From: James Procter Date: Thu, 16 Feb 2023 13:14:11 +0000 (+0000) Subject: Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects X-Git-Tag: Release_2_11_3_0~18^2~13 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0de37d1a047209510bab82225109ae2a47931f79;hp=01f8ff469a507604ed961418f7c80f9b245e60ca;p=jalview.git Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects Conflicts: src/jalview/bin/Jalview.java --- diff --git a/RELEASE b/RELEASE index bc0c6dd..cfbbf93 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ jalview.release=releases/Release_2_11_3_Branch -jalview.version=2.11.3 +jalview.version=2.11.3.0 diff --git a/build.gradle b/build.gradle index bde50b5..851c5f6 100644 --- a/build.gradle +++ b/build.gradle @@ -47,7 +47,7 @@ plugins { id 'eclipse' id "com.diffplug.gradle.spotless" version "3.28.0" id 'com.github.johnrengelman.shadow' version '4.0.3' - id 'com.install4j.gradle' version '9.0.6' + id 'com.install4j.gradle' version '10.0.3' id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree id 'com.palantir.git-version' version '0.13.0' apply false } @@ -483,16 +483,10 @@ ext { // for install4j JAVA_MIN_VERSION = JAVA_VERSION JAVA_MAX_VERSION = JAVA_VERSION - def jreInstallsDir = string(jre_installs_dir) + jreInstallsDir = string(jre_installs_dir) if (jreInstallsDir.startsWith("~/")) { jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1) } - macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre") - windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre") - linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre") - macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz") - windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz") - linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz") install4jDir = string("${jalviewDir}/${install4j_utils_dir}") install4jConfFileName = string("jalview-install4j-conf.install4j") install4jConfFile = file("${install4jDir}/${install4jConfFileName}") @@ -2411,12 +2405,6 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) { 'JAVA_VERSION': JAVA_VERSION, 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, 'VERSION': JALVIEW_VERSION, - 'MACOS_JAVA_VM_DIR': macosJavaVMDir, - 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, - 'LINUX_JAVA_VM_DIR': linuxJavaVMDir, - 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, - 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz, - 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz, 'COPYRIGHT_MESSAGE': install4j_copyright_message, 'BUNDLE_ID': install4jBundleId, 'INTERNAL_ID': install4jInternalId, @@ -2446,8 +2434,29 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) { 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile, 'PNG_ICON_FILE': install4jPngIconFile, 'BACKGROUND': install4jBackground, + ] + def varNameMap = [ + 'mac': 'MACOS', + 'windows': 'WINDOWS', + 'linux': 'LINUX' + ] + + // these are the bundled OS/architecture VMs needed by install4j + def osArch = [ + [ "mac", "x64" ], + [ "mac", "aarch64" ], + [ "windows", "x64" ], + [ "linux", "x64" ], + [ "linux", "aarch64" ] ] + osArch.forEach { os, arch -> + variables[ sprintf("%s_%s_JAVA_VM_DIR", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/jre-%s-%s-%s/jre", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch) + // N.B. For some reason install4j requires the below filename to have underscores and not hyphens + // otherwise running `gradle installers` generates a non-useful error: + // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"` + variables[ sprintf("%s_%s_JAVA_VM_TGZ", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/tgz/jre_%s_%s_%s.tar.gz", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch) + } //println("INSTALL4J VARIABLES:") //variables.each{k,v->println("${k}=${v}")} @@ -2481,8 +2490,6 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) { inputs.dir(getdownAppBaseDir) inputs.file(install4jConfFile) inputs.file("${install4jDir}/${install4j_info_plist_file_associations}") - inputs.dir(macosJavaVMDir) - inputs.dir(windowsJavaVMDir) outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}") } diff --git a/gradle.properties b/gradle.properties index acb65e9..e42f8b5 100644 --- a/gradle.properties +++ b/gradle.properties @@ -129,14 +129,14 @@ flexmark_css = utils/doc/github.css channel_properties_dir = utils/channels channel_props = channel.props -install4j_home_dir = ~/buildtools/install4j9 +install4j_home_dir = ~/buildtools/install4j10 install4j_copyright_message = ... install4j_bundle_id = org.jalview.jalview-desktop install4j_utils_dir = utils/install4j install4j_images_dir = utils/install4j -install4j_template = install4j9_template.install4j +install4j_template = install4j10_template.install4j install4j_info_plist_file_associations = file_associations_auto-Info_plist.xml -install4j_installer_file_associations = file_associations_auto-install4j8.xml +install4j_installer_file_associations = file_associations_auto-install4j10.xml #install4j_DMG_uninstaller_app_files = uninstall_old_jalview_files.xml install4j_build_dir = build/install4j install4j_executable_name = jalviewg diff --git a/help/help/help.jhm b/help/help/help.jhm index 1710bbc..cd415ea 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -105,6 +105,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 3308456..877c758 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -100,6 +100,7 @@ + diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html index e006618..9ba0578 100755 --- a/help/help/html/colourSchemes/index.html +++ b/help/help/html/colourSchemes/index.html @@ -459,13 +459,11 @@ td { I X - + R Y - N - W S @@ -481,7 +479,9 @@ td { D V - + + N + Nucleotide @@ -505,6 +505,27 @@ td { + Nucleotide Ambiguity + + + + + + + + + + + + + + + + + + + + Purine/Pyrimidine diff --git a/help/help/html/colourSchemes/nucleotideambiguity.html b/help/help/html/colourSchemes/nucleotideambiguity.html new file mode 100755 index 0000000..c1ab548 --- /dev/null +++ b/help/help/html/colourSchemes/nucleotideambiguity.html @@ -0,0 +1,122 @@ + + + +Nucleotide Colour Scheme + + + + +

+ Nucleotide Ambiguity Colours +

+ + +

+ This colour scheme was devised by Suzanne Duce and the Jalview Team to highlight ambiguity codes used in nucleotide sequences. +

+

+ The use of X to represent an unknown base is acknowledged, but this is not recommended as the symbol refers to xanthine (see IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents.) +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
AAdenine
CCytosine
GGuanine
TThymine
UUracil
IInosine
XUnknown (sometimes Xanthine)
RUnknown Purine
YUnknown Pyrimidine
WWeak nucleotide (A or T)
SStrong nucleotide (G or C)
MAmino (A or C)
KKeto (G or T)
BNot A (G or C or T)
HNot G (A or C or T)
DNot C (A or G or T)
VNot T (A or G or C)
NUnknown
+
+ + diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html index 1a7286f..6534d2d 100755 --- a/help/help/html/menus/alignmentMenu.html +++ b/help/help/html/menus/alignmentMenu.html @@ -489,7 +489,7 @@ Blosum62 Score, Percentage Identity, Zappo, Taylor, gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean, Hydrophobicity, Helix Propensity, Strand Propensity, Turn - Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User + Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User Defined
See colours for a description of all colour schemes. diff --git a/help/help/html/menus/alwcolour.html b/help/help/html/menus/alwcolour.html index 0e10f44..5b8d00b 100755 --- a/help/help/html/menus/alwcolour.html +++ b/help/help/html/menus/alwcolour.html @@ -40,7 +40,7 @@ Blosum62 Score, Percentage Identity, Zappo, Taylor, gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean, Hydrophobicity, Helix Propensity, Strand Propensity, Turn - Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User + Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User Defined
See colours for a description of all colour schemes. diff --git a/help/markdown/releases/release-2_11_3.md b/help/markdown/releases/release-2_11_3.md deleted file mode 100644 index 18b15ea..0000000 --- a/help/markdown/releases/release-2_11_3.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -version: 2.11.3 -date: 2022-12-12 -channel: "release" ---- - -## New Features - -- Find can search sequence features' type and description -- Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences -JAL-4089 use selected columns for superposition -JAL-4086 Highlight aligned positions on all associated structures when mousing over a column -JAL-4083 Exceptions for multiple residue highlights in Jmol -JAL-4075 Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows -JAL-4033 selections with visual feedback via contact matrix annotation -JAL-4027 contact matrix datatype in Jalview -JAL-3895 Alphafold red/orange/yellow/green colourscheme for structures -JAL-3855 Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ -JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ? -JAL-2961 Jmol view not always centred on structures when multiple structures are viewed -JAL-2382 Import and display sequence-associated contact predictions in CASP-RR format -JAL-2349 Contact prediction visualisation -JAL-2348 modularise annotation renderer -JAL-1551 Standard source code formatting and editing settings diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md new file mode 100644 index 0000000..46de783 --- /dev/null +++ b/help/markdown/releases/release-2_11_3_0.md @@ -0,0 +1,53 @@ +--- +version: 2.11.3.0 +date: 2023-03-07 +channel: "release" +--- + +## New Features +- Native M1 build for macOS using Adoptium JRE 11 macos-aarch64 +- Installers built with install4j10 +- Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button +- FlatLAF default look and feel on Linux, OSX and everywhere else ? + +- Ambiguous Base Colourscheme +- Find can search sequence features' type and description +- Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences +- Use selected columns for superposition +- Highlight aligned positions on all associated structures when mousing over a column + +- Alphafold red/orange/yellow/green colourscheme for structures +- Interactive picking of low pAE score regions +- contact matrix datatype in Jalview +- Selections with visual feedback via contact matrix annotation + +- Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows +- Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/ + +- Jmol view not always centred on structures when multiple structures are viewed + +- Overview window is saved in project file, and state of 'show hidden regions' is preserved. + +- Name of alignment and view included in overview window's title + +- Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows +- Shift+Click+Drag to adjust height of all annotation tracks of same type + + +## Still in progress (delete on release) + +- Import and display sequence-associated contact predictions in CASP-RR format +- Contact prediction visualisation +- modularise annotation renderer + + + +## Issues Resolved +- Cancelling interactive calculation leaves empty progress bar. +- Unsaved Alignment windows close without prompting to save, individually or at application quit. +- Can quit Jalview while 'save project' is in progress +- 'Use original colours' option of colour by annotation not honoured when restoring view from project +- PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch) +- Multiple overview windows can be opened for a particular alignment view when multiple views are present +- Overview windows opened automatically (due to preferences settings) lack title +- Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession \ No newline at end of file diff --git a/help/markdown/whatsnew/whatsnew-2_11_3_0.md b/help/markdown/whatsnew/whatsnew-2_11_3_0.md new file mode 100644 index 0000000..59495d5 --- /dev/null +++ b/help/markdown/whatsnew/whatsnew-2_11_3_0.md @@ -0,0 +1,5 @@ +The 2.11.3 series includes support for in-depth exploration of predicted alignment error matrices from AlphaFold in the context of multiple alignments, along with support for standard colourschemes for shading models according to their pLDDT. + +It also introduces new support for native ARM-based OSX architectures, and a few other goodies! + + diff --git a/j11lib/flatlaf-2.3.jar b/j11lib/flatlaf-2.3.jar deleted file mode 100644 index 9f292d2..0000000 Binary files a/j11lib/flatlaf-2.3.jar and /dev/null differ diff --git a/j11lib/flatlaf-3.0.jar b/j11lib/flatlaf-3.0.jar new file mode 100644 index 0000000..75d90d3 Binary files /dev/null and b/j11lib/flatlaf-3.0.jar differ diff --git a/j8lib/flatlaf-extras-2.3.jar b/j11lib/flatlaf-extras-3.0.jar similarity index 70% rename from j8lib/flatlaf-extras-2.3.jar rename to j11lib/flatlaf-extras-3.0.jar index 39e9701..1f6bbc3 100644 Binary files a/j8lib/flatlaf-extras-2.3.jar and b/j11lib/flatlaf-extras-3.0.jar differ diff --git a/j8lib/flatlaf-2.3.jar b/j8lib/flatlaf-2.3.jar deleted file mode 100644 index 9f292d2..0000000 Binary files a/j8lib/flatlaf-2.3.jar and /dev/null differ diff --git a/j8lib/flatlaf-3.0.jar b/j8lib/flatlaf-3.0.jar new file mode 100644 index 0000000..75d90d3 Binary files /dev/null and b/j8lib/flatlaf-3.0.jar differ diff --git a/j11lib/flatlaf-extras-2.3.jar b/j8lib/flatlaf-extras-3.0.jar similarity index 70% rename from j11lib/flatlaf-extras-2.3.jar rename to j8lib/flatlaf-extras-3.0.jar index 39e9701..1f6bbc3 100644 Binary files a/j11lib/flatlaf-extras-2.3.jar and b/j8lib/flatlaf-extras-3.0.jar differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 7f6e9a5..91ae958 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -32,7 +32,17 @@ action.load_project = Load Project action.save_project = Save Project action.save_project_as = Save Project as... action.quit = Quit -label.quit_jalview = Quit Jalview? +action.force_quit = Force quit +label.quit_jalview = Are you sure you want to quit Jalview? +label.wait_for_save = Wait for save +label.unsaved_changes = There are unsaved changes. +label.save_in_progress = Some files are still saving: +label.unknown = Unknown +label.quit_after_saving = Jalview will quit after saving. +label.all_saved = All files saved. +label.quitting_bye = Quitting, bye! +action.wait = Wait +action.cancel_quit = Cancel quit action.expand_views = Expand Views action.gather_views = Gather Views action.page_setup = Page Setup... @@ -203,6 +213,7 @@ label.colourScheme_turnpropensity = Turn Propensity label.colourScheme_buriedindex = Buried Index label.colourScheme_purine/pyrimidine = Purine/Pyrimidine label.colourScheme_nucleotide = Nucleotide +label.colourScheme_nucleotideambiguity = Nucleotide Ambiguity label.colourScheme_t-coffeescores = T-Coffee Scores label.colourScheme_rnahelices = By RNA Helices label.colourScheme_sequenceid = Sequence ID Colour diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 13eb15e..79274d0 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -32,7 +32,17 @@ action.load_project = Cargar proyecto action.save_project = Guardar proyecto action.save_project_as = Guardar proyecto como... action.quit = Salir -label.quit_jalview = Salir de Jalview? +action.force_quit = Forzar la salida +label.quit_jalview = ¿Estás seguro de que quieres salir de Jalview? +label.wait_for_save = Esperar a guardar +label.unsaved_changes = Hay cambios sin guardar. +label.save_in_progress = Algunos archivos aún se están guardando: +label.unknown = desconocido +label.quit_after_saving = Jalview se cerrará después de guardar. +label.all_saved = Todos los archivos guardados. +label.quitting_bye = Saliendo ¡chao! +action.wait = Espere +action.cancel_quit = Cancelar la salida action.expand_views = Expandir vistas action.gather_views = Capturar vistas action.page_setup = Configuración de la página @@ -194,6 +204,7 @@ label.colourScheme_turnpropensity = Tendencia de giro label.colourScheme_buriedindex = Índice de encubrimiento label.colourScheme_purine/pyrimidine = Purina/Pirimidina label.colourScheme_nucleotide = Nucleótido +label.colourScheme_nucleotideambiguity = Ambigüedad de nucleótido label.colourScheme_t-coffeescores = Puntuación del T-Coffee label.colourScheme_rnahelices = Por hélices de RNA label.colourScheme_sequenceid = Color de ID de secuencia diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index 1d2235e..cd05e5f 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -391,6 +391,16 @@ + + + + + + + + + + diff --git a/src/jalview/appletgui/#OverviewPanel.java# b/src/jalview/appletgui/#OverviewPanel.java# deleted file mode 100755 index 14c3158..0000000 --- a/src/jalview/appletgui/#OverviewPanel.java# +++ /dev/null @@ -1,453 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.appletgui; - -import jalview.datamodel.SequenceI; -import jalview.viewmodel.OverviewDimensions; -import jalview.datamodel.AlignmentI; -import jalview.renderer.seqfeatures.FeatureColourFinder; - -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Frame; -import java.awt.Graphics; -import java.awt.Image; -import java.awt.Panel; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; - -public class OverviewPanel extends Panel implements Runnable, - MouseMotionListener, MouseListener -{ - private OverviewDimensions od; - - private Image miniMe; - - private Image offscreen; - - private AlignViewport av; - - private AlignmentPanel ap; - - private boolean resizing = false; - - // This is set true if the user resizes whilst - // the overview is being calculated - private boolean resizeAgain = false; - - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; - - private FeatureRenderer fr; - - private Frame nullFrame; - - public OverviewPanel(AlignmentPanel alPanel) - { - this.av = alPanel.av; - this.ap = alPanel; - setLayout(null); - nullFrame = new Frame(); - nullFrame.addNotify(); - - sr = new SequenceRenderer(av); - sr.graphics = nullFrame.getGraphics(); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(av); - - od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation()); - - setSize(new Dimension(od.getWidth(), od.getHeight())); - addComponentListener(new ComponentAdapter() - { - - @Override - public void componentResized(ComponentEvent evt) - { - if ((getWidth() != od.getWidth()) - || (getHeight() != (od.getHeight()))) - { - updateOverviewImage(); - } - } - }); - - addMouseMotionListener(this); - - addMouseListener(this); - - updateOverviewImage(); - - } - - @Override - public void mouseEntered(MouseEvent evt) - { - } - - @Override - public void mouseExited(MouseEvent evt) - { - } - - @Override - public void mouseClicked(MouseEvent evt) - { - } - - @Override - public void mouseMoved(MouseEvent evt) - { - } - - @Override - public void mousePressed(MouseEvent evt) - { - mouseAction(evt); - } - - @Override - public void mouseReleased(MouseEvent evt) - { - mouseAction(evt); - } - - @Override - public void mouseDragged(MouseEvent evt) - { - mouseAction(evt); - } - - private void mouseAction(MouseEvent evt) - { - od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment() - .getHiddenSequences(), av.getColumnSelection(), av - .getRanges()); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); - ap.paintAlignment(false); - } - - /** - * Updates the overview image when the related alignment panel is updated - */ - public void updateOverviewImage() - { - if (resizing) - { - resizeAgain = true; - return; - } - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.seqPanel.seqCanvas.fr); - } - - resizing = true; - - if ((getSize().width > 0) && (getSize().height > 0)) - { - od.setWidth(getSize().width); - od.setHeight(getSize().height); - } - setSize(new Dimension(od.getWidth(), od.getHeight())); - - Thread thread = new Thread(this); - thread.start(); - repaint(); - } - - @Override - public void run() - { - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); - } - - if (getSize().width > 0 && getSize().height > 0) - { - od.setWidth(getSize().width); - od.setHeight(getSize().height); - } - - setSize(new Dimension(od.getWidth(), od.getHeight())); - - miniMe = nullFrame.createImage(od.getWidth(), od.getHeight()); - offscreen = nullFrame.createImage(od.getWidth(), od.getHeight()); - - Graphics mg = miniMe.getGraphics(); -<<<<<<< HEAD - - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getAbsoluteHeight(); - float sampleCol = alwidth / (float) od.getWidth(); - float sampleRow = alheight / (float) od.getSequencesHeight(); -======= - float sampleCol = (float) alwidth / (float) width; - float sampleRow = (float) alheight / (float) sequencesHeight; - - int lastcol = 0, lastrow = 0; - int xstart = 0, ystart = 0; - Color color = Color.yellow; - int row, col, sameRow = 0, sameCol = 0; - jalview.datamodel.SequenceI seq; - final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av - .hasHiddenColumns(); - boolean hiddenRow = false; - AlignmentI alignment = av.getAlignment(); - - FeatureColourFinder finder = new FeatureColourFinder(fr); - for (row = 0; row <= sequencesHeight; row++) - { - if (resizeAgain) - { - break; - } - if ((int) (row * sampleRow) == lastrow) - { - sameRow++; - continue; - } - - hiddenRow = false; - if (hasHiddenRows) - { - seq = alignment.getHiddenSequences().getHiddenSequence(lastrow); - if (seq == null) - { - int index = alignment.getHiddenSequences() - .findIndexWithoutHiddenSeqs(lastrow); - - seq = alignment.getSequenceAt(index); - } - else - { - hiddenRow = true; - } - } - else - { - seq = alignment.getSequenceAt(lastrow); - } - - for (col = 0; col < width; col++) - { - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) - { - sameCol++; - continue; - } - - lastcol = (int) (col * sampleCol); - - if (seq.getLength() > lastcol) - { - color = sr.getResidueColour(seq, lastcol, finder); - } - else - { - color = Color.white; - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection().isVisible( - lastcol))) - { - color = color.darker().darker(); - } - - mg.setColor(color); - if (sameCol == 1 && sameRow == 1) - { - mg.drawLine(xstart, ystart, xstart, ystart); - } - else - { - mg.fillRect(xstart, ystart, sameCol, sameRow); - } ->>>>>>> bug/JAL-2436featureRendererThreading - - buildImage(sampleRow, sampleCol, mg); - - if (av.isShowAnnotation()) - { - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - mg.translate(col, od.getSequencesHeight()); - ap.annotationPanel.renderer.drawGraph(mg, - av.getAlignmentConservationAnnotation(), - av.getAlignmentConservationAnnotation().annotations, - (int) (sampleCol) + 1, od.getGraphHeight(), - (int) (col * sampleCol), (int) (col * sampleCol) + 1); - mg.translate(-col, -od.getSequencesHeight()); - } - } - System.gc(); - - resizing = false; - - setBoxPosition(); - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - } - - /* - * Build the overview panel image - */ - private void buildImage(float sampleRow, float sampleCol, Graphics mg) - { - int lastcol = 0; - int lastrow = 0; - int xstart = 0; - int ystart = 0; - Color color = Color.yellow; - int sameRow = 0; - int sameCol = 0; - - SequenceI seq = null; - - final boolean hasHiddenCols = av.hasHiddenColumns(); - boolean hiddenRow = false; - - for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++) - { - if ((int) (row * sampleRow) == lastrow) - { - sameRow++; - } - else - { - // get the sequence which would be at alignment index 'lastrow' if no - // columns were hidden, and determine whether it is hidden or not - hiddenRow = av.getAlignment().isHidden(lastrow); - seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); - - for (int col = 0; col < od.getWidth(); col++) - { - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) - { - sameCol++; - } - else - { - lastcol = (int) (col * sampleCol); - - color = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol); - - mg.setColor(color); - if (sameCol == 1 && sameRow == 1) - { - mg.drawLine(xstart, ystart, xstart, ystart); - } - else - { - mg.fillRect(xstart, ystart, sameCol, sameRow); - } - - xstart = col; - sameCol = 1; - } - } - lastrow = (int) (row * sampleRow); - ystart = row; - sameRow = 1; - } - } - } - - /* - * Find the colour of a sequence at a specified column position - */ - private Color getColumnColourFromSequence( - jalview.datamodel.SequenceI seq, boolean hiddenRow, - boolean hasHiddenCols, int lastcol) - { - Color color; - if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white; - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = color.darker().darker(); - } - return color; - } - - /** - * Update the overview panel box when the associated alignment panel is - * changed - * - */ - public void setBoxPosition() - { - od.setBoxPosition(av.getAlignment() - .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); - repaint(); - } - - @Override - public void update(Graphics g) - { - paint(g); - } - - @Override - public void paint(Graphics g) - { - Graphics og = offscreen.getGraphics(); - if (miniMe != null) - { - og.drawImage(miniMe, 0, 0, this); - og.setColor(Color.red); - od.drawBox(og); - g.drawImage(offscreen, 0, 0, this); - } - } - -} diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 7ff7309..a75a27f 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1200,6 +1200,7 @@ public class Cache sb.append("Java version: "); sb.append(System.getProperty("java.version")); sb.append("\n"); + sb.append("Java platform: "); sb.append(System.getProperty("os.arch")); sb.append(" "); sb.append(System.getProperty("os.name")); @@ -1220,17 +1221,19 @@ public class Cache sb.append(" ("); sb.append(lafClass); sb.append(")\n"); + appendIfNotNull(sb, "Channel: ", + ChannelProperties.getProperty("channel"), "\n", null); if (Console.isDebugEnabled() || !"release".equals(ChannelProperties.getProperty("channel"))) { - appendIfNotNull(sb, "Channel: ", - ChannelProperties.getProperty("channel"), "\n", null); appendIfNotNull(sb, "Getdown appdir: ", System.getProperty("getdowninstanceappdir"), "\n", null); appendIfNotNull(sb, "Getdown appbase: ", System.getProperty("getdowninstanceappbase"), "\n", null); appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), "\n", "unknown"); + appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n", + "unknown"); } return sb.toString(); } diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index e259cc2..a988a09 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -49,6 +49,7 @@ import javax.swing.JOptionPane; import javax.swing.SwingUtilities; import javax.swing.UIManager; import javax.swing.UIManager.LookAndFeelInfo; +import javax.swing.UnsupportedLookAndFeelException; import com.formdev.flatlaf.FlatLightLaf; import com.formdev.flatlaf.util.SystemInfo; @@ -62,6 +63,8 @@ import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.PromptUserConfig; +import jalview.gui.QuitHandler; +import jalview.gui.QuitHandler.QResponse; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; @@ -272,6 +275,28 @@ public class Jalview if (!Platform.isJS()) { System.setSecurityManager(null); + + Runtime.getRuntime().addShutdownHook(new Thread() + { + public void run() + { + Console.debug("Running shutdown hook"); + if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT) + { + // Got to here by a SIGTERM signal. + // Note we will not actually cancel the quit from here -- it's too + // late -- but we can wait for saving files. + Console.debug("Checking for saving files"); + QuitHandler.getQuitResponse(false); + } + else + { + Console.debug("Nothing more to do"); + } + Console.debug("Exiting, bye!"); + // shutdownHook cannot be cancelled, JVM will now halt + } + }); } System.out @@ -280,6 +305,7 @@ public class Jalview System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); + String val = System.getProperty("sys.install4jVersion"); if (val != null) { @@ -301,6 +327,7 @@ public class Jalview // old ArgsParser ArgsParser aparser = new ArgsParser(args); + boolean headless = false; try @@ -315,7 +342,8 @@ public class Jalview } String usrPropsFile = aparser.getValue("props"); - Cache.loadProperties(usrPropsFile); // must do this before + Cache.loadProperties(usrPropsFile); // must do this + // before if (usrPropsFile != null) { System.out.println( @@ -587,8 +615,11 @@ public class Jalview } String file = null, data = null; + FileFormatI format = null; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); String groovyscript = null; // script to execute after all loading is @@ -602,6 +633,7 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } + long progress = -1; // Finally, deal with the remaining input data. if (file != null) @@ -861,6 +893,7 @@ public class Jalview } } } + AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user @@ -1030,7 +1063,7 @@ public class Jalview setSystemLookAndFeel(); if (Platform.isLinux()) { - setMetalLookAndFeel(); + setLinuxLookAndFeel(); } if (Platform.isMac()) { @@ -1121,8 +1154,29 @@ public class Jalview private static boolean setFlatLookAndFeel() { - boolean set = setSpecificLookAndFeel("flatlaf light", - "com.formdev.flatlaf.FlatLightLaf", false); + boolean set = false; + if (Platform.isMac()) { + try + { + UIManager.setLookAndFeel("com.formdev.flatlaf.themes.FlatMacLightLaf"); + set = true; + } catch (ClassNotFoundException | InstantiationException + | IllegalAccessException | UnsupportedLookAndFeelException e) + { + Console.debug("Exception loading FlatMacLightLaf", e); + } + } + if (!set) { + try + { + UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf"); + set = true; + } catch (ClassNotFoundException | InstantiationException + | IllegalAccessException | UnsupportedLookAndFeelException e) + { + Console.debug("Exception loading FlatLightLaf", e); + } + } if (set) { if (Platform.isMac()) @@ -1155,6 +1209,8 @@ public class Jalview UIManager.put("TabbedPane.tabWidthMode", "compact"); UIManager.put("TabbedPane.selectedBackground", Color.white); } + + Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true)); return set; } @@ -1191,6 +1247,18 @@ public class Jalview return set; } + private static boolean setLinuxLookAndFeel() + { + boolean set = false; + set = setFlatLookAndFeel(); + if (!set) + set = setMetalLookAndFeel(); + // avoid GtkLookAndFeel -- not good results especially on HiDPI + if (!set) + set = setNimbusLookAndFeel(); + return set; + } + private static void showUsage() { System.out.println( @@ -1401,19 +1469,12 @@ public class Jalview } /** - * Quit method delegates to Desktop.quit - unless running in headless mode - * when it just ends the JVM + * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit */ public void quit() { - if (desktop != null) - { - desktop.quit(); - } - else - { - System.exit(0); - } + // System.exit will run the shutdownHook first + System.exit(0); } public static AlignFrame getCurrentAlignFrame() diff --git a/src/jalview/datamodel/Profile.java~ b/src/jalview/datamodel/Profile.java~ deleted file mode 100644 index 5464596..0000000 --- a/src/jalview/datamodel/Profile.java~ +++ /dev/null @@ -1,143 +0,0 @@ -package jalview.datamodel; - - -/** - * A profile for one column of an alignment - * - * @author gmcarstairs - * - */ -public class Profile implements ProfileI -{ - /* - * an object holding counts of symbols in the profile - */ - private ResidueCount counts; - - /* - * the number of sequences (gapped or not) in the profile - */ - private int height; - - /* - * the number of non-gapped sequences in the profile - */ - private int gapped; - - /* - * the highest count for any residue in the profile - */ - private int maxCount; - - /* - * the residue (e.g. K) or residues (e.g. KQW) with the - * highest count in the profile - */ - private String modalResidue; - - /** - * Constructor which allows derived data to be stored without having to store - * the full profile - * - * @param seqCount - * the number of sequences in the profile - * @param gaps - * the number of gapped sequences - * @param max - * the highest count for any residue - * @param modalres - * the residue (or concatenated residues) with the highest count - */ - public Profile(int seqCount, int gaps, int max, String modalRes) - { - this.height = seqCount; - this.gapped = gaps; - this.maxCount = max; - this.modalResidue = modalRes; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#setCounts(jalview.datamodel.ResidueCount) - */ - @Override - public void setCounts(ResidueCount residueCounts) - { - this.counts = residueCounts; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getPercentageIdentity(boolean) - */ - @Override - public float getPercentageIdentity(boolean ignoreGaps) - { - if (height == 0) - { - return 0f; - } - float pid = 0f; - if (ignoreGaps && gapped < height) - { - pid = (maxCount * 100f) / (height - gapped); - } - else - { - pid = (maxCount * 100f) / height; - } - return pid; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getCounts() - */ - @Override - public ResidueCount getCounts() - { - return counts; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getHeight() - */ - @Override - public int getHeight() - { - return height; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getGapped() - */ - @Override - public int getGapped() - { - return gapped; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getMaxCount() - */ - @Override - public int getMaxCount() - { - return maxCount; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getModalResidue() - */ - @Override - public String getModalResidue() - { - return modalResidue; - } - - /* (non-Javadoc) - * @see jalview.datamodel.ProfileI#getNonGapped() - */ - @Override - public int getNonGapped() - { - return height - gapped; - } -} diff --git a/src/jalview/datamodel/ProfileI.java~ b/src/jalview/datamodel/ProfileI.java~ deleted file mode 100644 index cf2b394..0000000 --- a/src/jalview/datamodel/ProfileI.java~ +++ /dev/null @@ -1,67 +0,0 @@ -package jalview.datamodel; - -public interface ProfileI -{ - - /** - * Set the full profile of counts - * - * @param residueCounts - */ - public abstract void setCounts(ResidueCount residueCounts); - - /** - * Returns the percentage identity of the profile, i.e. the highest proportion - * of conserved (equal) symbols. The percentage is as a fraction of all - * sequences, or only ungapped sequences if flag ignoreGaps is set true. - * - * @param ignoreGaps - * @return - */ - public abstract float getPercentageIdentity(boolean ignoreGaps); - - /** - * Returns the full symbol counts for this profile - * - * @return - */ - public abstract ResidueCount getCounts(); - - /** - * Returns the number of sequences in the profile - * - * @return - */ - public abstract int getHeight(); - - /** - * Returns the number of sequences in the profile which had a gap character - * (or were too short to be included in this column's profile) - * - * @return - */ - public abstract int getGapped(); - - /** - * Returns the highest count for any symbol(s) in the profile - * - * @return - */ - public abstract int getMaxCount(); - - /** - * Returns the symbol (or concatenated symbols) which have the highest count - * in the profile, or an empty string if there were no symbols counted - * - * @return - */ - public abstract String getModalResidue(); - - /** - * Answers the number of non-gapped sequences in the profile - * - * @return - */ - public abstract int getNonGapped(); - -} \ No newline at end of file diff --git a/src/jalview/datamodel/Profiles.java~ b/src/jalview/datamodel/Profiles.java~ deleted file mode 100644 index 98a8c6d..0000000 --- a/src/jalview/datamodel/Profiles.java~ +++ /dev/null @@ -1,43 +0,0 @@ -package jalview.datamodel; - -public class Profiles implements ProfilesI -{ - - private ProfileI[] profiles; - - public Profiles(ProfileI[] p) - { - profiles = p; - } - - /** - * Returns the profile for the given column, or null if none found - * - * @param col - */ - @Override - public ProfileI get(int col) - { - return profiles != null && col >= 0 && col < profiles.length ? profiles[col] - : null; - } - - /** - * Returns the first column (base 0) covered by the profiles - */ - @Override - public int getStartColumn() - { - return 0; - } - - /** - * Returns the last column (base 0) covered by the profiles - */ - @Override - public int getEndColumn() - { - return profiles == null ? 0 : profiles.length - 1; - } - -} diff --git a/src/jalview/datamodel/ProfilesI.java~ b/src/jalview/datamodel/ProfilesI.java~ deleted file mode 100644 index 6719de6..0000000 --- a/src/jalview/datamodel/ProfilesI.java~ +++ /dev/null @@ -1,12 +0,0 @@ -package jalview.datamodel; - -public interface ProfilesI -{ - - ProfileI get(int i); - - int getStartColumn(); - - int getEndColumn(); - -} diff --git a/src/jalview/datamodel/ResidueCount.java~ b/src/jalview/datamodel/ResidueCount.java~ deleted file mode 100644 index 0d0348c..0000000 --- a/src/jalview/datamodel/ResidueCount.java~ +++ /dev/null @@ -1,621 +0,0 @@ -package jalview.datamodel; - -import jalview.util.Comparison; -import jalview.util.Format; -import jalview.util.QuickSort; -import jalview.util.SparseCount; - -/** - * A class to count occurrences of residues in a profile, optimised for speed - * and memory footprint. - * @author gmcarstairs - * - */ -public class ResidueCount -{ - /** - * A data bean to hold the results of counting symbols - */ - public class SymbolCounts - { - /** - * the symbols seen (as char values), in no particular order - */ - public final char[] symbols; - - /** - * the counts for each symbol, in the same order as the symbols - */ - public final int[] values; - - SymbolCounts(char[] s, int[] v) - { - symbols = s; - values = v; - } - } - - private static final int TOUPPERCASE = 'A' - 'a'; - - /* - * nucleotide symbols to count (including N unknown) - */ - private static final String NUCS = "ACGNTU"; - - /* - * amino acid symbols to count (including X unknown) - * NB we also include U so as to support counting of RNA bases - * in the "don't know" case of nucleotide / peptide - */ - private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY"; - - private static final int GAP_COUNT = 0; - - /* - * fast lookup tables holding the index into our count - * arrays of each symbol; index 0 is reserved for gap counting - */ - private static int[] NUC_INDEX = new int[26]; - - private static int[] AA_INDEX = new int[26]; - static - { - for (int i = 0; i < NUCS.length(); i++) - { - NUC_INDEX[NUCS.charAt(i) - 'A'] = i + 1; - } - for (int i = 0; i < AAS.length(); i++) - { - AA_INDEX[AAS.charAt(i) - 'A'] = i + 1; - } - } - - /* - * counts array, just big enough for the nucleotide or peptide - * character set (plus gap counts in position 0) - */ - private short[] counts; - - /* - * alternative array of int counts for use if any count - * exceeds the maximum value of short (32767) - */ - private int[] intCounts; - - /* - * flag set if we switch from short to int counts - */ - private boolean useIntCounts; - - /* - * general-purpose counter, only for use for characters - * that are not in the expected alphabet - */ - private SparseCount otherData; - - /* - * keeps track of the maximum count value recorded - * (if this class ever allows decrements, would need to - * calculate this on request instead) - */ - int maxCount; - - /* - * if we think we are counting nucleotide, can get by with smaller - * array to hold counts - */ - private boolean isNucleotide; - - /** - * Default constructor allocates arrays able to count either nucleotide or - * peptide bases. Use this constructor if not sure which the data is. - */ - public ResidueCount() - { - this(false); - } - - /** - * Constructor that allocates an array just big enough for the anticipated - * characters, plus one position to count gaps - */ - public ResidueCount(boolean nucleotide) - { - isNucleotide = nucleotide; - int charsToCount = nucleotide ? NUCS.length() : AAS.length(); - counts = new short[charsToCount + 1]; - } - - /** - * Increments the count for the given character. The supplied character may be - * upper or lower case but counts are for the upper case only. Gap characters - * (space, ., -) are all counted together. - * - * @param c - * @return the new value of the count for the character - */ - public int add(final char c) - { - char u = toUpperCase(c); - int newValue = 0; - int offset = getOffset(u); - - /* - * offset 0 is reserved for gap counting, so 0 here means either - * an unexpected character, or a gap character passed in error - */ - if (offset == 0) - { - if (Comparison.isGap(u)) - { - newValue = addGap(); - } - else - { - newValue = addOtherCharacter(u); - } - } - else - { - newValue = increment(offset); - } - return newValue; - } - - /** - * Increment the count at the specified offset. If this would result in short - * overflow, promote to counting int values instead. - * - * @param offset - * @return the new value of the count at this offset - */ - int increment(int offset) - { - int newValue = 0; - if (useIntCounts) - { - newValue = intCounts[offset]; - intCounts[offset] = ++newValue; - } - else - { - if (counts[offset] == Short.MAX_VALUE) - { - handleOverflow(); - newValue = intCounts[offset]; - intCounts[offset] = ++newValue; - } - else - { - newValue = counts[offset]; - counts[offset] = (short) ++newValue; - } - } - maxCount = Math.max(maxCount, newValue); - return newValue; - } - - /** - * Switch from counting in short to counting in int - */ - synchronized void handleOverflow() - { - intCounts = new int[counts.length]; - for (int i = 0; i < counts.length; i++) - { - intCounts[i] = counts[i]; - } - counts = null; - useIntCounts = true; - } - - /** - * Returns this character's offset in the count array - * - * @param c - * @return - */ - int getOffset(char c) - { - int offset = 0; - if ('A' <= c && c <= 'Z') - { - offset = isNucleotide ? NUC_INDEX[c - 'A'] : AA_INDEX[c - 'A']; - } - return offset; - } - - /** - * @param c - * @return - */ - protected char toUpperCase(final char c) - { - char u = c; - if ('a' <= c && c <= 'z') - { - u = (char) (c + TOUPPERCASE); - } - return u; - } - - /** - * Increment count for some unanticipated character. The first time this - * called, a SparseCount is instantiated to hold these 'extra' counts. - * - * @param c - * @return the new value of the count for the character - */ - int addOtherCharacter(char c) - { - if (otherData == null) - { - otherData = new SparseCount(); - } - int newValue = otherData.add(c, 1); - maxCount = Math.max(maxCount, newValue); - return newValue; - } - - /** - * Set count for some unanticipated character. The first time this called, a - * SparseCount is instantiated to hold these 'extra' counts. - * - * @param c - * @param value - */ - void setOtherCharacter(char c, int value) - { - if (otherData == null) - { - otherData = new SparseCount(); - } - otherData.put(c, value); - } - - /** - * Increment count of gap characters - * - * @return the new count of gaps - */ - public int addGap() - { - int newValue; - if (useIntCounts) - { - newValue = ++intCounts[GAP_COUNT]; - } - else - { - newValue = ++counts[GAP_COUNT]; - } - return newValue; - } - - /** - * Answers true if we are counting ints (only after overflow of short counts) - * - * @return - */ - boolean isCountingInts() - { - return useIntCounts; - } - - /** - * Sets the count for the given character. The supplied character may be upper - * or lower case but counts are for the upper case only. - * - * @param c - * @param count - */ - public void put(char c, int count) - { - char u = toUpperCase(c); - int offset = getOffset(u); - - /* - * offset 0 is reserved for gap counting, so 0 here means either - * an unexpected character, or a gap character passed in error - */ - if (offset == 0) - { - if (Comparison.isGap(u)) - { - set(0, count); - } - else - { - setOtherCharacter(u, count); - maxCount = Math.max(maxCount, count); - } - } - else - { - set(offset, count); - maxCount = Math.max(maxCount, count); - } - } - - /** - * Sets the count at the specified offset. If this would result in short - * overflow, promote to counting int values instead. - * - * @param offset - * @param value - */ - void set(int offset, int value) - { - if (useIntCounts) - { - intCounts[offset] = value; - } - else - { - if (value > Short.MAX_VALUE || value < Short.MIN_VALUE) - { - handleOverflow(); - intCounts[offset] = value; - } - else - { - counts[offset] = (short) value; - } - } - } - - /** - * Returns the count for the given character, or zero if no count held - * - * @param c - * @return - */ - public int getCount(char c) - { - char u = toUpperCase(c); - int offset = getOffset(u); - if (offset == 0) - { - if (!Comparison.isGap(u)) - { - // should have called getGapCount() - return otherData == null ? 0 : otherData.get(u); - } - } - return useIntCounts ? intCounts[offset] : counts[offset]; - } - - public int getGapCount() - { - return useIntCounts ? intCounts[0] : counts[0]; - } - - /** - * Answers true if this object wraps a counter for unexpected characters - * - * @return - */ - boolean isUsingOtherData() - { - return otherData != null; - } - - /** - * Returns the character (or concatenated characters) for the symbol(s) with - * the given count in the profile. Can be used to get the modal residue by - * supplying the modal count value. Returns an empty string if no symbol has - * the given count. The symbols are in alphabetic order of standard peptide or - * nucleotide characters, followed by 'other' symbols if any. - * - * @return - */ - public String getResiduesForCount(int count) - { - if (count == 0) - { - return ""; - } - - /* - * find counts for the given value and append the - * corresponding symbol - */ - StringBuilder modal = new StringBuilder(); - if (useIntCounts) - { - for (int i = 1; i < intCounts.length; i++) - { - if (intCounts[i] == count) - { - modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS - .charAt(i - 1)); - } - } - } - else - { - for (int i = 1; i < counts.length; i++) - { - if (counts[i] == count) - { - modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS - .charAt(i - 1)); - } - } - } - if (otherData != null) - { - for (int i = 0; i < otherData.size(); i++) - { - if (otherData.valueAt(i) == count) - { - modal.append((char) otherData.keyAt(i)); - } - } - } - return modal.toString(); - } - - /** - * Returns the highest count for any symbol(s) in the profile (excluding gap) - * - * @return - */ - public int getModalCount() - { - return maxCount; - } - - /** - * Returns the number of distinct symbols with a non-zero count (excluding the - * gap symbol) - * - * @return - */ - public int size() { - int size = 0; - if (useIntCounts) - { - for (int i = 1; i < intCounts.length; i++) - { - if (intCounts[i] > 0) - { - size++; - } - } - } - else - { - for (int i = 1; i < counts.length; i++) - { - if (counts[i] > 0) - { - size++; - } - } - } - - /* - * include 'other' characters recorded (even if count is zero - * though that would be a strange use case) - */ - if (otherData != null) - { - size += otherData.size(); - } - - return size; - } - - /** - * Returns a data bean holding those symbols that have a non-zero count - * (excluding the gap symbol), with their counts. - * - * @return - */ - public SymbolCounts getSymbolCounts() - { - int size = size(); - char[] symbols = new char[size]; - int[] values = new int[size]; - int j = 0; - - if (useIntCounts) - { - for (int i = 1; i < intCounts.length; i++) - { - if (intCounts[i] > 0) - { - char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS - .charAt(i - 1); - symbols[j] = symbol; - values[j] = intCounts[i]; - j++; - } - } - } - else - { - for (int i = 1; i < counts.length; i++) - { - if (counts[i] > 0) - { - char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS - .charAt(i - 1); - symbols[j] = symbol; - values[j] = counts[i]; - j++; - } - } - } - if (otherData != null) - { - for (int i = 0; i < otherData.size(); i++) - { - symbols[j] = (char) otherData.keyAt(i); - values[j] = otherData.valueAt(i); - j++; - } - } - - return new SymbolCounts(symbols, values); - } - - /** - * Returns a tooltip string showing residues in descending order of their - * percentage frequency in the profile - * - * @param normaliseBy - * the divisor for residue counts (may or may not include gapped - * sequence count) - * @param percentageDecPl - * the number of decimal places to show in percentages - * @return - */ - public String getTooltip(int normaliseBy, int percentageDecPl) - { - SymbolCounts symbolCounts = getSymbolCounts(); - char[] ca = symbolCounts.symbols; - int[] vl = symbolCounts.values; - - /* - * sort characters into ascending order of their counts - */ - QuickSort.sort(vl, ca); - - /* - * traverse in reverse order (highest count first) to build tooltip - */ - boolean first = true; - StringBuilder sb = new StringBuilder(64); - for (int c = ca.length - 1; c >= 0; c--) - { - final char residue = ca[c]; - // TODO combine residues which share a percentage - // (see AAFrequency.completeCdnaConsensus) - float tval = (vl[c] * 100f) / normaliseBy; - sb.append(first ? "" : "; ").append(residue).append(" "); - Format.appendPercentage(sb, tval, percentageDecPl); - sb.append("%"); - first = false; - } - return sb.toString(); - } - - /** - * Returns a string representation of the symbol counts, for debug purposes. - */ - @Override - public String toString() - { - StringBuilder sb = new StringBuilder(); - sb.append("[ "); - SymbolCounts sc = getSymbolCounts(); - for (int i = 0; i < sc.symbols.length; i++) - { - sb.append(sc.symbols[i]).append(":").append(sc.values[i]).append(" "); - } - sb.append("]"); - return sb.toString(); - } -} diff --git a/src/jalview/datamodel/SearchResultMatchI.java~ b/src/jalview/datamodel/SearchResultMatchI.java~ deleted file mode 100644 index 732f1dc..0000000 --- a/src/jalview/datamodel/SearchResultMatchI.java~ +++ /dev/null @@ -1,30 +0,0 @@ -package jalview.datamodel; - -/** - * An interface that describes one matched region of an alignment, as one - * contiguous portion of a single dataset sequence - */ -public interface SearchResultMatchI -{ - /** - * Returns the matched sequence - * - * @return - */ - SequenceI getSequence(); - - /** - * Returns the start position of the match in the sequence (base 1) - * - * @return - */ - int getStart(); - - /** - * Returns the end position of the match in the sequence (base 1) - * - * @return - */ - int getEnd(); - -} \ No newline at end of file diff --git a/src/jalview/datamodel/SearchResultsI.java~ b/src/jalview/datamodel/SearchResultsI.java~ deleted file mode 100644 index 93183f2..0000000 --- a/src/jalview/datamodel/SearchResultsI.java~ +++ /dev/null @@ -1,84 +0,0 @@ -package jalview.datamodel; - -import java.util.BitSet; -import java.util.List; - -/** - * An interface describing the result of a search or other operation which - * highlights matched regions of an alignment - */ -public interface SearchResultsI -{ - - /** - * Adds one region to the results - * - * @param seq - * Sequence - * @param start - * int - * @param end - * int - * @return - */ - SearchResultMatchI addResult(SequenceI seq, int start, int end); - - /** - * Answers true if the search results include the given sequence (or its - * dataset sequence), else false - * - * @param sequence - * @return - */ - boolean involvesSequence(SequenceI sequence); - - /** - * Returns an array of [from, to, from, to..] matched columns (base 0) between - * the given start and end columns of the given sequence. Returns null if no - * matches overlap the specified region. - *

