092 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java index f5a126a..e674452 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java index 33c194e..a00d698 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java index 45f654f..c9f169c 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java index 7cdaabd..c34a0f5 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java index 9edfb71..7b106fb 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java index 933a013..8d9d51d 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java index 8315a1c..e5f9fde 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java index fbd840b..49cd130 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java index ef8f052..9796260 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java index 711afca..9293a64 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java index dc8f920..dd3308b 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java index 27ea148..97522e2 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java index a7bc828..14f96df 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 PM GMT // diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java index 3f8b048..a7bc67c 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: 2023.03.09 at 07:45:04 AM GMT +// Generated on: 2023.03.17 at 05:31:46 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 0ab9dcb..fa6c25c 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -1568,6 +1568,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength()); assertEquals(vals[3][4],paevals[3][4]); dummyMat.makeGroups(0.5f, false); + Assert.assertNotSame(dummyMat.getNewick(), ""); AlignmentAnnotation paeCm = sq.addContactList(dummyMat); al.addAnnotation(paeCm); File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", -- 1.7.10.2