- * Implementations should provide an optimised method to return locations to - * highlight on a visible portion of an alignment. - * - * @param sequence - * @param start - * first column of range (base 0, inclusive) - * @param end - * last column of range base 0, inclusive) - * @return int[] - */ - int[] getResults(SequenceI sequence, int start, int end); - - /** - * Returns the number of matches found - * - * @return - */ - int getSize(); - - /** - * Returns true if no search result matches are held. - * - * @return - */ - boolean isEmpty(); - - /** - * Returns the list of matches. - * - * @return - */ - List getResults(); - - /** - * Set bits in a bitfield for all columns in the given sequence collection - * that are highlighted - * - * @param sqcol - * the set of sequences to search for highlighted regions - * @param bs - * bitset to set - * @return number of bits set - */ - int markColumns(SequenceCollectionI sqcol, BitSet bs); -} \ No newline at end of file diff --git a/src/jalview/ext/jmol/JmolParser.java~ b/src/jalview/ext/jmol/JmolParser.java~ deleted file mode 100644 index 9b32846..0000000 --- a/src/jalview/ext/jmol/JmolParser.java~ +++ /dev/null @@ -1,670 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.ext.jmol; - -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.io.FileParse; -import jalview.io.StructureFile; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureImportSettings; -import jalview.util.Format; -import jalview.util.MessageManager; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Vector; - -import javajs.awt.Dimension; - -import org.jmol.api.JmolStatusListener; -import org.jmol.api.JmolViewer; -import org.jmol.c.CBK; -import org.jmol.c.STR; -import org.jmol.modelset.ModelSet; -import org.jmol.viewer.Viewer; - -import MCview.Atom; -import MCview.PDBChain; -import MCview.Residue; - -/** - * Import and process files with Jmol for file like PDB, mmCIF - * - * @author jprocter - * - */ -public class JmolParser extends StructureFile implements JmolStatusListener -{ - Viewer viewer = null; - - public JmolParser(String inFile, String type) throws IOException - { - super(inFile, type); - } - - public JmolParser(FileParse fp) throws IOException - { - super(fp); - } - - public JmolParser() - { - } - - /** - * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the - * resulting object model to generate Jalview-style sequences, with secondary - * structure annotation added where available (i.e. where it has been computed - * by Jmol using DSSP). - * - * @see jalview.io.AlignFile#parse() - */ - @Override - public void parse() throws IOException - { - setChains(new Vector()); - Viewer jmolModel = getJmolData(); - jmolModel.openReader(getDataName(), getDataName(), getReader()); - waitForScript(jmolModel); - - /* - * Convert one or more Jmol Model objects to Jalview sequences - */ - if (jmolModel.ms.mc > 0) - { - // ideally we do this - // try - // { - // setStructureFileType(jmolModel.evalString("show _fileType")); - // } catch (Exception q) - // { - // } - // ; - // instead, we distinguish .cif from non-.cif by filename - setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF - .toString() : "PDB"); - - transformJmolModelToJalview(jmolModel.ms); - } - } - - /** - * create a headless jmol instance for dataprocessing - * - * @return - */ - private Viewer getJmolData() - { - if (viewer == null) - { - try - { - /* - * params -o (output to sysout) -n (nodisplay) -x (exit when finished) - * see http://wiki.jmol.org/index.php/Jmol_Application - */ - viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null, - null, "-x -o -n", this); - // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used - viewer.setBooleanProperty("defaultStructureDSSP", true); - } catch (ClassCastException x) - { - throw new Error(MessageManager.formatMessage( - "error.jmol_version_not_compatible_with_jalview_version", - new String[] { JmolViewer.getJmolVersion() }), x); - } - } - return viewer; - } - - public void transformJmolModelToJalview(ModelSet ms) throws IOException - { - try - { - String lastID = ""; - List rna = new ArrayList(); - List prot = new ArrayList(); - PDBChain tmpchain; - String pdbId = (String) ms.getInfo(0, "title"); - - if (pdbId == null) - { - setId(safeName(getDataName())); - setPDBIdAvailable(false); - } - else - { - setId(pdbId); - setPDBIdAvailable(true); - } - List significantAtoms = convertSignificantAtoms(ms); - for (Atom tmpatom : significantAtoms) - { - try - { - tmpchain = findChain(tmpatom.chain); - if (tmpatom.resNumIns.trim().equals(lastID)) - { - // phosphorylated protein - seen both CA and P.. - continue; - } - tmpchain.atoms.addElement(tmpatom); - } catch (Exception e) - { - tmpchain = new PDBChain(getId(), tmpatom.chain); - getChains().add(tmpchain); - tmpchain.atoms.addElement(tmpatom); - } - lastID = tmpatom.resNumIns.trim(); - } - xferSettings(); - - makeResidueList(); - makeCaBondList(); - -<<<<<<< HEAD -======= - if (getId() == null) - { - // always use resource name, not the hardwired file - // Does the value of ID get used ? Behaviour needs to be - // documented and tested - setId(getDataName()); - } ->>>>>>> spike/JAL-2040_JAL-2137_phyre2 - for (PDBChain chain : getChains()) - { - SequenceI chainseq = postProcessChain(chain); - if (isRNA(chainseq)) - { - rna.add(chainseq); - } - else - { - prot.add(chainseq); - } - - if (StructureImportSettings.isProcessSecondaryStructure()) - { - createAnnotation(chainseq, chain, ms.at); - } - } - } catch (OutOfMemoryError er) - { - System.out - .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL"); - throw new IOException( - MessageManager - .getString("exception.outofmemory_loading_mmcif_file")); - } - } - - private List convertSignificantAtoms(ModelSet ms) - { - List significantAtoms = new ArrayList(); - HashMap chainTerMap = new HashMap(); - org.jmol.modelset.Atom prevAtom = null; - for (org.jmol.modelset.Atom atom : ms.at) - { - if (atom.getAtomName().equalsIgnoreCase("CA") - || atom.getAtomName().equalsIgnoreCase("P")) - { - if (!atomValidated(atom, prevAtom, chainTerMap)) - { - continue; - } - Atom curAtom = new Atom(atom.x, atom.y, atom.z); - curAtom.atomIndex = atom.getIndex(); - curAtom.chain = atom.getChainIDStr(); - curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' ' - : atom.group.getInsertionCode(); - curAtom.name = atom.getAtomName(); - curAtom.number = atom.getAtomNumber(); - curAtom.resName = atom.getGroup3(true); - curAtom.resNumber = atom.getResno(); - curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom - .getIndex()] : Float.valueOf(atom.getOccupancy100()); - String fmt = new Format("%4i").form(curAtom.resNumber); - curAtom.resNumIns = (fmt + curAtom.insCode); - curAtom.tfactor = atom.getBfactor100() / 100f; - curAtom.type = 0; - // significantAtoms.add(curAtom); - // ignore atoms from subsequent models - if (!significantAtoms.contains(curAtom)) - { - significantAtoms.add(curAtom); - } - prevAtom = atom; - } - } - return significantAtoms; - } - - private boolean atomValidated(org.jmol.modelset.Atom curAtom, - org.jmol.modelset.Atom prevAtom, - HashMap chainTerMap) - { - // System.out.println("Atom: " + curAtom.getAtomNumber() - // + " Last atom index " + curAtom.group.lastAtomIndex); - if (chainTerMap == null || prevAtom == null) - { - return true; - } - String curAtomChId = curAtom.getChainIDStr(); - String prevAtomChId = prevAtom.getChainIDStr(); - // new chain encoutered - if (!prevAtomChId.equals(curAtomChId)) - { - // On chain switch add previous chain termination to xTerMap if not exists - if (!chainTerMap.containsKey(prevAtomChId)) - { - chainTerMap.put(prevAtomChId, prevAtom); - } - // if current atom belongs to an already terminated chain and the resNum - // diff < 5 then mark as valid and update termination Atom - if (chainTerMap.containsKey(curAtomChId)) - { - if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) - { - return false; - } - if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5) - { - chainTerMap.put(curAtomChId, curAtom); - return true; - } - return false; - } - } - // atom with previously terminated chain encountered - else if (chainTerMap.containsKey(curAtomChId)) - { - if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) - { - return false; - } - if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5) - { - chainTerMap.put(curAtomChId, curAtom); - return true; - } - return false; - } - // HETATM with resNum jump > 2 - return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom - .getResno()) > 2)); - } - - private void createAnnotation(SequenceI sequence, PDBChain chain, - org.jmol.modelset.Atom[] jmolAtoms) - { - char[] secstr = new char[sequence.getLength()]; - char[] secstrcode = new char[sequence.getLength()]; - - // Ensure Residue size equals Seq size - if (chain.residues.size() != sequence.getLength()) - { - return; - } - int annotIndex = 0; - for (Residue residue : chain.residues) - { - Atom repAtom = residue.getAtoms().get(0); - STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group - .getProteinStructureSubType(); - setSecondaryStructure(proteinStructureSubType, annotIndex, secstr, - secstrcode); - ++annotIndex; - } - addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr, - secstrcode, chain.id, sequence.getStart()); - } - - /** - * Helper method that adds an AlignmentAnnotation for secondary structure to - * the sequence, provided at least one secondary structure prediction has been - * made - * - * @param modelTitle - * @param seq - * @param secstr - * @param secstrcode - * @param chainId - * @param firstResNum - * @return - */ - protected void addSecondaryStructureAnnotation(String modelTitle, - SequenceI sq, char[] secstr, char[] secstrcode, String chainId, - int firstResNum) - { - char[] seq = sq.getSequence(); - boolean ssFound = false; - Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1]; - for (int p = 0; p < seq.length; p++) - { - if (secstr[p] >= 'A' && secstr[p] <= 'z') - { - try - { - asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, - secstrcode[p], Float.NaN); - ssFound = true; - } catch (Exception e) - { - // e.printStackTrace(); - } - } - } - - if (ssFound) - { - String mt = modelTitle == null ? getDataName() : modelTitle; - mt += chainId; - AlignmentAnnotation ann = new AlignmentAnnotation( - "Secondary Structure", "Secondary Structure for " + mt, - asecstr); - ann.belowAlignment = true; - ann.visible = true; - ann.autoCalculated = false; - ann.setCalcId(getClass().getName()); - ann.adjustForAlignment(); - ann.validateRangeAndDisplay(); - annotations.add(ann); - sq.addAlignmentAnnotation(ann); - } - } - - private void waitForScript(Viewer jmd) - { - while (jmd.isScriptExecuting()) - { - try - { - Thread.sleep(50); - - } catch (InterruptedException x) - { - } - } - } - - /** - * Convert Jmol's secondary structure code to Jalview's, and stored it in the - * secondary structure arrays at the given sequence position - * - * @param proteinStructureSubType - * @param pos - * @param secstr - * @param secstrcode - */ - protected void setSecondaryStructure(STR proteinStructureSubType, - int pos, char[] secstr, char[] secstrcode) - { - switch (proteinStructureSubType) - { - case HELIX310: - secstr[pos] = '3'; - break; - case HELIX: - case HELIXALPHA: - secstr[pos] = 'H'; - break; - case HELIXPI: - secstr[pos] = 'P'; - break; - case SHEET: - secstr[pos] = 'E'; - break; - default: - secstr[pos] = 0; - } - - switch (proteinStructureSubType) - { - case HELIX310: - case HELIXALPHA: - case HELIXPI: - case HELIX: - secstrcode[pos] = 'H'; - break; - case SHEET: - secstrcode[pos] = 'E'; - break; - default: - secstrcode[pos] = 0; - } - } - - /** - * Convert any non-standard peptide codes to their standard code table - * equivalent. (Initial version only does Selenomethionine MSE->MET.) - * - * @param threeLetterCode - * @param seq - * @param pos - */ - protected void replaceNonCanonicalResidue(String threeLetterCode, - char[] seq, int pos) - { - String canonical = ResidueProperties - .getCanonicalAminoAcid(threeLetterCode); - if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode)) - { - seq[pos] = ResidueProperties.getSingleCharacterCode(canonical); - } - } - - /** - * Not implemented - returns null - */ - @Override - public String print() - { - return null; - } - - /** - * Not implemented - */ - @Override - public void setCallbackFunction(String callbackType, - String callbackFunction) - { - } - - @Override - public void notifyCallback(CBK cbType, Object[] data) - { - String strInfo = (data == null || data[1] == null ? null : data[1] - .toString()); - switch (cbType) - { - case ECHO: - sendConsoleEcho(strInfo); - break; - case SCRIPT: - notifyScriptTermination((String) data[2], - ((Integer) data[3]).intValue()); - break; - case MEASURE: - String mystatus = (String) data[3]; - if (mystatus.indexOf("Picked") >= 0 - || mystatus.indexOf("Sequence") >= 0) - { - // Picking mode - sendConsoleMessage(strInfo); - } - else if (mystatus.indexOf("Completed") >= 0) - { - sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2, - strInfo.length() - 1)); - } - break; - case MESSAGE: - sendConsoleMessage(data == null ? null : strInfo); - break; - case PICK: - sendConsoleMessage(strInfo); - break; - default: - break; - } - } - - String lastConsoleEcho = ""; - - private void sendConsoleEcho(String string) - { - lastConsoleEcho += string; - lastConsoleEcho += "\n"; - } - - String lastConsoleMessage = ""; - - private void sendConsoleMessage(String string) - { - lastConsoleMessage += string; - lastConsoleMessage += "\n"; - } - - int lastScriptTermination = -1; - - String lastScriptMessage = ""; - - private void notifyScriptTermination(String string, int intValue) - { - lastScriptMessage += string; - lastScriptMessage += "\n"; - lastScriptTermination = intValue; - } - - @Override - public boolean notifyEnabled(CBK callbackPick) - { - switch (callbackPick) - { - case MESSAGE: - case SCRIPT: - case ECHO: - case LOADSTRUCT: - case ERROR: - return true; - default: - return false; - } - } - - /** - * Not implemented - returns null - */ - @Override - public String eval(String strEval) - { - return null; - } - - /** - * Not implemented - returns null - */ - @Override - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - /** - * Not implemented - returns null - */ - @Override - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) - { - return null; - } - - /** - * Not implemented - returns null - */ - @Override - public String createImage(String fileName, String imageType, - Object text_or_bytes, int quality) - { - return null; - } - - /** - * Not implemented - returns null - */ - @Override - public Map getRegistryInfo() - { - return null; - } - - /** - * Not implemented - */ - @Override - public void showUrl(String url) - { - } - - /** - * Not implemented - returns null - */ - @Override - public Dimension resizeInnerPanel(String data) - { - return null; - } - - @Override - public Map getJSpecViewProperty(String arg0) - { - return null; - } - - public boolean isPredictSecondaryStructure() - { - return predictSecondaryStructure; - } - - public void setPredictSecondaryStructure(boolean predictSecondaryStructure) - { - this.predictSecondaryStructure = predictSecondaryStructure; - } - - public boolean isVisibleChainAnnotation() - { - return visibleChainAnnotation; - } - - public void setVisibleChainAnnotation(boolean visibleChainAnnotation) - { - this.visibleChainAnnotation = visibleChainAnnotation; - } - -} diff --git a/src/jalview/gui/#OverviewPanel.java# b/src/jalview/gui/#OverviewPanel.java# deleted file mode 100755 index ce3abb5..0000000 --- a/src/jalview/gui/#OverviewPanel.java# +++ /dev/null @@ -1,468 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.gui; - -import jalview.datamodel.SequenceI; -import jalview.renderer.AnnotationRenderer; -import jalview.viewmodel.OverviewDimensions; -import jalview.renderer.seqfeatures.FeatureColourFinder; - -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Graphics; -import java.awt.event.ComponentAdapter; -import java.awt.event.ComponentEvent; -import java.awt.event.MouseAdapter; -import java.awt.event.MouseEvent; -import java.awt.event.MouseMotionAdapter; -import java.awt.image.BufferedImage; - -import javax.swing.JPanel; - -/** - * Panel displaying an overview of the full alignment, with an interactive box - * representing the viewport onto the alignment. - * - * @author $author$ - * @version $Revision$ - */ -public class OverviewPanel extends JPanel implements Runnable -{ - private static final Color TRANS_GREY = new Color(100, 100, 100, 25); - - private final AnnotationRenderer renderer = new AnnotationRenderer(); - - private OverviewDimensions od; - - private BufferedImage miniMe; - - private BufferedImage lastMiniMe = null; - - private AlignViewport av; - - private AlignmentPanel ap; - - // - private boolean resizing = false; - - // This is set true if the user resizes whilst - // the overview is being calculated - private boolean resizeAgain = false; - - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; - - private jalview.renderer.seqfeatures.FeatureRenderer fr; - - /** - * Creates a new OverviewPanel object. - * - * @param alPanel - * The alignment panel which is shown in the overview panel - */ - public OverviewPanel(AlignmentPanel alPanel) - { - this.av = alPanel.av; - this.ap = alPanel; - setLayout(null); - - sr = new SequenceRenderer(av); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(alPanel); - - od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation()); - - addComponentListener(new ComponentAdapter() - { - @Override - public void componentResized(ComponentEvent evt) - { - if ((getWidth() != od.getWidth()) - || (getHeight() != (od.getHeight()))) - { - updateOverviewImage(); - } - } - }); - - addMouseMotionListener(new MouseMotionAdapter() - { - @Override - public void mouseDragged(MouseEvent evt) - { - if (!av.getWrapAlignment()) - { - od.updateViewportFromMouse(evt.getX(), evt.getY(), av - .getAlignment().getHiddenSequences(), av - .getColumnSelection(), av.getRanges()); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); - } - } - }); - - addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (!av.getWrapAlignment()) - { - od.updateViewportFromMouse(evt.getX(), evt.getY(), av - .getAlignment().getHiddenSequences(), av - .getColumnSelection(), av.getRanges()); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); - } - } - }); - - updateOverviewImage(); - } - - /** - * Updates the overview image when the related alignment panel is updated - */ - public void updateOverviewImage() - { - if (resizing) - { - resizeAgain = true; - return; - } - - resizing = true; - - if ((getWidth() > 0) && (getHeight() > 0)) - { - od.setWidth(getWidth()); - od.setHeight(getHeight()); - } - - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - - Thread thread = new Thread(this); - thread.start(); - repaint(); - } - - @Override - public void run() - { - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); - } - - // why do we need to set preferred size again? was set in - // updateOverviewImage - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - - miniMe = new BufferedImage(od.getWidth(), od.getHeight(), - BufferedImage.TYPE_INT_RGB); - - Graphics mg = miniMe.getGraphics(); - mg.setColor(Color.orange); - mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight()); - -<<<<<<< HEAD - // calculate sampleCol and sampleRow - // alignment width is max number of residues/bases - // alignment height is number of sequences - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getAbsoluteHeight(); - - // sampleCol or sampleRow is the width/height allocated to each residue - // in particular, sometimes we may need more than one row/col of the - // BufferedImage allocated - // sampleCol is how much of a residue to assign to each pixel - // sampleRow is how many sequences to assign to each pixel - float sampleCol = alwidth / (float) od.getWidth(); - float sampleRow = alheight / (float) od.getSequencesHeight(); - - buildImage(sampleRow, sampleCol); -======= - float sampleCol = (float) alwidth / (float) width; - float sampleRow = (float) alheight / (float) sequencesHeight; - - int lastcol = -1, lastrow = -1; - Color color = Color.white; - int row, col; - jalview.datamodel.SequenceI seq; - final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av - .hasHiddenColumns(); - boolean hiddenRow = false; - // get hidden row and hidden column map once at beginning. - // clone featureRenderer settings to avoid race conditions... if state is - // updated just need to refresh again - - FeatureColourFinder finder = new FeatureColourFinder(fr); - - for (row = 0; row < sequencesHeight; row++) - { - if (resizeAgain) - { - break; - } - if ((int) (row * sampleRow) == lastrow) - { - // No need to recalculate the colours, - // Just copy from the row above - for (col = 0; col < width; col++) - { - if (resizeAgain) - { - break; - } - miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1)); - } - continue; - } - - lastrow = (int) (row * sampleRow); - - hiddenRow = false; - if (hasHiddenRows) - { - seq = av.getAlignment().getHiddenSequences() - .getHiddenSequence(lastrow); - if (seq == null) - { - int index = av.getAlignment().getHiddenSequences() - .findIndexWithoutHiddenSeqs(lastrow); - - seq = av.getAlignment().getSequenceAt(index); - } - else - { - hiddenRow = true; - } - } - else - { - seq = av.getAlignment().getSequenceAt(lastrow); - } - - if (seq == null) - { - System.out.println(lastrow + " null"); - continue; - } - - for (col = 0; col < width; col++) - { - if (resizeAgain) - { - break; - } - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) - { - miniMe.setRGB(col, row, color.getRGB()); - continue; - } - - lastcol = (int) (col * sampleCol); - - if (seq.getLength() > lastcol) - { - color = sr.getResidueColour(seq, lastcol, finder); - } - else - { - color = Color.WHITE; - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection().isVisible( - lastcol))) - { - color = color.darker().darker(); - } - - miniMe.setRGB(col, row, color.getRGB()); ->>>>>>> bug/JAL-2436featureRendererThreading - - if (av.isShowAnnotation()) - { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - mg.translate(col, od.getSequencesHeight()); - renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), - av.getAlignmentConservationAnnotation().annotations, - (int) (sampleCol) + 1, od.getGraphHeight(), - (int) (col * sampleCol), (int) (col * sampleCol) + 1); - mg.translate(-col, -od.getSequencesHeight()); - - } - } - System.gc(); - - resizing = false; - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - else - { - lastMiniMe = miniMe; - } - - setBoxPosition(); - } - - /* - * Build the overview panel image - */ - private void buildImage(float sampleRow, float sampleCol) - { - int lastcol = -1; - int lastrow = -1; - int color = Color.white.getRGB(); - - SequenceI seq = null; - - final boolean hasHiddenCols = av.hasHiddenColumns(); - boolean hiddenRow = false; - // get hidden row and hidden column map once at beginning. - // clone featureRenderer settings to avoid race conditions... if state is - // updated just need to refresh again - for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++) - { - boolean doCopy = true; - int currentrow = (int) (row * sampleRow); - if (currentrow != lastrow) - { - doCopy = false; - - lastrow = currentrow; - - // get the sequence which would be at alignment index 'lastrow' if no - // rows were hidden, and determine whether it is hidden or not - hiddenRow = av.getAlignment().isHidden(lastrow); - seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); - } - - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - if (doCopy) - { - color = miniMe.getRGB(col, row - 1); - } - else if ((int) (col * sampleCol) != lastcol - || (int) (row * sampleRow) != lastrow) - { - lastcol = (int) (col * sampleCol); - color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols, - lastcol); - } - // else we just use the color we already have , so don't need to set it - - miniMe.setRGB(col, row, color); - } - } - } - - /* - * Find the colour of a sequence at a specified column position - */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) - { - int color; - - if (seq == null) - { - color = Color.white.getRGB(); - } - else if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white.getRGB(); - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = new Color(color).darker().darker().getRGB(); - } - - return color; - } - - /** - * Update the overview panel box when the associated alignment panel is - * changed - * - */ - public void setBoxPosition() - { - od.setBoxPosition(av.getAlignment() - .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); - repaint(); - } - - - @Override - public void paintComponent(Graphics g) - { - if (resizing || resizeAgain) - { - if (lastMiniMe == null) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else - { - g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); - } - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else if (lastMiniMe != null) - { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) - { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - } - - g.setColor(Color.red); - od.drawBox(g); - } -} diff --git a/src/jalview/jbgui/APQHandlers.java b/src/jalview/gui/APQHandlers.java similarity index 55% rename from src/jalview/jbgui/APQHandlers.java rename to src/jalview/gui/APQHandlers.java index 1a7e971..00ec217 100644 --- a/src/jalview/jbgui/APQHandlers.java +++ b/src/jalview/gui/APQHandlers.java @@ -18,15 +18,11 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ -package jalview.jbgui; - -import javax.swing.JFrame; -import javax.swing.JOptionPane; +package jalview.gui; import com.formdev.flatlaf.extras.FlatDesktop; import com.formdev.flatlaf.extras.FlatDesktop.Action; -import jalview.util.MessageManager; import jalview.util.Platform; public class APQHandlers @@ -37,7 +33,7 @@ public class APQHandlers public static boolean setQuit = false; - public static boolean setAPQHandlers(GDesktop desktop) + public static boolean setAPQHandlers(Desktop desktop) { if (Platform.isJS()) { @@ -59,47 +55,7 @@ public class APQHandlers } if (FlatDesktop.isSupported(Action.APP_QUIT_HANDLER)) { - FlatDesktop.setQuitHandler(response -> { - boolean confirmQuit = jalview.bin.Cache.getDefault( - jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true); - boolean canQuit = !confirmQuit; - int n; - if (confirmQuit) - { - // ensure Jalview window is brought to front for Quit confirmation - // window to be visible - - // this method of raising the Jalview window is broken in java - // jalviewDesktop.setVisible(true); - // jalviewDesktop.toFront(); - - // a better hack which works instead - JFrame dialogParent = new JFrame(); - dialogParent.setAlwaysOnTop(true); - - n = JOptionPane.showConfirmDialog(dialogParent, - MessageManager.getString("label.quit_jalview"), - MessageManager.getString("action.quit"), - JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, - null); - - dialogParent.setAlwaysOnTop(false); - dialogParent.dispose(); - } - else - { - n = JOptionPane.OK_OPTION; - } - canQuit = (n == JOptionPane.OK_OPTION); - if (canQuit) - { - response.performQuit(); - } - else - { - response.cancelQuit(); - } - }); + QuitHandler.setQuitHandler(); setQuit = true; } // if we got to here, no exceptions occurred when we set the handlers. diff --git a/src/jalview/gui/AlignExportOptions.java b/src/jalview/gui/AlignExportOptions.java index 08ff021..a23cbfa 100644 --- a/src/jalview/gui/AlignExportOptions.java +++ b/src/jalview/gui/AlignExportOptions.java @@ -20,21 +20,22 @@ */ package jalview.gui; -import jalview.api.AlignExportSettingsI; -import jalview.api.AlignViewportI; -import jalview.io.FileFormatI; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; +import java.util.concurrent.Callable; import javax.swing.JCheckBox; import javax.swing.JPanel; +import jalview.api.AlignExportSettingsI; +import jalview.api.AlignViewportI; +import jalview.io.FileFormatI; +import jalview.util.MessageManager; + /** * A dialog that allows the user to specify whether to include hidden columns or * sequences in an alignment export, and possibly features, annotations and @@ -119,7 +120,7 @@ public class AlignExportOptions extends JPanel * * @param action */ - public void setResponseAction(Object response, Runnable action) + public void setResponseAction(Object response, Callable action) { dialog.setResponseHandler(response, action); } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f9381b4..7b310b1 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,6 +59,7 @@ import java.util.Hashtable; import java.util.List; import java.util.Locale; import java.util.Vector; +import java.util.concurrent.Callable; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; @@ -349,6 +350,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + setFrameIcon(null); + // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) @@ -1259,6 +1262,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); + Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); + if (lastSaveSuccessful) + { + this.getViewport().setSavedUpToDate(true); + } + statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { file, format })); @@ -1267,97 +1276,89 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Runnable cancelAction = new Runnable() - { - @Override - public void run() + Callable cancelAction = () -> { + lastSaveSuccessful = false; + return null; + }; + Callable outputAction = () -> { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport.getAlignExportData(options); + String output = new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns()); + if (output == null) { lastSaveSuccessful = false; } - }; - Runnable outputAction = new Runnable() - { - @Override - public void run() + else { - // todo defer this to inside formatSequences (or later) - AlignmentExportData exportData = viewport - .getAlignExportData(options); - String output = new FormatAdapter(alignPanel, options) - .formatSequences(format, exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getAlignment().getHiddenColumns()); - if (output == null) + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = null; + if (doBackup) { - lastSaveSuccessful = false; + Console.trace("ALIGNFRAME making backupfiles object for " + file); + backupfiles = new BackupFiles(file); } - else + try { - // create backupfiles object and get new temp filename destination - boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = null; - if (doBackup) + String tempFilePath = doBackup ? backupfiles.getTempFilePath() + : file; + Console.trace("ALIGNFRAME setting PrintWriter"); + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + + if (backupfiles != null) { - Console.trace( - "ALIGNFRAME making backupfiles object for " + file); - backupfiles = new BackupFiles(file); + Console.trace("ALIGNFRAME about to write to temp file " + + backupfiles.getTempFilePath()); } - try - { - String tempFilePath = doBackup ? backupfiles.getTempFilePath() - : file; - Console.trace("ALIGNFRAME setting PrintWriter"); - PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); - if (backupfiles != null) - { - Console.trace("ALIGNFRAME about to write to temp file " - + backupfiles.getTempFilePath()); - } + out.print(output); + Console.trace("ALIGNFRAME about to close file"); + out.close(); + Console.trace("ALIGNFRAME closed file"); + AlignFrame.this.setTitle(file); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { fileName, format.getName() })); + lastSaveSuccessful = true; + } catch (IOException e) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something happened writing the temp file"); + Console.error(e.getMessage()); + Console.debug(Cache.getStackTraceString(e)); + } catch (Exception ex) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); + } - out.print(output); - Console.trace("ALIGNFRAME about to close file"); - out.close(); - Console.trace("ALIGNFRAME closed file"); - AlignFrame.this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] - { fileName, format.getName() })); - lastSaveSuccessful = true; - } catch (IOException e) - { - lastSaveSuccessful = false; - Console.error( - "ALIGNFRAME Something happened writing the temp file"); - Console.error(e.getMessage()); - Console.debug(Cache.getStackTraceString(e)); - } catch (Exception ex) - { - lastSaveSuccessful = false; - Console.error( - "ALIGNFRAME Something unexpected happened writing the temp file"); - Console.error(ex.getMessage()); - Console.debug(Cache.getStackTraceString(ex)); - } + if (doBackup) + { + backupfiles.setWriteSuccess(lastSaveSuccessful); + Console.debug("ALIGNFRAME writing temp file was " + + (lastSaveSuccessful ? "" : "NOT ") + "successful"); + // do the backup file roll and rename the temp file to actual file + Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); + lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (lastSaveSuccessful ? "" : "un") + "successfully"); + } - if (doBackup) - { - backupfiles.setWriteSuccess(lastSaveSuccessful); - Console.debug("ALIGNFRAME writing temp file was " - + (lastSaveSuccessful ? "" : "NOT ") + "successful"); - // do the backup file roll and rename the temp file to actual file - Console.trace( - "ALIGNFRAME about to rollBackupsAndRenameTempFile"); - lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); - Console.debug( - "ALIGNFRAME performed rollBackupsAndRenameTempFile " - + (lastSaveSuccessful ? "" : "un") - + "successfully"); - } + Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); + if (lastSaveSuccessful) + { + AlignFrame.this.getViewport().setSavedUpToDate(true); } } + return null; }; /* @@ -1373,7 +1374,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - outputAction.run(); + try + { + outputAction.call(); + } catch (Exception e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } } } @@ -1390,34 +1398,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileFormatI fileFormat = FileFormats.getInstance() .forName(fileFormatName); AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Runnable outputAction = new Runnable() - { - @Override - public void run() + Callable outputAction = () -> { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport.getAlignExportData(options); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try { - // todo defer this to inside formatSequences (or later) - AlignmentExportData exportData = viewport - .getAlignExportData(options); - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); - try - { - FileFormatI format = fileFormat; - cap.setText(new FormatAdapter(alignPanel, options) - .formatSequences(format, exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getAlignment().getHiddenColumns())); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { fileFormat.getName() }), 600, 500); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Outputting alignment as " + fileFormat.getName(), - oom); - cap.dispose(); - } + FileFormatI format = fileFormat; + cap.setText(new FormatAdapter(alignPanel, options).formatSequences( + format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new Object[] + { fileFormat.getName() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + fileFormat.getName(), + oom); + cap.dispose(); } + return null; }; /* @@ -1432,7 +1435,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - outputAction.run(); + try + { + outputAction.call(); + } catch (Exception e) + { + e.printStackTrace(); + } } } @@ -1540,15 +1549,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.load_jalview_annotations"); chooser.setDialogTitle(tooltip); chooser.setToolTipText(tooltip); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); - } + chooser.setResponseHandler(0, () -> { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + return null; }); chooser.showOpenDialog(this); @@ -2470,36 +2475,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Runnable okAction = new Runnable() - { - @Override - public void run() - { - SequenceI[] cut = sg.getSequences() - .toArray(new SequenceI[sg.getSize()]); + Callable okAction = () -> { + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); - addHistoryItem(new EditCommand( - MessageManager.getString("label.cut_sequences"), Action.CUT, - cut, sg.getStartRes(), - sg.getEndRes() - sg.getStartRes() + 1, - viewport.getAlignment())); + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); - viewport.setSelectionGroup(null); - viewport.sendSelection(); - viewport.getAlignment().deleteGroup(sg); + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) { - try - { - AlignFrame.this.setClosed(true); - } catch (Exception ex) - { - } } } + return null; }; /* @@ -2523,7 +2523,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - okAction.run(); + try + { + okAction.call(); + } catch (Exception e) + { + e.printStackTrace(); + } } } @@ -2909,6 +2915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGatherViewsHere(true); } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } @@ -3424,28 +3431,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens an Overview panel for the alignment, unless one is open already * * @param e - * DOCUMENT ME! */ @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { + boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, + false); + openOverviewPanel(showHiddenRegions); + } + + public OverviewPanel openOverviewPanel(boolean showHidden) + { if (alignPanel.overviewPanel != null) { - return; + return alignPanel.overviewPanel; } - JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, MessageManager - .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), + Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(), true, true); + frame.setFrameIcon(null); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); + final AlignmentPanel thePanel = this.alignPanel; frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { @@ -3454,7 +3466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.event.InternalFrameEvent evt) { overview.dispose(); - alignPanel.setOverviewPanel(null); + thePanel.setOverviewPanel(null); } }); if (getKeyListeners().length > 0) @@ -3463,6 +3475,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.setOverviewPanel(overview); + alignPanel.setOverviewTitle(this); + + return overview; } @Override @@ -4076,36 +4091,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() + chooser.setResponseHandler(0, () -> { + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; + try { - String filePath = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try - { - fin = new NewickFile(new FileParse(chooser.getSelectedFile(), - DataSourceType.FILE)); - viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); - } catch (Exception ex) - { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - MessageManager - .getString("label.problem_reading_tree_file"), - JvOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - if (fin != null && fin.hasWarningMessage()) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager.getString( - "label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); - } + fin = new NewickFile(new FileParse(chooser.getSelectedFile(), + DataSourceType.FILE)); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) + { + JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + MessageManager.getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager + .getString("label.possible_problem_with_tree_file"), + JvOptionPane.WARNING_MESSAGE); } + return null; }); chooser.showOpenDialog(this); } @@ -4959,7 +4969,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (index > -1) { + /* + * update current Overview window title (if there is one) + * to add view name "Original" if necessary + */ + alignPanel.setOverviewTitle(this); + + /* + * switch panels and set Overview title (if there is one + * because it was opened automatically) + */ alignPanel = alignPanels.get(index); + alignPanel.setOverviewTitle(this); + viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); @@ -5884,16 +5906,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); final AlignFrame us = this; - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); - new VCFLoader(choice).loadVCF(seqs, us); - } + chooser.setResponseHandler(0, () -> { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + return null; }); chooser.showOpenDialog(null); diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 3b1b147..fea74db 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -801,27 +801,15 @@ public class AlignViewport extends AlignmentViewport * in reverse order) */ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop) - .setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - addDataToAlignment(al); - } - }).setResponseHandler(1, new Runnable() - { - @Override - public void run() - { - us.openLinkedAlignmentAs(al, title, true); - } - }).setResponseHandler(2, new Runnable() - { - @Override - public void run() - { - us.openLinkedAlignmentAs(al, title, false); - } + .setResponseHandler(0, () -> { + addDataToAlignment(al); + return null; + }).setResponseHandler(1, () -> { + us.openLinkedAlignmentAs(al, title, true); + return null; + }).setResponseHandler(2, () -> { + us.openLinkedAlignmentAs(al, title, false); + return null; }); dialog.showDialog(question, MessageManager.getString("label.open_split_window"), diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index e84aae0..e545776 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1742,4 +1742,42 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculationDialog; } + /** + * Constructs and sets the title for the Overview window (if there is one), + * including the align frame's title, and view name (if applicable). Returns + * the title, or null if this panel has no Overview window open. + * + * @param alignFrame + * @return + */ + public String setOverviewTitle(AlignFrame alignFrame) + { + if (this.overviewPanel == null) + { + return null; + } + String overviewTitle = MessageManager + .formatMessage("label.overview_params", new Object[] + { alignFrame.getTitle() }); + String viewName = getViewName(); + if (viewName != null) + { + overviewTitle += (" " + viewName); + } + overviewPanel.setTitle(overviewTitle); + return overviewTitle; + } + + /** + * If this alignment panel has an Overview panel open, closes it + */ + public void closeOverviewPanel() + { + if (overviewPanel != null) + { + overviewPanel.close(); + overviewPanel = null; + } + } + } diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java index 791421d..d976815 100644 --- a/src/jalview/gui/AnnotationChooser.java +++ b/src/jalview/gui/AnnotationChooser.java @@ -20,11 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceGroup; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Checkbox; import java.awt.CheckboxGroup; @@ -45,6 +40,11 @@ import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JPanel; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceGroup; +import jalview.util.MessageManager; + /** * A panel that allows the user to select which sequence-associated annotation * rows to show or hide. @@ -602,6 +602,7 @@ public class AnnotationChooser extends JPanel private void showFrame() { frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index f1e8402..a0ab709 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -86,6 +86,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java index 0b1ad93..c6c0e10 100644 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@ -97,6 +97,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter { super(av, ap); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 1efd100..894db79 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -20,24 +20,13 @@ */ package jalview.gui; -import java.util.Locale; - -import jalview.api.FeatureRenderer; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.SequenceI; -import jalview.io.AnnotationFile; -import jalview.io.FeaturesFile; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.FileWriter; import java.io.PrintWriter; +import java.util.Locale; import javax.swing.BoxLayout; import javax.swing.ButtonGroup; @@ -50,6 +39,16 @@ import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.SwingConstants; +import jalview.api.FeatureRenderer; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.util.MessageManager; + /** * * GUI dialog for exporting features or alignment annotations depending upon @@ -108,6 +107,7 @@ public class AnnotationExporter extends JPanel } frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Dimension preferredSize = frame.getPreferredSize(); diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 2c563f1..804ab7b 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -292,25 +292,21 @@ public class AnnotationLabels extends JPanel EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, name, description); - dialog.showDialog(ap.alignFrame, title, new Runnable() - { - @Override - public void run() + dialog.showDialog(ap.alignFrame, title, () -> { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) { - annotation.label = dialog.getName(); - String text = dialog.getDescription(); - if (text != null && text.length() == 0) - { - text = null; - } - annotation.description = text; - if (addNew) - { - ap.av.getAlignment().addAnnotation(annotation); - ap.av.getAlignment().setAnnotationIndex(annotation, 0); - } - ap.refresh(true); + text = null; + } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); } + ap.refresh(true); + return null; }); } diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index 3a64716..6fac8fc 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -20,23 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AlignSeq; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.RnaViewerModel; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.RnaModel; -import jalview.structure.SecondaryStructureListener; -import jalview.structure.SelectionListener; -import jalview.structure.SelectionSource; -import jalview.structure.StructureSelectionManager; -import jalview.structure.VamsasSource; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.util.ShiftList; - import java.awt.BorderLayout; import java.awt.Color; import java.util.Collection; @@ -60,6 +43,22 @@ import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; +import jalview.analysis.AlignSeq; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.RnaModel; +import jalview.structure.SecondaryStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.ShiftList; public class AppVarna extends JInternalFrame implements SelectionListener, SecondaryStructureListener, @@ -216,6 +215,7 @@ public class AppVarna extends JInternalFrame */ protected AppVarna(AlignmentPanel ap) { + this.setFrameIcon(null); this.ap = ap; this.viewId = System.currentTimeMillis() + "." + this.hashCode(); vab = new AppVarnaBinding(); diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index f7e5413..af41e58 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -20,15 +20,6 @@ */ package jalview.gui; -import jalview.analysis.TreeBuilder; -import jalview.analysis.scoremodels.ScoreModels; -import jalview.analysis.scoremodels.SimilarityParams; -import jalview.api.analysis.ScoreModelI; -import jalview.api.analysis.SimilarityParamsI; -import jalview.bin.Cache; -import jalview.datamodel.SequenceGroup; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -61,6 +52,15 @@ import javax.swing.JRadioButton; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.analysis.TreeBuilder; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Cache; +import jalview.datamodel.SequenceGroup; +import jalview.util.MessageManager; + /** * A dialog where a user can choose and action Tree or PCA calculation options */ @@ -130,6 +130,7 @@ public class CalculationChooser extends JPanel { setLayout(new BorderLayout()); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); this.setBackground(Color.white); frame.addFocusListener(new FocusListener() diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java index 9cf2cc9..5a23048 100644 --- a/src/jalview/gui/Console.java +++ b/src/jalview/gui/Console.java @@ -114,6 +114,7 @@ public class Console extends WindowAdapter Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); frame = initFrame("Java Console", screenSize.width / 2, screenSize.height / 2, -1, -1); + frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); initConsole(true); } @@ -551,10 +552,12 @@ public class Console extends WindowAdapter { } } + /* if (!frame.isVisible()) { frame.dispose(); } + */ // System.exit(0); } diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java index 6e0032f..4469ceb 100644 --- a/src/jalview/gui/CutAndPasteHtmlTransfer.java +++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java @@ -20,13 +20,6 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GCutAndPasteHtmlTransfer; -import jalview.util.MessageManager; -import jalview.viewmodel.AlignmentViewport; - import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.StringSelection; @@ -44,6 +37,13 @@ import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.HyperlinkListener; +import jalview.bin.Cache; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GCutAndPasteHtmlTransfer; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + /** * Cut'n'paste files into the desktop See JAL-1105 * @@ -58,6 +58,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer public CutAndPasteHtmlTransfer() { super(); + this.setFrameIcon(null); displaySource.setSelected(false); textarea.addKeyListener(new KeyListener() { diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 112d502..bc3c0d2 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -20,13 +20,29 @@ */ package jalview.gui; -import jalview.bin.Cache; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; + +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; + import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ComplexAlignFile; import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; import jalview.api.FeaturesSourceI; +import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; @@ -45,22 +61,6 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; -import java.io.FileWriter; -import java.io.IOException; -import java.io.PrintWriter; - -import javax.swing.JMenuItem; -import javax.swing.JPopupMenu; -import javax.swing.SwingUtilities; - /** * Cut'n'paste files into the desktop See JAL-1105 * @@ -78,6 +78,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer public CutAndPasteTransfer() { + this.setFrameIcon(null); SwingUtilities.invokeLater(new Runnable() { @Override diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 16603df..6a67148 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -64,6 +64,7 @@ import java.util.List; import java.util.ListIterator; import java.util.Locale; import java.util.Vector; +import java.util.concurrent.Callable; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; @@ -81,6 +82,7 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; +import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; @@ -90,6 +92,7 @@ import javax.swing.JProgressBar; import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; +import javax.swing.WindowConstants; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.InternalFrameAdapter; @@ -102,6 +105,7 @@ import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.QuitHandler.QResponse; import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -187,6 +191,16 @@ public class Desktop extends jalview.jbgui.GDesktop public static HashMap savingFiles = new HashMap(); + private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE; + + public static void setLiveDragMode(boolean b) + { + DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE + : JDesktopPane.OUTLINE_DRAG_MODE; + if (desktop != null) + desktop.setDragMode(DRAG_MODE); + } + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); public static boolean nosplash = false; @@ -451,13 +465,14 @@ public class Desktop extends jalview.jbgui.GDesktop setIconImages(ChannelProperties.getIconList()); + // override quit handling when GUI OS close [X] button pressed + this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { - @Override public void windowClosing(WindowEvent ev) { - quit(); + QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag } }); @@ -482,7 +497,7 @@ public class Desktop extends jalview.jbgui.GDesktop } getContentPane().add(desktop, BorderLayout.CENTER); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + desktop.setDragMode(DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised @@ -571,15 +586,6 @@ public class Desktop extends jalview.jbgui.GDesktop this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - this.addWindowListener(new WindowAdapter() - { - @Override - public void windowClosing(WindowEvent evt) - { - quit(); - } - }); - MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { @@ -1180,36 +1186,32 @@ public class Desktop extends jalview.jbgui.GDesktop MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - File selectedFile = chooser.getSelectedFile(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + chooser.setResponseHandler(0, () -> { + File selectedFile = chooser.getSelectedFile(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - FileFormatI format = chooser.getSelectedFormat(); + FileFormatI format = chooser.getSelectedFormat(); - /* - * Call IdentifyFile to verify the file contains what its extension implies. - * Skip this step for dynamically added file formats, because IdentifyFile does - * not know how to recognise them. - */ - if (FileFormats.getInstance().isIdentifiable(format)) + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because IdentifyFile does + * not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) + { + try { - try - { - format = new IdentifyFile().identify(selectedFile, - DataSourceType.FILE); - } catch (FileFormatException e) - { - // format = null; //?? - } + format = new IdentifyFile().identify(selectedFile, + DataSourceType.FILE); + } catch (FileFormatException e) + { + // format = null; //?? } - - new FileLoader().LoadFile(viewport, selectedFile, - DataSourceType.FILE, format); } + + new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, + format); + return null; }); chooser.showOpenDialog(this); } @@ -1265,64 +1267,60 @@ public class Desktop extends jalview.jbgui.GDesktop Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; - Runnable action = new Runnable() - { - @Override - public void run() - { - @SuppressWarnings("unchecked") - String url = (history instanceof JTextField - ? ((JTextField) history).getText() - : ((JComboBox) history).getEditor().getItem() - .toString().trim()); + Callable action = () -> { + @SuppressWarnings("unchecked") + String url = (history instanceof JTextField + ? ((JTextField) history).getText() + : ((JComboBox) history).getEditor().getItem() + .toString().trim()); - if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) + if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) + { + if (viewport != null) { - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - FileFormat.Jalview); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, - FileFormat.Jalview); - } + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); } else { - FileFormatI format = null; - try - { - format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) - { - // TODO revise error handling, distinguish between - // URL not found and response not valid - } + new FileLoader().LoadFile(url, DataSourceType.URL, + FileFormat.Jalview); + } + } + else + { + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - if (format == null) - { - String msg = MessageManager - .formatMessage("label.couldnt_locate", url); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, - MessageManager.getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); + if (format == null) + { + String msg = MessageManager.formatMessage("label.couldnt_locate", + url); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + MessageManager.getString("label.url_not_found"), + JvOptionPane.WARNING_MESSAGE); - return; - } + return null; // Void + } - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - format); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, format); - } + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, format); } } + return null; // Void }; String dialogOption = MessageManager .getString("label.input_alignment_from_url"); @@ -1352,39 +1350,79 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * Exit the program + * Check with user and saving files before actually quitting */ - @Override - public void quit() + public void desktopQuit() { - Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); - Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); - Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); - storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, - getWidth(), getHeight())); + desktopQuit(true, false); + } - if (jconsole != null) - { - storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); - jconsole.stopConsole(); - } - if (jvnews != null) - { - storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag) + { + final Callable doDesktopQuit = () -> { + Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); + Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); + Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); + storeLastKnownDimensions("", new Rectangle(getBounds().x, + getBounds().y, getWidth(), getHeight())); - } - if (dialogExecutor != null) - { - dialogExecutor.shutdownNow(); - } - closeAll_actionPerformed(null); + if (jconsole != null) + { + storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); + jconsole.stopConsole(); + } - if (groovyConsole != null) - { - // suppress a possible repeat prompt to save script - groovyConsole.setDirty(false); - groovyConsole.exit(); - } + if (jvnews != null) + { + storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + + } + + if (dialogExecutor != null) + { + dialogExecutor.shutdownNow(); + } + + closeAll_actionPerformed(null); + + if (groovyConsole != null) + { + // suppress a possible repeat prompt to save script + groovyConsole.setDirty(false); + groovyConsole.exit(); + } + + if (QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT) + { + // note that shutdown hook will not be run + jalview.bin.Console.debug("Force Quit selected by user"); + Runtime.getRuntime().halt(0); + } + + jalview.bin.Console.debug("Quit selected by user"); + if (disposeFlag) + { + instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); + // instance.dispose(); + } + instance.quit(); + + return null; // Void + }; + + return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, + QuitHandler.defaultCancelQuit); + } + + /** + * Don't call this directly, use desktopQuit() above. Exits the program. + */ + @Override + public void quit() + { + // this will run the shutdownHook but QuitHandler.getQuitResponse() should + // not run a second time if gotQuitResponse flag has been set (i.e. user + // confirmed quit of some kind). System.exit(0); } @@ -1794,7 +1832,7 @@ public class Desktop extends jalview.jbgui.GDesktop saveState_actionPerformed(true); } - private void setProjectFile(File choice) + protected void setProjectFile(File choice) { this.projectFile = choice; } @@ -1822,42 +1860,37 @@ public class Desktop extends jalview.jbgui.GDesktop // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() + chooser.setResponseHandler(0, () -> { + File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + String choice = selectedFile.getAbsolutePath(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + new Thread(new Runnable() { - File selectedFile = chooser.getSelectedFile(); - setProjectFile(selectedFile); - String choice = selectedFile.getAbsolutePath(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() + try { - try - { - new Jalview2XML().loadJalviewAlign(selectedFile); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) - { - jalview.bin.Console.error( - "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_whilst_loading_project_from", - new Object[] - { choice }), - MessageManager - .getString("label.couldnt_load_project"), - JvOptionPane.WARNING_MESSAGE); - } + new Jalview2XML().loadJalviewAlign(selectedFile); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst loading project from " + choice, oom); + } catch (Exception ex) + { + jalview.bin.Console.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), + MessageManager.getString("label.couldnt_load_project"), + JvOptionPane.WARNING_MESSAGE); } - }, "Project Loader").start(); - } + } + }, "Project Loader").start(); + return null; }); chooser.showOpenDialog(this); @@ -2521,7 +2554,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void actionPerformed(ActionEvent e) { - quit(); + desktopQuit(); } }); } diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java index 52791c8..ff0fe3a 100644 --- a/src/jalview/gui/EditNameDialog.java +++ b/src/jalview/gui/EditNameDialog.java @@ -20,10 +20,9 @@ */ package jalview.gui; -import jalview.util.MessageManager; - import java.awt.FlowLayout; import java.awt.Font; +import java.util.concurrent.Callable; import javax.swing.BoxLayout; import javax.swing.JButton; @@ -32,6 +31,8 @@ import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; +import jalview.util.MessageManager; + /** * A dialog where a name and description may be edited */ @@ -111,7 +112,7 @@ public class EditNameDialog * * @param action */ - public void showDialog(JComponent parent, String title, Runnable action) + public void showDialog(JComponent parent, String title, Callable action) { Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; diff --git a/src/jalview/gui/FeatureEditor.java b/src/jalview/gui/FeatureEditor.java index 844eee4..ba9da67 100644 --- a/src/jalview/gui/FeatureEditor.java +++ b/src/jalview/gui/FeatureEditor.java @@ -33,6 +33,7 @@ import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.ArrayList; import java.util.List; +import java.util.concurrent.Callable; import javax.swing.JComboBox; import javax.swing.JLabel; @@ -427,8 +428,9 @@ public class FeatureEditor */ public void showDialog() { - Runnable okAction = forCreate ? getCreateAction() : getAmendAction(); - Runnable cancelAction = getCancelAction(); + Callable okAction = forCreate ? getCreateAction() + : getAmendAction(); + Callable cancelAction = getCancelAction(); /* * set dialog action handlers for OK (create/Amend) and Cancel options @@ -474,16 +476,12 @@ public class FeatureEditor * * @return */ - protected Runnable getCancelAction() + protected Callable getCancelAction() { - Runnable okAction = new Runnable() - { - @Override - public void run() - { - ap.highlightSearchResults(null); - ap.paintAlignment(false, false); - } + Callable okAction = () -> { + ap.highlightSearchResults(null); + ap.paintAlignment(false, false); + return null; }; return okAction; } @@ -498,14 +496,14 @@ public class FeatureEditor * * @return */ - protected Runnable getCreateAction() + protected Callable getCreateAction() { - Runnable okAction = new Runnable() + Callable okAction = new Callable() { boolean useLastDefaults = features.get(0).getType() == null; @Override - public void run() + public Void call() { final String enteredType = name.getText().trim(); final String enteredGroup = group.getText().trim(); @@ -545,6 +543,7 @@ public class FeatureEditor repaintPanel(); } + return null; } }; return okAction; @@ -557,19 +556,15 @@ public class FeatureEditor * * @return */ - protected Runnable getDeleteAction() + protected Callable getDeleteAction() { - Runnable deleteAction = new Runnable() - { - @Override - public void run() - { - SequenceFeature sf = features.get(featureIndex); - sequences.get(0).getDatasetSequence().deleteFeature(sf); - fr.featuresAdded(); - ap.getSeqPanel().seqCanvas.highlightSearchResults(null); - ap.paintAlignment(true, true); - } + Callable deleteAction = () -> { + SequenceFeature sf = features.get(featureIndex); + sequences.get(0).getDatasetSequence().deleteFeature(sf); + fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.highlightSearchResults(null); + ap.paintAlignment(true, true); + return null; }; return deleteAction; } @@ -660,9 +655,9 @@ public class FeatureEditor * * @return */ - protected Runnable getAmendAction() + protected Callable getAmendAction() { - Runnable okAction = new Runnable() + Callable okAction = new Callable() { boolean useLastDefaults = features.get(0).getType() == null; @@ -671,7 +666,7 @@ public class FeatureEditor String featureGroup = group.getText(); @Override - public void run() + public Void call() { final String enteredType = name.getText().trim(); final String enteredGroup = group.getText().trim(); @@ -734,6 +729,7 @@ public class FeatureEditor fr.featuresAdded(); } repaintPanel(); + return null; } }; return okAction; diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index bb15b55..2c8f47a 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,8 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -54,6 +52,7 @@ import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Set; @@ -63,7 +62,6 @@ import javax.swing.BorderFactory; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; @@ -413,6 +411,7 @@ public class FeatureSettings extends JPanel { frame = new JInternalFrame(); frame.setContentPane(this); + frame.setFrameIcon(null); Rectangle bounds = af.getFeatureSettingsGeometry(); String title; if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( @@ -949,14 +948,10 @@ public class FeatureSettings extends JPanel chooser.setDialogTitle( MessageManager.getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - File file = chooser.getSelectedFile(); - load(file); - } + chooser.setResponseHandler(0, () -> { + File file = chooser.getSelectedFile(); + load(file); + return null; }); chooser.showOpenDialog(this); } diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index c40b958..2756b14 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -108,6 +108,7 @@ public class Finder extends GFinder focusFixed = fixedFocus; finders = new HashMap<>(); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new InternalFrameAdapter() diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 92cc4c6..f532706 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -20,10 +20,6 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.jbgui.GFontChooser; -import jalview.util.MessageManager; - import java.awt.Font; import java.awt.FontMetrics; import java.awt.geom.Rectangle2D; @@ -31,6 +27,10 @@ import java.awt.geom.Rectangle2D; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; +import jalview.bin.Cache; +import jalview.jbgui.GFontChooser; +import jalview.util.MessageManager; + /** * DOCUMENT ME! * @@ -112,6 +112,7 @@ public class FontChooser extends GFontChooser void init() { frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); smoothFont.setSelected(ap.av.antiAlias); diff --git a/src/jalview/gui/ImageExporter.java b/src/jalview/gui/ImageExporter.java index ce1cb46..d849ba2 100644 --- a/src/jalview/gui/ImageExporter.java +++ b/src/jalview/gui/ImageExporter.java @@ -20,6 +20,12 @@ */ package jalview.gui; +import java.awt.Component; +import java.awt.Graphics; +import java.io.File; +import java.util.concurrent.Callable; +import java.util.concurrent.atomic.AtomicBoolean; + import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.io.JalviewFileChooser; @@ -29,11 +35,6 @@ import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; -import java.awt.Component; -import java.awt.Graphics; -import java.io.File; -import java.util.concurrent.atomic.AtomicBoolean; - /** * A class that marshals steps in exporting a view in image graphics format *

    @@ -155,25 +156,22 @@ public class ImageExporter && !Jalview.isHeadlessMode()) { final File chosenFile = file; - Runnable okAction = new Runnable() - { - @Override - public void run() - { - exportImage(chosenFile, !textSelected.get(), width, height, - messageId); - } + Callable okAction = () -> { + exportImage(chosenFile, !textSelected.get(), width, height, + messageId); + return null; }; LineartOptions epsOption = new LineartOptions(TYPE.EPS.getName(), textSelected); - epsOption.setResponseAction(1, new Runnable() + epsOption.setResponseAction(1, new Callable() { @Override - public void run() + public Void call() { setStatus(MessageManager.formatMessage( "status.cancelled_image_export_operation", imageType.getName()), messageId); + return null; } }); epsOption.setResponseAction(0, okAction); diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java index 028e50b..0e0b13d 100644 --- a/src/jalview/gui/JvOptionPane.java +++ b/src/jalview/gui/JvOptionPane.java @@ -18,15 +18,22 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ - package jalview.gui; +import java.awt.AWTEvent; +import java.awt.ActiveEvent; import java.awt.Component; +import java.awt.Container; import java.awt.Dialog.ModalityType; +import java.awt.EventQueue; import java.awt.HeadlessException; +import java.awt.MenuComponent; +import java.awt.Toolkit; import java.awt.Window; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseMotionAdapter; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.util.ArrayList; @@ -34,16 +41,23 @@ import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; +import java.util.concurrent.Callable; import java.util.concurrent.Executors; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JDialog; +import javax.swing.JFrame; import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.SwingUtilities; import javax.swing.UIManager; +import javax.swing.event.InternalFrameEvent; +import javax.swing.event.InternalFrameListener; +import jalview.util.ChannelProperties; import jalview.util.Platform; import jalview.util.dialogrunner.DialogRunnerI; @@ -58,17 +72,18 @@ public class JvOptionPane extends JOptionPane private Component parentComponent; - private Map callbacks = new HashMap<>(); + private Map> callbacks = new HashMap<>(); /* - * JalviewJS reports user choice in the dialog as the selected - * option (text); this list allows conversion to index (int) + * JalviewJS reports user choice in the dialog as the selected option (text); + * this list allows conversion to index (int) */ List ourOptions; public JvOptionPane(final Component parent) { this.parentComponent = Platform.isJS() ? this : parent; + this.setIcon(null); } public static int showConfirmDialog(Component parentComponent, @@ -758,6 +773,11 @@ public class JvOptionPane extends JOptionPane * @param string2 * @return */ + public static JvOptionPane newOptionDialog() + { + return new JvOptionPane(null); + } + public static JvOptionPane newOptionDialog(Component parentComponent) { return new JvOptionPane(parentComponent); @@ -770,13 +790,22 @@ public class JvOptionPane extends JOptionPane initialValue, true); } - public void showDialog(String message, String title, int optionType, + public void showDialog(Object message, String title, int optionType, int messageType, Icon icon, Object[] options, Object initialValue, boolean modal) { + showDialog(message, title, optionType, messageType, icon, options, + initialValue, modal, null); + } + + public void showDialog(Object message, String title, int optionType, + int messageType, Icon icon, Object[] options, Object initialValue, + boolean modal, JButton[] buttons) + { if (!isInteractiveMode()) { handleResponse(getMockResponse()); + return; } // two uses: // @@ -797,13 +826,102 @@ public class JvOptionPane extends JOptionPane if (modal) { + boolean useButtons = false; + Object initialValueButton = null; + NOTNULL: if (buttons != null) + { + if (buttons.length != options.length) + { + jalview.bin.Console.error( + "Supplied buttons array not the same length as supplied options array."); + break NOTNULL; + } + int[] buttonActions = { JOptionPane.YES_OPTION, + JOptionPane.NO_OPTION, JOptionPane.CANCEL_OPTION }; + for (int i = 0; i < options.length; i++) + { + Object o = options[i]; + jalview.bin.Console.debug( + "Setting button " + i + " to '" + o.toString() + "'"); + JButton jb = buttons[i]; + + if (o.equals(initialValue)) + initialValueButton = jb; + + int buttonAction = buttonActions[i]; + Callable action = callbacks.get(buttonAction); + jb.setText((String) o); + jb.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + + Object obj = e.getSource(); + if (obj == null || !(obj instanceof Component)) + { + jalview.bin.Console.debug( + "Could not find Component source of event object " + + obj); + return; + } + Object joptionpaneObject = SwingUtilities.getAncestorOfClass( + JOptionPane.class, (Component) obj); + if (joptionpaneObject == null + || !(joptionpaneObject instanceof JOptionPane)) + { + jalview.bin.Console.debug( + "Could not find JOptionPane ancestor of event object " + + obj); + return; + } + JOptionPane joptionpane = (JOptionPane) joptionpaneObject; + joptionpane.setValue(buttonAction); + if (action != null) + Executors.newSingleThreadExecutor().submit(action); + joptionpane.transferFocusBackward(); + joptionpane.setVisible(false); + // put focus and raise parent window if possible, unless cancel or + // no button pressed + boolean raiseParent = (parentComponent != null); + if (buttonAction == JOptionPane.CANCEL_OPTION) + raiseParent = false; + if (optionType == JOptionPane.YES_NO_OPTION + && buttonAction == JOptionPane.NO_OPTION) + raiseParent = false; + if (raiseParent) + { + parentComponent.requestFocus(); + if (parentComponent instanceof JInternalFrame) + { + JInternalFrame jif = (JInternalFrame) parentComponent; + jif.show(); + jif.moveToFront(); + jif.grabFocus(); + } + else if (parentComponent instanceof Window) + { + Window w = (Window) parentComponent; + w.toFront(); + w.requestFocus(); + } + } + joptionpane.setVisible(false); + } + }); + + } + useButtons = true; + } // use a JOptionPane as usual int response = JOptionPane.showOptionDialog(parentComponent, message, - title, optionType, messageType, icon, options, initialValue); + title, optionType, messageType, icon, + useButtons ? buttons : options, + useButtons ? initialValueButton : initialValue); /* - * In Java, the response is returned to this thread and handled here; - * (for Javascript, see propertyChange) + * In Java, the response is returned to this thread and handled here; (for + * Javascript, see propertyChange) */ if (!Platform.isJS()) /** @@ -818,9 +936,9 @@ public class JvOptionPane extends JOptionPane else { /* - * This is java similar to the swingjs handling, with the callbacks - * attached to the button press of the dialog. This means we can use - * a non-modal JDialog for the confirmation without blocking the GUI. + * This is java similar to the swingjs handling, with the callbacks attached to + * the button press of the dialog. This means we can use a non-modal JDialog for + * the confirmation without blocking the GUI. */ JOptionPane joptionpane = new JOptionPane(); // Make button options @@ -849,13 +967,14 @@ public class JvOptionPane extends JOptionPane ArrayList options_btns = new ArrayList<>(); Object initialValue_btn = null; - if (!Platform.isJS()) // JalviewJS already uses callback, don't need to add them here + if (!Platform.isJS()) // JalviewJS already uses callback, don't need to + // add them here { for (int i = 0; i < options.length && i < 3; i++) { Object o = options[i]; int buttonAction = buttonActions[i]; - Runnable action = callbacks.get(buttonAction); + Callable action = callbacks.get(buttonAction); JButton jb = new JButton(); jb.setText((String) o); jb.addActionListener(new ActionListener() @@ -865,7 +984,7 @@ public class JvOptionPane extends JOptionPane { joptionpane.setValue(buttonAction); if (action != null) - Executors.defaultThreadFactory().newThread(action).start(); + Executors.newSingleThreadExecutor().submit(action); // joptionpane.transferFocusBackward(); joptionpane.transferFocusBackward(); joptionpane.setVisible(false); @@ -912,6 +1031,7 @@ public class JvOptionPane extends JOptionPane Platform.isJS() ? initialValue : initialValue_btn); JDialog dialog = joptionpane.createDialog(parentComponent, title); + dialog.setIconImages(ChannelProperties.getIconList()); dialog.setModalityType(modal ? ModalityType.APPLICATION_MODAL : ModalityType.MODELESS); dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); @@ -928,20 +1048,77 @@ public class JvOptionPane extends JOptionPane handleResponse(getMockResponse()); } + // need to set these separately so we can set the title bar icon later + this.setOptionType(yesNoCancelOption); + this.setMessageType(questionMessage); + this.setIcon(icon); + this.setInitialValue(initresponse); + this.setOptions(options); + this.setMessage(mainPanel); + ourOptions = Arrays.asList(options); int response; if (parentComponent != this) { - response = JOptionPane.showInternalOptionDialog(parentComponent, - mainPanel, title, yesNoCancelOption, questionMessage, icon, - options, initresponse); + JInternalFrame jif = this.createInternalFrame(parentComponent, title); + jif.setFrameIcon(null); + jif.addInternalFrameListener(new InternalFrameListener() + { + @Override + public void internalFrameActivated(InternalFrameEvent arg0) + { + } + + @Override + public void internalFrameClosed(InternalFrameEvent arg0) + { + JvOptionPane.this.internalDialogHandleResponse(); + } + + @Override + public void internalFrameClosing(InternalFrameEvent arg0) + { + } + + @Override + public void internalFrameDeactivated(InternalFrameEvent arg0) + { + } + + @Override + public void internalFrameDeiconified(InternalFrameEvent arg0) + { + } + + @Override + public void internalFrameIconified(InternalFrameEvent arg0) + { + } + + @Override + public void internalFrameOpened(InternalFrameEvent arg0) + { + } + }); + jif.setVisible(true); + startModal(jif); + return; } else { - response = JOptionPane.showOptionDialog(parentComponent, mainPanel, - title, yesNoCancelOption, questionMessage, icon, options, - initresponse); + JDialog dialog = this.createDialog(parentComponent, title); + dialog.setIconImages(ChannelProperties.getIconList()); + dialog.setVisible(true); // blocking + this.internalDialogHandleResponse(); + return; } + } + + private void internalDialogHandleResponse() + { + String responseString = (String) this.getValue(); + int response = ourOptions.indexOf(responseString); + if (!Platform.isJS()) /** * Java only @@ -953,14 +1130,105 @@ public class JvOptionPane extends JOptionPane } } + /* + * @Override public JvOptionPane setResponseHandler(Object response, Runnable + * action) { callbacks.put(response, new Callable() { + * + * @Override public Void call() { action.run(); return null; } }); return this; + * } + */ @Override - public JvOptionPane setResponseHandler(Object response, Runnable action) + public JvOptionPane setResponseHandler(Object response, + Callable action) { callbacks.put(response, action); return this; } /** + * showDialogOnTop will create a dialog that (attempts to) come to top of OS + * desktop windows + */ + public static int showDialogOnTop(String label, String actionString, + int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE) + { + if (!isInteractiveMode()) + { + return (int) getMockResponse(); + } + // Ensure Jalview window is brought to front (primarily for Quit + // confirmation window to be visible) + + // This method of raising the Jalview window is broken in java + // jalviewDesktop.setVisible(true); + // jalviewDesktop.toFront(); + + // A better hack which works is to create a new JFrame parent with + // setAlwaysOnTop(true) + JFrame dialogParent = new JFrame(); + dialogParent.setIconImages(ChannelProperties.getIconList()); + dialogParent.setAlwaysOnTop(true); + + int answer = JOptionPane.showConfirmDialog(dialogParent, label, + actionString, JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE); + + dialogParent.setAlwaysOnTop(false); + dialogParent.dispose(); + + return answer; + } + + public void showDialogOnTopAsync(String label, String actionString, + int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE, Icon icon, + Object[] options, Object initialValue, boolean modal) + { + JFrame frame = new JFrame(); + frame.setIconImages(ChannelProperties.getIconList()); + showDialogOnTopAsync(frame, label, actionString, JOPTIONPANE_OPTION, + JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal); + } + + public void showDialogOnTopAsync(JFrame dialogParent, Object label, + String actionString, int JOPTIONPANE_OPTION, + int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options, + Object initialValue, boolean modal) + { + showDialogOnTopAsync(dialogParent, label, actionString, + JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options, + initialValue, modal, null); + } + + public void showDialogOnTopAsync(JFrame dialogParent, Object label, + String actionString, int JOPTIONPANE_OPTION, + int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options, + Object initialValue, boolean modal, JButton[] buttons) + { + if (!isInteractiveMode()) + { + handleResponse(getMockResponse()); + return; + } + // Ensure Jalview window is brought to front (primarily for Quit + // confirmation window to be visible) + + // This method of raising the Jalview window is broken in java + // jalviewDesktop.setVisible(true); + // jalviewDesktop.toFront(); + + // A better hack which works is to create a new JFrame parent with + // setAlwaysOnTop(true) + dialogParent.setAlwaysOnTop(true); + parentComponent = dialogParent; + + showDialog(label, actionString, JOPTIONPANE_OPTION, + JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal, + buttons); + + dialogParent.setAlwaysOnTop(false); + dialogParent.dispose(); + } + + /** * JalviewJS signals option selection by a property change event for the * option e.g. "OK". This methods responds to that by running the response * action that corresponds to that option. @@ -987,17 +1255,248 @@ public class JvOptionPane extends JOptionPane public void handleResponse(Object response) { /* - * this test is for NaN in Chrome - */ + * this test is for NaN in Chrome + */ if (response != null && !response.equals(response)) { return; } - Runnable action = callbacks.get(response); + Callable action = callbacks.get(response); if (action != null) { - action.run(); - parentComponent.requestFocus(); + try + { + action.call(); + } catch (Exception e) + { + e.printStackTrace(); + } + if (parentComponent != null) + parentComponent.requestFocus(); + } + } + + /** + * Create a non-modal confirm dialog + */ + public JDialog createDialog(Component parentComponent, Object message, + String title, int optionType, int messageType, Icon icon, + Object[] options, Object initialValue, boolean modal) + { + return createDialog(parentComponent, message, title, optionType, + messageType, icon, options, initialValue, modal, null); + } + + public JDialog createDialog(Component parentComponent, Object message, + String title, int optionType, int messageType, Icon icon, + Object[] options, Object initialValue, boolean modal, + JButton[] buttons) + { + if (!isInteractiveMode()) + { + handleResponse(getMockResponse()); + return null; + } + JButton[] optionsButtons = null; + Object initialValueButton = null; + JOptionPane joptionpane = new JOptionPane(); + // Make button options + int[] buttonActions = { JOptionPane.YES_OPTION, JOptionPane.NO_OPTION, + JOptionPane.CANCEL_OPTION }; + + // we need the strings to make the buttons with actionEventListener + if (options == null) + { + ArrayList options_default = new ArrayList<>(); + options_default.add(UIManager.getString("OptionPane.yesButtonText")); + if (optionType == JOptionPane.YES_NO_OPTION + || optionType == JOptionPane.YES_NO_CANCEL_OPTION) + { + options_default.add(UIManager.getString("OptionPane.noButtonText")); + } + if (optionType == JOptionPane.YES_NO_CANCEL_OPTION) + { + options_default + .add(UIManager.getString("OptionPane.cancelButtonText")); + } + options = options_default.toArray(); + } + if (!Platform.isJS()) // JalviewJS already uses callback, don't need to + // add them here + { + if (((optionType == JOptionPane.YES_OPTION + || optionType == JOptionPane.NO_OPTION + || optionType == JOptionPane.CANCEL_OPTION + || optionType == JOptionPane.OK_OPTION + || optionType == JOptionPane.DEFAULT_OPTION) + && options.length < 1) + || ((optionType == JOptionPane.YES_NO_OPTION + || optionType == JOptionPane.OK_CANCEL_OPTION) + && options.length < 2) + || (optionType == JOptionPane.YES_NO_CANCEL_OPTION + && options.length < 3)) + { + jalview.bin.Console + .debug("JvOptionPane: not enough options for dialog type"); + } + optionsButtons = new JButton[options.length]; + for (int i = 0; i < options.length && i < 3; i++) + { + Object o = options[i]; + int buttonAction = buttonActions[i]; + Callable action = callbacks.get(buttonAction); + JButton jb; + if (buttons != null && buttons.length > i && buttons[i] != null) + { + jb = buttons[i]; + } + else + { + jb = new JButton(); + } + jb.setText((String) o); + jb.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + joptionpane.setValue(buttonAction); + if (action != null) + Executors.newSingleThreadExecutor().submit(action); + // joptionpane.transferFocusBackward(); + joptionpane.transferFocusBackward(); + joptionpane.setVisible(false); + // put focus and raise parent window if possible, unless cancel + // button pressed + boolean raiseParent = (parentComponent != null); + if (buttonAction == JOptionPane.CANCEL_OPTION) + raiseParent = false; + if (optionType == JOptionPane.YES_NO_OPTION + && buttonAction == JOptionPane.NO_OPTION) + raiseParent = false; + if (raiseParent) + { + parentComponent.requestFocus(); + if (parentComponent instanceof JInternalFrame) + { + JInternalFrame jif = (JInternalFrame) parentComponent; + jif.show(); + jif.moveToFront(); + jif.grabFocus(); + } + else if (parentComponent instanceof Window) + { + Window w = (Window) parentComponent; + w.toFront(); + w.requestFocus(); + } + } + joptionpane.setVisible(false); + } + }); + optionsButtons[i] = jb; + if (o.equals(initialValue)) + initialValueButton = jb; + } + } + joptionpane.setMessage(message); + joptionpane.setMessageType(messageType); + joptionpane.setOptionType(optionType); + joptionpane.setIcon(icon); + joptionpane.setOptions(Platform.isJS() ? options : optionsButtons); + joptionpane.setInitialValue( + Platform.isJS() ? initialValue : initialValueButton); + + JDialog dialog = joptionpane.createDialog(parentComponent, title); + dialog.setIconImages(ChannelProperties.getIconList()); + dialog.setModalityType( + modal ? ModalityType.APPLICATION_MODAL : ModalityType.MODELESS); + dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); + return dialog; + } + + /** + * Utility to programmatically click a button on a JOptionPane (as a JFrame) + * + * returns true if button was found + */ + public static boolean clickButton(JFrame frame, int buttonType) + { + + return false; + } + + /** + * This helper method makes the JInternalFrame wait until it is notified by an + * InternalFrameClosing event. This method also adds the given JOptionPane to + * the JInternalFrame and sizes it according to the JInternalFrame's preferred + * size. + * + * @param f + * The JInternalFrame to make modal. + */ + private static void startModal(JInternalFrame f) + { + // We need to add an additional glasspane-like component directly + // below the frame, which intercepts all mouse events that are not + // directed at the frame itself. + JPanel modalInterceptor = new JPanel(); + modalInterceptor.setOpaque(false); + JLayeredPane lp = JLayeredPane.getLayeredPaneAbove(f); + lp.setLayer(modalInterceptor, JLayeredPane.MODAL_LAYER.intValue()); + modalInterceptor.setBounds(0, 0, lp.getWidth(), lp.getHeight()); + modalInterceptor.addMouseListener(new MouseAdapter() + { + }); + modalInterceptor.addMouseMotionListener(new MouseMotionAdapter() + { + }); + lp.add(modalInterceptor); + f.toFront(); + + // We need to explicitly dispatch events when we are blocking the event + // dispatch thread. + EventQueue queue = Toolkit.getDefaultToolkit().getSystemEventQueue(); + try + { + while (!f.isClosed()) + { + if (EventQueue.isDispatchThread()) + { + // The getNextEventMethod() issues wait() when no + // event is available, so we don't need do explicitly wait(). + AWTEvent ev = queue.getNextEvent(); + // This mimics EventQueue.dispatchEvent(). We can't use + // EventQueue.dispatchEvent() directly, because it is + // protected, unfortunately. + if (ev instanceof ActiveEvent) + ((ActiveEvent) ev).dispatch(); + else if (ev.getSource() instanceof Component) + ((Component) ev.getSource()).dispatchEvent(ev); + else if (ev.getSource() instanceof MenuComponent) + ((MenuComponent) ev.getSource()).dispatchEvent(ev); + // Other events are ignored as per spec in + // EventQueue.dispatchEvent + } + else + { + // Give other threads a chance to become active. + Thread.yield(); + } + } + } catch (InterruptedException ex) + { + // If we get interrupted, then leave the modal state. + } finally + { + // Clean up the modal interceptor. + lp.remove(modalInterceptor); + + // Remove the internal frame from its parent, so it is no longer + // lurking around and clogging memory. + Container parent = f.getParent(); + if (parent != null) + parent.remove(f); } } } diff --git a/src/jalview/gui/LineartOptions.java b/src/jalview/gui/LineartOptions.java index 62ad108..8a530ac 100644 --- a/src/jalview/gui/LineartOptions.java +++ b/src/jalview/gui/LineartOptions.java @@ -23,6 +23,7 @@ package jalview.gui; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.util.concurrent.Callable; import java.util.concurrent.atomic.AtomicBoolean; import javax.swing.BorderFactory; @@ -95,7 +96,7 @@ public class LineartOptions extends JPanel * * @param action */ - public void setResponseAction(Object response, Runnable action) + public void setResponseAction(Object response, Callable action) { dialog.setResponseHandler(response, action); } diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index 470fd64..586ac2c 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -20,13 +20,6 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.bin.Cache; -import jalview.renderer.OverviewRenderer; -import jalview.renderer.OverviewResColourFinder; -import jalview.viewmodel.OverviewDimensions; -import jalview.viewmodel.seqfeatures.FeatureRendererModel; - import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics; @@ -34,8 +27,26 @@ import java.awt.image.BufferedImage; import javax.swing.JPanel; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; +import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; + public class OverviewCanvas extends JPanel { + public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white; + + public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white; + + public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray + .darker(); + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); // This is set true if the alignment view changes whilst @@ -79,10 +90,12 @@ public class OverviewCanvas extends JPanel boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false); Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + OVERVIEW_DEFAULT_GAP); Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); - cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol); + OVERVIEW_DEFAULT_HIDDEN); + Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE; + + cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol); setSize(od.getWidth(), od.getHeight()); } @@ -268,4 +281,31 @@ public class OverviewCanvas extends JPanel } } } + + public Color getGapColour() + { + return cf.getGapColour(); + } + + public Color getHiddenColour() + { + return cf.getHiddenColour(); + } + + public Color getResidueColour() + { + return cf.getResidueColour(); + } + + /** + * Sets the colours to use for gaps, residues and hidden regions + * + * @param gaps + * @param residues + * @param hidden + */ + public void setColours(Color gaps, Color residues, Color hidden) + { + cf = new OverviewResColourFinder(gaps, residues, hidden); + } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index adde919..872d142 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,18 +20,10 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.renderer.OverviewRenderer; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.viewmodel.OverviewDimensions; -import jalview.viewmodel.OverviewDimensionsHideHidden; -import jalview.viewmodel.OverviewDimensionsShowHidden; -import jalview.viewmodel.ViewportListenerI; - import java.awt.BorderLayout; import java.awt.Cursor; import java.awt.Dimension; +import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ComponentAdapter; @@ -48,6 +40,14 @@ import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; +import jalview.renderer.OverviewRenderer; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.OverviewDimensionsHideHidden; +import jalview.viewmodel.OverviewDimensionsShowHidden; +import jalview.viewmodel.ViewportListenerI; + /** * Panel displaying an overview of the full alignment, with an interactive box * representing the viewport onto the alignment. @@ -67,6 +67,8 @@ public class OverviewPanel extends JPanel private AlignmentPanel ap; + private JInternalFrame internalFrame; + protected JCheckBoxMenuItem displayToggle; protected boolean showHidden = true; @@ -80,14 +82,18 @@ public class OverviewPanel extends JPanel * * @param alPanel * The alignment panel which is shown in the overview panel + * @param frame + * @param isShowHidden + * TODO */ - public OverviewPanel(AlignmentPanel alPanel) + public OverviewPanel(AlignmentPanel alPanel, JInternalFrame frame, + boolean isShowHidden) { this.av = alPanel.av; this.ap = alPanel; + this.internalFrame = frame; - showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, - false); + showHidden = isShowHidden; if (showHidden) { od = new OverviewDimensionsShowHidden(av.getRanges(), @@ -420,6 +426,68 @@ public class OverviewPanel extends JPanel oviewCanvas = null; ap = null; od = null; + internalFrame = null; } } + + public boolean isShowHiddenRegions() + { + return showHidden; + } + + public OverviewCanvas getCanvas() + { + return oviewCanvas; + } + + /** + * Sets the title of the enclosing frame + * + * @param title + */ + public void setTitle(String title) + { + internalFrame.setTitle(title); + } + + /** + * Returns the title of the enclosing frame + * + * @return title + */ + public String getTitle() + { + return internalFrame.getTitle(); + } + + /** + * Sets the bounds of the frame holding the Overview panel + * + * @param xpos + * @param ypos + * @param width + * @param height + */ + public void setFrameBounds(int xpos, int ypos, int width, int height) + { + internalFrame.setBounds(xpos, ypos, width, height); + } + + /** + * Returns the bounds of the enclosing frame + * + * @return + */ + public Rectangle getFrameBounds() + { + return internalFrame.getBounds(); + } + + /** + * Closes the frame containing the overview panel + */ + public void close() + { + internalFrame.dispose(); + } } diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index e6b6b83..26db8c3 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -20,6 +20,23 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.awt.print.PrinterJob; + +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + import jalview.analysis.scoremodels.ScoreModels; import jalview.api.AlignViewportI; import jalview.api.analysis.ScoreModelI; @@ -39,23 +56,6 @@ import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Graphics; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.print.PageFormat; -import java.awt.print.Printable; -import java.awt.print.PrinterException; -import java.awt.print.PrinterJob; - -import javax.swing.ButtonGroup; -import javax.swing.JMenuItem; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.event.InternalFrameAdapter; -import javax.swing.event.InternalFrameEvent; - /** * The panel holding the Principal Component Analysis 3-D visualisation */ @@ -92,6 +92,7 @@ public class PCAPanel extends GPCAPanel SimilarityParamsI params) { super(); + this.setFrameIcon(null); this.av = alignPanel.av; this.ap = alignPanel; boolean nucleotide = av.getAlignment().isNucleotide(); diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6903034..1c03d6a 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,8 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; @@ -34,6 +32,7 @@ import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Objects; import java.util.SortedMap; @@ -1987,15 +1986,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("label.group_description")); dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - new Runnable() - { - @Override - public void run() - { - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); - } + () -> { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + return null; }); } @@ -2027,30 +2022,26 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequence.getDescription(), MessageManager.getString("label.sequence_name"), MessageManager.getString("label.sequence_description")); - dialog.showDialog(ap.alignFrame, MessageManager.getString( - "label.edit_sequence_name_description"), new Runnable() - { - @Override - public void run() + dialog.showDialog(ap.alignFrame, MessageManager + .getString("label.edit_sequence_name_description"), () -> { + if (dialog.getName() != null) { - if (dialog.getName() != null) + if (dialog.getName().indexOf(" ") > -1) { - if (dialog.getName().indexOf(" ") > -1) - { - JvOptionPane.showMessageDialog(ap, - MessageManager.getString( - "label.spaces_converted_to_underscores"), - MessageManager.getString( - "label.no_spaces_allowed_sequence_name"), - JvOptionPane.WARNING_MESSAGE); - } - sequence.setName(dialog.getName().replace(' ', '_')); - ap.paintAlignment(false, false); + JvOptionPane.showMessageDialog(ap, + MessageManager.getString( + "label.spaces_converted_to_underscores"), + MessageManager.getString( + "label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); } - sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + return null; }); } @@ -2272,25 +2263,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null); dialog.showDialog(ap.alignFrame, - MessageManager.getString("label.edit_sequence"), - new Runnable() - { - @Override - public void run() - { - EditCommand editCommand = new EditCommand( - MessageManager.getString("label.edit_sequences"), - Action.REPLACE, - dialog.getName().replace(' ', - ap.av.getGapCharacter()), - sg.getSequencesAsArray( - ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1, - ap.av.getAlignment()); - ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } + MessageManager.getString("label.edit_sequence"), () -> { + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), + Action.REPLACE, + dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray( + ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); + ap.alignFrame.addHistoryItem(editCommand); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + return null; }); } } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 06d3a60..493deee 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -249,6 +249,7 @@ public class Preferences extends GPreferences { super(); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); if (!Platform.isJS()) /** @@ -385,9 +386,9 @@ public class Preferences extends GPreferences * Set overview panel defaults */ gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); + OverviewCanvas.OVERVIEW_DEFAULT_GAP)); hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN)); useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); gapLabel.setEnabled(!useLegacyGap.isSelected()); gapColour.setEnabled(!useLegacyGap.isSelected()); @@ -1306,13 +1307,11 @@ public class Preferences extends GPreferences boolean enabled = useLegacyGap.isSelected(); if (enabled) { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP); } else { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP); } gapColour.setEnabled(!enabled); gapLabel.setEnabled(!enabled); @@ -1324,8 +1323,7 @@ public class Preferences extends GPreferences useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); showHiddenAtStart.setSelected(false); - hiddenColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN); } @Override diff --git a/src/jalview/gui/QuitHandler.java b/src/jalview/gui/QuitHandler.java new file mode 100644 index 0000000..77eed81 --- /dev/null +++ b/src/jalview/gui/QuitHandler.java @@ -0,0 +1,411 @@ +package jalview.gui; + +import java.io.File; +import java.util.List; +import java.util.concurrent.Callable; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.TimeUnit; +import java.util.concurrent.TimeoutException; + +import javax.swing.JButton; +import javax.swing.JFrame; +import javax.swing.JOptionPane; +import javax.swing.JTextPane; + +import com.formdev.flatlaf.extras.FlatDesktop; + +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.io.BackupFiles; +import jalview.project.Jalview2XML; +import jalview.util.MessageManager; +import jalview.util.Platform; + +public class QuitHandler +{ + private static final int MIN_WAIT_FOR_SAVE = 1000; + + private static final int MAX_WAIT_FOR_SAVE = 20000; + + private static boolean interactive = true; + + public static enum QResponse + { + NULL, QUIT, CANCEL_QUIT, FORCE_QUIT + }; + + private static ExecutorService executor = Executors.newFixedThreadPool(3); + + public static QResponse setQuitHandler() + { + FlatDesktop.setQuitHandler(response -> { + Callable performQuit = () -> { + response.performQuit(); + setResponse(QResponse.QUIT); + return null; + }; + Callable performForceQuit = () -> { + response.performQuit(); + setResponse(QResponse.FORCE_QUIT); + return null; + }; + Callable cancelQuit = () -> { + response.cancelQuit(); + // reset + setResponse(QResponse.NULL); + return null; + }; + getQuitResponse(true, performQuit, performForceQuit, cancelQuit); + }); + + return gotQuitResponse(); + } + + private static QResponse gotQuitResponse = QResponse.NULL; + + protected static QResponse setResponse(QResponse qresponse) + { + gotQuitResponse = qresponse; + return qresponse; + } + + public static QResponse gotQuitResponse() + { + return gotQuitResponse; + } + + public static final Callable defaultCancelQuit = () -> { + Console.debug("QuitHandler: (default) Quit action CANCELLED by user"); + // reset + setResponse(QResponse.CANCEL_QUIT); + return null; + }; + + public static final Callable defaultOkQuit = () -> { + Console.debug("QuitHandler: (default) Quit action CONFIRMED by user"); + setResponse(QResponse.QUIT); + return null; + }; + + public static final Callable defaultForceQuit = () -> { + Console.debug("QuitHandler: (default) Quit action FORCED by user"); + // note that shutdown hook will not be run + Runtime.getRuntime().halt(0); + setResponse(QResponse.FORCE_QUIT); // this line never reached! + return null; + }; + + public static QResponse getQuitResponse(boolean ui) + { + return getQuitResponse(ui, defaultOkQuit, defaultForceQuit, + defaultCancelQuit); + } + + public static QResponse getQuitResponse(boolean ui, Callable okQuit, + Callable forceQuit, Callable cancelQuit) + { + QResponse got = gotQuitResponse(); + if (got != QResponse.NULL && got != QResponse.CANCEL_QUIT) + { + // quit has already been selected, continue with calling quit method + return got; + } + + interactive = ui && !Platform.isHeadless(); + // confirm quit if needed and wanted + boolean confirmQuit = true; + + if (!interactive) + { + Console.debug("Non interactive quit -- not confirming"); + confirmQuit = false; + } + else if (Jalview2XML.allSavedUpToDate()) + { + Console.debug("Nothing changed -- not confirming quit"); + confirmQuit = false; + } + else + { + confirmQuit = jalview.bin.Cache + .getDefault(jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true); + Console.debug("Jalview property '" + + jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT + + "' is/defaults to " + confirmQuit + " -- " + + (confirmQuit ? "" : "not ") + "confirming quit"); + } + got = confirmQuit ? QResponse.NULL : QResponse.QUIT; + setResponse(got); + + if (confirmQuit) + { + JvOptionPane.newOptionDialog() + .setResponseHandler(JOptionPane.YES_OPTION, defaultOkQuit) + .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit) + .showDialogOnTopAsync( + new StringBuilder(MessageManager + .getString("label.quit_jalview")) + .append("\n") + .append(MessageManager + .getString("label.unsaved_changes")) + .toString(), + MessageManager.getString("action.quit"), + JOptionPane.YES_NO_OPTION, + JOptionPane.QUESTION_MESSAGE, null, new Object[] + { MessageManager.getString("action.quit"), + MessageManager.getString("action.cancel") }, + MessageManager.getString("action.quit"), true); + } + + got = gotQuitResponse(); + boolean wait = false; + if (got == QResponse.CANCEL_QUIT) + { + // reset + Console.debug("Cancelling quit. Resetting response to NULL"); + setResponse(QResponse.NULL); + // but return cancel + return QResponse.CANCEL_QUIT; + } + else if (got == QResponse.QUIT) + { + if (Cache.getDefault("WAIT_FOR_SAVE", true) + && BackupFiles.hasSavesInProgress()) + { + waitQuit(interactive, okQuit, forceQuit, cancelQuit); + QResponse waitResponse = gotQuitResponse(); + wait = waitResponse == QResponse.QUIT; + } + } + + Callable next = null; + switch (gotQuitResponse()) + { + case QUIT: + next = okQuit; + break; + case FORCE_QUIT: // not actually an option at this stage + next = forceQuit; + break; + default: + next = cancelQuit; + break; + } + try + { + executor.submit(next).get(); + got = gotQuitResponse(); + } catch (InterruptedException | ExecutionException e) + { + jalview.bin.Console + .debug("Exception during quit handling (final choice)", e); + } + setResponse(got); + + if (gotQuitResponse() == QResponse.CANCEL_QUIT) + { + // reset if cancelled + setResponse(QResponse.NULL); + return QResponse.CANCEL_QUIT; + } + return gotQuitResponse(); + } + + private static QResponse waitQuit(boolean interactive, + Callable okQuit, Callable forceQuit, + Callable cancelQuit) + { + // check for saves in progress + if (!BackupFiles.hasSavesInProgress()) + return QResponse.QUIT; + + int size = 0; + AlignFrame[] afArray = Desktop.getAlignFrames(); + if (!(afArray == null || afArray.length == 0)) + { + for (int i = 0; i < afArray.length; i++) + { + AlignFrame af = afArray[i]; + List avpList = af.getAlignPanels(); + for (AlignmentViewPanel avp : avpList) + { + AlignmentI a = avp.getAlignment(); + List sList = a.getSequences(); + for (SequenceI s : sList) + { + size += s.getLength(); + } + } + } + } + int waitTime = Math.min(MAX_WAIT_FOR_SAVE, + Math.max(MIN_WAIT_FOR_SAVE, size / 2)); + Console.debug("Set waitForSave to " + waitTime); + + int iteration = 0; + boolean doIterations = true; // note iterations not used in the gui now, + // only one pass without the "Wait" button + while (doIterations && BackupFiles.hasSavesInProgress() + && iteration++ < (interactive ? 100 : 5)) + { + // future that returns a Boolean when all files are saved + CompletableFuture filesAllSaved = new CompletableFuture<>(); + + // callback as each file finishes saving + for (CompletableFuture cf : BackupFiles + .savesInProgressCompletableFutures(false)) + { + // if this is the last one then complete filesAllSaved + cf.whenComplete((ret, e) -> { + if (!BackupFiles.hasSavesInProgress()) + { + filesAllSaved.complete(true); + } + }); + } + try + { + filesAllSaved.get(waitTime, TimeUnit.MILLISECONDS); + } catch (InterruptedException | ExecutionException e1) + { + Console.debug( + "Exception whilst waiting for files to save before quit", + e1); + } catch (TimeoutException e2) + { + // this Exception to be expected + } + + if (interactive && BackupFiles.hasSavesInProgress()) + { + boolean showForceQuit = iteration > 0; // iteration > 1 to not show + // force quit the first time + JFrame parent = new JFrame(); + JButton[] buttons = { new JButton(), new JButton() }; + JvOptionPane waitDialog = JvOptionPane.newOptionDialog(); + JTextPane messagePane = new JTextPane(); + messagePane.setBackground(waitDialog.getBackground()); + messagePane.setBorder(null); + messagePane.setText(waitingForSaveMessage()); + // callback as each file finishes saving + for (CompletableFuture cf : BackupFiles + .savesInProgressCompletableFutures(false)) + { + cf.whenComplete((ret, e) -> { + if (BackupFiles.hasSavesInProgress()) + { + // update the list of saving files as they save too + messagePane.setText(waitingForSaveMessage()); + } + else + { + if (!(QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT + || QuitHandler.gotQuitResponse() == QResponse.NULL)) + { + for (int i = 0; i < buttons.length; i++) + { + Console.debug("DISABLING BUTTON " + buttons[i].getText()); + buttons[i].setEnabled(false); + buttons[i].setVisible(false); + } + // if this is the last one then close the dialog + messagePane.setText(new StringBuilder() + .append(MessageManager.getString("label.all_saved")) + .append("\n") + .append(MessageManager + .getString("label.quitting_bye")) + .toString()); + messagePane.setEditable(false); + try + { + Thread.sleep(1500); + } catch (InterruptedException e1) + { + } + parent.dispose(); + } + } + }); + } + + String[] options; + int dialogType = -1; + if (showForceQuit) + { + options = new String[2]; + options[0] = MessageManager.getString("action.force_quit"); + options[1] = MessageManager.getString("action.cancel_quit"); + dialogType = JOptionPane.YES_NO_OPTION; + waitDialog.setResponseHandler(JOptionPane.YES_OPTION, forceQuit) + .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit); + } + else + { + options = new String[1]; + options[0] = MessageManager.getString("action.cancel_quit"); + dialogType = JOptionPane.YES_OPTION; + waitDialog.setResponseHandler(JOptionPane.YES_OPTION, cancelQuit); + } + waitDialog.showDialogOnTopAsync(parent, messagePane, + MessageManager.getString("label.wait_for_save"), dialogType, + JOptionPane.WARNING_MESSAGE, null, options, + MessageManager.getString("action.cancel_quit"), true, + buttons); + + parent.dispose(); + final QResponse thisWaitResponse = gotQuitResponse(); + switch (thisWaitResponse) + { + case QUIT: // wait -- do another iteration + break; + case FORCE_QUIT: + doIterations = false; + break; + case CANCEL_QUIT: + doIterations = false; + break; + case NULL: // already cancelled + doIterations = false; + break; + default: + } + } // end if interactive + + } // end while wait iteration loop + return gotQuitResponse(); + }; + + private static String waitingForSaveMessage() + { + StringBuilder messageSB = new StringBuilder(); + + messageSB.append(MessageManager.getString("label.save_in_progress")); + List files = BackupFiles.savesInProgressFiles(false); + boolean any = files.size() > 0; + if (any) + { + for (File file : files) + { + messageSB.append("\n\u2022 ").append(file.getName()); + } + } + else + { + messageSB.append(MessageManager.getString("label.unknown")); + } + messageSB.append("\n\n") + .append(MessageManager.getString("label.quit_after_saving")); + return messageSB.toString(); + } + + public static void abortQuit() + { + setResponse(QResponse.CANCEL_QUIT); + } +} \ No newline at end of file diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 6ed3248..8d66a44 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -20,15 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AlignSeq; -import jalview.commands.CommandI; -import jalview.commands.EditCommand; -import jalview.commands.EditCommand.Action; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GSliderPanel; -import jalview.util.MessageManager; - import java.awt.event.ActionEvent; import java.util.ArrayList; import java.util.List; @@ -42,6 +33,15 @@ import javax.swing.event.ChangeListener; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.analysis.AlignSeq; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GSliderPanel; +import jalview.util.MessageManager; + /** * DOCUMENT ME! * @@ -100,6 +100,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable worker.start(); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); Desktop.addInternalFrame(frame, MessageManager diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index e596fbf..6b4c74a 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -186,6 +186,7 @@ public class SequenceFetcher extends JPanel implements Runnable frame = new JInternalFrame(); frame.setContentPane(this); + frame.setFrameIcon(null); Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, Platform.isAMacAndNotJS() ? 240 : 180); } diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 5e1357a..1d59853 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -156,6 +156,7 @@ public class SliderPanel extends GSliderPanel { sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs); conservationSlider = new JInternalFrame(); + conservationSlider.setFrameIcon(null); conservationSlider.setContentPane(sliderPanel); conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -269,6 +270,7 @@ public class SliderPanel extends GSliderPanel { sliderPanel = new SliderPanel(ap, threshold, false, rs); PIDSlider = new JInternalFrame(); + PIDSlider.setFrameIcon(null); PIDSlider.setContentPane(sliderPanel); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); } diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java index 6ebedb7..08d6e03 100644 --- a/src/jalview/gui/SplitFrame.java +++ b/src/jalview/gui/SplitFrame.java @@ -105,6 +105,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI */ protected void init() { + setFrameIcon(null); getTopFrame().setSplitFrame(this); getBottomFrame().setSplitFrame(this); getTopFrame().setVisible(true); diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 30b3c06..9f259bb 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -31,6 +31,7 @@ import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; import java.util.Locale; +import java.util.concurrent.Callable; import java.util.concurrent.Executors; import javax.swing.JCheckBox; @@ -327,53 +328,43 @@ public class StructureChooser extends GStructureChooser }; // fetch db refs if OK pressed - final Runnable discoverCanonicalDBrefs = new Runnable() - { - @Override - public void run() + final Callable discoverCanonicalDBrefs = () -> { + btn_queryTDB.setEnabled(false); + populateSeqsWithoutSourceDBRef(); + + final int y = seqsWithoutSourceDBRef.size(); + if (y > 0) { - btn_queryTDB.setEnabled(false); - populateSeqsWithoutSourceDBRef(); + final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); + DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, + progressBar, new DbSourceProxy[] + { new jalview.ws.dbsources.Uniprot() }, null, false); + dbRefFetcher.addListener(afterDbRefFetch); + // ideally this would also gracefully run with callbacks - final int y = seqsWithoutSourceDBRef.size(); - if (y > 0) - { - final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef - .toArray(new SequenceI[y]); - DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, - progressBar, new DbSourceProxy[] - { new jalview.ws.dbsources.Uniprot() }, null, false); - dbRefFetcher.addListener(afterDbRefFetch); - // ideally this would also gracefully run with callbacks - - dbRefFetcher.fetchDBRefs(true); - } - else - { - // call finished action directly - afterDbRefFetch.finished(); - } + dbRefFetcher.fetchDBRefs(true); } - + else + { + // call finished action directly + afterDbRefFetch.finished(); + } + return null; }; - final Runnable revertview = new Runnable() - { - @Override - public void run() + final Callable revertview = () -> { + if (lastSelected != null) { - if (lastSelected != null) - { - cmb_filterOption.setSelectedItem(lastSelected); - } - }; + cmb_filterOption.setSelectedItem(lastSelected); + } + return null; }; int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); Console.debug("Using Uniprot fetch threshold of " + threshold); if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) { - Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs) - .start(); + Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs); return; } // need cancel and no to result in the discoverPDB action - mocked is diff --git a/src/jalview/gui/StructureChooser.java~ b/src/jalview/gui/StructureChooser.java~ deleted file mode 100644 index 5d6bef1..0000000 --- a/src/jalview/gui/StructureChooser.java~ +++ /dev/null @@ -1,1161 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ - -package jalview.gui; - -import jalview.bin.Jalview; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.fts.api.FTSData; -import jalview.fts.api.FTSDataColumnI; -import jalview.fts.api.FTSRestClientI; -import jalview.fts.core.FTSRestRequest; -import jalview.fts.core.FTSRestResponse; -import jalview.fts.service.pdb.PDBFTSRestClient; -import jalview.jbgui.GStructureChooser; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; -import jalview.ws.DBRefFetcher; -import jalview.ws.sifts.SiftsSettings; - -import java.awt.event.ItemEvent; -import java.util.ArrayList; -import java.util.Collection; -import java.util.HashSet; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Objects; -import java.util.Vector; - -import javax.swing.JCheckBox; -import javax.swing.JComboBox; -import javax.swing.JLabel; -import javax.swing.JOptionPane; -import javax.swing.table.AbstractTableModel; - -/** - * Provides the behaviors for the Structure chooser Panel - * - * @author tcnofoegbu - * - */ -@SuppressWarnings("serial") -public class StructureChooser extends GStructureChooser implements - IProgressIndicator -{ - private boolean structuresDiscovered = false; - - private SequenceI selectedSequence; - - private SequenceI[] selectedSequences; - - private IProgressIndicator progressIndicator; - - private Collection discoveredStructuresSet; - - private FTSRestRequest lastPdbRequest; - - private FTSRestClientI pdbRestCleint; - - private String selectedPdbFileName; - - private boolean isValidPBDEntry; - - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, - AlignmentPanel ap) - { - this.ap = ap; - this.selectedSequence = selectedSeq; - this.selectedSequences = selectedSeqs; - this.progressIndicator = (ap == null) ? null : ap.alignFrame; - init(); - } - - /** - * Initializes parameters used by the Structure Chooser Panel - */ - public void init() - { - if (!Jalview.isHeadlessMode()) - { - progressBar = new ProgressBar(this.statusPanel, this.statusBar); - } - - Thread discoverPDBStructuresThread = new Thread(new Runnable() - { - @Override - public void run() - { - long startTime = System.currentTimeMillis(); - updateProgressIndicator(MessageManager - .getString("status.loading_cached_pdb_entries"), startTime); - loadLocalCachedPDBEntries(); - updateProgressIndicator(null, startTime); - updateProgressIndicator(MessageManager - .getString("status.searching_for_pdb_structures"), - startTime); - fetchStructuresMetaData(); - populateFilterComboBox(); - updateProgressIndicator(null, startTime); - mainFrame.setVisible(true); - updateCurrentView(); - } - }); - discoverPDBStructuresThread.start(); - } - - /** - * Updates the progress indicator with the specified message - * - * @param message - * displayed message for the operation - * @param id - * unique handle for this indicator - */ - public void updateProgressIndicator(String message, long id) - { - if (progressIndicator != null) - { - progressIndicator.setProgressBar(message, id); - } - } - - /** - * Retrieve meta-data for all the structure(s) for a given sequence(s) in a - * selection group - */ - public void fetchStructuresMetaData() - { - long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); - Collection wantedFields = pdbDocFieldPrefs - .getStructureSummaryFields(); - - discoveredStructuresSet = new LinkedHashSet(); - HashSet errors = new HashSet(); - for (SequenceI seq : selectedSequences) - { - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("("); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq); - FTSRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - e.printStackTrace(); - errors.add(e.getMessage()); - continue; - } - lastPdbRequest = pdbRequest; - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) - { - discoveredStructuresSet.addAll(resultList.getSearchSummary()); - } - } - - int noOfStructuresFound = 0; - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - if (discoveredStructuresSet != null - && !discoveredStructuresSet.isEmpty()) - { - getResultTable().setModel( - FTSRestResponse.getTableModel(lastPdbRequest, - discoveredStructuresSet)); - structuresDiscovered = true; - noOfStructuresFound = discoveredStructuresSet.size(); - mainFrame.setTitle(MessageManager.formatMessage( - "label.structure_chooser_no_of_structures", - noOfStructuresFound, totalTime)); - } - else - { - mainFrame.setTitle(MessageManager - .getString("label.structure_chooser_manual_association")); - if (errors.size() > 0) - { - StringBuilder errorMsg = new StringBuilder(); - for (String error : errors) - { - errorMsg.append(error).append("\n"); - } - JOptionPane.showMessageDialog(this, errorMsg.toString(), - MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); - } - } - } - - public void loadLocalCachedPDBEntries() - { - ArrayList entries = new ArrayList(); - for (SequenceI seq : selectedSequences) - { - if (seq.getDatasetSequence() != null - && seq.getDatasetSequence().getAllPDBEntries() != null) - { - for (PDBEntry pdbEntry : seq.getDatasetSequence() - .getAllPDBEntries()) - { - if (pdbEntry.getFile() != null) - { - entries.add(new CachedPDB(seq, pdbEntry)); - } - } - } - } - - PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); - tbl_local_pdb.setModel(tableModelx); - } - - /** - * Builds a query string for a given sequences using its DBRef entries - * - * @param seq - * the sequences to build a query for - * @return the built query string - */ - - public static String buildQuery(SequenceI seq) - { - boolean isPDBRefsFound = false; - boolean isUniProtRefsFound = false; - StringBuilder queryBuilder = new StringBuilder(); - HashSet seqRefs = new LinkedHashSet(); - - if (seq.getAllPDBEntries() != null) - { - for (PDBEntry entry : seq.getAllPDBEntries()) - { - if (isValidSeqName(entry.getId())) - { - queryBuilder.append("pdb_id") - .append(":") -.append(entry.getId().toLowerCase()) - .append(" OR "); - isPDBRefsFound = true; - // seqRefs.add(entry.getId()); - } - } - } - - if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) - { - for (DBRefEntry dbRef : seq.getDBRefs()) - { - if (isValidSeqName(getDBRefId(dbRef))) - { - if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) - { - queryBuilder -.append("uniprot_accession").append(":") - .append(getDBRefId(dbRef)) - .append(" OR "); - queryBuilder -.append("uniprot_id") - .append(":") - .append(getDBRefId(dbRef)).append(" OR "); - isUniProtRefsFound = true; - } - else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB)) - { - - queryBuilder.append("pdb_id") - .append(":").append(getDBRefId(dbRef).toLowerCase()) - .append(" OR "); - isPDBRefsFound = true; - } - else - { - seqRefs.add(getDBRefId(dbRef)); - } - } - } - } - - if (!isPDBRefsFound && !isUniProtRefsFound) - { - String seqName = seq.getName(); - seqName = sanitizeSeqName(seqName); - String[] names = seqName.toLowerCase().split("\\|"); - for (String name : names) - { - // System.out.println("Found name : " + name); - name.trim(); - if (isValidSeqName(name)) - { - seqRefs.add(name); - } - } - - for (String seqRef : seqRefs) - { - queryBuilder.append("text:").append(seqRef).append(" OR "); - } - } - - int endIndex = queryBuilder.lastIndexOf(" OR "); - if (queryBuilder.toString().length() < 6) - { - return null; - } - String query = queryBuilder.toString().substring(0, endIndex); - return query; - } - - /** - * Remove the following special characters from input string +, -, &, !, (, ), - * {, }, [, ], ^, ", ~, *, ?, :, \ - * - * @param seqName - * @return - */ - static String sanitizeSeqName(String seqName) - { - Objects.requireNonNull(seqName); - return seqName.replaceAll("\\[\\d*\\]", "") - .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); - } - - - /** - * Ensures sequence ref names are not less than 3 characters and does not - * contain a database name - * - * @param seqName - * @return - */ - public static boolean isValidSeqName(String seqName) - { - // System.out.println("seqName : " + seqName); - String ignoreList = "pdb,uniprot,swiss-prot"; - if (seqName.length() < 3) - { - return false; - } - if (seqName.contains(":")) - { - return false; - } - seqName = seqName.toLowerCase(); - for (String ignoredEntry : ignoreList.split(",")) - { - if (seqName.contains(ignoredEntry)) - { - return false; - } - } - return true; - } - - public static String getDBRefId(DBRefEntry dbRef) - { - String ref = dbRef.getAccessionId().replaceAll("GO:", ""); - return ref; - } - - /** - * Filters a given list of discovered structures based on supplied argument - * - * @param fieldToFilterBy - * the field to filter by - */ - public void filterResultSet(final String fieldToFilterBy) - { - Thread filterThread = new Thread(new Runnable() - { - @Override - public void run() - { - long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); - lbl_loading.setVisible(true); - Collection wantedFields = pdbDocFieldPrefs - .getStructureSummaryFields(); - Collection filteredResponse = new HashSet(); - HashSet errors = new HashSet(); - - for (SequenceI seq : selectedSequences) - { - FTSRestRequest pdbRequest = new FTSRestRequest(); - if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage")) - { - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("("); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq); - pdbRequest.setFacet(true); - pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity"); - pdbRequest.setFacetPivotMinCount(1); - } - else - { - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("("); - pdbRequest.setFieldToSortBy(fieldToFilterBy, - !chk_invertFilter.isSelected()); - pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq); - } - FTSRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - e.printStackTrace(); - errors.add(e.getMessage()); - continue; - } - lastPdbRequest = pdbRequest; - if (resultList.getSearchSummary() != null - && !resultList.getSearchSummary().isEmpty()) - { - filteredResponse.addAll(resultList.getSearchSummary()); - } - } - - String totalTime = (System.currentTimeMillis() - startTime) - + " milli secs"; - if (!filteredResponse.isEmpty()) - { - final int filterResponseCount = filteredResponse.size(); - Collection reorderedStructuresSet = new LinkedHashSet(); - reorderedStructuresSet.addAll(filteredResponse); - reorderedStructuresSet.addAll(discoveredStructuresSet); - getResultTable().setModel( - FTSRestResponse.getTableModel( - lastPdbRequest, reorderedStructuresSet)); - - FTSRestResponse.configureTableColumn(getResultTable(), - wantedFields); - getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); - getResultTable().getColumn("Ref Sequence").setMinWidth(100); - getResultTable().getColumn("Ref Sequence").setMaxWidth(200); - // Update table selection model here - getResultTable().addRowSelectionInterval(0, - filterResponseCount - 1); - mainFrame.setTitle(MessageManager.formatMessage( - "label.structure_chooser_filter_time", totalTime)); - } - else - { - mainFrame.setTitle(MessageManager.formatMessage( - "label.structure_chooser_filter_time", totalTime)); - if (errors.size() > 0) - { - StringBuilder errorMsg = new StringBuilder(); - for (String error : errors) - { - errorMsg.append(error).append("\n"); - } - JOptionPane.showMessageDialog( - null, - errorMsg.toString(), - MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); - } - } - - lbl_loading.setVisible(false); - - validateSelections(); - } - }); - filterThread.start(); - } - - /** - * Handles action event for btn_pdbFromFile - */ - @Override - public void pdbFromFile_actionPerformed() - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", - selectedSequence.getDisplayId(false))); - chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", - selectedSequence.getDisplayId(false))); - - int value = chooser.showOpenDialog(null); - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - selectedPdbFileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); - validateSelections(); - } - } - - /** - * Populates the filter combo-box options dynamically depending on discovered - * structures - */ - @Override - protected void populateFilterComboBox() - { - if (isStructuresDiscovered()) - { - cmb_filterOption.addItem(new FilterOption("Best Quality", - "overall_quality", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Best Resolution", - "resolution", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - "number_of_protein_chains", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - "number_of_bound_molecules", VIEWS_FILTER)); - cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - "number_of_polymer_residues", VIEWS_FILTER)); - } - cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); - cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); - } - - /** - * Updates the displayed view based on the selected filter option - */ - @Override - protected void updateCurrentView() - { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - layout_switchableViews.show(pnl_switchableViews, - selectedFilterOpt.getView()); - String filterTitle = mainFrame.getTitle(); - mainFrame.setTitle(frameTitle); - chk_invertFilter.setVisible(false); - if (selectedFilterOpt.getView() == VIEWS_FILTER) - { - mainFrame.setTitle(filterTitle); - chk_invertFilter.setVisible(true); - filterResultSet(selectedFilterOpt.getValue()); - } - else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID - || selectedFilterOpt.getView() == VIEWS_FROM_FILE) - { - mainFrame.setTitle(MessageManager - .getString("label.structure_chooser_manual_association")); - idInputAssSeqPanel.loadCmbAssSeq(); - fileChooserAssSeqPanel.loadCmbAssSeq(); - } - validateSelections(); - } - - /** - * Validates user selection and activates the view button if all parameters - * are correct - */ - @Override - public void validateSelections() - { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - btn_view.setEnabled(false); - String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) - { - if (getResultTable().getSelectedRows().length > 0) - { - btn_view.setEnabled(true); - } - } - else if (currentView == VIEWS_LOCAL_PDB) - { - if (tbl_local_pdb.getSelectedRows().length > 0) - { - btn_view.setEnabled(true); - } - } - else if (currentView == VIEWS_ENTER_ID) - { - validateAssociationEnterPdb(); - } - else if (currentView == VIEWS_FROM_FILE) - { - validateAssociationFromFile(); - } - } - - /** - * Validates inputs from the Manual PDB entry panel - */ - public void validateAssociationEnterPdb() - { - AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem(); - lbl_pdbManualFetchStatus.setIcon(errorImage); - lbl_pdbManualFetchStatus.setToolTipText(""); - if (txt_search.getText().length() > 0) - { - lbl_pdbManualFetchStatus - .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager - .formatMessage("info.no_pdb_entry_found_for", - txt_search.getText()))); - } - - if (errorWarning.length() > 0) - { - lbl_pdbManualFetchStatus.setIcon(warningImage); - lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip( - true, errorWarning.toString())); - } - - if (selectedSequences.length == 1 - || !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-")) - { - txt_search.setEnabled(true); - if (isValidPBDEntry) - { - btn_view.setEnabled(true); - lbl_pdbManualFetchStatus.setToolTipText(""); - lbl_pdbManualFetchStatus.setIcon(goodImage); - } - } - else - { - txt_search.setEnabled(false); - lbl_pdbManualFetchStatus.setIcon(errorImage); - } - } - - /** - * Validates inputs for the manual PDB file selection options - */ - public void validateAssociationFromFile() - { - AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem(); - lbl_fromFileStatus.setIcon(errorImage); - if (selectedSequences.length == 1 - || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase( - "-Select Associated Seq-"))) - { - btn_pdbFromFile.setEnabled(true); - if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) - { - btn_view.setEnabled(true); - lbl_fromFileStatus.setIcon(goodImage); - } - } - else - { - btn_pdbFromFile.setEnabled(false); - lbl_fromFileStatus.setIcon(errorImage); - } - } - - @Override - public void cmbAssSeqStateChanged() - { - validateSelections(); - } - - /** - * Handles the state change event for the 'filter' combo-box and 'invert' - * check-box - */ - @Override - protected void stateChanged(ItemEvent e) - { - if (e.getSource() instanceof JCheckBox) - { - updateCurrentView(); - } - else - { - if (e.getStateChange() == ItemEvent.SELECTED) - { - updateCurrentView(); - } - } - - } - - /** - * Handles action event for btn_ok - */ - @Override - public void ok_ActionPerformed() - { - final StructureSelectionManager ssm = ap.getStructureSelectionManager(); - new Thread(new Runnable() - { - @Override - public void run() - { - FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption - .getSelectedItem()); - String currentView = selectedFilterOpt.getView(); - if (currentView == VIEWS_FILTER) - { - int pdbIdColIndex = getResultTable().getColumn("PDB Id") - .getModelIndex(); - int refSeqColIndex = getResultTable().getColumn("Ref Sequence") - .getModelIndex(); - int[] selectedRows = getResultTable().getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - String pdbIdStr = getResultTable().getValueAt(row, - pdbIdColIndex) - .toString(); - SequenceI selectedSeq = (SequenceI) getResultTable() - .getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = getFindEntry(pdbIdStr, - selectedSeq.getAllPDBEntries()); - } - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); - } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); - } - else if (currentView == VIEWS_LOCAL_PDB) - { - int[] selectedRows = tbl_local_pdb.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") - .getModelIndex(); - int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") - .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); - pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); - launchStructureViewer(ssm, pdbEntriesToView, ap, - selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - - String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - if (pdbIdStr.split(":").length > 1) - { - pdbEntry.setChainCode(pdbIdStr.split(":")[1]); - } - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - } - - PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; - launchStructureViewer(ssm, pdbEntriesToView, ap, - new SequenceI[] { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); - - launchStructureViewer(ssm, - new PDBEntry[] { fileEntry }, ap, - new SequenceI[] { selectedSequence }); - } - mainFrame.dispose(); - } - }).start(); - } - - private PDBEntry getFindEntry(String id, Vector pdbEntries) - { - Objects.requireNonNull(id); - Objects.requireNonNull(pdbEntries); - PDBEntry foundEntry = null; - for (PDBEntry entry : pdbEntries) - { - if (entry.getId().equalsIgnoreCase(id)) - { - return entry; - } - } - return foundEntry; - } - - private void launchStructureViewer(StructureSelectionManager ssm, - final PDBEntry[] pdbEntriesToView, - final AlignmentPanel alignPanel, SequenceI[] sequences) - { - long progressId = sequences.hashCode(); - setProgressBar(MessageManager - .getString("status.launching_3d_structure_viewer"), progressId); - final StructureViewer sViewer = new StructureViewer(ssm); - setProgressBar(null, progressId); - - if (SiftsSettings.isMapWithSifts()) - { - // TODO: prompt user if there are lots of sequences without dbrefs. - // It can take a long time if we need to fetch all dbrefs for all - // sequences! - ArrayList seqsWithoutSourceDBRef = new ArrayList(); - for (SequenceI seq : sequences) - { - if (seq.getSourceDBRef() == null && seq.getDBRefs() == null) - { - seqsWithoutSourceDBRef.add(seq); - continue; - } - } - if (!seqsWithoutSourceDBRef.isEmpty()) - { - int y = seqsWithoutSourceDBRef.size(); - setProgressBar(MessageManager.formatMessage( - "status.fetching_dbrefs_for_sequences_without_valid_refs", - y, - progressId); - SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; - int x = 0; - for (SequenceI fSeq : seqsWithoutSourceDBRef) - { - seqWithoutSrcDBRef[x++] = fSeq; - } - new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true); - setProgressBar("Fetch complete.", progressId); // todo i18n - } - } - if (pdbEntriesToView.length > 1) - { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); - } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); -<<<<<<< Updated upstream - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager - .getString("status.fetching_3d_structures_for_selected_entries")); -======= - setProgressBar("Fetching structure data", progressId); ->>>>>>> Stashed changes - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); - } - else - { -<<<<<<< Updated upstream - ssm.setProgressBar(null); - ssm.setProgressBar(MessageManager.formatMessage( - "status.fetching_3d_structures_for", - pdbEntriesToView[0].getId())); -======= - setProgressBar( - "Fetching structure for " + pdbEntriesToView[0].getId(), - progressId); ->>>>>>> Stashed changes - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } - setProgressBar(null, progressId); - } - - /** - * Populates the combo-box used in associating manually fetched structures to - * a unique sequence when more than one sequence selection is made. - */ - @Override - public void populateCmbAssociateSeqOptions( - JComboBox cmb_assSeq, JLabel lbl_associateSeq) - { - cmb_assSeq.removeAllItems(); - cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-", - null)); - lbl_associateSeq.setVisible(false); - if (selectedSequences.length > 1) - { - for (SequenceI seq : selectedSequences) - { - cmb_assSeq.addItem(new AssociateSeqOptions(seq)); - } - } - else - { - String seqName = selectedSequence.getDisplayId(false); - seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39); - lbl_associateSeq.setText(seqName); - lbl_associateSeq.setVisible(true); - cmb_assSeq.setVisible(false); - } - } - - public boolean isStructuresDiscovered() - { - return structuresDiscovered; - } - - public void setStructuresDiscovered(boolean structuresDiscovered) - { - this.structuresDiscovered = structuresDiscovered; - } - - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } - - @Override - protected void txt_search_ActionPerformed() - { - new Thread() - { - @Override - public void run() - { - errorWarning.setLength(0); - isValidPBDEntry = false; - if (txt_search.getText().length() > 0) - { - String searchTerm = txt_search.getText().toLowerCase(); - searchTerm = searchTerm.split(":")[0]; - // System.out.println(">>>>> search term : " + searchTerm); - List wantedFields = new ArrayList(); - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(1); - pdbRequest.setFieldToSearchBy("(pdb_id:"); - pdbRequest.setWantedFields(wantedFields); - pdbRequest -.setSearchTerm(searchTerm + ")"); - pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); - FTSRestResponse resultList; - try - { - resultList = pdbRestCleint.executeRequest(pdbRequest); - } catch (Exception e) - { - errorWarning.append(e.getMessage()); - return; - } finally - { - validateSelections(); - } - if (resultList.getSearchSummary() != null - && resultList.getSearchSummary().size() > 0) - { - isValidPBDEntry = true; - } - } - validateSelections(); - } - }.start(); - } - - @Override - public void tabRefresh() - { - if (selectedSequences != null) - { - Thread refreshThread = new Thread(new Runnable() - { - @Override - public void run() - { - fetchStructuresMetaData(); - filterResultSet(((FilterOption) cmb_filterOption - .getSelectedItem()).getValue()); - } - }); - refreshThread.start(); - } - } - - public class PDBEntryTableModel extends AbstractTableModel - { - String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" }; - - private List pdbEntries; - - public PDBEntryTableModel(List pdbEntries) - { - this.pdbEntries = new ArrayList(pdbEntries); - } - - @Override - public String getColumnName(int columnIndex) - { - return columns[columnIndex]; - } - - @Override - public int getRowCount() - { - return pdbEntries.size(); - } - - @Override - public int getColumnCount() - { - return columns.length; - } - - @Override - public boolean isCellEditable(int row, int column) - { - return false; - } - - @Override - public Object getValueAt(int rowIndex, int columnIndex) - { - Object value = "??"; - CachedPDB entry = pdbEntries.get(rowIndex); - switch (columnIndex) - { - case 0: - value = entry.getSequence(); - break; - case 1: - value = entry.getPdbEntry(); - break; - case 2: - value = entry.getPdbEntry().getChainCode() == null ? "_" : entry - .getPdbEntry().getChainCode(); - break; - case 3: - value = entry.getPdbEntry().getType(); - break; - case 4: - value = entry.getPdbEntry().getFile(); - break; - } - return value; - } - - @Override - public Class getColumnClass(int columnIndex) - { - return columnIndex == 0 ? SequenceI.class : PDBEntry.class; - } - - public CachedPDB getPDBEntryAt(int row) - { - return pdbEntries.get(row); - } - - } - - private class CachedPDB - { - private SequenceI sequence; - - private PDBEntry pdbEntry; - - public CachedPDB(SequenceI sequence, PDBEntry pdbEntry) - { - this.sequence = sequence; - this.pdbEntry = pdbEntry; - } - - public SequenceI getSequence() - { - return sequence; - } - - public PDBEntry getPdbEntry() - { - return pdbEntry; - } - - } - - private IProgressIndicator progressBar; - - @Override - public void setProgressBar(String message, long id) - { - progressBar.setProgressBar(message, id); - } - - @Override - public void registerHandler(long id, IProgressIndicatorHandler handler) - { - progressBar.registerHandler(id, handler); - } - - @Override - public boolean operationInProgress() - { - return progressBar.operationInProgress(); - } -} diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index ec5579c..1e12f7f 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -135,6 +135,7 @@ public abstract class StructureViewerBase extends GStructureViewer public StructureViewerBase() { super(); + setFrameIcon(null); } /** @@ -1280,6 +1281,9 @@ public abstract class StructureViewerBase extends GStructureViewer if (confirm == JvOptionPane.CANCEL_OPTION || confirm == JvOptionPane.CLOSED_OPTION) { + // abort possible quit handling if CANCEL chosen + if (confirm == JvOptionPane.CANCEL_OPTION) + QuitHandler.abortQuit(); return; } forceClose = confirm == JvOptionPane.YES_OPTION; diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index f9ff337..e72a084 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -27,6 +27,7 @@ import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.HashMap; import java.util.Map; +import java.util.concurrent.Callable; import javax.swing.BorderFactory; import javax.swing.JLabel; @@ -151,13 +152,10 @@ public class TextColourChooser MessageManager.getString("action.cancel") }; String title = MessageManager .getString("label.adjust_foreground_text_colour_threshold"); - Runnable action = new Runnable() // response for 1 = Cancel + Callable action = () -> // response for 1 = Cancel { - @Override - public void run() - { - restoreInitialSettings(); - } + restoreInitialSettings(); + return null; }; JvOptionPane.newOptionDialog(alignPanel.alignFrame) .setResponseHandler(1, action).showInternalDialog(bigpanel, diff --git a/src/jalview/gui/TreeCanvas.java~ b/src/jalview/gui/TreeCanvas.java~ deleted file mode 100755 index 90c74be..0000000 --- a/src/jalview/gui/TreeCanvas.java~ +++ /dev/null @@ -1,1080 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.gui; - -import jalview.analysis.Conservation; -import jalview.analysis.NJTree; -import jalview.api.AlignViewportI; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.datamodel.SequenceNode; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.ResidueProperties; -import jalview.schemes.UserColourScheme; -import jalview.structure.SelectionSource; -import jalview.util.Format; -import jalview.util.MappingUtils; -import jalview.util.MessageManager; - -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Graphics; -import java.awt.Graphics2D; -import java.awt.Point; -import java.awt.Rectangle; -import java.awt.RenderingHints; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; -import java.awt.print.PageFormat; -import java.awt.print.Printable; -import java.awt.print.PrinterException; -import java.awt.print.PrinterJob; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Vector; - -import javax.swing.JColorChooser; -import javax.swing.JPanel; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; -import javax.swing.ToolTipManager; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class TreeCanvas extends JPanel implements MouseListener, Runnable, - Printable, MouseMotionListener, SelectionSource -{ - /** DOCUMENT ME!! */ - public static final String PLACEHOLDER = " * "; - - NJTree tree; - - JScrollPane scrollPane; - - TreePanel tp; - - AlignViewport av; - - AlignmentPanel ap; - - Font font; - - FontMetrics fm; - - boolean fitToWindow = true; - - boolean showDistances = false; - - boolean showBootstrap = false; - - boolean markPlaceholders = false; - - int offx = 20; - - int offy; - - float threshold; - - String longestName; - - int labelLength = -1; - - Hashtable nameHash = new Hashtable(); - - Hashtable nodeHash = new Hashtable(); - - SequenceNode highlightNode; - - boolean applyToAllViews = false; - - /** - * Creates a new TreeCanvas object. - * - * @param av - * DOCUMENT ME! - * @param tree - * DOCUMENT ME! - * @param scroller - * DOCUMENT ME! - * @param label - * DOCUMENT ME! - */ - public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller) - { - this.tp = tp; - this.av = ap.av; - this.ap = ap; - font = av.getFont(); - scrollPane = scroller; - addMouseListener(this); - addMouseMotionListener(this); - ToolTipManager.sharedInstance().registerComponent(this); - } - - /** - * DOCUMENT ME! - * - * @param sequence - * DOCUMENT ME! - */ - public void treeSelectionChanged(SequenceI sequence) - { - AlignmentPanel[] aps = getAssociatedPanels(); - - for (int a = 0; a < aps.length; a++) - { - SequenceGroup selected = aps[a].av.getSelectionGroup(); - - if (selected == null) - { - selected = new SequenceGroup(); - aps[a].av.setSelectionGroup(selected); - } - - selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1); - selected.addOrRemove(sequence, true); - } - } - - /** - * DOCUMENT ME! - * - * @param tree - * DOCUMENT ME! - */ - public void setTree(NJTree tree) - { - this.tree = tree; - tree.findHeight(tree.getTopNode()); - - // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); - boolean has_placeholders = false; - longestName = ""; - - for (int i = 0; i < leaves.size(); i++) - { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); - - if (lf.isPlaceholder()) - { - has_placeholders = true; - } - - if (longestName.length() < ((Sequence) lf.element()).getName() - .length()) - { - longestName = TreeCanvas.PLACEHOLDER - + ((Sequence) lf.element()).getName(); - } - } - - setMarkPlaceholders(has_placeholders); - } - - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param node - * DOCUMENT ME! - * @param chunk - * DOCUMENT ME! - * @param scale - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param offx - * DOCUMENT ME! - * @param offy - * DOCUMENT ME! - */ - public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) - { - if (node == null) - { - return; - } - - if ((node.left() == null) && (node.right() == null)) - { - // Drawing leaf node - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; - - int ypos = (int) (node.ycount * chunk) + offy; - - if (node.element() instanceof SequenceI) - { - SequenceI seq = (SequenceI) node.element(); - - if (av.getSequenceColour(seq) == Color.white) - { - g.setColor(Color.black); - } - else - { - g.setColor(av.getSequenceColour(seq).darker()); - } - } - else - { - g.setColor(Color.black); - } - - // Draw horizontal line - g.drawLine(xstart, ypos, xend, ypos); - - String nodeLabel = ""; - - if (showDistances && (node.dist > 0)) - { - nodeLabel = new Format("%-.2f").form(node.dist); - } - - if (showBootstrap && node.bootstrap > -1) - { - if (showDistances) - { - nodeLabel = nodeLabel + " : "; - } - - nodeLabel = nodeLabel + String.valueOf(node.bootstrap); - } - - if (!nodeLabel.equals("")) - { - g.drawString(nodeLabel, xstart + 2, ypos - 2); - } - - String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node - .getName()) : node.getName(); - - int charWidth = fm.stringWidth(name) + 3; - int charHeight = font.getSize(); - - Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, - charWidth, charHeight); - - nameHash.put(node.element(), rect); - - // Colour selected leaves differently - SequenceGroup selected = av.getSelectionGroup(); - - if ((selected != null) - && selected.getSequences(null).contains(node.element())) - { - g.setColor(Color.gray); - - g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); - g.setColor(Color.white); - } - - g.drawString(name, xend + 10, ypos + fm.getDescent()); - g.setColor(Color.black); - } - else - { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, - offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, - offy); - - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; - int ypos = (int) (node.ycount * chunk) + offy; - - g.setColor(node.color.darker()); - - // Draw horizontal line - g.drawLine(xstart, ypos, xend, ypos); - if (node == highlightNode) - { - g.fillRect(xend - 3, ypos - 3, 6, 6); - } - else - { - g.fillRect(xend - 2, ypos - 2, 4, 4); - } - - int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) - + offy; - int yend = (int) (((SequenceNode) node.right()).ycount * chunk) - + offy; - - Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); - nodeHash.put(node, pos); - - g.drawLine((int) (height * scale) + offx, ystart, - (int) (height * scale) + offx, yend); - - String nodeLabel = ""; - - if (showDistances && (node.dist > 0)) - { - nodeLabel = new Format("%-.2f").form(node.dist); - } - - if (showBootstrap && node.bootstrap > -1) - { - if (showDistances) - { - nodeLabel = nodeLabel + " : "; - } - - nodeLabel = nodeLabel + String.valueOf(node.bootstrap); - } - - if (!nodeLabel.equals("")) - { - g.drawString(nodeLabel, xstart + 2, ypos - 2); - } - } - } - - /** - * DOCUMENT ME! - * - * @param x - * DOCUMENT ME! - * @param y - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Object findElement(int x, int y) - { - Enumeration keys = nameHash.keys(); - - while (keys.hasMoreElements()) - { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nameHash.get(ob); - - if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) - && (y <= (rect.y + rect.height))) - { - return ob; - } - } - - keys = nodeHash.keys(); - - while (keys.hasMoreElements()) - { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nodeHash.get(ob); - - if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) - && (y <= (rect.y + rect.height))) - { - return ob; - } - } - - return null; - } - - /** - * DOCUMENT ME! - * - * @param pickBox - * DOCUMENT ME! - */ - public void pickNodes(Rectangle pickBox) - { - int width = getWidth(); - int height = getHeight(); - - SequenceNode top = tree.getTopNode(); - - float wscale = (float) ((width * .8) - (offx * 2)) - / tree.getMaxHeight(); - - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; - } - - float chunk = (float) (height - (offy)) / top.count; - - pickNode(pickBox, top, chunk, wscale, width, offx, offy); - } - - /** - * DOCUMENT ME! - * - * @param pickBox - * DOCUMENT ME! - * @param node - * DOCUMENT ME! - * @param chunk - * DOCUMENT ME! - * @param scale - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param offx - * DOCUMENT ME! - * @param offy - * DOCUMENT ME! - */ - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) - { - if (node == null) - { - return; - } - - if ((node.left() == null) && (node.right() == null)) - { - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; - - int ypos = (int) (node.ycount * chunk) + offy; - - if (pickBox.contains(new Point(xend, ypos))) - { - if (node.element() instanceof SequenceI) - { - SequenceI seq = (SequenceI) node.element(); - SequenceGroup sg = av.getSelectionGroup(); - - if (sg != null) - { - sg.addOrRemove(seq, true); - } - } - } - } - else - { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, - offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, - offx, offy); - } - } - - /** - * DOCUMENT ME! - * - * @param node - * DOCUMENT ME! - * @param c - * DOCUMENT ME! - */ - public void setColor(SequenceNode node, Color c) - { - if (node == null) - { - return; - } - - if ((node.left() == null) && (node.right() == null)) // TODO: internal node - { - node.color = c; - - if (node.element() instanceof SequenceI) - { - AlignmentPanel[] aps = getAssociatedPanels(); - if (aps != null) - { - for (int a = 0; a < aps.length; a++) - { - final SequenceI seq = (SequenceI) node.element(); - aps[a].av.setSequenceColour(seq, c); - } - } - } - } - else - { - node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); - } - } - - /** - * DOCUMENT ME! - */ - void startPrinting() - { - Thread thread = new Thread(this); - thread.start(); - } - - // put printing in a thread to avoid painting problems - @Override - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - - printJob.setPrintable(this, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - - /** - * DOCUMENT ME! - * - * @param pg - * DOCUMENT ME! - * @param pf - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! - * - * @return DOCUMENT ME! - * - * @throws PrinterException - * DOCUMENT ME! - */ - @Override - public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException - { - pg.setFont(font); - pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - - int pwidth = (int) pf.getImageableWidth(); - int pheight = (int) pf.getImageableHeight(); - - int noPages = getHeight() / pheight; - - if (pi > noPages) - { - return Printable.NO_SUCH_PAGE; - } - - if (pwidth > getWidth()) - { - pwidth = getWidth(); - } - - if (fitToWindow) - { - if (pheight > getHeight()) - { - pheight = getHeight(); - } - - noPages = 0; - } - else - { - FontMetrics fm = pg.getFontMetrics(font); - int height = fm.getHeight() * nameHash.size(); - pg.translate(0, -pi * pheight); - pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight); - - // translate number of pages, - // height is screen size as this is the - // non overlapping text size - pheight = height; - } - - draw(pg, pwidth, pheight); - - return Printable.PAGE_EXISTS; - } - - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ - @Override - public void paintComponent(Graphics g) - { - super.paintComponent(g); - g.setFont(font); - - if (tree == null) - { - g.drawString(MessageManager.getString("label.calculating_tree") - + "....", 20, getHeight() / 2); - } - else - { - fm = g.getFontMetrics(font); - - if (nameHash.size() == 0) - { - repaint(); - } - - if (fitToWindow - || (!fitToWindow && (scrollPane.getHeight() > ((fm - .getHeight() * nameHash.size()) + offy)))) - { - draw(g, scrollPane.getWidth(), scrollPane.getHeight()); - setPreferredSize(null); - } - else - { - setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); - draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); - } - - scrollPane.revalidate(); - } - } - - /** - * DOCUMENT ME! - * - * @param fontSize - * DOCUMENT ME! - */ - @Override - public void setFont(Font font) - { - this.font = font; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param g1 - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param height - * DOCUMENT ME! - */ - public void draw(Graphics g1, int width, int height) - { - Graphics2D g2 = (Graphics2D) g1; - g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - g2.setColor(Color.white); - g2.fillRect(0, 0, width, height); - g2.setFont(font); - - if (longestName == null || tree == null) - { - g2.drawString("Calculating tree.", 20, 20); - } - offy = font.getSize() + 10; - - fm = g2.getFontMetrics(font); - - labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar - - float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); - - SequenceNode top = tree.getTopNode(); - - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; - } - - float chunk = (float) (height - (offy)) / top.count; - - drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); - - if (threshold != 0) - { - if (av.getCurrentTree() == tree) - { - g2.setColor(Color.red); - } - else - { - g2.setColor(Color.gray); - } - - int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx); - - g2.drawLine(x, 0, x, getHeight()); - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void mouseReleased(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void mouseEntered(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void mouseExited(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void mouseClicked(MouseEvent evt) - { - if (highlightNode != null) - { - if (SwingUtilities.isRightMouseButton(evt)) - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_subtree_colour"), - highlightNode.color); - if (col != null) - { - setColor(highlightNode, col); - } - } - else if (evt.getClickCount() > 1) - { - tree.swapNodes(highlightNode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - } - else - { - Vector leaves = new Vector(); - tree.findLeaves(highlightNode, leaves); - - for (int i = 0; i < leaves.size(); i++) - { - SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i)) - .element(); - treeSelectionChanged(seq); - } - av.sendSelection(); - } - - PaintRefresher.Refresh(tp, av.getSequenceSetId()); - repaint(); - } - } - - @Override - public void mouseMoved(MouseEvent evt) - { - av.setCurrentTree(tree); - - Object ob = findElement(evt.getX(), evt.getY()); - - if (ob instanceof SequenceNode) - { - highlightNode = (SequenceNode) ob; - this.setToolTipText("" - + MessageManager.getString("label.highlightnode")); - repaint(); - - } - else - { - if (highlightNode != null) - { - highlightNode = null; - setToolTipText(null); - repaint(); - } - } - } - - @Override - public void mouseDragged(MouseEvent ect) - { - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void mousePressed(MouseEvent e) - { - av.setCurrentTree(tree); - - int x = e.getX(); - int y = e.getY(); - - Object ob = findElement(x, y); - - if (ob instanceof SequenceI) - { - treeSelectionChanged((Sequence) ob); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); - repaint(); - av.sendSelection(); - return; - } - else if (!(ob instanceof SequenceNode)) - { - // Find threshold - if (tree.getMaxHeight() != 0) - { - threshold = (float) (x - offx) - / (float) (getWidth() - labelLength - (2 * offx)); - - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); - setColor(tree.getTopNode(), Color.black); - - AlignmentPanel[] aps = getAssociatedPanels(); - - // TODO push calls below into a single AlignViewportI method? - // see also AlignViewController.deleteGroups - for (int a = 0; a < aps.length; a++) - { - aps[a].av.setSelectionGroup(null); - aps[a].av.getAlignment().deleteAllGroups(); - aps[a].av.clearSequenceColours(); - if (aps[a].av.getCodingComplement() != null) - { - aps[a].av.getCodingComplement().setSelectionGroup(null); - aps[a].av.getCodingComplement().getAlignment() - .deleteAllGroups(); - aps[a].av.getCodingComplement().clearSequenceColours(); - } - } - colourGroups(); - } - - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); - repaint(); - } - - } - - void colourGroups() - { - AlignmentPanel[] aps = getAssociatedPanels(); - for (int i = 0; i < tree.getGroups().size(); i++) - { - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); - setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter()); - - Vector l = tree.findLeaves( - (SequenceNode) tree.getGroups().elementAt(i), new Vector()); - - Vector sequences = new Vector(); - - for (int j = 0; j < l.size(); j++) - { - SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)) - .element(); - - if (!sequences.contains(s1)) - { - sequences.addElement(s1); - } - } - - ColourSchemeI cs = null; - SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true, - false, 0, av.getAlignment().getWidth() - 1); - - if (av.getGlobalColourScheme() != null) - { - if (av.getGlobalColourScheme() instanceof UserColourScheme) - { - cs = new UserColourScheme( - ((UserColourScheme) av.getGlobalColourScheme()) - .getColours()); - - } - else - { - cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); - } - // cs is null if shading is an annotationColourGradient - if (cs != null) - { - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.isIgnoreGapsConsensus()); - } - } - sg.cs = cs; - // sg.recalcConservation(); - sg.setName("JTreeGroup:" + sg.hashCode()); - sg.setIdColour(col); - - for (int a = 0; a < aps.length; a++) - { - if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), - sg.getStartRes(), sg.getEndRes()); - - c.calculate(); - c.verdict(false, aps[a].av.getConsPercGaps()); - sg.cs.setConservation(c); - } - - aps[a].av.getAlignment().addGroup(new SequenceGroup(sg)); - // TODO can we push all of the below into AlignViewportI? - final AlignViewportI codingComplement = aps[a].av - .getCodingComplement(); - if (codingComplement != null) - { - if (codingComplement != null) - { - SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, - av, codingComplement); - if (mappedGroup.getSequences().size() > 0) - { - codingComplement.getAlignment().addGroup(mappedGroup); - for (SequenceI seq : mappedGroup.getSequences()) - { - codingComplement.setSequenceColour(seq, col.brighter()); - } - } - } - } - } - } - - // notify the panel(s) to redo any group specific stuff. - for (int a = 0; a < aps.length; a++) - { - aps[a].updateAnnotation(); - // TODO: JAL-868 - need to ensure view colour change message is broadcast - // to any Jmols listening in - final AlignViewportI codingComplement = aps[a].av - .getCodingComplement(); - if (codingComplement != null) - { - ((AlignViewport) codingComplement).getAlignPanel() - .updateAnnotation(); - - } - - } - - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowDistances(boolean state) - { - this.showDistances = state; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowBootstrap(boolean state) - { - this.showBootstrap = state; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setMarkPlaceholders(boolean state) - { - this.markPlaceholders = state; - repaint(); - } - - AlignmentPanel[] getAssociatedPanels() - { - if (applyToAllViews) - { - return PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); - } - else - { - return new AlignmentPanel[] { ap }; - } - } -} diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index d735402..76e1884 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,8 +20,26 @@ */ package jalview.gui; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileOutputStream; +import java.util.ArrayList; +import java.util.List; import java.util.Locale; +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +import org.jibble.epsgraphics.EpsGraphics2D; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; @@ -53,25 +71,6 @@ import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; -import java.awt.Font; -import java.awt.Graphics; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.io.File; -import java.io.FileOutputStream; -import java.util.ArrayList; -import java.util.List; - -import javax.swing.ButtonGroup; -import javax.swing.JMenuItem; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.event.InternalFrameAdapter; -import javax.swing.event.InternalFrameEvent; - -import org.jibble.epsgraphics.EpsGraphics2D; - /** * DOCUMENT ME! * @@ -106,6 +105,7 @@ public class TreePanel extends GTreePanel SimilarityParamsI options) { super(); + this.setFrameIcon(null); this.similarityParams = options; initTreePanel(ap, type, modelName, null, null); @@ -118,6 +118,7 @@ public class TreePanel extends GTreePanel String theTitle, AlignmentView inputData) { super(); + this.setFrameIcon(null); this.treeTitle = theTitle; initTreePanel(alignPanel, null, null, newtree, inputData); } diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 1836e33..298b8b4 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,25 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - -import jalview.bin.Cache; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GUserDefinedColours; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeLoader; -import jalview.schemes.ColourSchemes; -import jalview.schemes.ResidueProperties; -import jalview.schemes.UserColourScheme; -import jalview.util.ColorUtils; -import jalview.util.Format; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.xml.binding.jalview.JalviewUserColours; -import jalview.xml.binding.jalview.JalviewUserColours.Colour; -import jalview.xml.binding.jalview.ObjectFactory; - import java.awt.Color; import java.awt.Font; import java.awt.Insets; @@ -50,6 +31,7 @@ import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; +import java.util.Locale; import javax.swing.JButton; import javax.swing.JInternalFrame; @@ -58,6 +40,23 @@ import javax.swing.event.ChangeListener; import javax.xml.bind.JAXBContext; import javax.xml.bind.Marshaller; +import jalview.bin.Cache; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GUserDefinedColours; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeLoader; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueProperties; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; +import jalview.util.Format; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.ObjectFactory; + /** * This panel allows the user to assign colours to Amino Acid residue codes, and * save the colour scheme. @@ -149,6 +148,7 @@ public class UserDefinedColours extends GUserDefinedColours { colorChooser.getSelectionModel().addChangeListener(this); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), @@ -652,45 +652,41 @@ public class UserDefinedColours extends GUserDefinedColours chooser.setDialogTitle( MessageManager.getString("label.load_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.load")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - File choice = chooser.getSelectedFile(); - Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - - UserColourScheme ucs = ColourSchemeLoader - .loadColourScheme(choice.getAbsolutePath()); - Color[] colors = ucs.getColours(); - schemeName.setText(ucs.getSchemeName()); + chooser.setResponseHandler(0, () -> { + File choice = chooser.getSelectedFile(); + Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - if (ucs.getLowerCaseColours() != null) - { - caseSensitive.setSelected(true); - lcaseColour.setEnabled(true); - resetButtonPanel(true); - for (int i = 0; i < lowerCaseButtons.size(); i++) - { - JButton button = lowerCaseButtons.get(i); - button.setBackground(ucs.getLowerCaseColours()[i]); - } - } - else - { - caseSensitive.setSelected(false); - lcaseColour.setEnabled(false); - resetButtonPanel(false); - } + UserColourScheme ucs = ColourSchemeLoader + .loadColourScheme(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getSchemeName()); - for (int i = 0; i < upperCaseButtons.size(); i++) + if (ucs.getLowerCaseColours() != null) + { + caseSensitive.setSelected(true); + lcaseColour.setEnabled(true); + resetButtonPanel(true); + for (int i = 0; i < lowerCaseButtons.size(); i++) { - JButton button = upperCaseButtons.get(i); - button.setBackground(colors[i]); + JButton button = lowerCaseButtons.get(i); + button.setBackground(ucs.getLowerCaseColours()[i]); } + } + else + { + caseSensitive.setSelected(false); + lcaseColour.setEnabled(false); + resetButtonPanel(false); + } - addNewColourScheme(choice.getPath()); + for (int i = 0; i < upperCaseButtons.size(); i++) + { + JButton button = upperCaseButtons.get(i); + button.setBackground(colors[i]); } + + addNewColourScheme(choice.getPath()); + return null; }); chooser.showOpenDialog(this); diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index ee1b473..4aac062 100644 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -20,8 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -33,6 +31,7 @@ import java.awt.MediaTracker; import java.awt.RenderingHints; import java.awt.event.ActionEvent; import java.awt.image.BufferedImage; +import java.util.Locale; import java.util.Vector; import javax.swing.JComponent; @@ -324,6 +323,7 @@ public class WebserviceInfo extends GWebserviceInfo boolean makeVisible) { frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); Desktop.addInternalFrame(frame, title, makeVisible, width, height); frame.setClosable(false); @@ -626,8 +626,8 @@ public class WebserviceInfo extends GWebserviceInfo true, false); ((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport() .getComponent(0)) - .setText(ensureHtmlTagged( - txt + getHtmlFragment(text, false, true))); + .setText(ensureHtmlTagged( + txt + getHtmlFragment(text, false, true))); } else { diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java index 2039d3c..14c1260 100644 --- a/src/jalview/io/BackupFiles.java +++ b/src/jalview/io/BackupFiles.java @@ -29,8 +29,14 @@ import java.nio.file.StandardCopyOption; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.HashMap; +import java.util.List; import java.util.Map; import java.util.TreeMap; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.Executors; +import java.util.concurrent.Future; import jalview.bin.Cache; import jalview.bin.Console; @@ -105,6 +111,117 @@ public class BackupFiles private static final String oldTempFileSuffix = "_oldfile_tobedeleted"; + // thread pool used for completablefutures + private static final ExecutorService executorService = Executors + .newFixedThreadPool(3); + + private static List savesInProgress = new ArrayList<>(); + + private CompletableFuture myFuture = null; + + private boolean addSaveInProgress() + { + if (savesInProgress.contains(this)) + { + return false; + } + else + { + this.setMyFuture(); + savesInProgress.add(this); + return true; + } + } + + private boolean removeSaveInProgress(boolean ret) + { + if (savesInProgress.contains(this)) + { + this.getMyFuture().complete(ret); + // remove all occurrences + while (savesInProgress.remove(this)) + { + } + return true; + } + return false; + } + + private static CompletableFuture getNewFuture() + { + return new CompletableFuture() + { + }; + } + + private CompletableFuture getMyFuture() + { + return this.myFuture; + } + + private void setMyFuture() + { + this.myFuture = getNewFuture(); + } + + public static boolean hasSavesInProgress() + { + boolean has = false; + for (CompletableFuture cf : savesInProgressCompletableFutures(true)) + { + has |= !cf.isDone(); + } + return has; + } + + public static List savesInProgressFiles(boolean all) + { + List files = new ArrayList<>(); + for (BackupFiles bfile : savesInProgress) + { + if (all || !bfile.getMyFuture().isDone()) + files.add(bfile.getFile()); + } + return files; + } + + public static List> savesInProgressCompletableFutures( + boolean all) + { + List> cfs = new ArrayList<>(); + for (BackupFiles bfile : savesInProgress) + { + if (all || !bfile.getMyFuture().isDone()) + cfs.add(bfile.getMyFuture()); + } + return cfs; + } + + public static Future allSaved() + { + CompletableFuture f = new CompletableFuture<>(); + + executorService.submit(() -> { + for (BackupFiles buf : savesInProgress) + { + boolean allSaved = true; + try + { + allSaved &= buf.getMyFuture().get(); + } catch (InterruptedException e) + { + Console.debug("InterruptedException waiting for files to save", + e); + } catch (ExecutionException e) + { + Console.debug("ExecutionException waiting for files to save", e); + } + f.complete(allSaved); + } + }); + return f; + } + public BackupFiles(String filename) { this(new File(filename)); @@ -116,6 +233,10 @@ public class BackupFiles { classInit(); this.file = file; + + // add this file from the save in progress stack + addSaveInProgress(); + BackupFilesPresetEntry bfpe = BackupFilesPresetEntry .getSavedBackupEntry(); this.suffix = bfpe.suffix; @@ -132,6 +253,7 @@ public class BackupFiles { String tempfilename = file.getName(); File tempdir = file.getParentFile(); + tempdir.mkdirs(); Console.trace( "BACKUPFILES [file!=null] attempting to create temp file for " + tempfilename + " in dir " + tempdir); @@ -819,6 +941,9 @@ public class BackupFiles tidyUpFiles(); } + // remove this file from the save in progress stack + removeSaveInProgress(rename); + return rename; } @@ -890,6 +1015,11 @@ public class BackupFiles return ret; } + public File getFile() + { + return file; + } + public static boolean moveFileToFile(File oldFile, File newFile) { Console.initLogger(); diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index d3ac53f..1b82213 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -466,6 +466,7 @@ public class FileLoader implements Runnable { alignFrame.setFileName(file, format); alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS + alignFrame.getViewport().setSavedUpToDate(true); } if (proxyColourScheme != null) { @@ -485,6 +486,12 @@ public class FileLoader implements Runnable // that perform queries to find the 'current working alignment' Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + /* + * for an Overview automatically opened with alignment, + * set its title now alignFrame title has been set + */ + alignFrame.alignPanel.setOverviewTitle(alignFrame); } try diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 4b66f81..9fb3720 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -20,23 +20,24 @@ */ package jalview.io; -import jalview.bin.Cache; -import jalview.gui.AlignmentPanel; -import jalview.gui.LineartOptions; -import jalview.gui.OOMWarning; -import jalview.math.AlignmentDimension; -import jalview.util.MessageManager; - import java.awt.Graphics; import java.awt.print.PrinterException; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; +import java.util.concurrent.Callable; import java.util.concurrent.atomic.AtomicBoolean; import org.jfree.graphics2d.svg.SVGGraphics2D; import org.jfree.graphics2d.svg.SVGHints; +import jalview.bin.Cache; +import jalview.gui.AlignmentPanel; +import jalview.gui.LineartOptions; +import jalview.gui.OOMWarning; +import jalview.math.AlignmentDimension; +import jalview.util.MessageManager; + public class HtmlSvgOutput extends HTMLOutput { public HtmlSvgOutput(AlignmentPanel ap) @@ -211,13 +212,9 @@ public class HtmlSvgOutput extends HTMLOutput /* * configure the action to run on OK in the dialog */ - Runnable okAction = new Runnable() - { - @Override - public void run() - { - doOutput(textOption.get()); - } + Callable okAction = () -> { + doOutput(textOption.get()); + return null; }; /* @@ -226,15 +223,11 @@ public class HtmlSvgOutput extends HTMLOutput if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless()) { LineartOptions svgOption = new LineartOptions("HTML", textOption); - svgOption.setResponseAction(1, new Runnable() - { - @Override - public void run() - { - setProgressMessage(MessageManager.formatMessage( - "status.cancelled_image_export_operation", - getDescription())); - } + svgOption.setResponseAction(1, () -> { + setProgressMessage(MessageManager.formatMessage( + "status.cancelled_image_export_operation", + getDescription())); + return null; }); svgOption.setResponseAction(0, okAction); svgOption.showDialog(); diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index a9101a1..3b6e325 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -44,18 +44,28 @@ import java.util.List; import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; +import java.util.concurrent.Callable; import javax.swing.BoxLayout; import javax.swing.DefaultListCellRenderer; import javax.swing.JCheckBox; +import javax.swing.JDialog; import javax.swing.JFileChooser; import javax.swing.JList; +import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SpringLayout; import javax.swing.filechooser.FileFilter; import javax.swing.plaf.basic.BasicFileChooserUI; +import jalview.bin.Cache; +import jalview.gui.JvOptionPane; +import jalview.util.ChannelProperties; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.dialogrunner.DialogRunnerI; + /** * Enhanced file chooser dialog box. * @@ -70,7 +80,7 @@ public class JalviewFileChooser extends JFileChooser { private static final long serialVersionUID = 1L; - private Map callbacks = new HashMap<>(); + private Map callbacks = new HashMap<>(); File selectedFile = null; @@ -488,10 +498,13 @@ public class JalviewFileChooser extends JFileChooser if (selectedFile.exists()) { - int confirm = JvOptionPane.showConfirmDialog(this, - MessageManager.getString("label.overwrite_existing_file"), - MessageManager.getString("label.file_already_exists"), - JvOptionPane.YES_NO_OPTION); + int confirm = Cache.getDefault("CONFIRM_OVERWRITE_FILE", true) + ? JvOptionPane.showConfirmDialog(this, + MessageManager + .getString("label.overwrite_existing_file"), + MessageManager.getString("label.file_already_exists"), + JvOptionPane.YES_NO_OPTION) + : JOptionPane.YES_OPTION; if (confirm != JvOptionPane.YES_OPTION) { @@ -596,8 +609,26 @@ public class JalviewFileChooser extends JFileChooser } + /* @Override - public DialogRunnerI setResponseHandler(Object response, Runnable action) + public JalviewFileChooser setResponseHandler(Object response, + Runnable action) + { + callbacks.put(response, new Callable() + { + @Override + public Void call() + { + action.run(); + return null; + } + }); + return this; + } + */ + + @Override + public DialogRunnerI setResponseHandler(Object response, Callable action) { callbacks.put(response, action); return this; @@ -613,10 +644,16 @@ public class JalviewFileChooser extends JFileChooser { return; } - Runnable action = callbacks.get(response); + Callable action = callbacks.get(response); if (action != null) { - action.run(); + try + { + action.call(); + } catch (Exception e) + { + e.printStackTrace(); + } } } @@ -641,4 +678,13 @@ public class JalviewFileChooser extends JFileChooser break; } } + + @Override + protected JDialog createDialog(Component parent) throws HeadlessException + { + JDialog dialog = super.createDialog(parent); + dialog.setIconImages(ChannelProperties.getIconList()); + return dialog; + } + } diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index ca95222..b0079b4 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -32,6 +32,8 @@ import javax.swing.JMenuItem; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; +import jalview.gui.APQHandlers; +import jalview.gui.Desktop; import jalview.io.FileFormatException; import jalview.util.MessageManager; import jalview.util.Platform; @@ -140,7 +142,6 @@ public class GDesktop extends JFrame */ private void jbInit() throws Exception { - boolean apqHandlersSet = false; /** * APQHandlers sets handlers for About, Preferences and Quit actions * peculiar to macOS's application menu. APQHandlers will check to see if a @@ -148,7 +149,7 @@ public class GDesktop extends JFrame */ try { - apqHandlersSet = APQHandlers.setAPQHandlers(this); + APQHandlers.setAPQHandlers((Desktop) this); } catch (Exception e) { System.out.println("Cannot set APQHandlers"); @@ -213,7 +214,8 @@ public class GDesktop extends JFrame @Override public void actionPerformed(ActionEvent e) { - quit(); + if (Desktop.instance != null) + Desktop.instance.desktopQuit(); } }); aboutMenuItem.setText(MessageManager.getString("label.about")); diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index d4b2c04..8d2efe0 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -112,6 +112,7 @@ import jalview.gui.AppVarna; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; +import jalview.gui.OverviewPanel; import jalview.gui.PCAPanel; import jalview.gui.PaintRefresher; import jalview.gui.SplitFrame; @@ -185,6 +186,7 @@ import jalview.xml.binding.jalview.JalviewModel.UserColours; import jalview.xml.binding.jalview.JalviewModel.Viewport; import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam; import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns; +import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview; import jalview.xml.binding.jalview.JalviewUserColours; import jalview.xml.binding.jalview.JalviewUserColours.Colour; import jalview.xml.binding.jalview.MapListType.MapListFrom; @@ -229,6 +231,11 @@ public class Jalview2XML private static final String UTF_8 = "UTF-8"; /** + * used in decision if quit confirmation should be issued + */ + private static boolean stateSavedUpToDate = false; + + /** * prefix for recovering datasets for alignments with multiple views where * non-existent dataset IDs were written for some views */ @@ -616,6 +623,27 @@ public class Jalview2XML { AlignFrame[] frames = Desktop.getAlignFrames(); + setStateSavedUpToDate(true); + + if (Cache.getDefault("DEBUG_DELAY_SAVE", false)) + { + int n = debugDelaySave; + int i = 0; + while (i < n) + { + Console.debug("***** debugging save sleep " + i + "/" + n); + try + { + Thread.sleep(1000); + } catch (InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + i++; + } + } + if (frames == null) { return; @@ -763,6 +791,25 @@ public class Jalview2XML FileOutputStream fos = new FileOutputStream( doBackup ? backupfiles.getTempFilePath() : jarFile); + if (Cache.getDefault("DEBUG_DELAY_SAVE", false)) + { + int n = debugDelaySave; + int i = 0; + while (i < n) + { + Console.debug("***** debugging save sleep " + i + "/" + n); + try + { + Thread.sleep(1000); + } catch (InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + i++; + } + } + JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -1447,6 +1494,23 @@ public class Jalview2XML view.setStartRes(vpRanges.getStartRes()); view.setStartSeq(vpRanges.getStartSeq()); + OverviewPanel ov = ap.getOverviewPanel(); + if (ov != null) + { + Overview overview = new Overview(); + overview.setTitle(ov.getTitle()); + Rectangle bounds = ov.getFrameBounds(); + overview.setXpos(bounds.x); + overview.setYpos(bounds.y); + overview.setWidth(bounds.width); + overview.setHeight(bounds.height); + overview.setShowHidden(ov.isShowHiddenRegions()); + overview.setGapColour(ov.getCanvas().getGapColour().getRGB()); + overview.setResidueColour( + ov.getCanvas().getResidueColour().getRGB()); + overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB()); + view.setOverview(overview); + } if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(), @@ -4048,7 +4112,7 @@ public class Jalview2XML } /* - * Load any trees, PDB structures and viewers + * Load any trees, PDB structures and viewers, Overview * * Not done if flag is false (when this method is used for New View) */ @@ -4058,12 +4122,49 @@ public class Jalview2XML loadPCAViewers(jalviewModel, ap); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); + loadOverview(view, jalviewModel.getVersion(), af); } // and finally return. return af; } /** + * Load Overview window, restoring colours, 'show hidden regions' flag, title + * and geometry as saved + * + * @param view + * @param af + */ + protected void loadOverview(Viewport view, String version, AlignFrame af) + { + if (!isVersionStringLaterThan("2.11.3", + version) && view.getOverview()==null) + { + return; + } + /* + * first close any Overview that was opened automatically + * (if so configured in Preferences) so that the view is + * restored in the same state as saved + */ + af.alignPanel.closeOverviewPanel(); + + Overview overview = view.getOverview(); + if (overview != null) + { + OverviewPanel overviewPanel = af + .openOverviewPanel(overview.isShowHidden()); + overviewPanel.setTitle(overview.getTitle()); + overviewPanel.setFrameBounds(overview.getXpos(), overview.getYpos(), + overview.getWidth(), overview.getHeight()); + Color gap = new Color(overview.getGapColour()); + Color residue = new Color(overview.getResidueColour()); + Color hidden = new Color(overview.getHiddenColour()); + overviewPanel.getCanvas().setColours(gap, residue, hidden); + } + } + + /** * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna * panel is restored from separate jar entries, two (gapped and trimmed) per * sequence and secondary structure. @@ -4580,7 +4681,7 @@ public class Jalview2XML * - minimum version we are comparing against * @param version * - version of data being processsed - * @return + * @return true if version is equal to or later than supported */ public static boolean isVersionStringLaterThan(String supported, String version) @@ -4986,6 +5087,7 @@ public class Jalview2XML { splitFrameCandidates.put(view, af); } + return af; } @@ -5049,7 +5151,10 @@ public class Jalview2XML + annotationId); return null; } - if (matchedAnnotation.getThreshold() == null) + // belt-and-braces create a threshold line if the + // colourscheme needs one but the matchedAnnotation doesn't have one + if (safeInt(viewAnnColour.getAboveThreshold()) != 0 + && matchedAnnotation.getThreshold() == null) { matchedAnnotation.setThreshold( new GraphLine(safeFloat(viewAnnColour.getThreshold()), @@ -6537,4 +6642,44 @@ public class Jalview2XML return colour; } + + public static void setStateSavedUpToDate(boolean s) + { + Console.debug("Setting overall stateSavedUpToDate to " + s); + stateSavedUpToDate = s; + } + + public static boolean stateSavedUpToDate() + { + Console.debug("Returning overall stateSavedUpToDate value: " + + stateSavedUpToDate); + return stateSavedUpToDate; + } + + public static boolean allSavedUpToDate() + { + if (stateSavedUpToDate()) // nothing happened since last project save + return true; + + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames != null) + { + for (int i = 0; i < frames.length; i++) + { + if (frames[i] == null) + continue; + if (!frames[i].getViewport().savedUpToDate()) + return false; // at least one alignment is not individually saved + } + } + return true; + } + + // used for debugging and tests + private static int debugDelaySave = 20; + + public static void setDebugDelaySave(int n) + { + debugDelaySave = n; + } } diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java index 1b5d5da..1ff032b 100644 --- a/src/jalview/renderer/OverviewRenderer.java +++ b/src/jalview/renderer/OverviewRenderer.java @@ -225,7 +225,7 @@ public class OverviewRenderer int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq, int lastcol) { - Color color = resColFinder.GAP_COLOUR; + Color color = resColFinder.gapColour; if ((seq != null) && (seq.getLength() > lastcol)) { diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java index 57cae1c..ef4d04b 100644 --- a/src/jalview/renderer/OverviewResColourFinder.java +++ b/src/jalview/renderer/OverviewResColourFinder.java @@ -20,68 +20,60 @@ */ package jalview.renderer; +import java.awt.Color; + import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.Comparison; -import java.awt.Color; - public class OverviewResColourFinder extends ResidueColourFinder { - final Color GAP_COLOUR; // default colour to use at gaps - - final Color RESIDUE_COLOUR; // default colour to use at residues - - final Color HIDDEN_COLOUR; // colour for hidden regions - - boolean useLegacy = false; - - public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray; + /* + * colour for gaps (unless overridden by colour scheme) + * - as set in Preferences, _or_ read from a project file + */ + Color gapColour; - public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white; + /* + * colour for residues if no colour scheme set (before feature colouring) + * - as set in Preferences, _or_ read from a project file + */ + Color residueColour; - public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray - .darker(); + /* + * colour for hidden regions + * - as set in Preferences, _or_ read from a project file + */ + Color hiddenColour; /** * Constructor without colour settings (used by applet) + * @deprecated */ + @Deprecated public OverviewResColourFinder() { - this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN); + this(Color.lightGray, Color.white, Color.darkGray.darker()); } /** - * Constructor with colour settings + * Constructor given default colours for gaps, residues and hidden regions * - * @param useLegacyColouring - * whether to use legacy gap colouring (white gaps, grey residues) - * @param gapCol - * gap colour if not legacy - * @param hiddenCol - * hidden region colour (transparency applied by rendering code) + * @param gaps + * @param residues + * @param hidden */ - public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol, - Color hiddenCol) + public OverviewResColourFinder(Color gaps, Color residues, Color hidden) { - if (useLegacyColouring) - { - GAP_COLOUR = Color.white; - RESIDUE_COLOUR = Color.lightGray; - HIDDEN_COLOUR = hiddenCol; - } - else - { - GAP_COLOUR = gapCol; - RESIDUE_COLOUR = Color.white; - HIDDEN_COLOUR = hiddenCol; - } + gapColour = gaps; + residueColour = residues; + hiddenColour = hidden; } @Override public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i) { - Color resBoxColour = RESIDUE_COLOUR; + Color resBoxColour = residueColour; char currentChar = seq.getCharAt(i); // In the overview window, gaps are coloured grey, unless the colour scheme @@ -92,7 +84,7 @@ public class OverviewResColourFinder extends ResidueColourFinder if (Comparison.isGap(currentChar) && (!shader.getColourScheme().hasGapColour())) { - resBoxColour = GAP_COLOUR; + resBoxColour = gapColour; } else { @@ -101,7 +93,7 @@ public class OverviewResColourFinder extends ResidueColourFinder } else if (Comparison.isGap(currentChar)) { - resBoxColour = GAP_COLOUR; + resBoxColour = gapColour; } return resBoxColour; @@ -132,12 +124,34 @@ public class OverviewResColourFinder extends ResidueColourFinder } /** - * Supply hidden colour + * Returns the colour used for hidden regions + * + * @return + */ + public Color getHiddenColour() + { + return hiddenColour; + } + + /** + * Returns the colour used for gaps, if not overridden by the alignment colour + * scheme + * + * @return + */ + public Color getGapColour() + { + return gapColour; + } + + /** + * Returns the colour used for residues (before applying any feature + * colouring) if there is no alignment colour scheme * - * @return colour of hidden regions + * @return */ - protected Color getHiddenColour() + public Color getResidueColour() { - return HIDDEN_COLOUR; + return residueColour; } } diff --git a/src/jalview/schemes/JalviewColourScheme.java b/src/jalview/schemes/JalviewColourScheme.java index 965a26b..accdc8a 100644 --- a/src/jalview/schemes/JalviewColourScheme.java +++ b/src/jalview/schemes/JalviewColourScheme.java @@ -44,10 +44,12 @@ public enum JalviewColourScheme Turn("Turn Propensity", TurnColourScheme.class), Buried("Buried Index", BuriedColourScheme.class), Nucleotide("Nucleotide", NucleotideColourScheme.class), + NucleotideAmbiguity("Nucleotide Ambiguity", + NucleotideAmbiguityColourScheme.class), PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class), RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee("T-Coffee Scores", TCoffeeColourScheme.class), - IdColour("Sequence ID", IdColourScheme.class); + IdColour("Sequence ID", IdColourScheme.class),; // RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class) private String name; diff --git a/src/jalview/schemes/NucleotideAmbiguityColourScheme.java b/src/jalview/schemes/NucleotideAmbiguityColourScheme.java new file mode 100644 index 0000000..dd42db3 --- /dev/null +++ b/src/jalview/schemes/NucleotideAmbiguityColourScheme.java @@ -0,0 +1,40 @@ +package jalview.schemes; + +import jalview.api.AlignViewportI; +import jalview.datamodel.AnnotatedCollectionI; + +public class NucleotideAmbiguityColourScheme extends ResidueColourScheme +{ + /** + * Creates a new NucleotideColourScheme object. + */ + public NucleotideAmbiguityColourScheme() + { + super(ResidueProperties.nucleotideIndex, + ResidueProperties.nucleotideAmbiguity); + } + + @Override + public boolean isNucleotideSpecific() + { + return true; + } + + @Override + public String getSchemeName() + { + return JalviewColourScheme.NucleotideAmbiguity.toString(); + } + + /** + * Returns a new instance of this colour scheme with which the given data may + * be coloured + */ + @Override + public ColourSchemeI getInstance(AlignViewportI view, + AnnotatedCollectionI coll) + { + return new NucleotideAmbiguityColourScheme(); + } + +} diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 7ad35c3..42d03ec 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -20,10 +20,6 @@ */ package jalview.schemes; -import java.util.Locale; - -import jalview.analysis.GeneticCodes; - import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; @@ -31,9 +27,12 @@ import java.util.Enumeration; import java.util.HashMap; import java.util.Hashtable; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Vector; +import jalview.analysis.GeneticCodes; + public class ResidueProperties { // Stores residue codes/names and colours and other things @@ -49,6 +48,8 @@ public class ResidueProperties public static final Map nucleotideName = new HashMap<>(); + public static final Map nucleotideAmbiguityName = new HashMap<>(); + // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) public static final Map modifications = new HashMap<>(); @@ -119,73 +120,48 @@ public class ResidueProperties /** * maximum (gap) index for matrices involving nucleotide alphabet */ - public final static int maxNucleotideIndex = 10; + // public final static int maxNucleotideIndex = 10; + public final static int maxNucleotideIndex; static { + String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" }, + { "g", "Guanine" }, + { "t", "Thymine" }, + { "u", "Uracil" }, + { "i", "Inosine" }, + { "x", "Xanthine" }, + { "r", "Unknown Purine" }, + { "y", "Unknown Pyrimidine" }, + { "w", "Weak nucleotide (A or T)" }, + { "s", "Strong nucleotide (G or C)" }, + { "m", "Amino (A or C)" }, + { "k", "Keto (G or T)" }, + { "b", "Not A (G or C or T)" }, + { "h", "Not G (A or C or T)" }, + { "d", "Not C (A or G or T)" }, + { "v", "Not T (A or G or C)" }, + { "n", "Unknown" } }; + // "gap" index + maxNucleotideIndex = namesArray.length; + nucleotideIndex = new int[255]; for (int i = 0; i < 255; i++) { - nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps. + nucleotideIndex[i] = maxNucleotideIndex; // non-nucleotide symbols are all + // non-gap gaps. } - nucleotideIndex['A'] = 0; - nucleotideIndex['a'] = 0; - nucleotideIndex['C'] = 1; - nucleotideIndex['c'] = 1; - nucleotideIndex['G'] = 2; - nucleotideIndex['g'] = 2; - nucleotideIndex['T'] = 3; - nucleotideIndex['t'] = 3; - nucleotideIndex['U'] = 4; - nucleotideIndex['u'] = 4; - nucleotideIndex['I'] = 5; - nucleotideIndex['i'] = 5; - nucleotideIndex['X'] = 6; - nucleotideIndex['x'] = 6; - nucleotideIndex['R'] = 7; - nucleotideIndex['r'] = 7; - nucleotideIndex['Y'] = 8; - nucleotideIndex['y'] = 8; - nucleotideIndex['N'] = 9; - nucleotideIndex['n'] = 9; - - nucleotideName.put("A", "Adenine"); - nucleotideName.put("a", "Adenine"); - nucleotideName.put("G", "Guanine"); - nucleotideName.put("g", "Guanine"); - nucleotideName.put("C", "Cytosine"); - nucleotideName.put("c", "Cytosine"); - nucleotideName.put("T", "Thymine"); - nucleotideName.put("t", "Thymine"); - nucleotideName.put("U", "Uracil"); - nucleotideName.put("u", "Uracil"); - nucleotideName.put("I", "Inosine"); - nucleotideName.put("i", "Inosine"); - nucleotideName.put("X", "Xanthine"); - nucleotideName.put("x", "Xanthine"); - nucleotideName.put("R", "Unknown Purine"); - nucleotideName.put("r", "Unknown Purine"); - nucleotideName.put("Y", "Unknown Pyrimidine"); - nucleotideName.put("y", "Unknown Pyrimidine"); - nucleotideName.put("N", "Unknown"); - nucleotideName.put("n", "Unknown"); - nucleotideName.put("W", "Weak nucleotide (A or T)"); - nucleotideName.put("w", "Weak nucleotide (A or T)"); - nucleotideName.put("S", "Strong nucleotide (G or C)"); - nucleotideName.put("s", "Strong nucleotide (G or C)"); - nucleotideName.put("M", "Amino (A or C)"); - nucleotideName.put("m", "Amino (A or C)"); - nucleotideName.put("K", "Keto (G or T)"); - nucleotideName.put("k", "Keto (G or T)"); - nucleotideName.put("B", "Not A (G or C or T)"); - nucleotideName.put("b", "Not A (G or C or T)"); - nucleotideName.put("H", "Not G (A or C or T)"); - nucleotideName.put("h", "Not G (A or C or T)"); - nucleotideName.put("D", "Not C (A or G or T)"); - nucleotideName.put("d", "Not C (A or G or T)"); - nucleotideName.put("V", "Not T (A or G or C"); - nucleotideName.put("v", "Not T (A or G or C"); + for (int i = 0; i < namesArray.length; i++) + { + char c = namesArray[i][0].charAt(0); + nucleotideIndex[c] = i; + // Character.toUpperCase is Locale insensitive + nucleotideIndex[Character.toUpperCase(c)] = i; + nucleotideName.put(namesArray[i][0], namesArray[i][1]); + nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT), + namesArray[i][1]); + } } @@ -363,6 +339,37 @@ public class ResidueProperties Color.white, // R Color.white, // Y Color.white, // N + Color.white, // w + Color.white, // s + Color.white, // m + Color.white, // k + Color.white, // b + Color.white, // h + Color.white, // d + Color.white, // v + Color.white, // Gap + }; + + // this colour scheme devised by sduce + public static final Color[] nucleotideAmbiguity = { + Color.decode("#f0fff0"), // a + Color.decode("#f0fff0"), // c + Color.decode("#f0fff0"), // g + Color.decode("#f0fff0"), // t + Color.decode("#f0fff0"), // u + Color.decode("#ffffff"), // i + Color.decode("#4f6f6f"), // x + Color.decode("#CD5C5C"), // r + Color.decode("#008000"), // y + Color.decode("#4682B4"), // w + Color.decode("#FF8C00"), // s + Color.decode("#9ACD32"), // m + Color.decode("#9932CC"), // k + Color.decode("#8b4513"), // b + Color.decode("#808080"), // h + Color.decode("#483D8B"), // d + Color.decode("#b8860b"), // v + Color.decode("#2f4f4f"), // n Color.white, // Gap }; diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java index cd98ee7..9fea705 100644 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -20,11 +20,13 @@ */ package jalview.util; -import jalview.datamodel.SequenceI; - import java.util.ArrayList; import java.util.List; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.datamodel.SequenceI; + /** * Assorted methods for analysing or comparing sequences. */ @@ -32,7 +34,15 @@ public class Comparison { private static final int EIGHTY_FIVE = 85; - private static final int TO_UPPER_CASE = 'a' - 'A'; + private static final int NUCLEOTIDE_COUNT_PERCENT; + + private static final int NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT; + + private static final int NUCLEOTIDE_COUNT_SHORT_SEQUENCE; + + private static final int NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE; + + private static final boolean NUCLEOTIDE_AMBIGUITY_DETECTION; public static final char GAP_SPACE = ' '; @@ -44,6 +54,21 @@ public class Comparison new char[] { GAP_SPACE, GAP_DOT, GAP_DASH }); + static + { + // these options read only at start of session + NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT", + 55); + NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault( + "NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT", 95); + NUCLEOTIDE_COUNT_SHORT_SEQUENCE = Cache + .getDefault("NUCLEOTIDE_COUNT_SHORT", 100); + NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache + .getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4); + NUCLEOTIDE_AMBIGUITY_DETECTION = Cache + .getDefault("NUCLEOTIDE_AMBIGUITY_DETECTION", true); + } + /** * DOCUMENT ME! * @@ -91,7 +116,6 @@ public class Comparison jlen--; } - int count = 0; int match = 0; float pid = -1; @@ -104,8 +128,6 @@ public class Comparison { match++; } - - count++; } pid = (float) match / (float) ilen * 100; @@ -119,8 +141,6 @@ public class Comparison { match++; } - - count++; } pid = (float) match / (float) jlen * 100; @@ -256,7 +276,7 @@ public class Comparison */ public static final boolean isGap(char c) { - return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false; + return c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE; } /** @@ -268,19 +288,22 @@ public class Comparison */ public static final boolean isNucleotide(SequenceI seq) { - if (seq == null) + if (seq == null || seq.getLength() == 0) { return false; } - long ntCount = 0; - long aaCount = 0; - long nCount = 0; + long ntCount = 0; // nucleotide symbol count (does not include ntaCount) + long aaCount = 0; // non-nucleotide, non-gap symbol count (includes nCount + // and ntaCount) + long nCount = 0; // "Unknown" (N) symbol count + long xCount = 0; // Also used as "Unknown" (X) symbol count + long ntaCount = 0; // nucleotide ambiguity symbol count int len = seq.getLength(); for (int i = 0; i < len; i++) { char c = seq.getCharAt(i); - if (isNucleotide(c) || isX(c)) + if (isNucleotide(c)) { ntCount++; } @@ -291,21 +314,112 @@ public class Comparison { nCount++; } + else + { + if (isX(c)) + { + xCount++; + } + if (isNucleotideAmbiguity(c)) + { + ntaCount++; + } + } } } - /* - * Check for nucleotide count > 85% of total count (in a form that evades - * int / float conversion or divide by zero). - */ - if ((ntCount + nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount)) + long allCount = ntCount + aaCount; + + if (NUCLEOTIDE_AMBIGUITY_DETECTION) { - return ntCount > 0; // all N is considered protein. Could use a threshold - // here too + Console.debug("Performing new nucleotide detection routine"); + if (allCount > NUCLEOTIDE_COUNT_SHORT_SEQUENCE) + { + // a long sequence. + // check for at least 55% nucleotide, and nucleotide and ambiguity codes + // (including N) must make up 95% + return ntCount * 100 > NUCLEOTIDE_COUNT_PERCENT * allCount + && 100 * (ntCount + nCount + + ntaCount) > NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT + * allCount; + } + else if (allCount > NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE) + { + // a short sequence. + // check if a short sequence is at least 55% nucleotide and the rest of + // the symbols are all X or all N + if (ntCount * 100 > NUCLEOTIDE_COUNT_PERCENT * allCount + && (nCount == aaCount || xCount == aaCount)) + { + return true; + } + + // a short sequence. + // check for at least x% nucleotide and all the rest nucleotide + // ambiguity codes (including N), where x slides from 75% for sequences + // of length 4 (i.e. only one non-nucleotide) to 55% for sequences of + // length 100 + return myShortSequenceNucleotideProportionCount(ntCount, allCount) + && nCount + ntaCount == aaCount; + } + else + { + // a very short sequence. (<4) + // all bases must be nucleotide + return ntCount > 0 && ntCount == allCount; + } } else { - return false; + Console.debug("Performing old nucleotide detection routine"); + /* + * Check for nucleotide count > 85% of total count (in a form that evades + * int / float conversion or divide by zero). + */ + if ((ntCount + nCount) * 100 > EIGHTY_FIVE * allCount) + { + return ntCount > 0; // all N is considered protein. Could use a + // threshold here too + } } + return false; + } + + protected static boolean myShortSequenceNucleotideProportionCount( + long ntCount, long allCount) + { + /** + * this method is valid only for NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE <= + * allCount <= NUCLEOTIDE_COUNT_SHORT_SEQUENCE + */ + // the following is a simplified integer version of: + // + // a := allCount # the number of bases in the sequence + // n : = ntCount # the number of definite nucleotide bases + // vs := NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE + // s := NUCLEOTIDE_COUNT_SHORT_SEQUENCE + // lp := NUCLEOTIDE_COUNT_LOWER_PERCENT + // vsp := 1 - (1/a) # this is the proportion of required definite + // nucleotides + // # in a VERY_SHORT Sequence (4 bases). + // # This should be equivalent to all but one base in the sequence. + // p := (a - vs)/(s - vs) # proportion of the way between + // # VERY_SHORT and SHORT thresholds. + // tp := vsp + p * (lp/100 - vsp) # the proportion of definite nucleotides + // # required for this length of sequence. + // minNt := tp * a # the minimum number of definite nucleotide bases + // # required for this length of sequence. + // + // We are then essentially returning: + // # ntCount >= 55% of allCount and the rest are all nucleotide ambiguity: + // ntCount >= tp * allCount && nCount + ntaCount == aaCount + // but without going into float/double land + long LHS = 100 * allCount + * (NUCLEOTIDE_COUNT_SHORT_SEQUENCE + - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE) + * (ntCount - allCount + 1); + long RHS = allCount * (allCount - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE) + * (allCount * NUCLEOTIDE_COUNT_PERCENT - 100 * allCount + 100); + return LHS >= RHS; } /** @@ -350,11 +464,16 @@ public class Comparison */ public static boolean isNucleotide(char c) { - if ('a' <= c && c <= 'z') - { - c -= TO_UPPER_CASE; - } - switch (c) + return isNucleotide(c, false); + } + + /** + * includeAmbiguity = true also includes Nucleotide Ambiguity codes + */ + public static boolean isNucleotide(char c, boolean includeAmbiguity) + { + char C = Character.toUpperCase(c); + switch (C) { case 'A': case 'C': @@ -363,29 +482,48 @@ public class Comparison case 'U': return true; } + if (includeAmbiguity) + { + boolean ambiguity = isNucleotideAmbiguity(C); + if (ambiguity) + return true; + } return false; } - public static boolean isN(char c) + /** + * Tests *only* nucleotide ambiguity codes (and not definite nucleotide codes) + */ + public static boolean isNucleotideAmbiguity(char c) { - switch (c) + switch (Character.toUpperCase(c)) { - case 'N': - case 'n': + case 'I': + case 'X': + case 'R': + case 'Y': + case 'W': + case 'S': + case 'M': + case 'K': + case 'B': + case 'H': + case 'D': + case 'V': return true; + case 'N': // not counting N as nucleotide } return false; } + public static boolean isN(char c) + { + return 'n' == Character.toLowerCase(c); + } + public static boolean isX(char c) { - switch (c) - { - case 'X': - case 'x': - return true; - } - return false; + return 'x' == Character.toLowerCase(c); } /** @@ -398,6 +536,12 @@ public class Comparison */ public static boolean isNucleotideSequence(String s, boolean allowGaps) { + return isNucleotideSequence(s, allowGaps, false); + } + + public static boolean isNucleotideSequence(String s, boolean allowGaps, + boolean includeAmbiguous) + { if (s == null) { return false; @@ -405,7 +549,7 @@ public class Comparison for (int i = 0; i < s.length(); i++) { char c = s.charAt(i); - if (!isNucleotide(c)) + if (!isNucleotide(c, includeAmbiguous)) { if (!allowGaps || !isGap(c)) { @@ -456,13 +600,7 @@ public class Comparison public static boolean isSameResidue(char c1, char c2, boolean caseSensitive) { - if (caseSensitive) - { - return (c1 == c2); - } - else - { - return Character.toUpperCase(c1) == Character.toUpperCase(c2); - } + return caseSensitive ? c1 == c2 + : Character.toUpperCase(c1) == Character.toUpperCase(c2); } } diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index e17a336..98d5e11 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -30,6 +30,7 @@ import java.util.Map; import com.stevesoft.pat.Regex; +import jalview.bin.Console; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; @@ -810,9 +811,12 @@ public class DBRefUtils // toPromote.add(cand); if (!cand.isPrimaryCandidate()) { - System.out.println( - "Warning: Couldn't promote dbref " + cand.toString() - + " for sequence " + sequence.toString()); + if (Console.isDebugEnabled()) + { + Console.debug( + "Warning: Couldn't promote dbref " + cand.toString() + + " for sequence " + sequence.toString()); + } } } } diff --git a/src/jalview/util/SparseCount.java~ b/src/jalview/util/SparseCount.java~ deleted file mode 100644 index e6b45f2..0000000 --- a/src/jalview/util/SparseCount.java~ +++ /dev/null @@ -1,154 +0,0 @@ -package jalview.util; - -import jalview.ext.android.SparseIntArray; -import jalview.ext.android.SparseShortArray; - -/** - * A class to count occurrences of characters with minimal memory footprint. - * Sparse arrays of short values are used to hold the counts, with automatic - * promotion to arrays of int if any count exceeds the maximum value for a - * short. - * - * @author gmcarstairs - * - */ -public class SparseCount -{ - private static final int DEFAULT_PROFILE_SIZE = 2; - - /* - * array of keys (chars) and values (counts) - * held either as shorts or (if shorts overflow) as ints - */ - private SparseShortArray shortProfile; - - private SparseIntArray intProfile; - - /* - * flag is set true after short overflow occurs - */ - private boolean useInts; - - /** - * Constructor which initially creates a new sparse array of short values to - * hold counts. - * - * @param profileSize - */ - public SparseCount(int profileSize) - { - this.shortProfile = new SparseShortArray(profileSize); - } - - /** - * Constructor which allocates an initial count array for only two distinct - * values (the array will grow if needed) - */ - public SparseCount() - { - this(DEFAULT_PROFILE_SIZE); - } - - /** - * Adds the given value for the given key (or sets the initial value), and - * returns the new value - * - * @param key - * @param value - */ - public int add(int key, int value) - { - int newValue = 0; - if (useInts) - { - newValue = intProfile.add(key, value); - } - else - { - try { - newValue = shortProfile.add(key, value); - } catch (ArithmeticException e) { - handleOverflow(); - newValue = intProfile.add(key, value); - } - } - return newValue; - } - - /** - * Switch from counting shorts to counting ints - */ - synchronized void handleOverflow() - { - int size = shortProfile.size(); - intProfile = new SparseIntArray(size); - for (int i = 0; i < size; i++) - { - short key = shortProfile.keyAt(i); - short value = shortProfile.valueAt(i); - intProfile.put(key, value); - } - shortProfile = null; - useInts = true; - } - - /** - * Returns the size of the profile (number of distinct items counted) - * - * @return - */ - public int size() - { - return useInts ? intProfile.size() : shortProfile.size(); - } - - /** - * Returns the value for the key (zero if no such key) - * - * @param key - * @return - */ - public int get(int key) - { - return useInts ? intProfile.get(key) : shortProfile.get(key); - } - - /** - * Sets the value for the given key - * - * @param key - * @param value - */ - public void put(int key, int value) - { - if (useInts) - { - intProfile.put(key, value); - } - else - { - shortProfile.put(key, value); - } - } - - public int keyAt(int k) - { - return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k); - } - - public int valueAt(int k) - { - return useInts ? intProfile.valueAt(k) : shortProfile.valueAt(k); - } - - /** - * Answers true if this object wraps arrays of int values, false if using - * short values - * - * @return - */ - boolean isUsingInt() - { - return useInts; - } -} diff --git a/src/jalview/util/dialogrunner/DialogRunnerI.java b/src/jalview/util/dialogrunner/DialogRunnerI.java index fde80f7..1fc41e7 100644 --- a/src/jalview/util/dialogrunner/DialogRunnerI.java +++ b/src/jalview/util/dialogrunner/DialogRunnerI.java @@ -20,6 +20,8 @@ */ package jalview.util.dialogrunner; +import java.util.concurrent.Callable; + /** * An interface for blocking dialog response handling. This is motivated by * JalviewJS - when running as Javascript, there is only a single thread, and @@ -41,7 +43,9 @@ public interface DialogRunnerI * @param action * @return */ - DialogRunnerI setResponseHandler(Object response, Runnable action); + DialogRunnerI setResponseHandler(Object response, Callable action); + + // DialogRunnerI setResponseHandler(Object response, Runnable action); /** * Runs the registered handler (if any) for the given response. The default diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 7849c2d..a648b34 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -20,6 +20,18 @@ */ package jalview.viewmodel; +import java.awt.Color; +import java.beans.PropertyChangeSupport; +import java.util.ArrayDeque; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Deque; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.analysis.TreeModel; @@ -29,6 +41,7 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; @@ -46,6 +59,7 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.project.Jalview2XML; import jalview.renderer.ResidueShader; import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; @@ -62,18 +76,6 @@ import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; -import java.awt.Color; -import java.beans.PropertyChangeSupport; -import java.util.ArrayDeque; -import java.util.ArrayList; -import java.util.BitSet; -import java.util.Deque; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.List; -import java.util.Map; - /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -101,6 +103,11 @@ public abstract class AlignmentViewport protected Deque redoList = new ArrayDeque<>(); /** + * used to determine if quit should be confirmed + */ + private boolean savedUpToDate = false; + + /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; @@ -2615,6 +2622,8 @@ public abstract class AlignmentViewport { this.historyList.push(command); broadcastCommand(command, false); + setSavedUpToDate(false); + Jalview2XML.setStateSavedUpToDate(false); } } @@ -3103,4 +3112,18 @@ public abstract class AlignmentViewport return (alignment.getHiddenColumns().getVisContigsIterator(start, end, false)); } + + public void setSavedUpToDate(boolean s) + { + Console.debug( + "Setting " + this.getViewId() + " setSavedUpToDate to " + s); + savedUpToDate = s; + } + + public boolean savedUpToDate() + { + Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " + + savedUpToDate); + return savedUpToDate; + } } diff --git a/src/jalview/ws/dbsources/Pdb.java~ b/src/jalview/ws/dbsources/Pdb.java~ deleted file mode 100644 index 6c2f70a..0000000 --- a/src/jalview/ws/dbsources/Pdb.java~ +++ /dev/null @@ -1,294 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.ws.dbsources; - -import jalview.api.FeatureSettingsModelI; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.io.FormatAdapter; -import jalview.io.PDBFeatureSettings; -import jalview.util.MessageManager; -import jalview.ws.ebi.EBIFetchClient; - -import java.util.ArrayList; -import java.util.List; -import java.util.Vector; - -import com.stevesoft.pat.Regex; - -/** - * @author JimP - * - */ -public class Pdb extends EbiFileRetrievedProxy -{ - public Pdb() - { - super(); - } - - public static final String FEATURE_INSERTION = "INSERTION"; - - public static final String FEATURE_RES_NUM = "RESNUM"; - - private static String currentDefaultFormat = DBRefSource.PDB; - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#getAccessionSeparator() - */ - @Override - public String getAccessionSeparator() - { - // TODO Auto-generated method stub - return null; - } - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#getAccessionValidator() - */ - @Override - public Regex getAccessionValidator() - { - return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)"); - } - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#getDbSource() - */ - @Override - public String getDbSource() - { - return DBRefSource.PDB; - } - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#getDbVersion() - */ - @Override - public String getDbVersion() - { - return "0"; - } - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[]) - */ - @Override - public AlignmentI getSequenceRecords(String queries) throws Exception - { - AlignmentI pdbAlignment = null; - Vector result = new Vector(); - String chain = null; - String id = null; - if (queries.indexOf(":") > -1) - { - chain = queries.substring(queries.indexOf(":") + 1); - id = queries.substring(0, queries.indexOf(":")); - } - else - { - id = queries; - } - if (queries.length() > 4 && chain == null) - { - chain = queries.substring(4, 5); - id = queries.substring(0, 4); - } - if (!isValidReference(id)) - { - System.err.println("Ignoring invalid pdb query: '" + id + "'"); - stopQuery(); - return null; - } - String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif" - : ".xml"; - EBIFetchClient ebi = new EBIFetchClient(); - file = ebi.fetchDataAsFile("pdb:" + id, -<<<<<<< HEAD - getCurrentDefaultFomart().toLowerCase(), ext) -======= - getCurrentDefaultFormat().toLowerCase(), "raw", ext) ->>>>>>> develop - .getAbsolutePath(); - stopQuery(); - if (file == null) - { - return null; - } - try - { - - pdbAlignment = new FormatAdapter().readFile(file, - jalview.io.AppletFormatAdapter.FILE, - getCurrentDefaultFormat()); - if (pdbAlignment != null) - { - List toremove = new ArrayList(); - for (SequenceI pdbcs : pdbAlignment.getSequences()) - { - String chid = null; - // Mapping map=null; - for (PDBEntry pid : pdbcs.getAllPDBEntries()) - { - if (pid.getFile() == file) - { - chid = pid.getChainCode(); - - } - ; - - } - if (chain == null - || (chid != null && (chid.equals(chain) - || chid.trim().equals(chain.trim()) || (chain - .trim().length() == 0 && chid.equals("_"))))) - { - pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id - + "|" + pdbcs.getName()); - // Might need to add more metadata to the PDBEntry object - // like below - /* - * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry - * entry.setId(id); if (entry.getProperty() == null) - * entry.setProperty(new Hashtable()); - * entry.getProperty().put("chains", pdbchain.id + "=" + - * sq.getStart() + "-" + sq.getEnd()); - * sq.getDatasetSequence().addPDBId(entry); - */ - // Add PDB DB Refs - // We make a DBRefEtntry because we have obtained the PDB file from - // a - // verifiable source - // JBPNote - PDB DBRefEntry should also carry the chain and mapping - // information - DBRefEntry dbentry = new DBRefEntry(getDbSource(), - getDbVersion(), (chid == null ? id : id + chid)); - // dbentry.setMap() - pdbcs.addDBRef(dbentry); - } - else - { - // mark this sequence to be removed from the alignment - // - since it's not from the right chain - toremove.add(pdbcs); - } - } - // now remove marked sequences - for (SequenceI pdbcs : toremove) - { - pdbAlignment.deleteSequence(pdbcs); - if (pdbcs.getAnnotation() != null) - { - for (AlignmentAnnotation aa : pdbcs.getAnnotation()) - { - pdbAlignment.deleteAnnotation(aa); - } - } - } - } - - if (pdbAlignment == null || pdbAlignment.getHeight() < 1) - { - throw new Exception(MessageManager.formatMessage( - "exception.no_pdb_records_for_chain", new String[] { id, - ((chain == null) ? "' '" : chain) })); - } - - } catch (Exception ex) // Problem parsing PDB file - { - stopQuery(); - throw (ex); - } - return pdbAlignment; - } - - /* - * (non-Javadoc) - * - * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) - */ - @Override - public boolean isValidReference(String accession) - { - Regex r = getAccessionValidator(); - return r.search(accession.trim()); - } - - /** - * obtain human glyoxalase chain A sequence - */ - @Override - public String getTestQuery() - { - return "1QIPA"; - } - - @Override - public String getDbName() - { - return "PDB"; // getDbSource(); - } - - @Override - public int getTier() - { - return 0; - } - - public static String getCurrentDefaultFormat() - { - return currentDefaultFormat; - } - - public static void setCurrentDefaultFormat(String currentDefaultFomart) - { - Pdb.currentDefaultFormat = currentDefaultFomart; - } - - /** - * Returns a descriptor for suitable feature display settings with - *
      - *
    • ResNums or insertions features visible
      • - *
    • insertions features coloured red
      • - *
    • ResNum features coloured by label
      • - *
    • Insertions displayed above (on top of) ResNums
      • - *
    - */ - @Override - public FeatureSettingsModelI getFeatureColourScheme() - { - return new PDBFeatureSettings(); - } -} diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index 6e73e7b..7c061d7 100644 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.java @@ -2,9 +2,10 @@ // 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: 2018.09.14 at 02:46:00 PM BST +// Generated on: 2023.01.31 at 04:07:09 PM GMT // + package jalview.xml.binding.embl; import java.util.ArrayList; @@ -14,13 +15,11 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - *

    - * Java class for EntrySetType complex type. + *

    Java class for EntrySetType complex type. * - *

    - * The following schema fragment specifies the expected content contained within - * this class. + *

    The following schema fragment specifies the expected content contained within this class. * * 

      * <complexType name="EntrySetType">
@@ -37,42 +36,41 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = { "entry" })
-public class EntrySetType
-{
+@XmlType(name = "EntrySetType", propOrder = {
+    "entry"
+})
+public class EntrySetType {
 
-  @XmlElement(required = true)
-  protected List entry;
+    @XmlElement(required = true)
+    protected List entry;
 
-  /**
-   * Gets the value of the entry 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 entry property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEntry().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link EntryType }
-   * 
-   * 
-   */
-  public List getEntry()
-  {
-    if (entry == null)
-    {
-      entry = new ArrayList();
+    /**
+     * Gets the value of the entry 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 entry property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEntry().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType }
+     * 
+     * 
+     */
+    public List getEntry() {
+        if (entry == null) {
+            entry = new ArrayList();
+        }
+        return this.entry;
     }
-    return this.entry;
-  }
 
 }
diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java
index 6bdc35f..2791f66 100644
--- a/src/jalview/xml/binding/embl/EntryType.java
+++ b/src/jalview/xml/binding/embl/EntryType.java
@@ -2,9 +2,10 @@
 // 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: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import java.math.BigInteger;
@@ -19,13 +20,11 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * 
    
- * Java class for EntryType complex type.
+ * 
    Java class for EntryType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="EntryType">
@@ -226,1666 +225,669 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "EntryType",
-  propOrder =
-  { "secondaryAccession", "projectAccession", "description", "comment",
-      "keyword", "reference", "xref", "feature", "assembly", "contig",
-      "sequence" })
-public class EntryType
-{
-
-  protected List secondaryAccession;
-
-  protected List projectAccession;
-
-  @XmlElement(required = true)
-  protected String description;
-
-  protected String comment;
-
-  protected List keyword;
-
-  protected List reference;
-
-  protected List xref;
-
-  protected List feature;
-
-  protected EntryType.Assembly assembly;
-
-  protected EntryType.Contig contig;
-
-  protected String sequence;
-
-  @XmlAttribute(name = "accession", required = true)
-  protected String accession;
-
-  @XmlAttribute(name = "version", required = true)
-  protected BigInteger version;
-
-  @XmlAttribute(name = "entryVersion")
-  protected BigInteger entryVersion;
-
-  @XmlAttribute(name = "dataClass", required = true)
-  protected String dataClass;
-
-  @XmlAttribute(name = "taxonomicDivision", required = true)
-  protected String taxonomicDivision;
-
-  @XmlAttribute(name = "moleculeType", required = true)
-  protected String moleculeType;
-
-  @XmlAttribute(name = "sequenceLength", required = true)
-  protected BigInteger sequenceLength;
-
-  @XmlAttribute(name = "topology", required = true)
-  protected String topology;
-
-  @XmlAttribute(name = "firstPublic")
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar firstPublic;
-
-  @XmlAttribute(name = "firstPublicRelease")
-  protected BigInteger firstPublicRelease;
-
-  @XmlAttribute(name = "lastUpdated")
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar lastUpdated;
-
-  @XmlAttribute(name = "lastUpdatedRelease")
-  protected BigInteger lastUpdatedRelease;
-
-  /**
-   * Gets the value of the secondaryAccession 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 secondaryAccession property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getSecondaryAccession().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getSecondaryAccession()
-  {
-    if (secondaryAccession == null)
-    {
-      secondaryAccession = new ArrayList();
-    }
-    return this.secondaryAccession;
-  }
-
-  /**
-   * Gets the value of the projectAccession 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 projectAccession property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getProjectAccession().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getProjectAccession()
-  {
-    if (projectAccession == null)
-    {
-      projectAccession = new ArrayList();
-    }
-    return this.projectAccession;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the comment property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getComment()
-  {
-    return comment;
-  }
-
-  /**
-   * Sets the value of the comment property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setComment(String value)
-  {
-    this.comment = value;
-  }
-
-  /**
-   * Gets the value of the keyword 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 keyword property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getKeyword().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getKeyword()
-  {
-    if (keyword == null)
-    {
-      keyword = new ArrayList();
-    }
-    return this.keyword;
-  }
-
-  /**
-   * Gets the value of the reference 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 reference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EntryType.Reference }
-   * 
-   * 
-   */
-  public List getReference()
-  {
-    if (reference == null)
-    {
-      reference = new ArrayList();
-    }
-    return this.reference;
-  }
-
-  /**
-   * Gets the value of the xref 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 xref property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getXref().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link XrefType }
-   * 
-   * 
-   */
-  public List getXref()
-  {
-    if (xref == null)
-    {
-      xref = new ArrayList();
-    }
-    return this.xref;
-  }
-
-  /**
-   * Gets the value of the feature 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 feature property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getFeature().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EntryType.Feature }
-   * 
-   * 
-   */
-  public List getFeature()
-  {
-    if (feature == null)
-    {
-      feature = new ArrayList();
-    }
-    return this.feature;
-  }
-
-  /**
-   * Gets the value of the assembly property.
-   * 
-   * @return possible object is {@link EntryType.Assembly }
-   * 
-   */
-  public EntryType.Assembly getAssembly()
-  {
-    return assembly;
-  }
-
-  /**
-   * Sets the value of the assembly property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType.Assembly }
-   * 
-   */
-  public void setAssembly(EntryType.Assembly value)
-  {
-    this.assembly = value;
-  }
-
-  /**
-   * Gets the value of the contig property.
-   * 
-   * @return possible object is {@link EntryType.Contig }
-   * 
-   */
-  public EntryType.Contig getContig()
-  {
-    return contig;
-  }
-
-  /**
-   * Sets the value of the contig property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType.Contig }
-   * 
-   */
-  public void setContig(EntryType.Contig value)
-  {
-    this.contig = value;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the accession property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getAccession()
-  {
-    return accession;
-  }
-
-  /**
-   * Sets the value of the accession property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setAccession(String value)
-  {
-    this.accession = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setVersion(BigInteger value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the entryVersion property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getEntryVersion()
-  {
-    return entryVersion;
-  }
-
-  /**
-   * Sets the value of the entryVersion property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setEntryVersion(BigInteger value)
-  {
-    this.entryVersion = value;
-  }
-
-  /**
-   * Gets the value of the dataClass property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDataClass()
-  {
-    return dataClass;
-  }
-
-  /**
-   * Sets the value of the dataClass property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDataClass(String value)
-  {
-    this.dataClass = value;
-  }
-
-  /**
-   * Gets the value of the taxonomicDivision property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTaxonomicDivision()
-  {
-    return taxonomicDivision;
-  }
-
-  /**
-   * Sets the value of the taxonomicDivision property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTaxonomicDivision(String value)
-  {
-    this.taxonomicDivision = value;
-  }
-
-  /**
-   * Gets the value of the moleculeType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMoleculeType()
-  {
-    return moleculeType;
-  }
-
-  /**
-   * Sets the value of the moleculeType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMoleculeType(String value)
-  {
-    this.moleculeType = value;
-  }
-
-  /**
-   * Gets the value of the sequenceLength property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getSequenceLength()
-  {
-    return sequenceLength;
-  }
-
-  /**
-   * Sets the value of the sequenceLength property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setSequenceLength(BigInteger value)
-  {
-    this.sequenceLength = value;
-  }
-
-  /**
-   * Gets the value of the topology property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTopology()
-  {
-    return topology;
-  }
-
-  /**
-   * Sets the value of the topology property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTopology(String value)
-  {
-    this.topology = value;
-  }
-
-  /**
-   * Gets the value of the firstPublic property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getFirstPublic()
-  {
-    return firstPublic;
-  }
-
-  /**
-   * Sets the value of the firstPublic property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setFirstPublic(XMLGregorianCalendar value)
-  {
-    this.firstPublic = value;
-  }
-
-  /**
-   * Gets the value of the firstPublicRelease property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getFirstPublicRelease()
-  {
-    return firstPublicRelease;
-  }
-
-  /**
-   * Sets the value of the firstPublicRelease property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setFirstPublicRelease(BigInteger value)
-  {
-    this.firstPublicRelease = value;
-  }
-
-  /**
-   * Gets the value of the lastUpdated property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getLastUpdated()
-  {
-    return lastUpdated;
-  }
-
-  /**
-   * Sets the value of the lastUpdated property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setLastUpdated(XMLGregorianCalendar value)
-  {
-    this.lastUpdated = value;
-  }
-
-  /**
-   * Gets the value of the lastUpdatedRelease property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getLastUpdatedRelease()
-  {
-    return lastUpdatedRelease;
-  }
-
-  /**
-   * Sets the value of the lastUpdatedRelease property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setLastUpdatedRelease(BigInteger value)
-  {
-    this.lastUpdatedRelease = value;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="range" maxOccurs="unbounded">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "range" })
-  public static class Assembly
-  {
-
+@XmlType(name = "EntryType", propOrder = {
+    "secondaryAccession",
+    "projectAccession",
+    "description",
+    "comment",
+    "keyword",
+    "reference",
+    "xref",
+    "feature",
+    "assembly",
+    "contig",
+    "sequence"
+})
+public class EntryType {
+
+    protected List secondaryAccession;
+    protected List projectAccession;
     @XmlElement(required = true)
-    protected List range;
+    protected String description;
+    protected String comment;
+    protected List keyword;
+    protected List reference;
+    protected List xref;
+    protected List feature;
+    protected EntryType.Assembly assembly;
+    protected EntryType.Contig contig;
+    protected String sequence;
+    @XmlAttribute(name = "accession", required = true)
+    protected String accession;
+    @XmlAttribute(name = "version", required = true)
+    protected BigInteger version;
+    @XmlAttribute(name = "entryVersion")
+    protected BigInteger entryVersion;
+    @XmlAttribute(name = "dataClass", required = true)
+    protected String dataClass;
+    @XmlAttribute(name = "taxonomicDivision", required = true)
+    protected String taxonomicDivision;
+    @XmlAttribute(name = "moleculeType", required = true)
+    protected String moleculeType;
+    @XmlAttribute(name = "sequenceLength", required = true)
+    protected BigInteger sequenceLength;
+    @XmlAttribute(name = "topology", required = true)
+    protected String topology;
+    @XmlAttribute(name = "firstPublic")
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar firstPublic;
+    @XmlAttribute(name = "firstPublicRelease")
+    protected BigInteger firstPublicRelease;
+    @XmlAttribute(name = "lastUpdated")
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar lastUpdated;
+    @XmlAttribute(name = "lastUpdatedRelease")
+    protected BigInteger lastUpdatedRelease;
 
     /**
-     * Gets the value of the range property.
+     * Gets the value of the secondaryAccession 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 range 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 secondaryAccession property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getRange().add(newItem);
+     *    getSecondaryAccession().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Assembly.Range }
+     * {@link String }
      * 
      * 
      */
-    public List getRange()
-    {
-      if (range == null)
-      {
-        range = new ArrayList();
-      }
-      return this.range;
+    public List getSecondaryAccession() {
+        if (secondaryAccession == null) {
+            secondaryAccession = new ArrayList();
+        }
+        return this.secondaryAccession;
     }
 
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * Gets the value of the projectAccession property.
      * 
      * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 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 projectAccession property.
      * 
+     * 
    
+     * For example, to add a new item, do as follows:
      * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     *    getProjectAccession().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Range
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "primaryBegin")
-      protected BigInteger primaryBegin;
-
-      @XmlAttribute(name = "primaryEnd")
-      protected BigInteger primaryEnd;
-
-      @XmlAttribute(name = "accession", required = true)
-      protected String accession;
-
-      @XmlAttribute(name = "version", required = true)
-      protected BigInteger version;
-
-      @XmlAttribute(name = "complement")
-      protected Boolean complement;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the primaryBegin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryBegin()
-      {
-        return primaryBegin;
-      }
-
-      /**
-       * Sets the value of the primaryBegin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryBegin(BigInteger value)
-      {
-        this.primaryBegin = value;
-      }
-
-      /**
-       * Gets the value of the primaryEnd property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryEnd()
-      {
-        return primaryEnd;
-      }
-
-      /**
-       * Sets the value of the primaryEnd property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryEnd(BigInteger value)
-      {
-        this.primaryEnd = value;
-      }
-
-      /**
-       * Gets the value of the accession property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getAccession()
-      {
-        return accession;
-      }
-
-      /**
-       * Sets the value of the accession property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setAccession(String value)
-      {
-        this.accession = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setVersion(BigInteger value)
-      {
-        this.version = value;
-      }
-
-      /**
-       * Gets the value of the complement property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isComplement()
-      {
-        if (complement == null)
-        {
-          return false;
-        }
-        else
-        {
-          return complement;
+    public List getProjectAccession() {
+        if (projectAccession == null) {
+            projectAccession = new ArrayList();
         }
-      }
-
-      /**
-       * Sets the value of the complement property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setComplement(Boolean value)
-      {
-        this.complement = value;
-      }
+        return this.projectAccession;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
 
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the comment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getComment() {
+        return comment;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <choice maxOccurs="unbounded" minOccurs="0">
-   *           <element name="range">
-   *             <complexType>
-   *               <complexContent>
-   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 </restriction>
-   *               </complexContent>
-   *             </complexType>
-   *           </element>
-   *           <element name="gap">
-   *             <complexType>
-   *               <complexContent>
-   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 </restriction>
-   *               </complexContent>
-   *             </complexType>
-   *           </element>
-   *         </choice>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "rangeOrGap" })
-  public static class Contig
-  {
-
-    @XmlElements({
-        @XmlElement(name = "range", type = EntryType.Contig.Range.class),
-        @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
-    protected List rangeOrGap;
+    /**
+     * Sets the value of the comment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setComment(String value) {
+        this.comment = value;
+    }
 
     /**
-     * Gets the value of the rangeOrGap property.
+     * Gets the value of the keyword 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 rangeOrGap 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 keyword property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getRangeOrGap().add(newItem);
+     *    getKeyword().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
+     * {@link String }
      * 
      * 
      */
-    public List getRangeOrGap()
-    {
-      if (rangeOrGap == null)
-      {
-        rangeOrGap = new ArrayList();
-      }
-      return this.rangeOrGap;
+    public List getKeyword() {
+        if (keyword == null) {
+            keyword = new ArrayList();
+        }
+        return this.keyword;
     }
 
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * Gets the value of the reference property.
      * 
      * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 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 reference property.
      * 
+     * 
    
+     * For example, to add a new item, do as follows:
      * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     *    getReference().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType.Reference }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Gap
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "length", required = true)
-      protected BigInteger length;
-
-      @XmlAttribute(name = "unknownLength")
-      protected Boolean unknownLength;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the length property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getLength()
-      {
-        return length;
-      }
-
-      /**
-       * Sets the value of the length property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setLength(BigInteger value)
-      {
-        this.length = value;
-      }
-
-      /**
-       * Gets the value of the unknownLength property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isUnknownLength()
-      {
-        if (unknownLength == null)
-        {
-          return false;
+    public List getReference() {
+        if (reference == null) {
+            reference = new ArrayList();
         }
-        else
-        {
-          return unknownLength;
-        }
-      }
-
-      /**
-       * Sets the value of the unknownLength property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setUnknownLength(Boolean value)
-      {
-        this.unknownLength = value;
-      }
-
+        return this.reference;
     }
 
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * Gets the value of the xref property.
      * 
      * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 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 xref property.
      * 
+     * 
    
+     * For example, to add a new item, do as follows:
      * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     *    getXref().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link XrefType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Range
-    {
-
-      @XmlAttribute(name = "begin", required = true)
-      protected BigInteger begin;
-
-      @XmlAttribute(name = "end", required = true)
-      protected BigInteger end;
-
-      @XmlAttribute(name = "primaryBegin")
-      protected BigInteger primaryBegin;
-
-      @XmlAttribute(name = "primaryEnd")
-      protected BigInteger primaryEnd;
-
-      @XmlAttribute(name = "accession", required = true)
-      protected String accession;
-
-      @XmlAttribute(name = "version", required = true)
-      protected BigInteger version;
-
-      @XmlAttribute(name = "complement")
-      protected Boolean complement;
-
-      /**
-       * Gets the value of the begin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getBegin()
-      {
-        return begin;
-      }
-
-      /**
-       * Sets the value of the begin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setBegin(BigInteger value)
-      {
-        this.begin = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setEnd(BigInteger value)
-      {
-        this.end = value;
-      }
-
-      /**
-       * Gets the value of the primaryBegin property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryBegin()
-      {
-        return primaryBegin;
-      }
-
-      /**
-       * Sets the value of the primaryBegin property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryBegin(BigInteger value)
-      {
-        this.primaryBegin = value;
-      }
-
-      /**
-       * Gets the value of the primaryEnd property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getPrimaryEnd()
-      {
-        return primaryEnd;
-      }
-
-      /**
-       * Sets the value of the primaryEnd property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setPrimaryEnd(BigInteger value)
-      {
-        this.primaryEnd = value;
-      }
-
-      /**
-       * Gets the value of the accession property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getAccession()
-      {
-        return accession;
-      }
-
-      /**
-       * Sets the value of the accession property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setAccession(String value)
-      {
-        this.accession = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setVersion(BigInteger value)
-      {
-        this.version = value;
-      }
-
-      /**
-       * Gets the value of the complement property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isComplement()
-      {
-        if (complement == null)
-        {
-          return false;
-        }
-        else
-        {
-          return complement;
+    public List getXref() {
+        if (xref == null) {
+            xref = new ArrayList();
         }
-      }
-
-      /**
-       * Sets the value of the complement property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setComplement(Boolean value)
-      {
-        this.complement = value;
-      }
-
+        return this.xref;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="taxon" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="lineage" minOccurs="0">
-   *                     <complexType>
-   *                       <complexContent>
-   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           <sequence>
-   *                             <element name="taxon" maxOccurs="unbounded">
-   *                               <complexType>
-   *                                 <complexContent>
-   *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                                   </restriction>
-   *                                 </complexContent>
-   *                               </complexType>
-   *                             </element>
-   *                           </sequence>
-   *                         </restriction>
-   *                       </complexContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *                 </sequence>
-   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
-  public static class Feature
-  {
-
-    protected EntryType.Feature.FeatureTaxon taxon;
-
-    protected List xref;
+    /**
+     * Gets the value of the feature 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 feature property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getFeature().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType.Feature }
+     * 
+     * 
+     */
+    public List getFeature() {
+        if (feature == null) {
+            feature = new ArrayList();
+        }
+        return this.feature;
+    }
 
-    protected List qualifier;
+    /**
+     * Gets the value of the assembly property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType.Assembly }
+     *     
+     */
+    public EntryType.Assembly getAssembly() {
+        return assembly;
+    }
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+    /**
+     * Sets the value of the assembly property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntryType.Assembly }
+     *     
+     */
+    public void setAssembly(EntryType.Assembly value) {
+        this.assembly = value;
+    }
 
-    @XmlAttribute(name = "location", required = true)
-    protected String location;
+    /**
+     * Gets the value of the contig property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType.Contig }
+     *     
+     */
+    public EntryType.Contig getContig() {
+        return contig;
+    }
 
     /**
-     * Gets the value of the taxon property.
+     * Sets the value of the contig property.
      * 
-     * @return possible object is {@link EntryType.Feature.FeatureTaxon }
+     * @param value
+     *     allowed object is
+     *     {@link EntryType.Contig }
+     *     
+     */
+    public void setContig(EntryType.Contig value) {
+        this.contig = value;
+    }
+
+    /**
+     * Gets the value of the sequence property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public EntryType.Feature.FeatureTaxon getTaxon()
-    {
-      return taxon;
+    public String getSequence() {
+        return sequence;
     }
 
     /**
-     * Sets the value of the taxon property.
+     * Sets the value of the sequence property.
      * 
      * @param value
-     *          allowed object is {@link EntryType.Feature.FeatureTaxon }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
+
+    /**
+     * Gets the value of the accession property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setTaxon(EntryType.Feature.FeatureTaxon value)
-    {
-      this.taxon = value;
+    public String getAccession() {
+        return accession;
     }
 
     /**
-     * Gets the value of the xref property.
+     * Sets the value of the accession 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 xref property.
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setAccession(String value) {
+        this.accession = value;
+    }
+
+    /**
+     * Gets the value of the version property.
      * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
      * 
-     * 
    -     * getXref().add(newItem);
-     * 
    
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setVersion(BigInteger value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the entryVersion property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getEntryVersion() {
+        return entryVersion;
+    }
+
+    /**
+     * Sets the value of the entryVersion property.
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link XrefType
-     * }
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setEntryVersion(BigInteger value) {
+        this.entryVersion = value;
+    }
+
+    /**
+     * Gets the value of the dataClass property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDataClass() {
+        return dataClass;
+    }
+
+    /**
+     * Sets the value of the dataClass property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public List getXref()
-    {
-      if (xref == null)
-      {
-        xref = new ArrayList();
-      }
-      return this.xref;
+    public void setDataClass(String value) {
+        this.dataClass = value;
     }
 
     /**
-     * Gets the value of the qualifier property.
+     * Gets the value of the taxonomicDivision 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 qualifier property.
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTaxonomicDivision() {
+        return taxonomicDivision;
+    }
+
+    /**
+     * Sets the value of the taxonomicDivision property.
      * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTaxonomicDivision(String value) {
+        this.taxonomicDivision = value;
+    }
+
+    /**
+     * Gets the value of the moleculeType property.
      * 
-     * 
    -     * getQualifier().add(newItem);
-     * 
    
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMoleculeType() {
+        return moleculeType;
+    }
+
+    /**
+     * Sets the value of the moleculeType property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMoleculeType(String value) {
+        this.moleculeType = value;
+    }
+
+    /**
+     * Gets the value of the sequenceLength property.
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Feature.Qualifier }
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getSequenceLength() {
+        return sequenceLength;
+    }
+
+    /**
+     * Sets the value of the sequenceLength property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setSequenceLength(BigInteger value) {
+        this.sequenceLength = value;
+    }
+
+    /**
+     * Gets the value of the topology property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public List getQualifier()
-    {
-      if (qualifier == null)
-      {
-        qualifier = new ArrayList();
-      }
-      return this.qualifier;
+    public String getTopology() {
+        return topology;
     }
 
     /**
-     * Gets the value of the name property.
+     * Sets the value of the topology property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTopology(String value) {
+        this.topology = value;
+    }
+
+    /**
+     * Gets the value of the firstPublic property.
      * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public XMLGregorianCalendar getFirstPublic() {
+        return firstPublic;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the firstPublic property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setFirstPublic(XMLGregorianCalendar value) {
+        this.firstPublic = value;
+    }
+
+    /**
+     * Gets the value of the firstPublicRelease property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public BigInteger getFirstPublicRelease() {
+        return firstPublicRelease;
     }
 
     /**
-     * Gets the value of the location property.
+     * Sets the value of the firstPublicRelease property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setFirstPublicRelease(BigInteger value) {
+        this.firstPublicRelease = value;
+    }
+
+    /**
+     * Gets the value of the lastUpdated property.
      * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public String getLocation()
-    {
-      return location;
+    public XMLGregorianCalendar getLastUpdated() {
+        return lastUpdated;
     }
 
     /**
-     * Sets the value of the location property.
+     * Sets the value of the lastUpdated property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public void setLocation(String value)
-    {
-      this.location = value;
+    public void setLastUpdated(XMLGregorianCalendar value) {
+        this.lastUpdated = value;
     }
 
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * Gets the value of the lastUpdatedRelease property.
      * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getLastUpdatedRelease() {
+        return lastUpdatedRelease;
+    }
+
+    /**
+     * Sets the value of the lastUpdatedRelease property.
      * 
-     * 
    -     * <complexType>
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setLastUpdatedRelease(BigInteger value) {
+        this.lastUpdatedRelease = value;
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="lineage" minOccurs="0">
+     *         <element name="range" maxOccurs="unbounded">
      *           <complexType>
      *             <complexContent>
      *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="taxon" maxOccurs="unbounded">
-     *                     <complexType>
-     *                       <complexContent>
-     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         </restriction>
-     *                       </complexContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
+     *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
      *               </restriction>
      *             </complexContent>
      *           </complexType>
      *         </element>
      *       </sequence>
-     *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -1894,198 +896,366 @@ public class EntryType
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "lineage" })
-    public static class FeatureTaxon
-    {
-
-      protected EntryType.Feature.FeatureTaxon.Lineage lineage;
-
-      @XmlAttribute(name = "scientificName", required = true)
-      protected String scientificName;
-
-      @XmlAttribute(name = "commonName")
-      protected String commonName;
-
-      @XmlAttribute(name = "taxId")
-      protected BigInteger taxId;
-
-      /**
-       * Gets the value of the lineage property.
-       * 
-       * @return possible object is
-       *         {@link EntryType.Feature.FeatureTaxon.Lineage }
-       * 
-       */
-      public EntryType.Feature.FeatureTaxon.Lineage getLineage()
-      {
-        return lineage;
-      }
-
-      /**
-       * Sets the value of the lineage property.
-       * 
-       * @param value
-       *          allowed object is
-       *          {@link EntryType.Feature.FeatureTaxon.Lineage }
-       * 
-       */
-      public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
-      {
-        this.lineage = value;
-      }
-
-      /**
-       * Gets the value of the scientificName property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getScientificName()
-      {
-        return scientificName;
-      }
-
-      /**
-       * Sets the value of the scientificName property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setScientificName(String value)
-      {
-        this.scientificName = value;
-      }
-
-      /**
-       * Gets the value of the commonName property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCommonName()
-      {
-        return commonName;
-      }
-
-      /**
-       * Sets the value of the commonName property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCommonName(String value)
-      {
-        this.commonName = value;
-      }
-
-      /**
-       * Gets the value of the taxId property.
-       * 
-       * @return possible object is {@link BigInteger }
-       * 
-       */
-      public BigInteger getTaxId()
-      {
-        return taxId;
-      }
-
-      /**
-       * Sets the value of the taxId property.
-       * 
-       * @param value
-       *          allowed object is {@link BigInteger }
-       * 
-       */
-      public void setTaxId(BigInteger value)
-      {
-        this.taxId = value;
-      }
-
-      /**
-       * 
    
-       * Java class for anonymous complex type.
-       * 
-       * 
    
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * 
    -       * <complexType>
-       *   <complexContent>
-       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       <sequence>
-       *         <element name="taxon" maxOccurs="unbounded">
-       *           <complexType>
-       *             <complexContent>
-       *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *               </restriction>
-       *             </complexContent>
-       *           </complexType>
-       *         </element>
-       *       </sequence>
-       *     </restriction>
-       *   </complexContent>
-       * </complexType>
-       * 
    
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "taxon" })
-      public static class Lineage
-      {
+    @XmlType(name = "", propOrder = {
+        "range"
+    })
+    public static class Assembly {
 
         @XmlElement(required = true)
-        protected List taxon;
+        protected List range;
 
         /**
-         * Gets the value of the taxon property.
+         * Gets the value of the range 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 taxon 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 range property.
          * 
          * 
    
          * For example, to add a new item, do as follows:
-         * 
          * 
    -         * getTaxon().add(newItem);
+         *    getRange().add(newItem);
          * 
    
          * 
          * 
          * 
    
          * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+         * {@link EntryType.Assembly.Range }
+         * 
+         * 
+         */
+        public List getRange() {
+            if (range == null) {
+                range = new ArrayList();
+            }
+            return this.range;
+        }
+
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
          * 
          * 
          */
-        public List getTaxon()
-        {
-          if (taxon == null)
-          {
-            taxon = new ArrayList();
-          }
-          return this.taxon;
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Range {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "primaryBegin")
+            protected BigInteger primaryBegin;
+            @XmlAttribute(name = "primaryEnd")
+            protected BigInteger primaryEnd;
+            @XmlAttribute(name = "accession", required = true)
+            protected String accession;
+            @XmlAttribute(name = "version", required = true)
+            protected BigInteger version;
+            @XmlAttribute(name = "complement")
+            protected Boolean complement;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the primaryBegin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryBegin() {
+                return primaryBegin;
+            }
+
+            /**
+             * Sets the value of the primaryBegin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryBegin(BigInteger value) {
+                this.primaryBegin = value;
+            }
+
+            /**
+             * Gets the value of the primaryEnd property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryEnd() {
+                return primaryEnd;
+            }
+
+            /**
+             * Sets the value of the primaryEnd property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryEnd(BigInteger value) {
+                this.primaryEnd = value;
+            }
+
+            /**
+             * Gets the value of the accession property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getAccession() {
+                return accession;
+            }
+
+            /**
+             * Sets the value of the accession property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setAccession(String value) {
+                this.accession = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setVersion(BigInteger value) {
+                this.version = value;
+            }
+
+            /**
+             * Gets the value of the complement property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isComplement() {
+                if (complement == null) {
+                    return false;
+                } else {
+                    return complement;
+                }
+            }
+
+            /**
+             * Sets the value of the complement property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setComplement(Boolean value) {
+                this.complement = value;
+            }
+
         }
 
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <choice maxOccurs="unbounded" minOccurs="0">
+     *           <element name="range">
+     *             <complexType>
+     *               <complexContent>
+     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 </restriction>
+     *               </complexContent>
+     *             </complexType>
+     *           </element>
+     *           <element name="gap">
+     *             <complexType>
+     *               <complexContent>
+     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 </restriction>
+     *               </complexContent>
+     *             </complexType>
+     *           </element>
+     *         </choice>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "rangeOrGap"
+    })
+    public static class Contig {
+
+        @XmlElements({
+            @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+            @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
+        })
+        protected List rangeOrGap;
+
         /**
+         * Gets the value of the rangeOrGap property.
+         * 
          * 
    
-         * Java class for anonymous complex type.
+         * 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 rangeOrGap property.
          * 
          * 
    
-         * The following schema fragment specifies the expected content
-         * contained within this class.
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getRangeOrGap().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EntryType.Contig.Range }
+         * {@link EntryType.Contig.Gap }
+         * 
+         * 
+         */
+        public List getRangeOrGap() {
+            if (rangeOrGap == null) {
+                rangeOrGap = new ArrayList();
+            }
+            return this.rangeOrGap;
+        }
+
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
          * 
          * 
              * <complexType>
          *   <complexContent>
          *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
          *     </restriction>
          *   </complexContent>
          * </complexType>
@@ -2095,57 +1265,397 @@ public class EntryType
          */
         @XmlAccessorType(XmlAccessType.FIELD)
         @XmlType(name = "")
-        public static class Taxon
-        {
-
-          @XmlAttribute(name = "scientificName", required = true)
-          protected String scientificName;
-
-          /**
-           * Gets the value of the scientificName property.
-           * 
-           * @return possible object is {@link String }
-           * 
-           */
-          public String getScientificName()
-          {
-            return scientificName;
-          }
-
-          /**
-           * Sets the value of the scientificName property.
-           * 
-           * @param value
-           *          allowed object is {@link String }
-           * 
-           */
-          public void setScientificName(String value)
-          {
-            this.scientificName = value;
-          }
+        public static class Gap {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "length", required = true)
+            protected BigInteger length;
+            @XmlAttribute(name = "unknownLength")
+            protected Boolean unknownLength;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the length property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getLength() {
+                return length;
+            }
+
+            /**
+             * Sets the value of the length property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setLength(BigInteger value) {
+                this.length = value;
+            }
+
+            /**
+             * Gets the value of the unknownLength property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isUnknownLength() {
+                if (unknownLength == null) {
+                    return false;
+                } else {
+                    return unknownLength;
+                }
+            }
+
+            /**
+             * Sets the value of the unknownLength property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setUnknownLength(Boolean value) {
+                this.unknownLength = value;
+            }
 
         }
 
-      }
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Range {
+
+            @XmlAttribute(name = "begin", required = true)
+            protected BigInteger begin;
+            @XmlAttribute(name = "end", required = true)
+            protected BigInteger end;
+            @XmlAttribute(name = "primaryBegin")
+            protected BigInteger primaryBegin;
+            @XmlAttribute(name = "primaryEnd")
+            protected BigInteger primaryEnd;
+            @XmlAttribute(name = "accession", required = true)
+            protected String accession;
+            @XmlAttribute(name = "version", required = true)
+            protected BigInteger version;
+            @XmlAttribute(name = "complement")
+            protected Boolean complement;
+
+            /**
+             * Gets the value of the begin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getBegin() {
+                return begin;
+            }
+
+            /**
+             * Sets the value of the begin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setBegin(BigInteger value) {
+                this.begin = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setEnd(BigInteger value) {
+                this.end = value;
+            }
+
+            /**
+             * Gets the value of the primaryBegin property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryBegin() {
+                return primaryBegin;
+            }
+
+            /**
+             * Sets the value of the primaryBegin property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryBegin(BigInteger value) {
+                this.primaryBegin = value;
+            }
+
+            /**
+             * Gets the value of the primaryEnd property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getPrimaryEnd() {
+                return primaryEnd;
+            }
+
+            /**
+             * Sets the value of the primaryEnd property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setPrimaryEnd(BigInteger value) {
+                this.primaryEnd = value;
+            }
+
+            /**
+             * Gets the value of the accession property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getAccession() {
+                return accession;
+            }
+
+            /**
+             * Sets the value of the accession property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setAccession(String value) {
+                this.accession = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setVersion(BigInteger value) {
+                this.version = value;
+            }
+
+            /**
+             * Gets the value of the complement property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isComplement() {
+                if (complement == null) {
+                    return false;
+                } else {
+                    return complement;
+                }
+            }
+
+            /**
+             * Sets the value of the complement property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setComplement(Boolean value) {
+                this.complement = value;
+            }
+
+        }
 
     }
 
+
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
          * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="taxon" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="lineage" minOccurs="0">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <sequence>
+     *                             <element name="taxon" maxOccurs="unbounded">
+     *                               <complexType>
+     *                                 <complexContent>
+     *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                                   </restriction>
+     *                                 </complexContent>
+     *                               </complexType>
+     *                             </element>
+     *                           </sequence>
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *                 </sequence>
+     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
      *       </sequence>
      *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -2154,578 +1664,1017 @@ public class EntryType
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "value" })
-    public static class Qualifier
-    {
-
-      protected String value;
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      /**
-       * Gets the value of the value property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getValue()
-      {
-        return value;
-      }
-
-      /**
-       * Sets the value of the value property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setValue(String value)
-      {
-        this.value = value;
-      }
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-    }
+    @XmlType(name = "", propOrder = {
+        "taxon",
+        "xref",
+        "qualifier"
+    })
+    public static class Feature {
+
+        protected EntryType.Feature.FeatureTaxon taxon;
+        protected List xref;
+        protected List qualifier;
+        @XmlAttribute(name = "name", required = true)
+        protected String name;
+        @XmlAttribute(name = "location", required = true)
+        protected String location;
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
-   *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="type" use="required">
-   *         <simpleType>
-   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             <enumeration value="submission"/>
-   *             <enumeration value="book"/>
-   *             <enumeration value="article"/>
-   *             <enumeration value="patent"/>
-   *             <enumeration value="thesis"/>
-   *             <enumeration value="unpublished"/>
-   *           </restriction>
-   *         </simpleType>
-   *       </attribute>
-   *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "title", "author", "applicant", "consortium", "submissionDate",
-        "journal", "year", "volume", "issue", "firstPage", "lastPage",
-        "comment", "referenceLocation", "xref" })
-  public static class Reference
-  {
-
-    protected String title;
-
-    protected List author;
-
-    protected List applicant;
-
-    protected String consortium;
+        /**
+         * Gets the value of the taxon property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EntryType.Feature.FeatureTaxon }
+         *     
+         */
+        public EntryType.Feature.FeatureTaxon getTaxon() {
+            return taxon;
+        }
 
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar submissionDate;
+        /**
+         * Sets the value of the taxon property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EntryType.Feature.FeatureTaxon }
+         *     
+         */
+        public void setTaxon(EntryType.Feature.FeatureTaxon value) {
+            this.taxon = value;
+        }
 
-    protected String journal;
+        /**
+         * Gets the value of the xref 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 xref property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getXref().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link XrefType }
+         * 
+         * 
+         */
+        public List getXref() {
+            if (xref == null) {
+                xref = new ArrayList();
+            }
+            return this.xref;
+        }
 
-    protected String year;
+        /**
+         * Gets the value of the qualifier 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 qualifier property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getQualifier().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EntryType.Feature.Qualifier }
+         * 
+         * 
+         */
+        public List getQualifier() {
+            if (qualifier == null) {
+                qualifier = new ArrayList();
+            }
+            return this.qualifier;
+        }
 
-    protected String volume;
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
 
-    protected String issue;
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
 
-    protected String firstPage;
+        /**
+         * Gets the value of the location property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLocation() {
+            return location;
+        }
 
-    protected String lastPage;
+        /**
+         * Sets the value of the location property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLocation(String value) {
+            this.location = value;
+        }
 
-    protected String comment;
 
-    protected String referenceLocation;
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="lineage" minOccurs="0">
+         *           <complexType>
+         *             <complexContent>
+         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 <sequence>
+         *                   <element name="taxon" maxOccurs="unbounded">
+         *                     <complexType>
+         *                       <complexContent>
+         *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                         </restriction>
+         *                       </complexContent>
+         *                     </complexType>
+         *                   </element>
+         *                 </sequence>
+         *               </restriction>
+         *             </complexContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "lineage"
+        })
+        public static class FeatureTaxon {
+
+            protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+            @XmlAttribute(name = "scientificName", required = true)
+            protected String scientificName;
+            @XmlAttribute(name = "commonName")
+            protected String commonName;
+            @XmlAttribute(name = "taxId")
+            protected BigInteger taxId;
+
+            /**
+             * Gets the value of the lineage property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
+             *     
+             */
+            public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
+                return lineage;
+            }
+
+            /**
+             * Sets the value of the lineage property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
+             *     
+             */
+            public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
+                this.lineage = value;
+            }
+
+            /**
+             * Gets the value of the scientificName property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getScientificName() {
+                return scientificName;
+            }
+
+            /**
+             * Sets the value of the scientificName property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setScientificName(String value) {
+                this.scientificName = value;
+            }
+
+            /**
+             * Gets the value of the commonName property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getCommonName() {
+                return commonName;
+            }
+
+            /**
+             * Sets the value of the commonName property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setCommonName(String value) {
+                this.commonName = value;
+            }
+
+            /**
+             * Gets the value of the taxId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link BigInteger }
+             *     
+             */
+            public BigInteger getTaxId() {
+                return taxId;
+            }
+
+            /**
+             * Sets the value of the taxId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link BigInteger }
+             *     
+             */
+            public void setTaxId(BigInteger value) {
+                this.taxId = value;
+            }
+
+
+            /**
+             * 
    Java class for anonymous complex type.
+             * 
+             * 
    The following schema fragment specifies the expected content contained within this class.
+             * 
+             * 
    +             * <complexType>
+             *   <complexContent>
+             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       <sequence>
+             *         <element name="taxon" maxOccurs="unbounded">
+             *           <complexType>
+             *             <complexContent>
+             *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *               </restriction>
+             *             </complexContent>
+             *           </complexType>
+             *         </element>
+             *       </sequence>
+             *     </restriction>
+             *   </complexContent>
+             * </complexType>
+             * 
    
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "", propOrder = {
+                "taxon"
+            })
+            public static class Lineage {
+
+                @XmlElement(required = true)
+                protected List taxon;
+
+                /**
+                 * Gets the value of the taxon 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 taxon property.
+                 * 
+                 * 
    
+                 * For example, to add a new item, do as follows:
+                 * 
    +                 *    getTaxon().add(newItem);
+                 * 
    
+                 * 
+                 * 
+                 * 
    
+                 * Objects of the following type(s) are allowed in the list
+                 * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+                 * 
+                 * 
+                 */
+                public List getTaxon() {
+                    if (taxon == null) {
+                        taxon = new ArrayList();
+                    }
+                    return this.taxon;
+                }
+
+
+                /**
+                 * 
    Java class for anonymous complex type.
+                 * 
+                 * 
    The following schema fragment specifies the expected content contained within this class.
+                 * 
+                 * 
    +                 * <complexType>
+                 *   <complexContent>
+                 *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+                 *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+                 *     </restriction>
+                 *   </complexContent>
+                 * </complexType>
+                 * 
    
+                 * 
+                 * 
+                 */
+                @XmlAccessorType(XmlAccessType.FIELD)
+                @XmlType(name = "")
+                public static class Taxon {
+
+                    @XmlAttribute(name = "scientificName", required = true)
+                    protected String scientificName;
+
+                    /**
+                     * Gets the value of the scientificName property.
+                     * 
+                     * @return
+                     *     possible object is
+                     *     {@link String }
+                     *     
+                     */
+                    public String getScientificName() {
+                        return scientificName;
+                    }
+
+                    /**
+                     * Sets the value of the scientificName property.
+                     * 
+                     * @param value
+                     *     allowed object is
+                     *     {@link String }
+                     *     
+                     */
+                    public void setScientificName(String value) {
+                        this.scientificName = value;
+                    }
+
+                }
+
+            }
 
-    protected List xref;
+        }
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
 
-    @XmlAttribute(name = "number", required = true)
-    protected BigInteger number;
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+         *       </sequence>
+         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "value"
+        })
+        public static class Qualifier {
+
+            protected String value;
+            @XmlAttribute(name = "name", required = true)
+            protected String name;
+
+            /**
+             * Gets the value of the value property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getValue() {
+                return value;
+            }
+
+            /**
+             * Sets the value of the value property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setValue(String value) {
+                this.value = value;
+            }
+
+            /**
+             * Gets the value of the name property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getName() {
+                return name;
+            }
+
+            /**
+             * Sets the value of the name property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setName(String value) {
+                this.name = value;
+            }
 
-    @XmlAttribute(name = "location")
-    protected String location;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
     }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
 
     /**
-     * Gets the value of the author property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 author property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getAuthor().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+     *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="type" use="required">
+     *         <simpleType>
+     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             <enumeration value="submission"/>
+     *             <enumeration value="book"/>
+     *             <enumeration value="article"/>
+     *             <enumeration value="patent"/>
+     *             <enumeration value="thesis"/>
+     *             <enumeration value="unpublished"/>
+     *           </restriction>
+     *         </simpleType>
+     *       </attribute>
+     *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
      */
-    public List getAuthor()
-    {
-      if (author == null)
-      {
-        author = new ArrayList();
-      }
-      return this.author;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "title",
+        "author",
+        "applicant",
+        "consortium",
+        "submissionDate",
+        "journal",
+        "year",
+        "volume",
+        "issue",
+        "firstPage",
+        "lastPage",
+        "comment",
+        "referenceLocation",
+        "xref"
+    })
+    public static class Reference {
+
+        protected String title;
+        protected List author;
+        protected List applicant;
+        protected String consortium;
+        @XmlSchemaType(name = "date")
+        protected XMLGregorianCalendar submissionDate;
+        protected String journal;
+        protected String year;
+        protected String volume;
+        protected String issue;
+        protected String firstPage;
+        protected String lastPage;
+        protected String comment;
+        protected String referenceLocation;
+        protected List xref;
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "number", required = true)
+        protected BigInteger number;
+        @XmlAttribute(name = "location")
+        protected String location;
 
-    /**
-     * Gets the value of the applicant 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 applicant property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getApplicant().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
-     */
-    public List getApplicant()
-    {
-      if (applicant == null)
-      {
-        applicant = new ArrayList();
-      }
-      return this.applicant;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the consortium property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getConsortium()
-    {
-      return consortium;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the consortium property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setConsortium(String value)
-    {
-      this.consortium = value;
-    }
+        /**
+         * Gets the value of the author 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 author property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getAuthor().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getAuthor() {
+            if (author == null) {
+                author = new ArrayList();
+            }
+            return this.author;
+        }
 
-    /**
-     * Gets the value of the submissionDate property.
-     * 
-     * @return possible object is {@link XMLGregorianCalendar }
-     * 
-     */
-    public XMLGregorianCalendar getSubmissionDate()
-    {
-      return submissionDate;
-    }
+        /**
+         * Gets the value of the applicant 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 applicant property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getApplicant().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getApplicant() {
+            if (applicant == null) {
+                applicant = new ArrayList();
+            }
+            return this.applicant;
+        }
 
-    /**
-     * Sets the value of the submissionDate property.
-     * 
-     * @param value
-     *          allowed object is {@link XMLGregorianCalendar }
-     * 
-     */
-    public void setSubmissionDate(XMLGregorianCalendar value)
-    {
-      this.submissionDate = value;
-    }
+        /**
+         * Gets the value of the consortium property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getConsortium() {
+            return consortium;
+        }
 
-    /**
-     * Gets the value of the journal property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getJournal()
-    {
-      return journal;
-    }
+        /**
+         * Sets the value of the consortium property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setConsortium(String value) {
+            this.consortium = value;
+        }
 
-    /**
-     * Sets the value of the journal property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setJournal(String value)
-    {
-      this.journal = value;
-    }
+        /**
+         * Gets the value of the submissionDate property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link XMLGregorianCalendar }
+         *     
+         */
+        public XMLGregorianCalendar getSubmissionDate() {
+            return submissionDate;
+        }
 
-    /**
-     * Gets the value of the year property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getYear()
-    {
-      return year;
-    }
+        /**
+         * Sets the value of the submissionDate property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link XMLGregorianCalendar }
+         *     
+         */
+        public void setSubmissionDate(XMLGregorianCalendar value) {
+            this.submissionDate = value;
+        }
 
-    /**
-     * Sets the value of the year property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setYear(String value)
-    {
-      this.year = value;
-    }
+        /**
+         * Gets the value of the journal property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getJournal() {
+            return journal;
+        }
 
-    /**
-     * Gets the value of the volume property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getVolume()
-    {
-      return volume;
-    }
+        /**
+         * Sets the value of the journal property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setJournal(String value) {
+            this.journal = value;
+        }
 
-    /**
-     * Sets the value of the volume property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setVolume(String value)
-    {
-      this.volume = value;
-    }
+        /**
+         * Gets the value of the year property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getYear() {
+            return year;
+        }
 
-    /**
-     * Gets the value of the issue property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getIssue()
-    {
-      return issue;
-    }
+        /**
+         * Sets the value of the year property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setYear(String value) {
+            this.year = value;
+        }
 
-    /**
-     * Sets the value of the issue property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setIssue(String value)
-    {
-      this.issue = value;
-    }
+        /**
+         * Gets the value of the volume property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVolume() {
+            return volume;
+        }
 
-    /**
-     * Gets the value of the firstPage property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFirstPage()
-    {
-      return firstPage;
-    }
+        /**
+         * Sets the value of the volume property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVolume(String value) {
+            this.volume = value;
+        }
 
-    /**
-     * Sets the value of the firstPage property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFirstPage(String value)
-    {
-      this.firstPage = value;
-    }
+        /**
+         * Gets the value of the issue property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getIssue() {
+            return issue;
+        }
 
-    /**
-     * Gets the value of the lastPage property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getLastPage()
-    {
-      return lastPage;
-    }
+        /**
+         * Sets the value of the issue property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setIssue(String value) {
+            this.issue = value;
+        }
 
-    /**
-     * Sets the value of the lastPage property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setLastPage(String value)
-    {
-      this.lastPage = value;
-    }
+        /**
+         * Gets the value of the firstPage property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFirstPage() {
+            return firstPage;
+        }
 
-    /**
-     * Gets the value of the comment property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComment()
-    {
-      return comment;
-    }
+        /**
+         * Sets the value of the firstPage property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFirstPage(String value) {
+            this.firstPage = value;
+        }
 
-    /**
-     * Sets the value of the comment property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComment(String value)
-    {
-      this.comment = value;
-    }
+        /**
+         * Gets the value of the lastPage property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLastPage() {
+            return lastPage;
+        }
 
-    /**
-     * Gets the value of the referenceLocation property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getReferenceLocation()
-    {
-      return referenceLocation;
-    }
+        /**
+         * Sets the value of the lastPage property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLastPage(String value) {
+            this.lastPage = value;
+        }
 
-    /**
-     * Sets the value of the referenceLocation property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setReferenceLocation(String value)
-    {
-      this.referenceLocation = value;
-    }
+        /**
+         * Gets the value of the comment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getComment() {
+            return comment;
+        }
 
-    /**
-     * Gets the value of the xref 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 xref property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getXref().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link XrefType
-     * }
-     * 
-     * 
-     */
-    public List getXref()
-    {
-      if (xref == null)
-      {
-        xref = new ArrayList();
-      }
-      return this.xref;
-    }
+        /**
+         * Sets the value of the comment property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setComment(String value) {
+            this.comment = value;
+        }
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getType()
-    {
-      return type;
-    }
+        /**
+         * Gets the value of the referenceLocation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getReferenceLocation() {
+            return referenceLocation;
+        }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setType(String value)
-    {
-      this.type = value;
-    }
+        /**
+         * Sets the value of the referenceLocation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setReferenceLocation(String value) {
+            this.referenceLocation = value;
+        }
 
-    /**
-     * Gets the value of the number property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getNumber()
-    {
-      return number;
-    }
+        /**
+         * Gets the value of the xref 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 xref property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getXref().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link XrefType }
+         * 
+         * 
+         */
+        public List getXref() {
+            if (xref == null) {
+                xref = new ArrayList();
+            }
+            return this.xref;
+        }
 
-    /**
-     * Sets the value of the number property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setNumber(BigInteger value)
-    {
-      this.number = value;
-    }
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getLocation()
-    {
-      return location;
-    }
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
 
-    /**
-     * Sets the value of the location property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setLocation(String value)
-    {
-      this.location = value;
-    }
+        /**
+         * Gets the value of the number property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getNumber() {
+            return number;
+        }
+
+        /**
+         * Sets the value of the number property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setNumber(BigInteger value) {
+            this.number = value;
+        }
+
+        /**
+         * Gets the value of the location property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLocation() {
+            return location;
+        }
+
+        /**
+         * Sets the value of the location property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLocation(String value) {
+            this.location = value;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java
index f622bd6..3e9d660 100644
--- a/src/jalview/xml/binding/embl/ObjectFactory.java
+++ b/src/jalview/xml/binding/embl/ObjectFactory.java
@@ -2,170 +2,158 @@
 // 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: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlRegistry;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.embl package.
- * 
    
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.embl package. 
+ * 
    An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.embl
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link EntryType }
-   * 
-   */
-  public EntryType createEntryType()
-  {
-    return new EntryType();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig }
-   * 
-   */
-  public EntryType.Contig createEntryTypeContig()
-  {
-    return new EntryType.Contig();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Assembly }
-   * 
-   */
-  public EntryType.Assembly createEntryTypeAssembly()
-  {
-    return new EntryType.Assembly();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature }
-   * 
-   */
-  public EntryType.Feature createEntryTypeFeature()
-  {
-    return new EntryType.Feature();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
-  {
-    return new EntryType.Feature.FeatureTaxon();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
-  {
-    return new EntryType.Feature.FeatureTaxon.Lineage();
-  }
-
-  /**
-   * Create an instance of {@link ROOT }
-   * 
-   */
-  public ROOT createROOT()
-  {
-    return new ROOT();
-  }
-
-  /**
-   * Create an instance of {@link EntrySetType }
-   * 
-   */
-  public EntrySetType createEntrySetType()
-  {
-    return new EntrySetType();
-  }
-
-  /**
-   * Create an instance of {@link XrefType }
-   * 
-   */
-  public XrefType createXrefType()
-  {
-    return new XrefType();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Reference }
-   * 
-   */
-  public EntryType.Reference createEntryTypeReference()
-  {
-    return new EntryType.Reference();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig.Range }
-   * 
-   */
-  public EntryType.Contig.Range createEntryTypeContigRange()
-  {
-    return new EntryType.Contig.Range();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Contig.Gap }
-   * 
-   */
-  public EntryType.Contig.Gap createEntryTypeContigGap()
-  {
-    return new EntryType.Contig.Gap();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Assembly.Range }
-   * 
-   */
-  public EntryType.Assembly.Range createEntryTypeAssemblyRange()
-  {
-    return new EntryType.Assembly.Range();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.Qualifier }
-   * 
-   */
-  public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
-  {
-    return new EntryType.Feature.Qualifier();
-  }
-
-  /**
-   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
-   * 
-   */
-  public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
-  {
-    return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
-  }
+public class ObjectFactory {
+
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link EntryType }
+     * 
+     */
+    public EntryType createEntryType() {
+        return new EntryType();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig }
+     * 
+     */
+    public EntryType.Contig createEntryTypeContig() {
+        return new EntryType.Contig();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Assembly }
+     * 
+     */
+    public EntryType.Assembly createEntryTypeAssembly() {
+        return new EntryType.Assembly();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature }
+     * 
+     */
+    public EntryType.Feature createEntryTypeFeature() {
+        return new EntryType.Feature();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
+        return new EntryType.Feature.FeatureTaxon();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
+        return new EntryType.Feature.FeatureTaxon.Lineage();
+    }
+
+    /**
+     * Create an instance of {@link ROOT }
+     * 
+     */
+    public ROOT createROOT() {
+        return new ROOT();
+    }
+
+    /**
+     * Create an instance of {@link EntrySetType }
+     * 
+     */
+    public EntrySetType createEntrySetType() {
+        return new EntrySetType();
+    }
+
+    /**
+     * Create an instance of {@link XrefType }
+     * 
+     */
+    public XrefType createXrefType() {
+        return new XrefType();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Reference }
+     * 
+     */
+    public EntryType.Reference createEntryTypeReference() {
+        return new EntryType.Reference();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig.Range }
+     * 
+     */
+    public EntryType.Contig.Range createEntryTypeContigRange() {
+        return new EntryType.Contig.Range();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Contig.Gap }
+     * 
+     */
+    public EntryType.Contig.Gap createEntryTypeContigGap() {
+        return new EntryType.Contig.Gap();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Assembly.Range }
+     * 
+     */
+    public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
+        return new EntryType.Assembly.Range();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.Qualifier }
+     * 
+     */
+    public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
+        return new EntryType.Feature.Qualifier();
+    }
+
+    /**
+     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+     * 
+     */
+    public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
+        return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java
index 6a09d79..6b8b2ea 100644
--- a/src/jalview/xml/binding/embl/ROOT.java
+++ b/src/jalview/xml/binding/embl/ROOT.java
@@ -2,9 +2,10 @@
 // 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: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType>
@@ -36,59 +35,62 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entrySet", "entry" })
+@XmlType(name = "", propOrder = {
+    "entrySet",
+    "entry"
+})
 @XmlRootElement(name = "ROOT")
-public class ROOT
-{
-
-  protected EntrySetType entrySet;
+public class ROOT {
 
-  protected EntryType entry;
+    protected EntrySetType entrySet;
+    protected EntryType entry;
 
-  /**
-   * Gets the value of the entrySet property.
-   * 
-   * @return possible object is {@link EntrySetType }
-   * 
-   */
-  public EntrySetType getEntrySet()
-  {
-    return entrySet;
-  }
+    /**
+     * Gets the value of the entrySet property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntrySetType }
+     *     
+     */
+    public EntrySetType getEntrySet() {
+        return entrySet;
+    }
 
-  /**
-   * Sets the value of the entrySet property.
-   * 
-   * @param value
-   *          allowed object is {@link EntrySetType }
-   * 
-   */
-  public void setEntrySet(EntrySetType value)
-  {
-    this.entrySet = value;
-  }
+    /**
+     * Sets the value of the entrySet property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntrySetType }
+     *     
+     */
+    public void setEntrySet(EntrySetType value) {
+        this.entrySet = value;
+    }
 
-  /**
-   * Gets the value of the entry property.
-   * 
-   * @return possible object is {@link EntryType }
-   * 
-   */
-  public EntryType getEntry()
-  {
-    return entry;
-  }
+    /**
+     * Gets the value of the entry property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link EntryType }
+     *     
+     */
+    public EntryType getEntry() {
+        return entry;
+    }
 
-  /**
-   * Sets the value of the entry property.
-   * 
-   * @param value
-   *          allowed object is {@link EntryType }
-   * 
-   */
-  public void setEntry(EntryType value)
-  {
-    this.entry = value;
-  }
+    /**
+     * Sets the value of the entry property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link EntryType }
+     *     
+     */
+    public void setEntry(EntryType value) {
+        this.entry = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java
index cdfd438..4aa7e5e 100644
--- a/src/jalview/xml/binding/embl/XrefType.java
+++ b/src/jalview/xml/binding/embl/XrefType.java
@@ -2,9 +2,10 @@
 // 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: 2018.09.14 at 02:46:00 PM BST 
+// Generated on: 2023.01.31 at 04:07:09 PM GMT 
 //
 
+
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,15 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Database cross-reference.
  * 
- * 
    
- * Java class for XrefType complex type.
+ * 
    Java class for XrefType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="XrefType">
@@ -38,85 +37,85 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "XrefType")
-public class XrefType
-{
-
-  @XmlAttribute(name = "db", required = true)
-  protected String db;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
+public class XrefType {
 
-  @XmlAttribute(name = "secondaryId")
-  protected String secondaryId;
+    @XmlAttribute(name = "db", required = true)
+    protected String db;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "secondaryId")
+    protected String secondaryId;
 
-  /**
-   * Gets the value of the db property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDb()
-  {
-    return db;
-  }
+    /**
+     * Gets the value of the db property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDb() {
+        return db;
+    }
 
-  /**
-   * Sets the value of the db property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDb(String value)
-  {
-    this.db = value;
-  }
+    /**
+     * Sets the value of the db property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDb(String value) {
+        this.db = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the secondaryId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSecondaryId()
-  {
-    return secondaryId;
-  }
+    /**
+     * Gets the value of the secondaryId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSecondaryId() {
+        return secondaryId;
+    }
 
-  /**
-   * Sets the value of the secondaryId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSecondaryId(String value)
-  {
-    this.secondaryId = value;
-  }
+    /**
+     * Sets the value of the secondaryId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSecondaryId(String value) {
+        this.secondaryId = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 9a2c488..bee5c06 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,288 +18,309 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="alcodon" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute
- * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ *                 </sequence>
+ *                 <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+    "alcodon",
+    "alcodMap"
+})
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
-  protected List alcodon;
-
-  protected List alcodMap;
+public class AlcodonFrame {
 
-  /**
-   * Gets the value of the alcodon property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the alcodon property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAlcodon().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.Alcodon }
-   * 
-   * 
-   */
-  public List getAlcodon()
-  {
-    if (alcodon == null)
-    {
-      alcodon = new ArrayList();
-    }
-    return this.alcodon;
-  }
-
-  /**
-   * Gets the value of the alcodMap property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the alcodMap property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAlcodMap().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.AlcodMap }
-   * 
-   * 
-   */
-  public List getAlcodMap()
-  {
-    if (alcodMap == null)
-    {
-      alcodMap = new ArrayList();
-    }
-    return this.alcodMap;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class AlcodMap
-  {
-
-    @XmlElement(name = "Mapping", required = true)
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "dnasq", required = true)
-    protected String dnasq;
+    protected List alcodon;
+    protected List alcodMap;
 
     /**
+     * Gets the value of the alcodon property.
      * 
-     * a Mapping entry and an associated protein sequence
+     * 
    
+     * 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 alcodon property.
      * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAlcodon().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link Mapping }
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.Alcodon }
      * 
-     * @param value
-     *          allowed object is {@link Mapping }
      * 
      */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
+    public List getAlcodon() {
+        if (alcodon == null) {
+            alcodon = new ArrayList();
+        }
+        return this.alcodon;
     }
 
     /**
-     * Gets the value of the dnasq property.
+     * Gets the value of the alcodMap 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 alcodMap property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAlcodMap().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.AlcodMap }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getDnasq()
-    {
-      return dnasq;
+    public List getAlcodMap() {
+        if (alcodMap == null) {
+            alcodMap = new ArrayList();
+        }
+        return this.alcodMap;
     }
 
+
     /**
-     * Sets the value of the dnasq property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+     *       </sequence>
+     *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setDnasq(String value)
-    {
-      this.dnasq = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class AlcodMap {
 
-  }
+        @XmlElement(name = "Mapping", required = true)
+        protected Mapping mapping;
+        @XmlAttribute(name = "dnasq", required = true)
+        protected String dnasq;
 
-  /**
-   * 
-   * specifies a series of aligned codons from an associated DNA sequence
-   * alignment that when translated correspond to columns of a peptide
-   * alignment. Element may have either all pos1,2,3 attributes specified, or
-   * none at all (indicating a gapped column with no translated peptide).
-   * 
-   * 
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
-   * &lt;attribute name="pos2"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
-   * &lt;attribute name="pos3"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Alcodon
-  {
+        /**
+         * 
+         * 										a Mapping entry and an associated protein sequence
+         * 									
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
 
-    @XmlAttribute(name = "pos1")
-    protected BigInteger pos1;
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
 
-    @XmlAttribute(name = "pos2")
-    protected BigInteger pos2;
+        /**
+         * Gets the value of the dnasq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDnasq() {
+            return dnasq;
+        }
 
-    @XmlAttribute(name = "pos3")
-    protected BigInteger pos3;
+        /**
+         * Sets the value of the dnasq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDnasq(String value) {
+            this.dnasq = value;
+        }
 
-    /**
-     * Gets the value of the pos1 property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getPos1()
-    {
-      return pos1;
     }
 
-    /**
-     * Sets the value of the pos1 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos1(BigInteger value)
-    {
-      this.pos1 = value;
-    }
 
     /**
-     * Gets the value of the pos2 property.
      * 
-     * @return possible object is {@link BigInteger }
+     * 								specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+     * 								Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+     * 							
      * 
-     */
-    public BigInteger getPos2()
-    {
-      return pos2;
-    }
-
-    /**
-     * Sets the value of the pos2 property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link BigInteger }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setPos2(BigInteger value)
-    {
-      this.pos2 = value;
-    }
-
-    /**
-     * Gets the value of the pos3 property.
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link BigInteger }
      * 
      */
-    public BigInteger getPos3()
-    {
-      return pos3;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Alcodon {
 
-    /**
-     * Sets the value of the pos3 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos3(BigInteger value)
-    {
-      this.pos3 = value;
-    }
+        @XmlAttribute(name = "pos1")
+        protected BigInteger pos1;
+        @XmlAttribute(name = "pos2")
+        protected BigInteger pos2;
+        @XmlAttribute(name = "pos3")
+        protected BigInteger pos3;
+
+        /**
+         * Gets the value of the pos1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos1() {
+            return pos1;
+        }
 
-  }
+        /**
+         * Sets the value of the pos1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos1(BigInteger value) {
+            this.pos1 = value;
+        }
+
+        /**
+         * Gets the value of the pos2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos2() {
+            return pos2;
+        }
+
+        /**
+         * Sets the value of the pos2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos2(BigInteger value) {
+            this.pos2 = value;
+        }
+
+        /**
+         * Gets the value of the pos3 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos3() {
+            return pos3;
+        }
+
+        /**
+         * Sets the value of the pos3 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos3(BigInteger value) {
+            this.pos3 = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 8d66aa3..8c07465 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,846 +17,841 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
- * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="label"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&gt; &lt;element name="thresholdLine"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="property" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="graph" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="graphColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphHeight"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreOnly"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="score"
- * type="{http://www.w3.org/2001/XMLSchema}double" /&gt; &lt;attribute
- * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showAllColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="belowAlignment"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="calcId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="thresholdLine" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *       <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "annotationElement", "label", "description", "thresholdLine",
-      "property" })
+@XmlType(name = "", propOrder = {
+    "annotationElement",
+    "label",
+    "description",
+    "thresholdLine",
+    "property"
+})
 @XmlRootElement(name = "Annotation")
-public class Annotation
-{
+public class Annotation {
 
-  protected List annotationElement;
+    protected List annotationElement;
+    @XmlElement(required = true)
+    protected String label;
+    protected String description;
+    protected Annotation.ThresholdLine thresholdLine;
+    protected List property;
+    @XmlAttribute(name = "graph", required = true)
+    protected boolean graph;
+    @XmlAttribute(name = "graphType")
+    protected Integer graphType;
+    @XmlAttribute(name = "sequenceRef")
+    protected String sequenceRef;
+    @XmlAttribute(name = "groupRef")
+    protected String groupRef;
+    @XmlAttribute(name = "graphColour")
+    protected Integer graphColour;
+    @XmlAttribute(name = "graphGroup")
+    protected Integer graphGroup;
+    @XmlAttribute(name = "graphHeight")
+    protected Integer graphHeight;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "scoreOnly")
+    protected Boolean scoreOnly;
+    @XmlAttribute(name = "score")
+    protected Double score;
+    @XmlAttribute(name = "visible")
+    protected Boolean visible;
+    @XmlAttribute(name = "centreColLabels")
+    protected Boolean centreColLabels;
+    @XmlAttribute(name = "scaleColLabels")
+    protected Boolean scaleColLabels;
+    @XmlAttribute(name = "showAllColLabels")
+    protected Boolean showAllColLabels;
+    @XmlAttribute(name = "autoCalculated")
+    protected Boolean autoCalculated;
+    @XmlAttribute(name = "belowAlignment")
+    protected Boolean belowAlignment;
+    @XmlAttribute(name = "calcId")
+    protected String calcId;
 
-  @XmlElement(required = true)
-  protected String label;
-
-  protected String description;
-
-  protected Annotation.ThresholdLine thresholdLine;
-
-  protected List property;
-
-  @XmlAttribute(name = "graph", required = true)
-  protected boolean graph;
-
-  @XmlAttribute(name = "graphType")
-  protected Integer graphType;
-
-  @XmlAttribute(name = "sequenceRef")
-  protected String sequenceRef;
-
-  @XmlAttribute(name = "groupRef")
-  protected String groupRef;
-
-  @XmlAttribute(name = "graphColour")
-  protected Integer graphColour;
-
-  @XmlAttribute(name = "graphGroup")
-  protected Integer graphGroup;
-
-  @XmlAttribute(name = "graphHeight")
-  protected Integer graphHeight;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "scoreOnly")
-  protected Boolean scoreOnly;
-
-  @XmlAttribute(name = "score")
-  protected Double score;
-
-  @XmlAttribute(name = "visible")
-  protected Boolean visible;
-
-  @XmlAttribute(name = "centreColLabels")
-  protected Boolean centreColLabels;
-
-  @XmlAttribute(name = "scaleColLabels")
-  protected Boolean scaleColLabels;
-
-  @XmlAttribute(name = "showAllColLabels")
-  protected Boolean showAllColLabels;
-
-  @XmlAttribute(name = "autoCalculated")
-  protected Boolean autoCalculated;
-
-  @XmlAttribute(name = "belowAlignment")
-  protected Boolean belowAlignment;
-
-  @XmlAttribute(name = "calcId")
-  protected String calcId;
-
-  /**
-   * Gets the value of the annotationElement property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the annotationElement property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAnnotationElement().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link AnnotationElement }
-   * 
-   * 
-   */
-  public List getAnnotationElement()
-  {
-    if (annotationElement == null)
-    {
-      annotationElement = new ArrayList();
-    }
-    return this.annotationElement;
-  }
-
-  /**
-   * Gets the value of the label property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLabel()
-  {
-    return label;
-  }
-
-  /**
-   * Sets the value of the label property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLabel(String value)
-  {
-    this.label = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the thresholdLine property.
-   * 
-   * @return possible object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine getThresholdLine()
-  {
-    return thresholdLine;
-  }
-
-  /**
-   * Sets the value of the thresholdLine property.
-   * 
-   * @param value
-   *          allowed object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public void setThresholdLine(Annotation.ThresholdLine value)
-  {
-    this.thresholdLine = value;
-  }
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the property property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getProperty().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Annotation.Property }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the graph property.
-   * 
-   */
-  public boolean isGraph()
-  {
-    return graph;
-  }
-
-  /**
-   * Sets the value of the graph property.
-   * 
-   */
-  public void setGraph(boolean value)
-  {
-    this.graph = value;
-  }
-
-  /**
-   * Gets the value of the graphType property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphType()
-  {
-    return graphType;
-  }
-
-  /**
-   * Sets the value of the graphType property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphType(Integer value)
-  {
-    this.graphType = value;
-  }
-
-  /**
-   * Gets the value of the sequenceRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequenceRef()
-  {
-    return sequenceRef;
-  }
-
-  /**
-   * Sets the value of the sequenceRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequenceRef(String value)
-  {
-    this.sequenceRef = value;
-  }
-
-  /**
-   * Gets the value of the groupRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGroupRef()
-  {
-    return groupRef;
-  }
-
-  /**
-   * Sets the value of the groupRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGroupRef(String value)
-  {
-    this.groupRef = value;
-  }
-
-  /**
-   * Gets the value of the graphColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphColour()
-  {
-    return graphColour;
-  }
-
-  /**
-   * Sets the value of the graphColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphColour(Integer value)
-  {
-    this.graphColour = value;
-  }
-
-  /**
-   * Gets the value of the graphGroup property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphGroup()
-  {
-    return graphGroup;
-  }
-
-  /**
-   * Sets the value of the graphGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphGroup(Integer value)
-  {
-    this.graphGroup = value;
-  }
-
-  /**
-   * Gets the value of the graphHeight property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphHeight()
-  {
-    return graphHeight;
-  }
-
-  /**
-   * Sets the value of the graphHeight property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphHeight(Integer value)
-  {
-    this.graphHeight = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the scoreOnly property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isScoreOnly()
-  {
-    if (scoreOnly == null)
-    {
-      return false;
-    }
-    else
-    {
-      return scoreOnly;
-    }
-  }
-
-  /**
-   * Sets the value of the scoreOnly property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScoreOnly(Boolean value)
-  {
-    this.scoreOnly = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Double }
-   * 
-   */
-  public Double getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Double }
-   * 
-   */
-  public void setScore(Double value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * Gets the value of the visible property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isVisible()
-  {
-    return visible;
-  }
-
-  /**
-   * Sets the value of the visible property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setVisible(Boolean value)
-  {
-    this.visible = value;
-  }
-
-  /**
-   * Gets the value of the centreColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isCentreColLabels()
-  {
-    return centreColLabels;
-  }
-
-  /**
-   * Sets the value of the centreColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setCentreColLabels(Boolean value)
-  {
-    this.centreColLabels = value;
-  }
-
-  /**
-   * Gets the value of the scaleColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isScaleColLabels()
-  {
-    return scaleColLabels;
-  }
-
-  /**
-   * Sets the value of the scaleColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScaleColLabels(Boolean value)
-  {
-    this.scaleColLabels = value;
-  }
-
-  /**
-   * Gets the value of the showAllColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isShowAllColLabels()
-  {
-    return showAllColLabels;
-  }
-
-  /**
-   * Sets the value of the showAllColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setShowAllColLabels(Boolean value)
-  {
-    this.showAllColLabels = value;
-  }
-
-  /**
-   * Gets the value of the autoCalculated property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isAutoCalculated()
-  {
-    if (autoCalculated == null)
-    {
-      return false;
-    }
-    else
-    {
-      return autoCalculated;
-    }
-  }
-
-  /**
-   * Sets the value of the autoCalculated property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setAutoCalculated(Boolean value)
-  {
-    this.autoCalculated = value;
-  }
-
-  /**
-   * Gets the value of the belowAlignment property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isBelowAlignment()
-  {
-    if (belowAlignment == null)
-    {
-      return true;
-    }
-    else
-    {
-      return belowAlignment;
-    }
-  }
-
-  /**
-   * Sets the value of the belowAlignment property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setBelowAlignment(Boolean value)
-  {
-    this.belowAlignment = value;
-  }
-
-  /**
-   * Gets the value of the calcId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCalcId()
-  {
-    return calcId;
-  }
-
-  /**
-   * Sets the value of the calcId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCalcId(String value)
-  {
-    this.calcId = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "value")
-    protected String value;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
+    /**
+     * Gets the value of the annotationElement 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 annotationElement property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAnnotationElement().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link AnnotationElement }
+     * 
+     * 
+     */
+    public List getAnnotationElement() {
+        if (annotationElement == null) {
+            annotationElement = new ArrayList();
+        }
+        return this.annotationElement;
+    }
+
+    /**
+     * Gets the value of the label property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLabel() {
+        return label;
+    }
+
+    /**
+     * Sets the value of the label property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLabel(String value) {
+        this.label = value;
+    }
+
+    /**
+     * Gets the value of the description property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public String getDescription() {
+        return description;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the description property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the thresholdLine property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Annotation.ThresholdLine }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public Annotation.ThresholdLine getThresholdLine() {
+        return thresholdLine;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the thresholdLine property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
-
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class ThresholdLine
-  {
-
-    @XmlAttribute(name = "label")
-    protected String label;
+     *     allowed object is
+     *     {@link Annotation.ThresholdLine }
+     *     
+     */
+    public void setThresholdLine(Annotation.ThresholdLine value) {
+        this.thresholdLine = value;
+    }
 
-    @XmlAttribute(name = "value")
-    protected Float value;
+    /**
+     * Gets the value of the property 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 property property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getProperty().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation.Property }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
+    }
 
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
+    /**
+     * Gets the value of the graph property.
+     * 
+     */
+    public boolean isGraph() {
+        return graph;
+    }
 
     /**
-     * Gets the value of the label property.
+     * Sets the value of the graph property.
      * 
-     * @return possible object is {@link String }
+     */
+    public void setGraph(boolean value) {
+        this.graph = value;
+    }
+
+    /**
+     * Gets the value of the graphType property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public String getLabel()
-    {
-      return label;
+    public Integer getGraphType() {
+        return graphType;
     }
 
     /**
-     * Sets the value of the label property.
+     * Sets the value of the graphType property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphType(Integer value) {
+        this.graphType = value;
+    }
+
+    /**
+     * Gets the value of the sequenceRef property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequenceRef() {
+        return sequenceRef;
+    }
+
+    /**
+     * Sets the value of the sequenceRef property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequenceRef(String value) {
+        this.sequenceRef = value;
+    }
+
+    /**
+     * Gets the value of the groupRef property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getGroupRef() {
+        return groupRef;
+    }
+
+    /**
+     * Sets the value of the groupRef property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setLabel(String value)
-    {
-      this.label = value;
+    public void setGroupRef(String value) {
+        this.groupRef = value;
     }
 
     /**
-     * Gets the value of the value property.
+     * Gets the value of the graphColour property.
      * 
-     * @return possible object is {@link Float }
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getGraphColour() {
+        return graphColour;
+    }
+
+    /**
+     * Sets the value of the graphColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphColour(Integer value) {
+        this.graphColour = value;
+    }
+
+    /**
+     * Gets the value of the graphGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public Float getValue()
-    {
-      return value;
+    public Integer getGraphGroup() {
+        return graphGroup;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the graphGroup property.
      * 
      * @param value
-     *          allowed object is {@link Float }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphGroup(Integer value) {
+        this.graphGroup = value;
+    }
+
+    /**
+     * Gets the value of the graphHeight property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public void setValue(Float value)
-    {
-      this.value = value;
+    public Integer getGraphHeight() {
+        return graphHeight;
     }
 
     /**
-     * Gets the value of the colour property.
+     * Sets the value of the graphHeight property.
      * 
-     * @return possible object is {@link Integer }
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphHeight(Integer value) {
+        this.graphHeight = value;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Integer getColour()
-    {
-      return colour;
+    public String getId() {
+        return id;
     }
 
     /**
-     * Sets the value of the colour property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the scoreOnly property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
      */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
+    public boolean isScoreOnly() {
+        if (scoreOnly == null) {
+            return false;
+        } else {
+            return scoreOnly;
+        }
     }
 
-  }
+    /**
+     * Sets the value of the scoreOnly property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScoreOnly(Boolean value) {
+        this.scoreOnly = value;
+    }
+
+    /**
+     * Gets the value of the score property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Double }
+     *     
+     */
+    public Double getScore() {
+        return score;
+    }
+
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Double }
+     *     
+     */
+    public void setScore(Double value) {
+        this.score = value;
+    }
+
+    /**
+     * Gets the value of the visible property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isVisible() {
+        return visible;
+    }
+
+    /**
+     * Sets the value of the visible property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setVisible(Boolean value) {
+        this.visible = value;
+    }
+
+    /**
+     * Gets the value of the centreColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isCentreColLabels() {
+        return centreColLabels;
+    }
+
+    /**
+     * Sets the value of the centreColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setCentreColLabels(Boolean value) {
+        this.centreColLabels = value;
+    }
+
+    /**
+     * Gets the value of the scaleColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isScaleColLabels() {
+        return scaleColLabels;
+    }
+
+    /**
+     * Sets the value of the scaleColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScaleColLabels(Boolean value) {
+        this.scaleColLabels = value;
+    }
+
+    /**
+     * Gets the value of the showAllColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isShowAllColLabels() {
+        return showAllColLabels;
+    }
+
+    /**
+     * Sets the value of the showAllColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setShowAllColLabels(Boolean value) {
+        this.showAllColLabels = value;
+    }
+
+    /**
+     * Gets the value of the autoCalculated property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isAutoCalculated() {
+        if (autoCalculated == null) {
+            return false;
+        } else {
+            return autoCalculated;
+        }
+    }
+
+    /**
+     * Sets the value of the autoCalculated property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setAutoCalculated(Boolean value) {
+        this.autoCalculated = value;
+    }
+
+    /**
+     * Gets the value of the belowAlignment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isBelowAlignment() {
+        if (belowAlignment == null) {
+            return true;
+        } else {
+            return belowAlignment;
+        }
+    }
+
+    /**
+     * Sets the value of the belowAlignment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setBelowAlignment(Boolean value) {
+        this.belowAlignment = value;
+    }
+
+    /**
+     * Gets the value of the calcId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCalcId() {
+        return calcId;
+    }
+
+    /**
+     * Sets the value of the calcId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCalcId(String value) {
+        this.calcId = value;
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @XmlAttribute(name = "name")
+        protected String name;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class ThresholdLine {
+
+        @XmlAttribute(name = "label")
+        protected String label;
+        @XmlAttribute(name = "value")
+        protected Float value;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+
+        /**
+         * Gets the value of the label property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLabel() {
+            return label;
+        }
+
+        /**
+         * Sets the value of the label property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLabel(String value) {
+            this.label = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setValue(Float value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
+
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index e697228..522d9c6 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,243 +13,242 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for AnnotationColourScheme complex type.
+ * 
    Java class for AnnotationColourScheme complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="AnnotationColourScheme"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="annotation"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="maxColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="predefinedColours"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="AnnotationColourScheme">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme
-{
-
-  @XmlAttribute(name = "aboveThreshold")
-  protected Integer aboveThreshold;
-
-  @XmlAttribute(name = "annotation")
-  protected String annotation;
-
-  @XmlAttribute(name = "minColour")
-  protected Integer minColour;
-
-  @XmlAttribute(name = "maxColour")
-  protected Integer maxColour;
-
-  @XmlAttribute(name = "colourScheme")
-  protected String colourScheme;
-
-  @XmlAttribute(name = "threshold")
-  protected Float threshold;
-
-  @XmlAttribute(name = "perSequence")
-  protected Boolean perSequence;
-
-  @XmlAttribute(name = "predefinedColours")
-  protected Boolean predefinedColours;
-
-  /**
-   * Gets the value of the aboveThreshold property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getAboveThreshold()
-  {
-    return aboveThreshold;
-  }
-
-  /**
-   * Sets the value of the aboveThreshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setAboveThreshold(Integer value)
-  {
-    this.aboveThreshold = value;
-  }
-
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getAnnotation()
-  {
-    return annotation;
-  }
-
-  /**
-   * Sets the value of the annotation property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setAnnotation(String value)
-  {
-    this.annotation = value;
-  }
-
-  /**
-   * Gets the value of the minColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMinColour()
-  {
-    return minColour;
-  }
-
-  /**
-   * Sets the value of the minColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMinColour(Integer value)
-  {
-    this.minColour = value;
-  }
-
-  /**
-   * Gets the value of the maxColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMaxColour()
-  {
-    return maxColour;
-  }
-
-  /**
-   * Sets the value of the maxColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMaxColour(Integer value)
-  {
-    this.maxColour = value;
-  }
-
-  /**
-   * Gets the value of the colourScheme property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getColourScheme()
-  {
-    return colourScheme;
-  }
-
-  /**
-   * Sets the value of the colourScheme property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setColourScheme(String value)
-  {
-    this.colourScheme = value;
-  }
-
-  /**
-   * Gets the value of the threshold property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * Sets the value of the threshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setThreshold(Float value)
-  {
-    this.threshold = value;
-  }
-
-  /**
-   * Gets the value of the perSequence property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPerSequence()
-  {
-    return perSequence;
-  }
-
-  /**
-   * Sets the value of the perSequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPerSequence(Boolean value)
-  {
-    this.perSequence = value;
-  }
-
-  /**
-   * Gets the value of the predefinedColours property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPredefinedColours()
-  {
-    return predefinedColours;
-  }
-
-  /**
-   * Sets the value of the predefinedColours property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPredefinedColours(Boolean value)
-  {
-    this.predefinedColours = value;
-  }
+public class AnnotationColourScheme {
+
+    @XmlAttribute(name = "aboveThreshold")
+    protected Integer aboveThreshold;
+    @XmlAttribute(name = "annotation")
+    protected String annotation;
+    @XmlAttribute(name = "minColour")
+    protected Integer minColour;
+    @XmlAttribute(name = "maxColour")
+    protected Integer maxColour;
+    @XmlAttribute(name = "colourScheme")
+    protected String colourScheme;
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+    @XmlAttribute(name = "perSequence")
+    protected Boolean perSequence;
+    @XmlAttribute(name = "predefinedColours")
+    protected Boolean predefinedColours;
+
+    /**
+     * Gets the value of the aboveThreshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getAboveThreshold() {
+        return aboveThreshold;
+    }
+
+    /**
+     * Sets the value of the aboveThreshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setAboveThreshold(Integer value) {
+        this.aboveThreshold = value;
+    }
+
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getAnnotation() {
+        return annotation;
+    }
+
+    /**
+     * Sets the value of the annotation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setAnnotation(String value) {
+        this.annotation = value;
+    }
+
+    /**
+     * Gets the value of the minColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMinColour() {
+        return minColour;
+    }
+
+    /**
+     * Sets the value of the minColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMinColour(Integer value) {
+        this.minColour = value;
+    }
+
+    /**
+     * Gets the value of the maxColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMaxColour() {
+        return maxColour;
+    }
+
+    /**
+     * Sets the value of the maxColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMaxColour(Integer value) {
+        this.maxColour = value;
+    }
+
+    /**
+     * Gets the value of the colourScheme property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getColourScheme() {
+        return colourScheme;
+    }
+
+    /**
+     * Sets the value of the colourScheme property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setColourScheme(String value) {
+        this.colourScheme = value;
+    }
+
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getThreshold() {
+        return threshold;
+    }
+
+    /**
+     * Sets the value of the threshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setThreshold(Float value) {
+        this.threshold = value;
+    }
+
+    /**
+     * Gets the value of the perSequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPerSequence() {
+        return perSequence;
+    }
+
+    /**
+     * Sets the value of the perSequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPerSequence(Boolean value) {
+        this.perSequence = value;
+    }
+
+    /**
+     * Gets the value of the predefinedColours property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPredefinedColours() {
+        return predefinedColours;
+    }
+
+    /**
+     * Sets the value of the predefinedColours property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPredefinedColours(Boolean value) {
+        this.predefinedColours = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index ec1216b..99d82a7 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,186 +14,190 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="displayCharacter"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="secondaryStructure" minOccurs="0"&gt;
- * &lt;simpleType&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;length
- * value="1"/&gt; &lt;/restriction&gt; &lt;/simpleType&gt;
- * &lt;/element&gt; &lt;element name="value"
- * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="position" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="secondaryStructure" minOccurs="0">
+ *           <simpleType>
+ *             <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               <length value="1"/>
+ *             </restriction>
+ *           </simpleType>
+ *         </element>
+ *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "displayCharacter", "description", "secondaryStructure", "value" })
+@XmlType(name = "", propOrder = {
+    "displayCharacter",
+    "description",
+    "secondaryStructure",
+    "value"
+})
 @XmlRootElement(name = "annotationElement")
-public class AnnotationElement
-{
-
-  protected String displayCharacter;
-
-  protected String description;
-
-  protected String secondaryStructure;
-
-  protected Float value;
-
-  @XmlAttribute(name = "position", required = true)
-  protected int position;
-
-  @XmlAttribute(name = "colour")
-  protected Integer colour;
-
-  /**
-   * Gets the value of the displayCharacter property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDisplayCharacter()
-  {
-    return displayCharacter;
-  }
-
-  /**
-   * Sets the value of the displayCharacter property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDisplayCharacter(String value)
-  {
-    this.displayCharacter = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the secondaryStructure property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSecondaryStructure()
-  {
-    return secondaryStructure;
-  }
-
-  /**
-   * Sets the value of the secondaryStructure property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSecondaryStructure(String value)
-  {
-    this.secondaryStructure = value;
-  }
-
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getValue()
-  {
-    return value;
-  }
-
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setValue(Float value)
-  {
-    this.value = value;
-  }
-
-  /**
-   * Gets the value of the position property.
-   * 
-   */
-  public int getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   */
-  public void setPosition(int value)
-  {
-    this.position = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColour()
-  {
-    return colour;
-  }
-
-  /**
-   * Sets the value of the colour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColour(Integer value)
-  {
-    this.colour = value;
-  }
+public class AnnotationElement {
+
+    protected String displayCharacter;
+    protected String description;
+    protected String secondaryStructure;
+    protected Float value;
+    @XmlAttribute(name = "position", required = true)
+    protected int position;
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
+
+    /**
+     * Gets the value of the displayCharacter property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDisplayCharacter() {
+        return displayCharacter;
+    }
+
+    /**
+     * Sets the value of the displayCharacter property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDisplayCharacter(String value) {
+        this.displayCharacter = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the secondaryStructure property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSecondaryStructure() {
+        return secondaryStructure;
+    }
+
+    /**
+     * Sets the value of the secondaryStructure property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSecondaryStructure(String value) {
+        this.secondaryStructure = value;
+    }
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getValue() {
+        return value;
+    }
+
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setValue(Float value) {
+        this.value = value;
+    }
+
+    /**
+     * Gets the value of the position property.
+     * 
+     */
+    public int getPosition() {
+        return position;
+    }
+
+    /**
+     * Sets the value of the position property.
+     * 
+     */
+    public void setPosition(int value) {
+        this.position = value;
+    }
+
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColour() {
+        return colour;
+    }
+
+    /**
+     * Sets the value of the colour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColour(Integer value) {
+        this.colour = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 7ce2892..77c6bb7 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,167 +16,171 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for DoubleMatrix complex type.
+ * 
    Java class for DoubleMatrix complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="DoubleMatrix"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="row"
- * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="D"
- * type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; &lt;element
- * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="rows"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="DoubleMatrix">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *         <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleMatrix",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "row", "d", "e" })
-public class DoubleMatrix
-{
-
-  protected List row;
-
-  @XmlElement(name = "D")
-  protected DoubleVector d;
-
-  @XmlElement(name = "E")
-  protected DoubleVector e;
-
-  @XmlAttribute(name = "rows")
-  protected Integer rows;
-
-  @XmlAttribute(name = "columns")
-  protected Integer columns;
-
-  /**
-   * Gets the value of the row property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the row property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getRow().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link DoubleVector }
-   * 
-   * 
-   */
-  public List getRow()
-  {
-    if (row == null)
-    {
-      row = new ArrayList();
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+    "row",
+    "d",
+    "e"
+})
+public class DoubleMatrix {
+
+    protected List row;
+    @XmlElement(name = "D")
+    protected DoubleVector d;
+    @XmlElement(name = "E")
+    protected DoubleVector e;
+    @XmlAttribute(name = "rows")
+    protected Integer rows;
+    @XmlAttribute(name = "columns")
+    protected Integer columns;
+
+    /**
+     * Gets the value of the row 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 row property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getRow().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link DoubleVector }
+     * 
+     * 
+     */
+    public List getRow() {
+        if (row == null) {
+            row = new ArrayList();
+        }
+        return this.row;
+    }
+
+    /**
+     * Gets the value of the d property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getD() {
+        return d;
+    }
+
+    /**
+     * Sets the value of the d property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setD(DoubleVector value) {
+        this.d = value;
+    }
+
+    /**
+     * Gets the value of the e property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getE() {
+        return e;
+    }
+
+    /**
+     * Sets the value of the e property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setE(DoubleVector value) {
+        this.e = value;
+    }
+
+    /**
+     * Gets the value of the rows property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getRows() {
+        return rows;
+    }
+
+    /**
+     * Sets the value of the rows property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setRows(Integer value) {
+        this.rows = value;
+    }
+
+    /**
+     * Gets the value of the columns property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColumns() {
+        return columns;
+    }
+
+    /**
+     * Sets the value of the columns property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColumns(Integer value) {
+        this.columns = value;
     }
-    return this.row;
-  }
-
-  /**
-   * Gets the value of the d property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getD()
-  {
-    return d;
-  }
-
-  /**
-   * Sets the value of the d property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setD(DoubleVector value)
-  {
-    this.d = value;
-  }
-
-  /**
-   * Gets the value of the e property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getE()
-  {
-    return e;
-  }
-
-  /**
-   * Sets the value of the e property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setE(DoubleVector value)
-  {
-    this.e = value;
-  }
-
-  /**
-   * Gets the value of the rows property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getRows()
-  {
-    return rows;
-  }
-
-  /**
-   * Sets the value of the rows property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setRows(Integer value)
-  {
-    this.rows = value;
-  }
-
-  /**
-   * Gets the value of the columns property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColumns()
-  {
-    return columns;
-  }
-
-  /**
-   * Sets the value of the columns property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColumns(Integer value)
-  {
-    this.columns = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 4995dd3..f1dad96 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,58 +15,62 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for DoubleVector complex type.
+ * 
    Java class for DoubleVector complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="DoubleVector"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="v"
- * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="DoubleVector">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleVector",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "v" })
-public class DoubleVector
-{
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+    "v"
+})
+public class DoubleVector {
 
-  @XmlElement(type = Double.class)
-  protected List v;
+    @XmlElement(type = Double.class)
+    protected List v;
 
-  /**
-   * Gets the value of the v property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the v property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getV().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Double }
-   * 
-   * 
-   */
-  public List getV()
-  {
-    if (v == null)
-    {
-      v = new ArrayList();
+    /**
+     * Gets the value of the v 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 v property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getV().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Double }
+     * 
+     * 
+     */
+    public List getV() {
+        if (v == null) {
+            v = new ArrayList();
+        }
+        return this.v;
     }
-    return this.v;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 4c496e5..dac24c4 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,350 +15,349 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for feature complex type.
+ * 
    Java class for feature complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="feature"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="otherData"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="key2"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="begin" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="status"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="feature">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "feature",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "otherData" })
-public class Feature
-{
-
-  protected List otherData;
-
-  @XmlAttribute(name = "begin", required = true)
-  protected int begin;
-
-  @XmlAttribute(name = "end", required = true)
-  protected int end;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  @XmlAttribute(name = "status")
-  protected String status;
-
-  @XmlAttribute(name = "featureGroup")
-  protected String featureGroup;
-
-  @XmlAttribute(name = "score")
-  protected Float score;
-
-  /**
-   * Gets the value of the otherData property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the otherData property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getOtherData().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Feature.OtherData }
-   * 
-   * 
-   */
-  public List getOtherData()
-  {
-    if (otherData == null)
-    {
-      otherData = new ArrayList();
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+    "otherData"
+})
+public class Feature {
+
+    protected List otherData;
+    @XmlAttribute(name = "begin", required = true)
+    protected int begin;
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "description")
+    protected String description;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "featureGroup")
+    protected String featureGroup;
+    @XmlAttribute(name = "score")
+    protected Float score;
+
+    /**
+     * Gets the value of the otherData 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 otherData property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getOtherData().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Feature.OtherData }
+     * 
+     * 
+     */
+    public List getOtherData() {
+        if (otherData == null) {
+            otherData = new ArrayList();
+        }
+        return this.otherData;
     }
-    return this.otherData;
-  }
-
-  /**
-   * Gets the value of the begin property.
-   * 
-   */
-  public int getBegin()
-  {
-    return begin;
-  }
-
-  /**
-   * Sets the value of the begin property.
-   * 
-   */
-  public void setBegin(int value)
-  {
-    this.begin = value;
-  }
-
-  /**
-   * Gets the value of the end property.
-   * 
-   */
-  public int getEnd()
-  {
-    return end;
-  }
-
-  /**
-   * Sets the value of the end property.
-   * 
-   */
-  public void setEnd(int value)
-  {
-    this.end = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
-
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
-
-  /**
-   * Gets the value of the featureGroup property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFeatureGroup()
-  {
-    return featureGroup;
-  }
-
-  /**
-   * Sets the value of the featureGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFeatureGroup(String value)
-  {
-    this.featureGroup = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setScore(Float value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="key2"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class OtherData
-  {
-
-    @XmlAttribute(name = "key", required = true)
-    protected String key;
-
-    @XmlAttribute(name = "key2")
-    protected String key2;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
 
     /**
-     * Gets the value of the key property.
+     * Gets the value of the begin property.
      * 
-     * @return possible object is {@link String }
+     */
+    public int getBegin() {
+        return begin;
+    }
+
+    /**
+     * Sets the value of the begin property.
      * 
      */
-    public String getKey()
-    {
-      return key;
+    public void setBegin(int value) {
+        this.begin = value;
     }
 
     /**
-     * Sets the value of the key property.
+     * Gets the value of the end property.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     */
+    public int getEnd() {
+        return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     */
+    public void setEnd(int value) {
+        this.end = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the key2 property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the description property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getKey2()
-    {
-      return key2;
+    public String getDescription() {
+        return description;
     }
 
     /**
-     * Sets the value of the key2 property.
+     * Sets the value of the description property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the status property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey2(String value)
-    {
-      this.key2 = value;
+    public String getStatus() {
+        return status;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the status property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
+
+    /**
+     * Gets the value of the featureGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFeatureGroup() {
+        return featureGroup;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the featureGroup property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFeatureGroup(String value) {
+        this.featureGroup = value;
+    }
+
+    /**
+     * Gets the value of the score property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public Float getScore() {
+        return score;
     }
 
-  }
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setScore(Float value) {
+        this.score = value;
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class OtherData {
+
+        @XmlAttribute(name = "key", required = true)
+        protected String key;
+        @XmlAttribute(name = "key2")
+        protected String key2;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the key2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey2() {
+            return key2;
+        }
+
+        /**
+         * Sets the value of the key2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey2(String value) {
+            this.key2 = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index 7fd14fa..8a30d89 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,141 +16,145 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for FeatureMatcher complex type.
+ * 
    Java class for FeatureMatcher complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="FeatureMatcher"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="condition"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="by"
- * type="{www.jalview.org/colours}FilterBy" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="FeatureMatcher">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *         <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       </sequence>
+ *       <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcher",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "attributeName", "condition", "value" })
-public class FeatureMatcher
-{
-
-  @XmlElement(namespace = "")
-  protected List attributeName;
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+    "attributeName",
+    "condition",
+    "value"
+})
+public class FeatureMatcher {
 
-  @XmlElement(namespace = "", required = true)
-  protected String condition;
+    @XmlElement(namespace = "")
+    protected List attributeName;
+    @XmlElement(namespace = "", required = true)
+    protected String condition;
+    @XmlElement(namespace = "", required = true)
+    protected String value;
+    @XmlAttribute(name = "by")
+    protected FilterBy by;
 
-  @XmlElement(namespace = "", required = true)
-  protected String value;
-
-  @XmlAttribute(name = "by")
-  protected FilterBy by;
-
-  /**
-   * Gets the value of the attributeName property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the attributeName property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAttributeName().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List getAttributeName()
-  {
-    if (attributeName == null)
-    {
-      attributeName = new ArrayList();
+    /**
+     * Gets the value of the attributeName 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 attributeName property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAttributeName().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getAttributeName() {
+        if (attributeName == null) {
+            attributeName = new ArrayList();
+        }
+        return this.attributeName;
     }
-    return this.attributeName;
-  }
 
-  /**
-   * Gets the value of the condition property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCondition()
-  {
-    return condition;
-  }
+    /**
+     * Gets the value of the condition property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCondition() {
+        return condition;
+    }
 
-  /**
-   * Sets the value of the condition property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCondition(String value)
-  {
-    this.condition = value;
-  }
+    /**
+     * Sets the value of the condition property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCondition(String value) {
+        this.condition = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the by property.
-   * 
-   * @return possible object is {@link FilterBy }
-   * 
-   */
-  public FilterBy getBy()
-  {
-    return by;
-  }
+    /**
+     * Gets the value of the by property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link FilterBy }
+     *     
+     */
+    public FilterBy getBy() {
+        return by;
+    }
 
-  /**
-   * Sets the value of the by property.
-   * 
-   * @param value
-   *          allowed object is {@link FilterBy }
-   * 
-   */
-  public void setBy(FilterBy value)
-  {
-    this.by = value;
-  }
+    /**
+     * Sets the value of the by property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link FilterBy }
+     *     
+     */
+    public void setBy(FilterBy value) {
+        this.by = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index d2bdaaa..a902a83 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,167 +16,177 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * A feature match condition, which may be simple or compound
  * 
- * <p>Java class for FeatureMatcherSet complex type.
+ * 
    Java class for FeatureMatcherSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="FeatureMatcherSet"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;choice&gt; &lt;element name="matchCondition"
- * type="{www.jalview.org/colours}FeatureMatcher"/&gt; &lt;element
- * name="compoundMatcher"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
- * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute name="and"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;/choice&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="FeatureMatcherSet">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <choice>
+ *         <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ *         <element name="compoundMatcher">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ *                 </sequence>
+ *                 <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </choice>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcherSet",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "matchCondition", "compoundMatcher" })
-public class FeatureMatcherSet
-{
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcher matchCondition;
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
-
-  /**
-   * Gets the value of the matchCondition property.
-   * 
-   * @return possible object is {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher getMatchCondition()
-  {
-    return matchCondition;
-  }
-
-  /**
-   * Sets the value of the matchCondition property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcher }
-   * 
-   */
-  public void setMatchCondition(FeatureMatcher value)
-  {
-    this.matchCondition = value;
-  }
-
-  /**
-   * Gets the value of the compoundMatcher property.
-   * 
-   * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
-  {
-    return compoundMatcher;
-  }
-
-  /**
-   * Sets the value of the compoundMatcher property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
-  {
-    this.compoundMatcher = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
-   * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute
-   * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class CompoundMatcher
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected List matcherSet;
-
-    @XmlAttribute(name = "and", required = true)
-    protected boolean and;
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+    "matchCondition",
+    "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+    @XmlElement(namespace = "")
+    protected FeatureMatcher matchCondition;
+    @XmlElement(namespace = "")
+    protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
 
     /**
-     * Gets the value of the matcherSet property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the matcherSet property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getMatcherSet().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link FeatureMatcherSet }
+     * Gets the value of the matchCondition property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcher }
+     *     
+     */
+    public FeatureMatcher getMatchCondition() {
+        return matchCondition;
+    }
+
+    /**
+     * Sets the value of the matchCondition property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcher }
+     *     
      */
-    public List getMatcherSet()
-    {
-      if (matcherSet == null)
-      {
-        matcherSet = new ArrayList();
-      }
-      return this.matcherSet;
+    public void setMatchCondition(FeatureMatcher value) {
+        this.matchCondition = value;
     }
 
     /**
-     * Gets the value of the and property.
+     * Gets the value of the compoundMatcher property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public boolean isAnd()
-    {
-      return and;
+    public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+        return compoundMatcher;
     }
 
     /**
-     * Sets the value of the and property.
+     * Sets the value of the compoundMatcher property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public void setAnd(boolean value)
-    {
-      this.and = value;
+    public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+        this.compoundMatcher = value;
     }
 
-  }
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+     *       </sequence>
+     *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class CompoundMatcher {
+
+        @XmlElement(namespace = "", required = true)
+        protected List matcherSet;
+        @XmlAttribute(name = "and", required = true)
+        protected boolean and;
+
+        /**
+         * Gets the value of the matcherSet 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 matcherSet property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getMatcherSet().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link FeatureMatcherSet }
+         * 
+         * 
+         */
+        public List getMatcherSet() {
+            if (matcherSet == null) {
+                matcherSet = new ArrayList();
+            }
+            return this.matcherSet;
+        }
+
+        /**
+         * Gets the value of the and property.
+         * 
+         */
+        public boolean isAnd() {
+            return and;
+        }
+
+        /**
+         * Sets the value of the and property.
+         * 
+         */
+        public void setAnd(boolean value) {
+            this.and = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index 9614490..a95d432 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -1,60 +1,61 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for FilterBy.
+ * 
    Java class for FilterBy.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="FilterBy"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="byLabel"/&gt; &lt;enumeration value="byScore"/&gt;
- * &lt;enumeration value="byAttribute"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * 
    The following schema fragment specifies the expected content contained within this class.
+ * 
    
+ * 
    + * <simpleType name="FilterBy">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="byLabel"/>
+ *     <enumeration value="byScore"/>
+ *     <enumeration value="byAttribute"/>
+ *   </restriction>
+ * </simpleType>
+ * 
    
  * 
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy
-{
-
-  @XmlEnumValue("byLabel")
-  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
-  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
-  BY_ATTRIBUTE("byAttribute");
-
-  private final String value;
-
-  FilterBy(String v)
-  {
-    value = v;
-  }
-
-  public String value()
-  {
-    return value;
-  }
-
-  public static FilterBy fromValue(String v)
-  {
-    for (FilterBy c : FilterBy.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+public enum FilterBy {
+
+    @XmlEnumValue("byLabel")
+    BY_LABEL("byLabel"),
+    @XmlEnumValue("byScore")
+    BY_SCORE("byScore"),
+    @XmlEnumValue("byAttribute")
+    BY_ATTRIBUTE("byAttribute");
+    private final String value;
+
+    FilterBy(String v) {
+        value = v;
+    }
+
+    public String value() {
+        return value;
+    }
+
+    public static FilterBy fromValue(String v) {
+        for (FilterBy c: FilterBy.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 9909b08..2de1eba 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -21,6393 +22,6677 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * <p>Java class for JalviewModel complex type.
+ * 
    Java class for JalviewModel complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="creationDate"
- * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel"
- * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
- * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequencePoint"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="seqPointMax"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; &lt;attGroup
- * ref="{www.jalview.org}SimilarityParams"/&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="zDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&gt; &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="JalviewModel">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         <sequence>
+ *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org}pdbentry">
+ *                             <sequence>
+ *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 <complexType>
+ *                                   <simpleContent>
+ *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </extension>
+ *                                   </simpleContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 <complexType>
+ *                                   <complexContent>
+ *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </restriction>
+ *                                   </complexContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="overview" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   </sequence>
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence minOccurs="0">
+ *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="sequencePoint" maxOccurs="unbounded">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                             <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="axis" maxOccurs="3" minOccurs="3">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="seqPointMin">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="seqPointMax">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ *                   </sequence>
+ *                   <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" />
+ *                   <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="FeatureSettings" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             </sequence>
+ *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *         </sequence>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewModel",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
-      "userColours", "tree", "pcaViewer", "featureSettings" })
-public class JalviewModel
-{
-
-  @XmlElement(required = true)
-  @XmlSchemaType(name = "dateTime")
-  protected XMLGregorianCalendar creationDate;
-
-  @XmlElement(required = true)
-  protected String version;
-
-  @XmlElement(required = true)
-  protected VAMSAS vamsasModel;
-
-  @XmlElement(name = "JSeq")
-  protected List jSeq;
-
-  @XmlElement(name = "JGroup")
-  protected List jGroup;
-
-  @XmlElement(name = "Viewport")
-  protected List viewport;
-
-  @XmlElement(name = "UserColours")
-  protected List userColours;
-
-  protected List tree;
-
-  @XmlElement(name = "PcaViewer")
-  protected List pcaViewer;
-
-  @XmlElement(name = "FeatureSettings")
-  protected JalviewModel.FeatureSettings featureSettings;
-
-  /**
-   * Gets the value of the creationDate property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreationDate()
-  {
-    return creationDate;
-  }
-
-  /**
-   * Sets the value of the creationDate property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreationDate(XMLGregorianCalendar value)
-  {
-    this.creationDate = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the vamsasModel property.
-   * 
-   * @return possible object is {@link VAMSAS }
-   * 
-   */
-  public VAMSAS getVamsasModel()
-  {
-    return vamsasModel;
-  }
-
-  /**
-   * Sets the value of the vamsasModel property.
-   * 
-   * @param value
-   *          allowed object is {@link VAMSAS }
-   * 
-   */
-  public void setVamsasModel(VAMSAS value)
-  {
-    this.vamsasModel = value;
-  }
-
-  /**
-   * Gets the value of the jSeq property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the jSeq property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getJSeq().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JSeq }
-   * 
-   * 
-   */
-  public List getJSeq()
-  {
-    if (jSeq == null)
-    {
-      jSeq = new ArrayList();
-    }
-    return this.jSeq;
-  }
-
-  /**
-   * Gets the value of the jGroup property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the jGroup property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getJGroup().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JGroup }
-   * 
-   * 
-   */
-  public List getJGroup()
-  {
-    if (jGroup == null)
-    {
-      jGroup = new ArrayList();
-    }
-    return this.jGroup;
-  }
-
-  /**
-   * Gets the value of the viewport property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the viewport property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getViewport().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Viewport }
-   * 
-   * 
-   */
-  public List getViewport()
-  {
-    if (viewport == null)
-    {
-      viewport = new ArrayList();
-    }
-    return this.viewport;
-  }
-
-  /**
-   * Gets the value of the userColours property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the userColours property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getUserColours().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.UserColours }
-   * 
-   * 
-   */
-  public List getUserColours()
-  {
-    if (userColours == null)
-    {
-      userColours = new ArrayList();
-    }
-    return this.userColours;
-  }
-
-  /**
-   * Gets the value of the tree property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the tree property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getTree().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Tree }
-   * 
-   * 
-   */
-  public List getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList();
-    }
-    return this.tree;
-  }
-
-  /**
-   * Gets the value of the pcaViewer property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the pcaViewer property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getPcaViewer().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.PcaViewer }
-   * 
-   * 
-   */
-  public List getPcaViewer()
-  {
-    if (pcaViewer == null)
-    {
-      pcaViewer = new ArrayList();
-    }
-    return this.pcaViewer;
-  }
-
-  /**
-   * Gets the value of the featureSettings property.
-   * 
-   * @return possible object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings getFeatureSettings()
-  {
-    return featureSettings;
-  }
-
-  /**
-   * Sets the value of the featureSettings property.
-   * 
-   * @param value
-   *          allowed object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public void setFeatureSettings(JalviewModel.FeatureSettings value)
-  {
-    this.featureSettings = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="setting"
-   * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="attributeName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-   * minOccurs="0"/&gt; &lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="type" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;attribute name="display" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="order"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="noValueColour"
-   * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
-   * &lt;attribute name="threshold"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
-   * /&gt; &lt;attribute name="min"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;attribute name="autoScale"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt; &lt;element
-   * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
-   * &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="display" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt;
-   * &lt;/sequence&gt; &lt;/restriction&gt;
-   * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "setting", "group" })
-  public static class FeatureSettings
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List setting;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List group;
-
-    /**
-     * Gets the value of the setting property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the setting property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getSetting().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Setting }
-     * 
-     * 
-     */
-    public List getSetting()
-    {
-      if (setting == null)
-      {
-        setting = new ArrayList();
-      }
-      return this.setting;
-    }
-
-    /**
-     * Gets the value of the group property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the group property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getGroup().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Group }
-     * 
-     * 
-     */
-    public List getGroup()
-    {
-      if (group == null)
-      {
-        group = new ArrayList();
-      }
-      return this.group;
-    }
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-     * &lt;attribute name="name" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="display" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Group
-    {
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-    }
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-     * &lt;sequence&gt; &lt;element name="attributeName"
-     * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-     * minOccurs="0"/&gt; &lt;element name="matcherSet"
-     * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
-     * &lt;/sequence&gt; &lt;attribute name="type" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="colour" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-     * name="display" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;attribute name="order"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-     * &lt;attribute name="mincolour"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-     * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
-     * default="Min" /&gt; &lt;attribute name="threshold"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-     * &lt;attribute name="threshstate"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-     * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-     * &lt;attribute name="min"
-     * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-     * &lt;attribute name="colourByLabel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;attribute name="autoScale"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
-    public static class Setting
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List attributeName;
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected FeatureMatcherSet matcherSet;
-
-      @XmlAttribute(name = "type", required = true)
-      protected String type;
-
-      @XmlAttribute(name = "colour", required = true)
-      protected int colour;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      @XmlAttribute(name = "order")
-      protected Float order;
-
-      @XmlAttribute(name = "mincolour")
-      protected Integer mincolour;
-
-      @XmlAttribute(name = "noValueColour")
-      protected NoValueColour noValueColour;
-
-      @XmlAttribute(name = "threshold")
-      protected Float threshold;
-
-      @XmlAttribute(name = "threshstate")
-      protected Integer threshstate;
-
-      @XmlAttribute(name = "max")
-      protected Float max;
-
-      @XmlAttribute(name = "min")
-      protected Float min;
-
-      @XmlAttribute(name = "colourByLabel")
-      protected Boolean colourByLabel;
-
-      @XmlAttribute(name = "autoScale")
-      protected Boolean autoScale;
-
-      /**
-       * Gets the value of the attributeName property.
-       * 
-       * <p> 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
-       * <CODE>set</CODE> method for the attributeName property.
-       * 
-       * <p> For example, to add a new item, do as follows: <pre>
-       * getAttributeName().add(newItem); </pre>
-       * 
-       * 
-       * <p> Objects of the following type(s) are allowed in the list
-       * {@link String }
-       * 
-       * 
-       */
-      public List getAttributeName()
-      {
-        if (attributeName == null)
-        {
-          attributeName = new ArrayList();
-        }
-        return this.attributeName;
-      }
-
-      /**
-       * Gets the value of the matcherSet property.
-       * 
-       * @return possible object is {@link FeatureMatcherSet }
-       * 
-       */
-      public FeatureMatcherSet getMatcherSet()
-      {
-        return matcherSet;
-      }
-
-      /**
-       * Sets the value of the matcherSet property.
-       * 
-       * @param value
-       *          allowed object is {@link FeatureMatcherSet }
-       * 
-       */
-      public void setMatcherSet(FeatureMatcherSet value)
-      {
-        this.matcherSet = value;
-      }
-
-      /**
-       * Gets the value of the type property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getType()
-      {
-        return type;
-      }
-
-      /**
-       * Sets the value of the type property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setType(String value)
-      {
-        this.type = value;
-      }
-
-      /**
-       * Gets the value of the colour property.
-       * 
-       */
-      public int getColour()
-      {
-        return colour;
-      }
-
-      /**
-       * Sets the value of the colour property.
-       * 
-       */
-      public void setColour(int value)
-      {
-        this.colour = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-      /**
-       * Gets the value of the order property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getOrder()
-      {
-        return order;
-      }
-
-      /**
-       * Sets the value of the order property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setOrder(Float value)
-      {
-        this.order = value;
-      }
-
-      /**
-       * Gets the value of the mincolour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getMincolour()
-      {
-        return mincolour;
-      }
-
-      /**
-       * Sets the value of the mincolour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setMincolour(Integer value)
-      {
-        this.mincolour = value;
-      }
-
-      /**
-       * Gets the value of the noValueColour property.
-       * 
-       * @return possible object is {@link NoValueColour }
-       * 
-       */
-      public NoValueColour getNoValueColour()
-      {
-        if (noValueColour == null)
-        {
-          return NoValueColour.MIN;
-        }
-        else
-        {
-          return noValueColour;
-        }
-      }
-
-      /**
-       * Sets the value of the noValueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link NoValueColour }
-       * 
-       */
-      public void setNoValueColour(NoValueColour value)
-      {
-        this.noValueColour = value;
-      }
-
-      /**
-       * Gets the value of the threshold property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getThreshold()
-      {
-        return threshold;
-      }
-
-      /**
-       * Sets the value of the threshold property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setThreshold(Float value)
-      {
-        this.threshold = value;
-      }
-
-      /**
-       * Gets the value of the threshstate property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getThreshstate()
-      {
-        return threshstate;
-      }
-
-      /**
-       * Sets the value of the threshstate property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setThreshstate(Integer value)
-      {
-        this.threshstate = value;
-      }
-
-      /**
-       * Gets the value of the max property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMax()
-      {
-        return max;
-      }
-
-      /**
-       * Sets the value of the max property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMax(Float value)
-      {
-        this.max = value;
-      }
-
-      /**
-       * Gets the value of the min property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMin()
-      {
-        return min;
-      }
-
-      /**
-       * Sets the value of the min property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMin(Float value)
-      {
-        this.min = value;
-      }
-
-      /**
-       * Gets the value of the colourByLabel property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isColourByLabel()
-      {
-        return colourByLabel;
-      }
-
-      /**
-       * Sets the value of the colourByLabel property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setColourByLabel(Boolean value)
-      {
-        this.colourByLabel = value;
-      }
-
-      /**
-       * Gets the value of the autoScale property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isAutoScale()
-      {
-        return autoScale;
-      }
-
-      /**
-       * Sets the value of the autoScale property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setAutoScale(Boolean value)
-      {
-        this.autoScale = value;
-      }
-
-    }
-
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="seq"
-   * type="{http://www.w3.org/2001/XMLSchema}string"
-   * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
-   * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="start"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="name"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="consThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="outlineColour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;attribute name="displayText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="colourText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="textCol1"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="textColThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;attribute name="ignoreGapsinConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="showConsensusHistogram"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="showSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="normaliseSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
-  public static class JGroup
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List seq;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlAttribute(name = "start")
-    protected Integer start;
-
-    @XmlAttribute(name = "end")
-    protected Integer end;
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "colour")
-    protected String colour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "outlineColour")
-    protected Integer outlineColour;
-
-    @XmlAttribute(name = "displayBoxes")
-    protected Boolean displayBoxes;
-
-    @XmlAttribute(name = "displayText")
-    protected Boolean displayText;
-
-    @XmlAttribute(name = "colourText")
-    protected Boolean colourText;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the seq property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the seq property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getSeq().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getSeq()
-    {
-      if (seq == null)
-      {
-        seq = new ArrayList();
-      }
-      return this.seq;
-    }
-
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+    "creationDate",
+    "version",
+    "vamsasModel",
+    "jSeq",
+    "jGroup",
+    "viewport",
+    "userColours",
+    "tree",
+    "pcaViewer",
+    "featureSettings"
+})
+public class JalviewModel {
+
+    @XmlElement(required = true)
+    @XmlSchemaType(name = "dateTime")
+    protected XMLGregorianCalendar creationDate;
+    @XmlElement(required = true)
+    protected String version;
+    @XmlElement(required = true)
+    protected VAMSAS vamsasModel;
+    @XmlElement(name = "JSeq")
+    protected List jSeq;
+    @XmlElement(name = "JGroup")
+    protected List jGroup;
+    @XmlElement(name = "Viewport")
+    protected List viewport;
+    @XmlElement(name = "UserColours")
+    protected List userColours;
+    protected List tree;
+    @XmlElement(name = "PcaViewer")
+    protected List pcaViewer;
+    @XmlElement(name = "FeatureSettings")
+    protected JalviewModel.FeatureSettings featureSettings;
+
+    /**
+     * Gets the value of the creationDate property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getCreationDate() {
+        return creationDate;
+    }
+
+    /**
+     * Sets the value of the creationDate property.
      * 
      * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
      */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
+    public void setCreationDate(XMLGregorianCalendar value) {
+        this.creationDate = value;
     }
 
     /**
-     * Gets the value of the start property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the version property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Integer getStart()
-    {
-      return start;
+    public String getVersion() {
+        return version;
     }
 
     /**
-     * Sets the value of the start property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setStart(Integer value)
-    {
-      this.start = value;
+    public void setVersion(String value) {
+        this.version = value;
     }
 
     /**
-     * Gets the value of the end property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the vamsasModel property.
      * 
+     * @return
+     *     possible object is
+     *     {@link VAMSAS }
+     *     
      */
-    public Integer getEnd()
-    {
-      return end;
+    public VAMSAS getVamsasModel() {
+        return vamsasModel;
     }
 
     /**
-     * Sets the value of the end property.
+     * Sets the value of the vamsasModel property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
+     *     allowed object is
+     *     {@link VAMSAS }
+     *     
      */
-    public void setEnd(Integer value)
-    {
-      this.end = value;
+    public void setVamsasModel(VAMSAS value) {
+        this.vamsasModel = value;
     }
 
     /**
-     * Gets the value of the name property.
+     * Gets the value of the jSeq property.
      * 
-     * @return possible object is {@link String }
+     * 
    
+     * 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 jSeq property.
      * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getJSeq().add(newItem);
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getColour()
-    {
-      return colour;
+    public List getJSeq() {
+        if (jSeq == null) {
+            jSeq = new ArrayList();
+        }
+        return this.jSeq;
     }
 
     /**
-     * Sets the value of the colour property.
+     * Gets the value of the jGroup property.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     * 
    
+     * 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 jGroup property.
      * 
-     */
-    public void setColour(String value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getJGroup().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link Integer }
      * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JGroup }
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
+    public List getJGroup() {
+        if (jGroup == null) {
+            jGroup = new ArrayList();
+        }
+        return this.jGroup;
     }
 
     /**
-     * Gets the value of the pidThreshold property.
+     * Gets the value of the viewport property.
      * 
-     * @return possible object is {@link Integer }
+     * 
    
+     * 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 viewport property.
      * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getViewport().add(newItem);
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the outlineColour property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport }
      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getOutlineColour()
-    {
-      return outlineColour;
+    public List getViewport() {
+        if (viewport == null) {
+            viewport = new ArrayList();
+        }
+        return this.viewport;
     }
 
     /**
-     * Sets the value of the outlineColour property.
+     * Gets the value of the userColours property.
      * 
-     * @param value
-     *          allowed object is {@link Integer }
+     * 
    
+     * 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 userColours property.
      * 
-     */
-    public void setOutlineColour(Integer value)
-    {
-      this.outlineColour = value;
-    }
-
-    /**
-     * Gets the value of the displayBoxes property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getUserColours().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link Boolean }
      * 
-     */
-    public Boolean isDisplayBoxes()
-    {
-      return displayBoxes;
-    }
-
-    /**
-     * Sets the value of the displayBoxes property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.UserColours }
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
      * 
      */
-    public void setDisplayBoxes(Boolean value)
-    {
-      this.displayBoxes = value;
+    public List getUserColours() {
+        if (userColours == null) {
+            userColours = new ArrayList();
+        }
+        return this.userColours;
     }
 
     /**
-     * Gets the value of the displayText property.
+     * Gets the value of the tree property.
      * 
-     * @return possible object is {@link Boolean }
+     * 
    
+     * 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 tree property.
      * 
-     */
-    public Boolean isDisplayText()
-    {
-      return displayText;
-    }
-
-    /**
-     * Sets the value of the displayText property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getTree().add(newItem);
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
      * 
-     */
-    public void setDisplayText(Boolean value)
-    {
-      this.displayText = value;
-    }
-
-    /**
-     * Gets the value of the colourText property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Tree }
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public Boolean isColourText()
-    {
-      return colourText;
+    public List getTree() {
+        if (tree == null) {
+            tree = new ArrayList();
+        }
+        return this.tree;
     }
 
     /**
-     * Sets the value of the colourText property.
+     * Gets the value of the pcaViewer property.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * 
    
+     * 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 pcaViewer property.
      * 
-     */
-    public void setColourText(Boolean value)
-    {
-      this.colourText = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getPcaViewer().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link Integer }
      * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer }
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
+    public List getPcaViewer() {
+        if (pcaViewer == null) {
+            pcaViewer = new ArrayList();
+        }
+        return this.pcaViewer;
     }
 
     /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
+     * Gets the value of the featureSettings property.
      * 
+     * @return
+     *     possible object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
      */
-    public Integer getTextCol2()
-    {
-      return textCol2;
+    public JalviewModel.FeatureSettings getFeatureSettings() {
+        return featureSettings;
     }
 
     /**
-     * Sets the value of the textCol2 property.
+     * Sets the value of the featureSettings property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
+     *     allowed object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
+     */
+    public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+        this.featureSettings = value;
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 </sequence>
+     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "setting",
+        "group"
+    })
+    public static class FeatureSettings {
 
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
+        @XmlElement(namespace = "www.jalview.org")
+        protected List setting;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List group;
 
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowUnconserved()
-    {
-      return showUnconserved;
-    }
+        /**
+         * Gets the value of the setting 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 setting property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getSetting().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Setting }
+         * 
+         * 
+         */
+        public List getSetting() {
+            if (setting == null) {
+                setting = new ArrayList();
+            }
+            return this.setting;
+        }
 
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
+        /**
+         * Gets the value of the group 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 group property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getGroup().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Group }
+         * 
+         * 
+         */
+        public List getGroup() {
+            if (group == null) {
+                group = new ArrayList();
+            }
+            return this.group;
+        }
 
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
 
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Group {
+
+            @XmlAttribute(name = "name", required = true)
+            protected String name;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+
+            /**
+             * Gets the value of the name property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getName() {
+                return name;
+            }
+
+            /**
+             * Sets the value of the name property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setName(String value) {
+                this.name = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
 
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
+        }
 
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
 
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       </sequence>
+         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "attributeName",
+            "matcherSet"
+        })
+        public static class Setting {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List attributeName;
+            @XmlElement(namespace = "www.jalview.org")
+            protected FeatureMatcherSet matcherSet;
+            @XmlAttribute(name = "type", required = true)
+            protected String type;
+            @XmlAttribute(name = "colour", required = true)
+            protected int colour;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+            @XmlAttribute(name = "order")
+            protected Float order;
+            @XmlAttribute(name = "mincolour")
+            protected Integer mincolour;
+            @XmlAttribute(name = "noValueColour")
+            protected NoValueColour noValueColour;
+            @XmlAttribute(name = "threshold")
+            protected Float threshold;
+            @XmlAttribute(name = "threshstate")
+            protected Integer threshstate;
+            @XmlAttribute(name = "max")
+            protected Float max;
+            @XmlAttribute(name = "min")
+            protected Float min;
+            @XmlAttribute(name = "colourByLabel")
+            protected Boolean colourByLabel;
+            @XmlAttribute(name = "autoScale")
+            protected Boolean autoScale;
+
+            /**
+             * Gets the value of the attributeName 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 attributeName property.
+             * 
+             * 
    
+             * For example, to add a new item, do as follows:
+             * 
    +             *    getAttributeName().add(newItem);
+             * 
    
+             * 
+             * 
+             * 
    
+             * Objects of the following type(s) are allowed in the list
+             * {@link String }
+             * 
+             * 
+             */
+            public List getAttributeName() {
+                if (attributeName == null) {
+                    attributeName = new ArrayList();
+                }
+                return this.attributeName;
+            }
+
+            /**
+             * Gets the value of the matcherSet property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public FeatureMatcherSet getMatcherSet() {
+                return matcherSet;
+            }
+
+            /**
+             * Sets the value of the matcherSet property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public void setMatcherSet(FeatureMatcherSet value) {
+                this.matcherSet = value;
+            }
+
+            /**
+             * Gets the value of the type property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getType() {
+                return type;
+            }
+
+            /**
+             * Sets the value of the type property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setType(String value) {
+                this.type = value;
+            }
+
+            /**
+             * Gets the value of the colour property.
+             * 
+             */
+            public int getColour() {
+                return colour;
+            }
+
+            /**
+             * Sets the value of the colour property.
+             * 
+             */
+            public void setColour(int value) {
+                this.colour = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
+
+            /**
+             * Gets the value of the order property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getOrder() {
+                return order;
+            }
+
+            /**
+             * Sets the value of the order property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setOrder(Float value) {
+                this.order = value;
+            }
+
+            /**
+             * Gets the value of the mincolour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getMincolour() {
+                return mincolour;
+            }
+
+            /**
+             * Sets the value of the mincolour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setMincolour(Integer value) {
+                this.mincolour = value;
+            }
+
+            /**
+             * Gets the value of the noValueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public NoValueColour getNoValueColour() {
+                if (noValueColour == null) {
+                    return NoValueColour.MIN;
+                } else {
+                    return noValueColour;
+                }
+            }
+
+            /**
+             * Sets the value of the noValueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public void setNoValueColour(NoValueColour value) {
+                this.noValueColour = value;
+            }
+
+            /**
+             * Gets the value of the threshold property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getThreshold() {
+                return threshold;
+            }
+
+            /**
+             * Sets the value of the threshold property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setThreshold(Float value) {
+                this.threshold = value;
+            }
+
+            /**
+             * Gets the value of the threshstate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getThreshstate() {
+                return threshstate;
+            }
+
+            /**
+             * Sets the value of the threshstate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setThreshstate(Integer value) {
+                this.threshstate = value;
+            }
+
+            /**
+             * Gets the value of the max property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMax() {
+                return max;
+            }
+
+            /**
+             * Sets the value of the max property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMax(Float value) {
+                this.max = value;
+            }
+
+            /**
+             * Gets the value of the min property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMin() {
+                return min;
+            }
+
+            /**
+             * Sets the value of the min property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMin(Float value) {
+                this.min = value;
+            }
+
+            /**
+             * Gets the value of the colourByLabel property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isColourByLabel() {
+                return colourByLabel;
+            }
+
+            /**
+             * Sets the value of the colourByLabel property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setColourByLabel(Boolean value) {
+                this.colourByLabel = value;
+            }
+
+            /**
+             * Gets the value of the autoScale property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isAutoScale() {
+                return autoScale;
+            }
+
+            /**
+             * Sets the value of the autoScale property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setAutoScale(Boolean value) {
+                this.autoScale = value;
+            }
 
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
+        }
 
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
     }
 
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
 
     /**
-     * Gets the value of the id property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @return possible object is {@link String }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "seq",
+        "annotationColours"
+    })
+    public static class JGroup {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List seq;
+        @XmlElement(namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlAttribute(name = "start")
+        protected Integer start;
+        @XmlAttribute(name = "end")
+        protected Integer end;
+        @XmlAttribute(name = "name")
+        protected String name;
+        @XmlAttribute(name = "colour")
+        protected String colour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "outlineColour")
+        protected Integer outlineColour;
+        @XmlAttribute(name = "displayBoxes")
+        protected Boolean displayBoxes;
+        @XmlAttribute(name = "displayText")
+        protected Boolean displayText;
+        @XmlAttribute(name = "colourText")
+        protected Boolean colourText;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "id")
+        protected String id;
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="features"
-   * type="{www.jalview.org}feature" maxOccurs="unbounded"
-   * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
-   * minOccurs="0"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;extension
-   * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
-   * &lt;element name="structureState" maxOccurs="unbounded"
-   * minOccurs="0"&gt; &lt;complexType&gt;
-   * &lt;simpleContent&gt; &lt;extension
-   * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
-   * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
-   * &lt;attribute name="visible"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="viewId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="colourByJmol"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="type"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/extension&gt; &lt;/simpleContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt;
-   * &lt;/sequence&gt; &lt;/extension&gt;
-   * &lt;/complexContent&gt; &lt;/complexType&gt;
-   * &lt;/element&gt; &lt;element name="hiddenSequences"
-   * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
-   * minOccurs="0"/&gt; &lt;element name="rnaViewer"
-   * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="secondaryStructure"
-   * maxOccurs="unbounded"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="annotationId" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="viewerState"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt;
-   * &lt;/sequence&gt; &lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="dividerLocation"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt;
-   * &lt;/sequence&gt; &lt;attribute name="colour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="hidden"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="viewreference"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
-  public static class JSeq
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List features;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List pdbids;
-
-    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-    protected List hiddenSequences;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List rnaViewer;
-
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-
-    @XmlAttribute(name = "hidden")
-    protected Boolean hidden;
-
-    @XmlAttribute(name = "viewreference")
-    protected Boolean viewreference;
-
-    /**
-     * Gets the value of the features property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the features property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getFeatures().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link Feature }
-     * 
-     * 
-     */
-    public List getFeatures()
-    {
-      if (features == null)
-      {
-        features = new ArrayList();
-      }
-      return this.features;
-    }
-
-    /**
-     * Gets the value of the pdbids property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the pdbids property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getPdbids().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.Pdbids }
-     * 
-     * 
-     */
-    public List getPdbids()
-    {
-      if (pdbids == null)
-      {
-        pdbids = new ArrayList();
-      }
-      return this.pdbids;
-    }
-
-    /**
-     * Gets the value of the hiddenSequences property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the hiddenSequences property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getHiddenSequences().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getHiddenSequences()
-    {
-      if (hiddenSequences == null)
-      {
-        hiddenSequences = new ArrayList();
-      }
-      return this.hiddenSequences;
-    }
-
-    /**
-     * Gets the value of the rnaViewer property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the rnaViewer property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getRnaViewer().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.RnaViewer }
-     * 
-     * 
-     */
-    public List getRnaViewer()
-    {
-      if (rnaViewer == null)
-      {
-        rnaViewer = new ArrayList();
-      }
-      return this.rnaViewer;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     */
-    public int getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     */
-    public void setStart(int value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the hidden property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isHidden()
-    {
-      return hidden;
-    }
-
-    /**
-     * Sets the value of the hidden property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setHidden(Boolean value)
-    {
-      this.hidden = value;
-    }
-
-    /**
-     * Gets the value of the viewreference property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isViewreference()
-    {
-      return viewreference;
-    }
-
-    /**
-     * Sets the value of the viewreference property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setViewreference(Boolean value)
-    {
-      this.viewreference = value;
-    }
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;extension base="{www.jalview.org}pdbentry"&gt;
-     * &lt;sequence&gt; &lt;element name="structureState"
-     * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
-     * &lt;simpleContent&gt; &lt;extension
-     * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
-     * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
-     * &lt;attribute name="visible"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;attribute name="viewId"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="alignwithAlignPanel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-     * &lt;attribute name="colourwithAlignPanel"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-     * /&gt; &lt;attribute name="colourByJmol"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-     * &lt;attribute name="type"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;/extension&gt; &lt;/simpleContent&gt;
-     * &lt;/complexType&gt; &lt;/element&gt;
-     * &lt;/sequence&gt; &lt;/extension&gt;
-     * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "structureState" })
-    public static class Pdbids extends Pdbentry
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List structureState;
-
-      /**
-       * Gets the value of the structureState property.
-       * 
-       * <p> 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
-       * <CODE>set</CODE> method for the structureState property.
-       * 
-       * <p> For example, to add a new item, do as follows: <pre>
-       * getStructureState().add(newItem); </pre>
-       * 
-       * 
-       * <p> Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.Pdbids.StructureState }
-       * 
-       * 
-       */
-      public List getStructureState()
-      {
-        if (structureState == null)
-        {
-          structureState = new ArrayList();
-        }
-        return this.structureState;
-      }
-
-      /**
-       * <p>Java class for anonymous complex type.
-       * 
-       * <p>The following schema fragment specifies the expected content
-       * contained within this class.
-       * 
-       * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
-       * &lt;extension
-       * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
-       * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
-       * &lt;attribute name="visible"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-       * &lt;attribute name="viewId"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-       * &lt;attribute name="alignwithAlignPanel"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
-       * /&gt; &lt;attribute name="colourwithAlignPanel"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-       * /&gt; &lt;attribute name="colourByJmol"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
-       * /&gt; &lt;attribute name="type"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-       * &lt;/extension&gt; &lt;/simpleContent&gt;
-       * &lt;/complexType&gt; </pre>
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "value" })
-      public static class StructureState
-      {
-
-        @XmlValue
-        protected String value;
-
-        @XmlAttribute(name = "visible")
-        protected Boolean visible;
-
-        @XmlAttribute(name = "viewId")
-        protected String viewId;
-
-        @XmlAttribute(name = "alignwithAlignPanel")
-        protected Boolean alignwithAlignPanel;
-
-        @XmlAttribute(name = "colourwithAlignPanel")
-        protected Boolean colourwithAlignPanel;
-
-        @XmlAttribute(name = "colourByJmol")
-        protected Boolean colourByJmol;
-
-        @XmlAttribute(name = "type")
-        protected String type;
-
-        @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 seq 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 seq property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getSeq().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getSeq() {
+            if (seq == null) {
+                seq = new ArrayList();
+            }
+            return this.seq;
+        }
 
         /**
-         * Gets the value of the value property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the annotationColours property.
          * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
          */
-        public String getValue()
-        {
-          return value;
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
         }
 
         /**
-         * Sets the value of the value property.
+         * Sets the value of the annotationColours property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
          */
-        public void setValue(String value)
-        {
-          this.value = value;
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
         }
 
         /**
-         * Gets the value of the visible property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the start property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Boolean isVisible()
-        {
-          return visible;
+        public Integer getStart() {
+            return start;
         }
 
         /**
-         * Sets the value of the visible property.
+         * Sets the value of the start property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setVisible(Boolean value)
-        {
-          this.visible = value;
+        public void setStart(Integer value) {
+            this.start = value;
         }
 
         /**
-         * Gets the value of the viewId property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the end property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getViewId()
-        {
-          return viewId;
+        public Integer getEnd() {
+            return end;
         }
 
         /**
-         * Sets the value of the viewId property.
+         * Sets the value of the end property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setViewId(String value)
-        {
-          this.viewId = value;
+        public void setEnd(Integer value) {
+            this.end = value;
         }
 
         /**
-         * Gets the value of the alignwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the name property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isAlignwithAlignPanel()
-        {
-          if (alignwithAlignPanel == null)
-          {
-            return true;
-          }
-          else
-          {
-            return alignwithAlignPanel;
-          }
+        public String getName() {
+            return name;
         }
 
         /**
-         * Sets the value of the alignwithAlignPanel property.
+         * Sets the value of the name property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setAlignwithAlignPanel(Boolean value)
-        {
-          this.alignwithAlignPanel = value;
+        public void setName(String value) {
+            this.name = value;
         }
 
         /**
-         * Gets the value of the colourwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the colour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isColourwithAlignPanel()
-        {
-          if (colourwithAlignPanel == null)
-          {
-            return false;
-          }
-          else
-          {
-            return colourwithAlignPanel;
-          }
+        public String getColour() {
+            return colour;
         }
 
         /**
-         * Sets the value of the colourwithAlignPanel property.
+         * Sets the value of the colour property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setColourwithAlignPanel(Boolean value)
-        {
-          this.colourwithAlignPanel = value;
+        public void setColour(String value) {
+            this.colour = value;
         }
 
         /**
-         * Gets the value of the colourByJmol property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the consThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public boolean isColourByJmol()
-        {
-          if (colourByJmol == null)
-          {
-            return true;
-          }
-          else
-          {
-            return colourByJmol;
-          }
+        public Integer getConsThreshold() {
+            return consThreshold;
         }
 
         /**
-         * Sets the value of the colourByJmol property.
+         * Sets the value of the consThreshold property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setColourByJmol(Boolean value)
-        {
-          this.colourByJmol = value;
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
         }
 
         /**
-         * Gets the value of the type property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the pidThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getType()
-        {
-          return type;
+        public Integer getPidThreshold() {
+            return pidThreshold;
         }
 
         /**
-         * Sets the value of the type property.
+         * Sets the value of the pidThreshold property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setType(String value)
-        {
-          this.type = value;
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
         }
 
         /**
-         * Gets the value of the width property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the outlineColour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Integer getWidth()
-        {
-          return width;
+        public Integer getOutlineColour() {
+            return outlineColour;
         }
 
         /**
-         * Sets the value of the width property.
+         * Sets the value of the outlineColour property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setWidth(Integer value)
-        {
-          this.width = value;
+        public void setOutlineColour(Integer value) {
+            this.outlineColour = value;
         }
 
         /**
-         * Gets the value of the height property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayBoxes property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getHeight()
-        {
-          return height;
+        public Boolean isDisplayBoxes() {
+            return displayBoxes;
         }
 
         /**
-         * Sets the value of the height property.
+         * Sets the value of the displayBoxes property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setHeight(Integer value)
-        {
-          this.height = value;
+        public void setDisplayBoxes(Boolean value) {
+            this.displayBoxes = value;
         }
 
         /**
-         * Gets the value of the xpos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getXpos()
-        {
-          return xpos;
+        public Boolean isDisplayText() {
+            return displayText;
         }
 
         /**
-         * Sets the value of the xpos property.
+         * Sets the value of the displayText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setXpos(Integer value)
-        {
-          this.xpos = value;
+        public void setDisplayText(Boolean value) {
+            this.displayText = value;
         }
 
         /**
-         * Gets the value of the ypos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the colourText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getYpos()
-        {
-          return ypos;
+        public Boolean isColourText() {
+            return colourText;
         }
 
         /**
-         * Sets the value of the ypos property.
+         * Sets the value of the colourText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setYpos(Integer value)
-        {
-          this.ypos = value;
+        public void setColourText(Boolean value) {
+            this.colourText = value;
         }
 
-      }
-
-    }
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-     * &lt;sequence&gt; &lt;element name="secondaryStructure"
-     * maxOccurs="unbounded"&gt; &lt;complexType&gt;
-     * &lt;complexContent&gt; &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-     * &lt;attribute name="title"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="annotationId" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="gapped"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;attribute name="viewerState"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; &lt;/element&gt;
-     * &lt;/sequence&gt; &lt;attGroup
-     * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
-     * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="viewId"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="dividerLocation"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-     * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-     * &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "secondaryStructure" })
-    public static class RnaViewer
-    {
-
-      @XmlElement(namespace = "www.jalview.org", required = true)
-      protected List secondaryStructure;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "viewId")
-      protected String viewId;
-
-      @XmlAttribute(name = "dividerLocation")
-      protected Integer dividerLocation;
-
-      @XmlAttribute(name = "selectedRna")
-      protected Integer selectedRna;
-
-      @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 secondaryStructure property.
-       * 
-       * <p> 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
-       * <CODE>set</CODE> method for the secondaryStructure
-       * property.
-       * 
-       * <p> For example, to add a new item, do as follows: <pre>
-       * getSecondaryStructure().add(newItem); </pre>
-       * 
-       * 
-       * <p> Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-       * 
-       * 
-       */
-      public List getSecondaryStructure()
-      {
-        if (secondaryStructure == null)
-        {
-          secondaryStructure = new ArrayList();
-        }
-        return this.secondaryStructure;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the viewId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getViewId()
-      {
-        return viewId;
-      }
-
-      /**
-       * Sets the value of the viewId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setViewId(String value)
-      {
-        this.viewId = value;
-      }
-
-      /**
-       * Gets the value of the dividerLocation property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getDividerLocation()
-      {
-        return dividerLocation;
-      }
-
-      /**
-       * Sets the value of the dividerLocation property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setDividerLocation(Integer value)
-      {
-        this.dividerLocation = value;
-      }
-
-      /**
-       * Gets the value of the selectedRna property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getSelectedRna()
-      {
-        return selectedRna;
-      }
-
-      /**
-       * Sets the value of the selectedRna property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setSelectedRna(Integer value)
-      {
-        this.selectedRna = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
-
-      /**
-       * <p>Java class for anonymous complex type.
-       * 
-       * <p>The following schema fragment specifies the expected content
-       * contained within this class.
-       * 
-       * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-       * &lt;restriction
-       * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-       * &lt;attribute name="title"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-       * &lt;attribute name="annotationId" use="required"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-       * &lt;attribute name="gapped"
-       * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-       * &lt;attribute name="viewerState"
-       * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-       * &lt;/restriction&gt; &lt;/complexContent&gt;
-       * &lt;/complexType&gt; </pre>
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "")
-      public static class SecondaryStructure
-      {
-
-        @XmlAttribute(name = "title")
-        protected String title;
-
-        @XmlAttribute(name = "annotationId", required = true)
-        protected String annotationId;
-
-        @XmlAttribute(name = "gapped")
-        protected Boolean gapped;
-
-        @XmlAttribute(name = "viewerState")
-        protected String viewerState;
+        /**
+         * Gets the value of the textCol1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol1() {
+            return textCol1;
+        }
 
         /**
-         * Gets the value of the title property.
+         * Sets the value of the textCol1 property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
+        }
+
+        /**
+         * Gets the value of the textCol2 property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getTitle()
-        {
-          return title;
+        public Integer getTextCol2() {
+            return textCol2;
         }
 
         /**
-         * Sets the value of the title property.
+         * Sets the value of the textCol2 property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
+        }
+
+        /**
+         * Gets the value of the textColThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public void setTitle(String value)
-        {
-          this.title = value;
+        public Integer getTextColThreshold() {
+            return textColThreshold;
         }
 
         /**
-         * Gets the value of the annotationId property.
+         * Sets the value of the textColThreshold property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
+        }
+
+        /**
+         * Gets the value of the showUnconserved property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public String getAnnotationId()
-        {
-          return annotationId;
+        public Boolean isShowUnconserved() {
+            return showUnconserved;
         }
 
         /**
-         * Sets the value of the annotationId property.
+         * Sets the value of the showUnconserved property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
+        }
+
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public void setAnnotationId(String value)
-        {
-          this.annotationId = value;
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
         }
 
         /**
-         * Gets the value of the gapped property.
+         * Sets the value of the ignoreGapsinConsensus property.
          * 
-         * @return possible object is {@link Boolean }
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
+
+        /**
+         * Gets the value of the showConsensusHistogram property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Boolean isGapped()
-        {
-          return gapped;
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
         }
 
         /**
-         * Sets the value of the gapped property.
+         * Sets the value of the showConsensusHistogram property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
+
+        /**
+         * Gets the value of the showSequenceLogo property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public void setGapped(Boolean value)
-        {
-          this.gapped = value;
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
         }
 
         /**
-         * Gets the value of the viewerState property.
+         * Sets the value of the showSequenceLogo property.
          * 
-         * @return possible object is {@link String }
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public String getViewerState()
-        {
-          return viewerState;
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
         }
 
         /**
-         * Sets the value of the viewerState property.
+         * Sets the value of the normaliseSequenceLogo property.
          * 
          * @param value
-         *          allowed object is {@link String }
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the id property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public void setViewerState(String value)
-        {
-          this.viewerState = value;
+        public String getId() {
+            return id;
         }
 
-      }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
     }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="sequencePoint"
-   * maxOccurs="unbounded"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-   * ref="{www.jalview.org}position"/&gt; &lt;attribute
-   * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt; &lt;element
-   * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-   * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-   * &lt;/complexContent&gt; &lt;/complexType&gt;
-   * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
-   * &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-   * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-   * &lt;/complexContent&gt; &lt;/complexType&gt;
-   * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
-   * &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-   * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-   * &lt;/complexContent&gt; &lt;/complexType&gt;
-   * &lt;/element&gt; &lt;element name="pcaData"
-   * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
-   * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
-   * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
-   * &lt;attribute name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="xDim"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;attribute name="bgColour"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-   * &lt;attribute name="showLabels"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="linkToAllViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
-  public static class PcaViewer
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List sequencePoint;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List axis;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected PcaDataType pcaData;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "scoreModelName")
-    protected String scoreModelName;
-
-    @XmlAttribute(name = "xDim")
-    protected Integer xDim;
-
-    @XmlAttribute(name = "yDim")
-    protected Integer yDim;
-
-    @XmlAttribute(name = "zDim")
-    protected Integer zDim;
-
-    @XmlAttribute(name = "bgColour")
-    protected Integer bgColour;
-
-    @XmlAttribute(name = "scaleFactor")
-    protected Float scaleFactor;
-
-    @XmlAttribute(name = "showLabels")
-    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")
-    protected Boolean matchGaps;
-
-    @XmlAttribute(name = "includeGappedColumns")
-    protected Boolean includeGappedColumns;
-
-    @XmlAttribute(name = "denominateByShortestLength")
-    protected Boolean denominateByShortestLength;
 
     /**
-     * Gets the value of the sequencePoint property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the sequencePoint property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getSequencePoint().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.SequencePoint }
-     * 
-     * 
-     */
-    public List getSequencePoint()
-    {
-      if (sequencePoint == null)
-      {
-        sequencePoint = new ArrayList();
-      }
-      return this.sequencePoint;
-    }
-
-    /**
-     * Gets the value of the axis property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the axis property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getAxis().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.Axis }
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org}pdbentry">
+     *                 <sequence>
+     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     <complexType>
+     *                       <simpleContent>
+     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </extension>
+     *                       </simpleContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="secondaryStructure" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
      * 
      */
-    public List getAxis()
-    {
-      if (axis == null)
-      {
-        axis = new ArrayList();
-      }
-      return this.axis;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "features",
+        "pdbids",
+        "hiddenSequences",
+        "rnaViewer"
+    })
+    public static class JSeq {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List features;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List pdbids;
+        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+        protected List hiddenSequences;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List rnaViewer;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+        @XmlAttribute(name = "id", required = true)
+        protected String id;
+        @XmlAttribute(name = "hidden")
+        protected Boolean hidden;
+        @XmlAttribute(name = "viewreference")
+        protected Boolean viewreference;
 
-    /**
-     * Gets the value of the seqPointMin property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
-    {
-      return seqPointMin;
-    }
+        /**
+         * Gets the value of the features 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 features property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getFeatures().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Feature }
+         * 
+         * 
+         */
+        public List getFeatures() {
+            if (features == null) {
+                features = new ArrayList();
+            }
+            return this.features;
+        }
 
-    /**
-     * Sets the value of the seqPointMin property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
-    {
-      this.seqPointMin = value;
-    }
+        /**
+         * Gets the value of the pdbids 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 pdbids property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getPdbids().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.Pdbids }
+         * 
+         * 
+         */
+        public List getPdbids() {
+            if (pdbids == null) {
+                pdbids = new ArrayList();
+            }
+            return this.pdbids;
+        }
 
-    /**
-     * Gets the value of the seqPointMax property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
-    {
-      return seqPointMax;
-    }
+        /**
+         * Gets the value of the hiddenSequences 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 hiddenSequences property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getHiddenSequences().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getHiddenSequences() {
+            if (hiddenSequences == null) {
+                hiddenSequences = new ArrayList();
+            }
+            return this.hiddenSequences;
+        }
 
-    /**
-     * Sets the value of the seqPointMax property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
-    {
-      this.seqPointMax = value;
-    }
+        /**
+         * Gets the value of the rnaViewer 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 rnaViewer property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getRnaViewer().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.RnaViewer }
+         * 
+         * 
+         */
+        public List getRnaViewer() {
+            if (rnaViewer == null) {
+                rnaViewer = new ArrayList();
+            }
+            return this.rnaViewer;
+        }
 
-    /**
-     * Gets the value of the pcaData property.
-     * 
-     * @return possible object is {@link PcaDataType }
-     * 
-     */
-    public PcaDataType getPcaData()
-    {
-      return pcaData;
-    }
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
 
-    /**
-     * Sets the value of the pcaData property.
-     * 
-     * @param value
-     *          allowed object is {@link PcaDataType }
-     * 
-     */
-    public void setPcaData(PcaDataType value)
-    {
-      this.pcaData = value;
-    }
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
 
-    /**
-     * Gets the value of the scoreModelName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getScoreModelName()
-    {
-      return scoreModelName;
-    }
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
 
-    /**
-     * Sets the value of the scoreModelName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setScoreModelName(String value)
-    {
-      this.scoreModelName = value;
-    }
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
 
-    /**
-     * Gets the value of the xDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXDim()
-    {
-      return xDim;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Sets the value of the xDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXDim(Integer value)
-    {
-      this.xDim = value;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Gets the value of the yDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYDim()
-    {
-      return yDim;
-    }
+        /**
+         * Gets the value of the hidden property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isHidden() {
+            return hidden;
+        }
 
-    /**
-     * Sets the value of the yDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYDim(Integer value)
-    {
-      this.yDim = value;
-    }
+        /**
+         * Sets the value of the hidden property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setHidden(Boolean value) {
+            this.hidden = value;
+        }
 
-    /**
-     * Gets the value of the zDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getZDim()
-    {
-      return zDim;
-    }
+        /**
+         * Gets the value of the viewreference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isViewreference() {
+            return viewreference;
+        }
 
-    /**
-     * Sets the value of the zDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setZDim(Integer value)
-    {
-      this.zDim = value;
-    }
+        /**
+         * Sets the value of the viewreference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setViewreference(Boolean value) {
+            this.viewreference = value;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getBgColour()
-    {
-      return bgColour;
-    }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setBgColour(Integer value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org}pdbentry">
+         *       <sequence>
+         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           <complexType>
+         *             <simpleContent>
+         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </extension>
+         *             </simpleContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "structureState"
+        })
+        public static class Pdbids
+            extends Pdbentry
+        {
 
-    /**
-     * Gets the value of the scaleFactor property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getScaleFactor()
-    {
-      return scaleFactor;
-    }
+            @XmlElement(namespace = "www.jalview.org")
+            protected List structureState;
+
+            /**
+             * Gets the value of the structureState 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 structureState property.
+             * 
+             * 
    
+             * For example, to add a new item, do as follows:
+             * 
    +             *    getStructureState().add(newItem);
+             * 
    
+             * 
+             * 
+             * 
    
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.Pdbids.StructureState }
+             * 
+             * 
+             */
+            public List getStructureState() {
+                if (structureState == null) {
+                    structureState = new ArrayList();
+                }
+                return this.structureState;
+            }
+
+
+            /**
+             * 
    Java class for anonymous complex type.
+             * 
+             * 
    The following schema fragment specifies the expected content contained within this class.
+             * 
+             * 
    +             * <complexType>
+             *   <simpleContent>
+             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+             *       <attGroup ref="{www.jalview.org}swingwindow"/>
+             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </extension>
+             *   </simpleContent>
+             * </complexType>
+             * 
    
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "", propOrder = {
+                "value"
+            })
+            public static class StructureState {
+
+                @XmlValue
+                protected String value;
+                @XmlAttribute(name = "visible")
+                protected Boolean visible;
+                @XmlAttribute(name = "viewId")
+                protected String viewId;
+                @XmlAttribute(name = "alignwithAlignPanel")
+                protected Boolean alignwithAlignPanel;
+                @XmlAttribute(name = "colourwithAlignPanel")
+                protected Boolean colourwithAlignPanel;
+                @XmlAttribute(name = "colourByJmol")
+                protected Boolean colourByJmol;
+                @XmlAttribute(name = "type")
+                protected String type;
+                @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 value property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getValue() {
+                    return value;
+                }
+
+                /**
+                 * Sets the value of the value property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setValue(String value) {
+                    this.value = value;
+                }
+
+                /**
+                 * Gets the value of the visible property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isVisible() {
+                    return visible;
+                }
+
+                /**
+                 * Sets the value of the visible property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setVisible(Boolean value) {
+                    this.visible = value;
+                }
+
+                /**
+                 * Gets the value of the viewId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewId() {
+                    return viewId;
+                }
+
+                /**
+                 * Sets the value of the viewId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewId(String value) {
+                    this.viewId = value;
+                }
+
+                /**
+                 * Gets the value of the alignwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isAlignwithAlignPanel() {
+                    if (alignwithAlignPanel == null) {
+                        return true;
+                    } else {
+                        return alignwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the alignwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setAlignwithAlignPanel(Boolean value) {
+                    this.alignwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourwithAlignPanel() {
+                    if (colourwithAlignPanel == null) {
+                        return false;
+                    } else {
+                        return colourwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourwithAlignPanel(Boolean value) {
+                    this.colourwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourByJmol property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourByJmol() {
+                    if (colourByJmol == null) {
+                        return true;
+                    } else {
+                        return colourByJmol;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourByJmol property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourByJmol(Boolean value) {
+                    this.colourByJmol = value;
+                }
+
+                /**
+                 * Gets the value of the type property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getType() {
+                    return type;
+                }
+
+                /**
+                 * Sets the value of the type property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setType(String value) {
+                    this.type = value;
+                }
+
+                /**
+                 * Gets the value of the width property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getWidth() {
+                    return width;
+                }
+
+                /**
+                 * Sets the value of the width property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setWidth(Integer value) {
+                    this.width = value;
+                }
+
+                /**
+                 * Gets the value of the height property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getHeight() {
+                    return height;
+                }
+
+                /**
+                 * Sets the value of the height property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setHeight(Integer value) {
+                    this.height = value;
+                }
+
+                /**
+                 * Gets the value of the xpos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getXpos() {
+                    return xpos;
+                }
+
+                /**
+                 * Sets the value of the xpos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setXpos(Integer value) {
+                    this.xpos = value;
+                }
+
+                /**
+                 * Gets the value of the ypos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getYpos() {
+                    return ypos;
+                }
+
+                /**
+                 * Sets the value of the ypos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setYpos(Integer value) {
+                    this.ypos = value;
+                }
+
+            }
 
-    /**
-     * Sets the value of the scaleFactor property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setScaleFactor(Float value)
-    {
-      this.scaleFactor = value;
-    }
+        }
 
-    /**
-     * Gets the value of the showLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowLabels()
-    {
-      return showLabels;
-    }
 
-    /**
-     * Sets the value of the showLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowLabels(Boolean value)
-    {
-      this.showLabels = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="secondaryStructure" maxOccurs="unbounded">
+         *           <complexType>
+         *             <complexContent>
+         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </restriction>
+         *             </complexContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "secondaryStructure"
+        })
+        public static class RnaViewer {
+
+            @XmlElement(namespace = "www.jalview.org", required = true)
+            protected List secondaryStructure;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @XmlAttribute(name = "viewId")
+            protected String viewId;
+            @XmlAttribute(name = "dividerLocation")
+            protected Integer dividerLocation;
+            @XmlAttribute(name = "selectedRna")
+            protected Integer selectedRna;
+            @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 secondaryStructure 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 secondaryStructure property.
+             * 
+             * 
    
+             * For example, to add a new item, do as follows:
+             * 
    +             *    getSecondaryStructure().add(newItem);
+             * 
    
+             * 
+             * 
+             * 
    
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+             * 
+             * 
+             */
+            public List getSecondaryStructure() {
+                if (secondaryStructure == null) {
+                    secondaryStructure = new ArrayList();
+                }
+                return this.secondaryStructure;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the viewId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getViewId() {
+                return viewId;
+            }
+
+            /**
+             * Sets the value of the viewId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setViewId(String value) {
+                this.viewId = value;
+            }
+
+            /**
+             * Gets the value of the dividerLocation property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getDividerLocation() {
+                return dividerLocation;
+            }
+
+            /**
+             * Sets the value of the dividerLocation property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setDividerLocation(Integer value) {
+                this.dividerLocation = value;
+            }
+
+            /**
+             * Gets the value of the selectedRna property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getSelectedRna() {
+                return selectedRna;
+            }
+
+            /**
+             * Sets the value of the selectedRna property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setSelectedRna(Integer value) {
+                this.selectedRna = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
+
+
+            /**
+             * 
    Java class for anonymous complex type.
+             * 
+             * 
    The following schema fragment specifies the expected content contained within this class.
+             * 
+             * 
    +             * <complexType>
+             *   <complexContent>
+             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </restriction>
+             *   </complexContent>
+             * </complexType>
+             * 
    
+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "")
+            public static class SecondaryStructure {
+
+                @XmlAttribute(name = "title")
+                protected String title;
+                @XmlAttribute(name = "annotationId", required = true)
+                protected String annotationId;
+                @XmlAttribute(name = "gapped")
+                protected Boolean gapped;
+                @XmlAttribute(name = "viewerState")
+                protected String viewerState;
+
+                /**
+                 * Gets the value of the title property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getTitle() {
+                    return title;
+                }
+
+                /**
+                 * Sets the value of the title property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setTitle(String value) {
+                    this.title = value;
+                }
+
+                /**
+                 * Gets the value of the annotationId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getAnnotationId() {
+                    return annotationId;
+                }
+
+                /**
+                 * Sets the value of the annotationId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setAnnotationId(String value) {
+                    this.annotationId = value;
+                }
+
+                /**
+                 * Gets the value of the gapped property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isGapped() {
+                    return gapped;
+                }
+
+                /**
+                 * Sets the value of the gapped property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setGapped(Boolean value) {
+                    this.gapped = value;
+                }
+
+                /**
+                 * Gets the value of the viewerState property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewerState() {
+                    return viewerState;
+                }
+
+                /**
+                 * Sets the value of the viewerState property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewerState(String value) {
+                    this.viewerState = value;
+                }
+
+            }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isLinkToAllViews()
-    {
-      return linkToAllViews;
-    }
+        }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
     }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
 
     /**
-     * Sets the value of the width property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="sequencePoint" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="axis" maxOccurs="3" minOccurs="3">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMin">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMax">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+     *       </sequence>
+     *       <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" />
+     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "sequencePoint",
+        "axis",
+        "seqPointMin",
+        "seqPointMax",
+        "pcaData"
+    })
+    public static class PcaViewer {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List sequencePoint;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List axis;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected PcaDataType pcaData;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "scoreModelName")
+        protected String scoreModelName;
+        @XmlAttribute(name = "xDim")
+        protected Integer xDim;
+        @XmlAttribute(name = "yDim")
+        protected Integer yDim;
+        @XmlAttribute(name = "zDim")
+        protected Integer zDim;
+        @XmlAttribute(name = "bgColour")
+        protected Integer bgColour;
+        @XmlAttribute(name = "scaleFactor")
+        protected Float scaleFactor;
+        @XmlAttribute(name = "showLabels")
+        protected Boolean showLabels;
+        @XmlAttribute(name = "linkToAllViews")
+        protected Boolean linkToAllViews;
+        @XmlAttribute(name = "includeGaps")
+        protected Boolean includeGaps;
+        @XmlAttribute(name = "matchGaps")
+        protected Boolean matchGaps;
+        @XmlAttribute(name = "includeGappedColumns")
+        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 height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        /**
+         * Gets the value of the sequencePoint 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 sequencePoint property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getSequencePoint().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.SequencePoint }
+         * 
+         * 
+         */
+        public List getSequencePoint() {
+            if (sequencePoint == null) {
+                sequencePoint = new ArrayList();
+            }
+            return this.sequencePoint;
+        }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * Gets the value of the axis 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 axis property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getAxis().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.Axis }
+         * 
+         * 
+         */
+        public List getAxis() {
+            if (axis == null) {
+                axis = new ArrayList();
+            }
+            return this.axis;
+        }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * Gets the value of the seqPointMin property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+            return seqPointMin;
+        }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        /**
+         * Sets the value of the seqPointMin property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+            this.seqPointMin = value;
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
+        /**
+         * Gets the value of the seqPointMax property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+            return seqPointMax;
+        }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * Sets the value of the seqPointMax property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+            this.seqPointMax = value;
+        }
 
-    /**
-     * Gets the value of the includeGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGaps()
-    {
-      return includeGaps;
-    }
+        /**
+         * Gets the value of the pcaData property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public PcaDataType getPcaData() {
+            return pcaData;
+        }
 
-    /**
-     * Sets the value of the includeGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGaps(Boolean value)
-    {
-      this.includeGaps = value;
-    }
+        /**
+         * Sets the value of the pcaData property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public void setPcaData(PcaDataType value) {
+            this.pcaData = value;
+        }
 
-    /**
-     * Gets the value of the matchGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMatchGaps()
-    {
-      return matchGaps;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Sets the value of the matchGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMatchGaps(Boolean value)
-    {
-      this.matchGaps = value;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Gets the value of the includeGappedColumns property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGappedColumns()
-    {
-      return includeGappedColumns;
-    }
+        /**
+         * Gets the value of the scoreModelName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getScoreModelName() {
+            return scoreModelName;
+        }
 
-    /**
-     * Sets the value of the includeGappedColumns property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGappedColumns(Boolean value)
-    {
-      this.includeGappedColumns = value;
-    }
+        /**
+         * Sets the value of the scoreModelName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setScoreModelName(String value) {
+            this.scoreModelName = value;
+        }
 
-    /**
-     * Gets the value of the denominateByShortestLength property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDenominateByShortestLength()
-    {
-      return denominateByShortestLength;
-    }
+        /**
+         * Gets the value of the xDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXDim() {
+            return xDim;
+        }
 
-    /**
-     * Sets the value of the denominateByShortestLength property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDenominateByShortestLength(Boolean value)
-    {
-      this.denominateByShortestLength = value;
-    }
+        /**
+         * Sets the value of the xDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXDim(Integer value) {
+            this.xDim = value;
+        }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-     * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-     * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Axis
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the yDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYDim() {
+            return yDim;
+        }
 
-    }
+        /**
+         * Sets the value of the yDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYDim(Integer value) {
+            this.yDim = value;
+        }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-     * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-     * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMax
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the zDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getZDim() {
+            return zDim;
+        }
 
-    }
+        /**
+         * Sets the value of the zDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setZDim(Integer value) {
+            this.zDim = value;
+        }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-     * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
-     * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMin
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getBgColour() {
+            return bgColour;
+        }
 
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setBgColour(Integer value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
-     * ref="{www.jalview.org}position"/&gt; &lt;attribute
-     * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
-     * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SequencePoint
-    {
-
-      @XmlAttribute(name = "sequenceRef")
-      protected String sequenceRef;
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the sequenceRef property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getSequenceRef()
-      {
-        return sequenceRef;
-      }
-
-      /**
-       * Sets the value of the sequenceRef property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setSequenceRef(String value)
-      {
-        this.sequenceRef = value;
-      }
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the scaleFactor property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getScaleFactor() {
+            return scaleFactor;
+        }
 
-    }
+        /**
+         * Sets the value of the scaleFactor property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setScaleFactor(Float value) {
+            this.scaleFactor = value;
+        }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
-   * minOccurs="0"&gt; &lt;element name="title"
-   * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
-   * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
-   * &lt;/sequence&gt; &lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
-   * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="fontSize"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="threshold"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;attribute name="showDistances"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="markUnlinked"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="fitToWindow"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="currentTree"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID"
-   * /&gt; &lt;attribute name="linkToAllViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "title", "newick" })
-  public static class Tree
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String title;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String newick;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "showBootstrap")
-    protected Boolean showBootstrap;
-
-    @XmlAttribute(name = "showDistances")
-    protected Boolean showDistances;
-
-    @XmlAttribute(name = "markUnlinked")
-    protected Boolean markUnlinked;
-
-    @XmlAttribute(name = "fitToWindow")
-    protected Boolean fitToWindow;
-
-    @XmlAttribute(name = "currentTree")
-    protected Boolean currentTree;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @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;
+        /**
+         * Gets the value of the showLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowLabels() {
+            return showLabels;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the showLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowLabels(Boolean value) {
+            this.showLabels = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isLinkToAllViews() {
+            return linkToAllViews;
+        }
 
-    /**
-     * Gets the value of the newick property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getNewick()
-    {
-      return newick;
-    }
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    /**
-     * Sets the value of the newick property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setNewick(String value)
-    {
-      this.newick = value;
-    }
+        /**
+         * Gets the value of the includeGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGaps() {
+            return includeGaps;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Sets the value of the includeGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGaps(Boolean value) {
+            this.includeGaps = value;
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Gets the value of the matchGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMatchGaps() {
+            return matchGaps;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Sets the value of the matchGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMatchGaps(Boolean value) {
+            this.matchGaps = value;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Gets the value of the includeGappedColumns property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGappedColumns() {
+            return includeGappedColumns;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Sets the value of the includeGappedColumns property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGappedColumns(Boolean value) {
+            this.includeGappedColumns = value;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Gets the value of the denominateByShortestLength property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isDenominateByShortestLength() {
+            return denominateByShortestLength;
+        }
 
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getThreshold()
-    {
-      return threshold;
-    }
+        /**
+         * Sets the value of the denominateByShortestLength property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setDenominateByShortestLength(Boolean value) {
+            this.denominateByShortestLength = value;
+        }
 
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Gets the value of the showBootstrap property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBootstrap()
-    {
-      return showBootstrap;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Sets the value of the showBootstrap property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBootstrap(Boolean value)
-    {
-      this.showBootstrap = value;
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Gets the value of the showDistances property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDistances()
-    {
-      return showDistances;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Sets the value of the showDistances property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDistances(Boolean value)
-    {
-      this.showDistances = value;
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Gets the value of the markUnlinked property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMarkUnlinked()
-    {
-      return markUnlinked;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Sets the value of the markUnlinked property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMarkUnlinked(Boolean value)
-    {
-      this.markUnlinked = value;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    /**
-     * Gets the value of the fitToWindow property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isFitToWindow()
-    {
-      return fitToWindow;
-    }
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Sets the value of the fitToWindow property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFitToWindow(Boolean value)
-    {
-      this.fitToWindow = value;
-    }
 
-    /**
-     * Gets the value of the currentTree property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isCurrentTree()
-    {
-      return currentTree;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Axis {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Sets the value of the currentTree property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCurrentTree(Boolean value)
-    {
-      this.currentTree = value;
-    }
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMax {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLinkToAllViews()
-    {
-      if (linkToAllViews == null)
-      {
-        return false;
-      }
-      else
-      {
-        return linkToAllViews;
-      }
-    }
+        }
+
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMin {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
+
+        }
+
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SequencePoint {
+
+            @XmlAttribute(name = "sequenceRef")
+            protected String sequenceRef;
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the sequenceRef property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getSequenceRef() {
+                return sequenceRef;
+            }
+
+            /**
+             * Sets the value of the sequenceRef property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setSequenceRef(String value) {
+                this.sequenceRef = value;
+            }
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
+
+        }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
     }
 
+
     /**
-     * Gets the value of the width property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @return possible object is {@link Integer }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence minOccurs="0">
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "title",
+        "newick"
+    })
+    public static class Tree {
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        @XmlElement(namespace = "www.jalview.org")
+        protected String title;
+        @XmlElement(namespace = "www.jalview.org")
+        protected String newick;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "showBootstrap")
+        protected Boolean showBootstrap;
+        @XmlAttribute(name = "showDistances")
+        protected Boolean showDistances;
+        @XmlAttribute(name = "markUnlinked")
+        protected Boolean markUnlinked;
+        @XmlAttribute(name = "fitToWindow")
+        protected Boolean fitToWindow;
+        @XmlAttribute(name = "currentTree")
+        protected Boolean currentTree;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @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;
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        /**
+         * Gets the value of the newick property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getNewick() {
+            return newick;
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
+        /**
+         * Sets the value of the newick property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setNewick(String value) {
+            this.newick = value;
+        }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="UserColourScheme"
-   * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="id"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "userColourScheme" })
-  public static class UserColours
-  {
-
-    @XmlElement(
-      name = "UserColourScheme",
-      namespace = "www.jalview.org",
-      required = true)
-    protected JalviewUserColours userColourScheme;
-
-    @XmlAttribute(name = "id")
-    protected String id;
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    /**
-     * Gets the value of the userColourScheme property.
-     * 
-     * @return possible object is {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours getUserColourScheme()
-    {
-      return userColourScheme;
-    }
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    /**
-     * Sets the value of the userColourScheme property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewUserColours }
-     * 
-     */
-    public void setUserColourScheme(JalviewUserColours value)
-    {
-      this.userColourScheme = value;
-    }
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="AnnotationColours"
-   * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
-   * &lt;element name="hiddenColumns" maxOccurs="unbounded"
-   * minOccurs="0"&gt; &lt;complexType&gt;
-   * &lt;complexContent&gt; &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt; &lt;element
-   * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
-   * &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;extension
-   * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
-   * &lt;attribute name="calcId" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="false" /&gt; &lt;attribute name="autoUpdate"
-   * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/extension&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; &lt;/element&gt;
-   * &lt;/sequence&gt; &lt;attGroup
-   * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
-   * name="conservationSelected"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="pidSelected"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="bgColour"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="pidThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="showFullId"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="rightAlignIds"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showColourText"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showUnconserved"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="showBoxes"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="wrapAlignment"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="renderGaps"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showSequenceFeatures"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showNPfeatureTooltip"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="showDbRefTooltip"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="followHighlight"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="followSelection"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="showAnnotation"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="centreColumnLabels"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="showGroupConservation"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="showGroupConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="showConsensusHistogram"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="showSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="normaliseSequenceLogo"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="ignoreGapsinConsensus"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
-   * &lt;attribute name="startRes"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="fontName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="fontStyle"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="true" /&gt; &lt;attribute name="viewName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="gatheredViews"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;attribute name="textCol1"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;attribute name="textColThreshold"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-   * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
-   * &lt;attribute name="complementId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="showComplementFeatures"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;attribute name="showComplementFeaturesOnTop"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "annotationColours", "hiddenColumns", "calcIdParam" })
-  public static class Viewport
-  {
-
-    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List hiddenColumns;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List calcIdParam;
-
-    @XmlAttribute(name = "conservationSelected")
-    protected Boolean conservationSelected;
-
-    @XmlAttribute(name = "pidSelected")
-    protected Boolean pidSelected;
-
-    @XmlAttribute(name = "bgColour")
-    protected String bgColour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "showFullId")
-    protected Boolean showFullId;
-
-    @XmlAttribute(name = "rightAlignIds")
-    protected Boolean rightAlignIds;
-
-    @XmlAttribute(name = "showText")
-    protected Boolean showText;
-
-    @XmlAttribute(name = "showColourText")
-    protected Boolean showColourText;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "showBoxes")
-    protected Boolean showBoxes;
-
-    @XmlAttribute(name = "wrapAlignment")
-    protected Boolean wrapAlignment;
-
-    @XmlAttribute(name = "renderGaps")
-    protected Boolean renderGaps;
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
 
-    @XmlAttribute(name = "showSequenceFeatures")
-    protected Boolean showSequenceFeatures;
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
 
-    @XmlAttribute(name = "showNPfeatureTooltip")
-    protected Boolean showNPfeatureTooltip;
+        /**
+         * Gets the value of the showBootstrap property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBootstrap() {
+            return showBootstrap;
+        }
 
-    @XmlAttribute(name = "showDbRefTooltip")
-    protected Boolean showDbRefTooltip;
+        /**
+         * Sets the value of the showBootstrap property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBootstrap(Boolean value) {
+            this.showBootstrap = value;
+        }
 
-    @XmlAttribute(name = "followHighlight")
-    protected Boolean followHighlight;
+        /**
+         * Gets the value of the showDistances property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDistances() {
+            return showDistances;
+        }
 
-    @XmlAttribute(name = "followSelection")
-    protected Boolean followSelection;
+        /**
+         * Sets the value of the showDistances property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDistances(Boolean value) {
+            this.showDistances = value;
+        }
 
-    @XmlAttribute(name = "showAnnotation")
-    protected Boolean showAnnotation;
+        /**
+         * Gets the value of the markUnlinked property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMarkUnlinked() {
+            return markUnlinked;
+        }
 
-    @XmlAttribute(name = "centreColumnLabels")
-    protected Boolean centreColumnLabels;
+        /**
+         * Sets the value of the markUnlinked property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMarkUnlinked(Boolean value) {
+            this.markUnlinked = value;
+        }
 
-    @XmlAttribute(name = "showGroupConservation")
-    protected Boolean showGroupConservation;
+        /**
+         * Gets the value of the fitToWindow property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isFitToWindow() {
+            return fitToWindow;
+        }
 
-    @XmlAttribute(name = "showGroupConsensus")
-    protected Boolean showGroupConsensus;
+        /**
+         * Sets the value of the fitToWindow property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFitToWindow(Boolean value) {
+            this.fitToWindow = value;
+        }
 
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
+        /**
+         * Gets the value of the currentTree property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isCurrentTree() {
+            return currentTree;
+        }
 
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
+        /**
+         * Sets the value of the currentTree property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCurrentTree(Boolean value) {
+            this.currentTree = value;
+        }
 
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    @XmlAttribute(name = "startRes")
-    protected Integer startRes;
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLinkToAllViews() {
+            if (linkToAllViews == null) {
+                return false;
+            } else {
+                return linkToAllViews;
+            }
+        }
 
-    @XmlAttribute(name = "startSeq")
-    protected Integer startSeq;
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    @XmlAttribute(name = "scaleProteinAsCdna")
-    protected Boolean scaleProteinAsCdna;
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    @XmlAttribute(name = "viewName")
-    protected String viewName;
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    @XmlAttribute(name = "sequenceSetId")
-    protected String sequenceSetId;
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    @XmlAttribute(name = "gatheredViews")
-    protected Boolean gatheredViews;
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
+    }
 
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
 
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       </sequence>
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "userColourScheme"
+    })
+    public static class UserColours {
 
-    @XmlAttribute(name = "complementId")
-    protected String complementId;
+        @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+        protected JalviewUserColours userColourScheme;
+        @XmlAttribute(name = "id")
+        protected String id;
 
-    @XmlAttribute(name = "showComplementFeatures")
-    protected Boolean showComplementFeatures;
+        /**
+         * Gets the value of the userColourScheme property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public JalviewUserColours getUserColourScheme() {
+            return userColourScheme;
+        }
 
-    @XmlAttribute(name = "showComplementFeaturesOnTop")
-    protected Boolean showComplementFeaturesOnTop;
+        /**
+         * Sets the value of the userColourScheme property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public void setUserColourScheme(JalviewUserColours value) {
+            this.userColourScheme = value;
+        }
 
-    @XmlAttribute(name = "width")
-    protected Integer width;
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    @XmlAttribute(name = "height")
-    protected Integer height;
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
+    }
 
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
 
     /**
-     * Gets the value of the annotationColours property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="overview" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link AnnotationColourScheme }
      * 
      */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "annotationColours",
+        "hiddenColumns",
+        "calcIdParam",
+        "overview"
+    })
+    public static class Viewport {
+
+        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List hiddenColumns;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List calcIdParam;
+        @XmlElement(namespace = "www.jalview.org")
+        protected JalviewModel.Viewport.Overview overview;
+        @XmlAttribute(name = "conservationSelected")
+        protected Boolean conservationSelected;
+        @XmlAttribute(name = "pidSelected")
+        protected Boolean pidSelected;
+        @XmlAttribute(name = "bgColour")
+        protected String bgColour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "showFullId")
+        protected Boolean showFullId;
+        @XmlAttribute(name = "rightAlignIds")
+        protected Boolean rightAlignIds;
+        @XmlAttribute(name = "showText")
+        protected Boolean showText;
+        @XmlAttribute(name = "showColourText")
+        protected Boolean showColourText;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "showBoxes")
+        protected Boolean showBoxes;
+        @XmlAttribute(name = "wrapAlignment")
+        protected Boolean wrapAlignment;
+        @XmlAttribute(name = "renderGaps")
+        protected Boolean renderGaps;
+        @XmlAttribute(name = "showSequenceFeatures")
+        protected Boolean showSequenceFeatures;
+        @XmlAttribute(name = "showNPfeatureTooltip")
+        protected Boolean showNPfeatureTooltip;
+        @XmlAttribute(name = "showDbRefTooltip")
+        protected Boolean showDbRefTooltip;
+        @XmlAttribute(name = "followHighlight")
+        protected Boolean followHighlight;
+        @XmlAttribute(name = "followSelection")
+        protected Boolean followSelection;
+        @XmlAttribute(name = "showAnnotation")
+        protected Boolean showAnnotation;
+        @XmlAttribute(name = "centreColumnLabels")
+        protected Boolean centreColumnLabels;
+        @XmlAttribute(name = "showGroupConservation")
+        protected Boolean showGroupConservation;
+        @XmlAttribute(name = "showGroupConsensus")
+        protected Boolean showGroupConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "startRes")
+        protected Integer startRes;
+        @XmlAttribute(name = "startSeq")
+        protected Integer startSeq;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "scaleProteinAsCdna")
+        protected Boolean scaleProteinAsCdna;
+        @XmlAttribute(name = "viewName")
+        protected String viewName;
+        @XmlAttribute(name = "sequenceSetId")
+        protected String sequenceSetId;
+        @XmlAttribute(name = "gatheredViews")
+        protected Boolean gatheredViews;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @XmlAttribute(name = "complementId")
+        protected String complementId;
+        @XmlAttribute(name = "showComplementFeatures")
+        protected Boolean showComplementFeatures;
+        @XmlAttribute(name = "showComplementFeaturesOnTop")
+        protected Boolean showComplementFeaturesOnTop;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
+        /**
+         * Gets the value of the annotationColours property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
+        }
 
-    /**
-     * Gets the value of the hiddenColumns property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the hiddenColumns property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getHiddenColumns().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.HiddenColumns }
-     * 
-     * 
-     */
-    public List getHiddenColumns()
-    {
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList();
-      }
-      return this.hiddenColumns;
-    }
+        /**
+         * Sets the value of the annotationColours property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
+        }
 
-    /**
-     * Gets the value of the calcIdParam property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the calcIdParam property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getCalcIdParam().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.CalcIdParam }
-     * 
-     * 
-     */
-    public List getCalcIdParam()
-    {
-      if (calcIdParam == null)
-      {
-        calcIdParam = new ArrayList();
-      }
-      return this.calcIdParam;
-    }
+        /**
+         * Gets the value of the hiddenColumns 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 hiddenColumns property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getHiddenColumns().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.HiddenColumns }
+         * 
+         * 
+         */
+        public List getHiddenColumns() {
+            if (hiddenColumns == null) {
+                hiddenColumns = new ArrayList();
+            }
+            return this.hiddenColumns;
+        }
 
-    /**
-     * Gets the value of the conservationSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isConservationSelected()
-    {
-      return conservationSelected;
-    }
+        /**
+         * Gets the value of the calcIdParam 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 calcIdParam property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getCalcIdParam().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.CalcIdParam }
+         * 
+         * 
+         */
+        public List getCalcIdParam() {
+            if (calcIdParam == null) {
+                calcIdParam = new ArrayList();
+            }
+            return this.calcIdParam;
+        }
 
-    /**
-     * Sets the value of the conservationSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setConservationSelected(Boolean value)
-    {
-      this.conservationSelected = value;
-    }
+        /**
+         * Gets the value of the overview property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public JalviewModel.Viewport.Overview getOverview() {
+            return overview;
+        }
 
-    /**
-     * Gets the value of the pidSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isPidSelected()
-    {
-      return pidSelected;
-    }
+        /**
+         * Sets the value of the overview property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public void setOverview(JalviewModel.Viewport.Overview value) {
+            this.overview = value;
+        }
 
-    /**
-     * Sets the value of the pidSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setPidSelected(Boolean value)
-    {
-      this.pidSelected = value;
-    }
+        /**
+         * Gets the value of the conservationSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isConservationSelected() {
+            return conservationSelected;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getBgColour()
-    {
-      return bgColour;
-    }
+        /**
+         * Sets the value of the conservationSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setConservationSelected(Boolean value) {
+            this.conservationSelected = value;
+        }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setBgColour(String value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * Gets the value of the pidSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isPidSelected() {
+            return pidSelected;
+        }
 
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
+        /**
+         * Sets the value of the pidSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setPidSelected(Boolean value) {
+            this.pidSelected = value;
+        }
 
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getBgColour() {
+            return bgColour;
+        }
 
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setBgColour(String value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
+        /**
+         * Gets the value of the consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the consThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
 
-    /**
-     * Gets the value of the showFullId property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowFullId()
-    {
-      return showFullId;
-    }
+        /**
+         * Sets the value of the pidThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
+        }
 
-    /**
-     * Sets the value of the showFullId property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowFullId(Boolean value)
-    {
-      this.showFullId = value;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the rightAlignIds property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRightAlignIds()
-    {
-      return rightAlignIds;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the rightAlignIds property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRightAlignIds(Boolean value)
-    {
-      this.rightAlignIds = value;
-    }
+        /**
+         * Gets the value of the showFullId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowFullId() {
+            return showFullId;
+        }
 
-    /**
-     * Gets the value of the showText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowText()
-    {
-      return showText;
-    }
+        /**
+         * Sets the value of the showFullId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowFullId(Boolean value) {
+            this.showFullId = value;
+        }
 
-    /**
-     * Sets the value of the showText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowText(Boolean value)
-    {
-      this.showText = value;
-    }
+        /**
+         * Gets the value of the rightAlignIds property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRightAlignIds() {
+            return rightAlignIds;
+        }
 
-    /**
-     * Gets the value of the showColourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowColourText()
-    {
-      return showColourText;
-    }
+        /**
+         * Sets the value of the rightAlignIds property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRightAlignIds(Boolean value) {
+            this.rightAlignIds = value;
+        }
 
-    /**
-     * Sets the value of the showColourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowColourText(Boolean value)
-    {
-      this.showColourText = value;
-    }
+        /**
+         * Gets the value of the showText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowText() {
+            return showText;
+        }
+
+        /**
+         * Sets the value of the showText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowText(Boolean value) {
+            this.showText = value;
+        }
+
+        /**
+         * Gets the value of the showColourText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowColourText() {
+            return showColourText;
+        }
+
+        /**
+         * Sets the value of the showColourText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowColourText(Boolean value) {
+            this.showColourText = value;
+        }
+
+        /**
+         * Gets the value of the showUnconserved property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowUnconserved() {
+            if (showUnconserved == null) {
+                return false;
+            } else {
+                return showUnconserved;
+            }
+        }
+
+        /**
+         * Sets the value of the showUnconserved property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
+        }
+
+        /**
+         * Gets the value of the showBoxes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBoxes() {
+            return showBoxes;
+        }
+
+        /**
+         * Sets the value of the showBoxes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBoxes(Boolean value) {
+            this.showBoxes = value;
+        }
+
+        /**
+         * Gets the value of the wrapAlignment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isWrapAlignment() {
+            return wrapAlignment;
+        }
 
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowUnconserved()
-    {
-      if (showUnconserved == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showUnconserved;
-      }
-    }
+        /**
+         * Sets the value of the wrapAlignment property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setWrapAlignment(Boolean value) {
+            this.wrapAlignment = value;
+        }
 
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
+        /**
+         * Gets the value of the renderGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRenderGaps() {
+            return renderGaps;
+        }
 
-    /**
-     * Gets the value of the showBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBoxes()
-    {
-      return showBoxes;
-    }
+        /**
+         * Sets the value of the renderGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRenderGaps(Boolean value) {
+            this.renderGaps = value;
+        }
 
-    /**
-     * Sets the value of the showBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBoxes(Boolean value)
-    {
-      this.showBoxes = value;
-    }
+        /**
+         * Gets the value of the showSequenceFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowSequenceFeatures() {
+            return showSequenceFeatures;
+        }
 
-    /**
-     * Gets the value of the wrapAlignment property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isWrapAlignment()
-    {
-      return wrapAlignment;
-    }
+        /**
+         * Sets the value of the showSequenceFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceFeatures(Boolean value) {
+            this.showSequenceFeatures = value;
+        }
 
-    /**
-     * Sets the value of the wrapAlignment property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setWrapAlignment(Boolean value)
-    {
-      this.wrapAlignment = value;
-    }
+        /**
+         * Gets the value of the showNPfeatureTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowNPfeatureTooltip() {
+            return showNPfeatureTooltip;
+        }
 
-    /**
-     * Gets the value of the renderGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRenderGaps()
-    {
-      return renderGaps;
-    }
+        /**
+         * Sets the value of the showNPfeatureTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowNPfeatureTooltip(Boolean value) {
+            this.showNPfeatureTooltip = value;
+        }
 
-    /**
-     * Sets the value of the renderGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRenderGaps(Boolean value)
-    {
-      this.renderGaps = value;
-    }
+        /**
+         * Gets the value of the showDbRefTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDbRefTooltip() {
+            return showDbRefTooltip;
+        }
 
-    /**
-     * Gets the value of the showSequenceFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
+        /**
+         * Sets the value of the showDbRefTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDbRefTooltip(Boolean value) {
+            this.showDbRefTooltip = value;
+        }
 
-    /**
-     * Sets the value of the showSequenceFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceFeatures(Boolean value)
-    {
-      this.showSequenceFeatures = value;
-    }
+        /**
+         * Gets the value of the followHighlight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowHighlight() {
+            if (followHighlight == null) {
+                return true;
+            } else {
+                return followHighlight;
+            }
+        }
 
-    /**
-     * Gets the value of the showNPfeatureTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowNPfeatureTooltip()
-    {
-      return showNPfeatureTooltip;
-    }
+        /**
+         * Sets the value of the followHighlight property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowHighlight(Boolean value) {
+            this.followHighlight = value;
+        }
 
-    /**
-     * Sets the value of the showNPfeatureTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowNPfeatureTooltip(Boolean value)
-    {
-      this.showNPfeatureTooltip = value;
-    }
+        /**
+         * Gets the value of the followSelection property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowSelection() {
+            if (followSelection == null) {
+                return true;
+            } else {
+                return followSelection;
+            }
+        }
 
-    /**
-     * Gets the value of the showDbRefTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDbRefTooltip()
-    {
-      return showDbRefTooltip;
-    }
+        /**
+         * Sets the value of the followSelection property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowSelection(Boolean value) {
+            this.followSelection = value;
+        }
 
-    /**
-     * Sets the value of the showDbRefTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDbRefTooltip(Boolean value)
-    {
-      this.showDbRefTooltip = value;
-    }
+        /**
+         * Gets the value of the showAnnotation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAnnotation() {
+            return showAnnotation;
+        }
 
-    /**
-     * Gets the value of the followHighlight property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowHighlight()
-    {
-      if (followHighlight == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followHighlight;
-      }
-    }
+        /**
+         * Sets the value of the showAnnotation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowAnnotation(Boolean value) {
+            this.showAnnotation = value;
+        }
 
-    /**
-     * Sets the value of the followHighlight property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowHighlight(Boolean value)
-    {
-      this.followHighlight = value;
-    }
+        /**
+         * Gets the value of the centreColumnLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCentreColumnLabels() {
+            if (centreColumnLabels == null) {
+                return false;
+            } else {
+                return centreColumnLabels;
+            }
+        }
 
-    /**
-     * Gets the value of the followSelection property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowSelection()
-    {
-      if (followSelection == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followSelection;
-      }
-    }
+        /**
+         * Sets the value of the centreColumnLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCentreColumnLabels(Boolean value) {
+            this.centreColumnLabels = value;
+        }
 
-    /**
-     * Sets the value of the followSelection property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowSelection(Boolean value)
-    {
-      this.followSelection = value;
-    }
+        /**
+         * Gets the value of the showGroupConservation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConservation() {
+            if (showGroupConservation == null) {
+                return false;
+            } else {
+                return showGroupConservation;
+            }
+        }
 
-    /**
-     * Gets the value of the showAnnotation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowAnnotation()
-    {
-      return showAnnotation;
-    }
+        /**
+         * Sets the value of the showGroupConservation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConservation(Boolean value) {
+            this.showGroupConservation = value;
+        }
 
-    /**
-     * Sets the value of the showAnnotation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowAnnotation(Boolean value)
-    {
-      this.showAnnotation = value;
-    }
+        /**
+         * Gets the value of the showGroupConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConsensus() {
+            if (showGroupConsensus == null) {
+                return false;
+            } else {
+                return showGroupConsensus;
+            }
+        }
 
-    /**
-     * Gets the value of the centreColumnLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isCentreColumnLabels()
-    {
-      if (centreColumnLabels == null)
-      {
-        return false;
-      }
-      else
-      {
-        return centreColumnLabels;
-      }
-    }
+        /**
+         * Sets the value of the showGroupConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConsensus(Boolean value) {
+            this.showGroupConsensus = value;
+        }
 
-    /**
-     * Sets the value of the centreColumnLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCentreColumnLabels(Boolean value)
-    {
-      this.centreColumnLabels = value;
-    }
+        /**
+         * Gets the value of the showConsensusHistogram property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConservation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConservation()
-    {
-      if (showGroupConservation == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConservation;
-      }
-    }
+        /**
+         * Sets the value of the showConsensusHistogram property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
 
-    /**
-     * Sets the value of the showGroupConservation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConservation(Boolean value)
-    {
-      this.showGroupConservation = value;
-    }
+        /**
+         * Gets the value of the showSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConsensus()
-    {
-      if (showGroupConsensus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConsensus;
-      }
-    }
+        /**
+         * Sets the value of the showSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
+
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
+        }
 
-    /**
-     * Sets the value of the showGroupConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConsensus(Boolean value)
-    {
-      this.showGroupConsensus = value;
-    }
+        /**
+         * Sets the value of the normaliseSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
 
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
+        }
 
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
+        /**
+         * Sets the value of the ignoreGapsinConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
 
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
+        /**
+         * Gets the value of the startRes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartRes() {
+            return startRes;
+        }
 
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
+        /**
+         * Sets the value of the startRes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartRes(Integer value) {
+            this.startRes = value;
+        }
 
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
+        /**
+         * Gets the value of the startSeq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartSeq() {
+            return startSeq;
+        }
 
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
+        /**
+         * Sets the value of the startSeq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartSeq(Integer value) {
+            this.startSeq = value;
+        }
 
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    /**
-     * Gets the value of the startRes property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartRes()
-    {
-      return startRes;
-    }
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    /**
-     * Sets the value of the startRes property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartRes(Integer value)
-    {
-      this.startRes = value;
-    }
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    /**
-     * Gets the value of the startSeq property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartSeq()
-    {
-      return startSeq;
-    }
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    /**
-     * Sets the value of the startSeq property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartSeq(Integer value)
-    {
-      this.startSeq = value;
-    }
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Gets the value of the scaleProteinAsCdna property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isScaleProteinAsCdna() {
+            if (scaleProteinAsCdna == null) {
+                return true;
+            } else {
+                return scaleProteinAsCdna;
+            }
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Sets the value of the scaleProteinAsCdna property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setScaleProteinAsCdna(Boolean value) {
+            this.scaleProteinAsCdna = value;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Gets the value of the viewName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getViewName() {
+            return viewName;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Sets the value of the viewName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setViewName(String value) {
+            this.viewName = value;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Gets the value of the sequenceSetId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSequenceSetId() {
+            return sequenceSetId;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Sets the value of the sequenceSetId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSequenceSetId(String value) {
+            this.sequenceSetId = value;
+        }
 
-    /**
-     * Gets the value of the scaleProteinAsCdna property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isScaleProteinAsCdna()
-    {
-      if (scaleProteinAsCdna == null)
-      {
-        return true;
-      }
-      else
-      {
-        return scaleProteinAsCdna;
-      }
-    }
+        /**
+         * Gets the value of the gatheredViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isGatheredViews() {
+            return gatheredViews;
+        }
 
-    /**
-     * Sets the value of the scaleProteinAsCdna property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setScaleProteinAsCdna(Boolean value)
-    {
-      this.scaleProteinAsCdna = value;
-    }
+        /**
+         * Sets the value of the gatheredViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setGatheredViews(Boolean value) {
+            this.gatheredViews = value;
+        }
 
-    /**
-     * Gets the value of the viewName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getViewName()
-    {
-      return viewName;
-    }
+        /**
+         * Gets the value of the textCol1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol1() {
+            return textCol1;
+        }
 
-    /**
-     * Sets the value of the viewName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setViewName(String value)
-    {
-      this.viewName = value;
-    }
+        /**
+         * Sets the value of the textCol1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
+        }
 
-    /**
-     * Gets the value of the sequenceSetId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getSequenceSetId()
-    {
-      return sequenceSetId;
-    }
+        /**
+         * Gets the value of the textCol2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol2() {
+            return textCol2;
+        }
 
-    /**
-     * Sets the value of the sequenceSetId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setSequenceSetId(String value)
-    {
-      this.sequenceSetId = value;
-    }
+        /**
+         * Sets the value of the textCol2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
+        }
 
-    /**
-     * Gets the value of the gatheredViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isGatheredViews()
-    {
-      return gatheredViews;
-    }
+        /**
+         * Gets the value of the textColThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextColThreshold() {
+            return textColThreshold;
+        }
 
-    /**
-     * Sets the value of the gatheredViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setGatheredViews(Boolean value)
-    {
-      this.gatheredViews = value;
-    }
+        /**
+         * Sets the value of the textColThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
+        }
 
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
+        /**
+         * Gets the value of the complementId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getComplementId() {
+            return complementId;
+        }
 
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
+        /**
+         * Sets the value of the complementId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setComplementId(String value) {
+            this.complementId = value;
+        }
 
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
+        /**
+         * Gets the value of the showComplementFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeatures() {
+            if (showComplementFeatures == null) {
+                return false;
+            } else {
+                return showComplementFeatures;
+            }
+        }
 
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
+        /**
+         * Sets the value of the showComplementFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeatures(Boolean value) {
+            this.showComplementFeatures = value;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Gets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeaturesOnTop() {
+            if (showComplementFeaturesOnTop == null) {
+                return false;
+            } else {
+                return showComplementFeaturesOnTop;
+            }
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * Sets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeaturesOnTop(Boolean value) {
+            this.showComplementFeaturesOnTop = value;
+        }
 
-    /**
-     * Gets the value of the complementId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComplementId()
-    {
-      return complementId;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Sets the value of the complementId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComplementId(String value)
-    {
-      this.complementId = value;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Gets the value of the showComplementFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeatures()
-    {
-      if (showComplementFeatures == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeatures;
-      }
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Sets the value of the showComplementFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeatures(Boolean value)
-    {
-      this.showComplementFeatures = value;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Gets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeaturesOnTop()
-    {
-      if (showComplementFeaturesOnTop == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeaturesOnTop;
-      }
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Sets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeaturesOnTop(Boolean value)
-    {
-      this.showComplementFeaturesOnTop = value;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class CalcIdParam
+            extends WebServiceParameterSet
+        {
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+            @XmlAttribute(name = "calcId", required = true)
+            protected String calcId;
+            @XmlAttribute(name = "needsUpdate")
+            protected Boolean needsUpdate;
+            @XmlAttribute(name = "autoUpdate", required = true)
+            protected boolean autoUpdate;
+
+            /**
+             * Gets the value of the calcId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getCalcId() {
+                return calcId;
+            }
+
+            /**
+             * Sets the value of the calcId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setCalcId(String value) {
+                this.calcId = value;
+            }
+
+            /**
+             * Gets the value of the needsUpdate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isNeedsUpdate() {
+                if (needsUpdate == null) {
+                    return false;
+                } else {
+                    return needsUpdate;
+                }
+            }
+
+            /**
+             * Sets the value of the needsUpdate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setNeedsUpdate(Boolean value) {
+                this.needsUpdate = value;
+            }
+
+            /**
+             * Gets the value of the autoUpdate property.
+             * 
+             */
+            public boolean isAutoUpdate() {
+                return autoUpdate;
+            }
+
+            /**
+             * Sets the value of the autoUpdate property.
+             * 
+             */
+            public void setAutoUpdate(boolean value) {
+                this.autoUpdate = value;
+            }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class HiddenColumns {
+
+            @XmlAttribute(name = "start")
+            protected Integer start;
+            @XmlAttribute(name = "end")
+            protected Integer end;
+
+            /**
+             * Gets the value of the start property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getStart() {
+                return start;
+            }
+
+            /**
+             * Sets the value of the start property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setStart(Integer value) {
+                this.start = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setEnd(Integer value) {
+                this.end = value;
+            }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;extension
-     * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
-     * &lt;attribute name="calcId" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-     * &lt;attribute name="needsUpdate"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
-     * /&gt; &lt;attribute name="autoUpdate" use="required"
-     * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-     * &lt;/extension&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class CalcIdParam extends WebServiceParameterSet
-    {
-
-      @XmlAttribute(name = "calcId", required = true)
-      protected String calcId;
-
-      @XmlAttribute(name = "needsUpdate")
-      protected Boolean needsUpdate;
-
-      @XmlAttribute(name = "autoUpdate", required = true)
-      protected boolean autoUpdate;
-
-      /**
-       * Gets the value of the calcId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCalcId()
-      {
-        return calcId;
-      }
-
-      /**
-       * Sets the value of the calcId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCalcId(String value)
-      {
-        this.calcId = value;
-      }
-
-      /**
-       * Gets the value of the needsUpdate property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isNeedsUpdate()
-      {
-        if (needsUpdate == null)
-        {
-          return false;
         }
-        else
-        {
-          return needsUpdate;
-        }
-      }
-
-      /**
-       * Sets the value of the needsUpdate property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setNeedsUpdate(Boolean value)
-      {
-        this.needsUpdate = value;
-      }
-
-      /**
-       * Gets the value of the autoUpdate property.
-       * 
-       */
-      public boolean isAutoUpdate()
-      {
-        return autoUpdate;
-      }
-
-      /**
-       * Sets the value of the autoUpdate property.
-       * 
-       */
-      public void setAutoUpdate(boolean value)
-      {
-        this.autoUpdate = value;
-      }
 
-    }
 
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content
-     * contained within this class.
-     * 
-     * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-     * &lt;restriction
-     * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-     * &lt;attribute name="start"
-     * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
-     * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-     * &lt;/restriction&gt; &lt;/complexContent&gt;
-     * &lt;/complexType&gt; </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class HiddenColumns
-    {
-
-      @XmlAttribute(name = "start")
-      protected Integer start;
-
-      @XmlAttribute(name = "end")
-      protected Integer end;
-
-      /**
-       * Gets the value of the start property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getStart()
-      {
-        return start;
-      }
-
-      /**
-       * Sets the value of the start property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setStart(Integer value)
-      {
-        this.start = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setEnd(Integer value)
-      {
-        this.end = value;
-      }
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Overview {
+
+            @XmlAttribute(name = "showHidden")
+            protected Boolean showHidden;
+            @XmlAttribute(name = "residueColour")
+            protected Integer residueColour;
+            @XmlAttribute(name = "gapColour")
+            protected Integer gapColour;
+            @XmlAttribute(name = "hiddenColour")
+            protected Integer hiddenColour;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @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 showHidden property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isShowHidden() {
+                return showHidden;
+            }
+
+            /**
+             * Sets the value of the showHidden property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setShowHidden(Boolean value) {
+                this.showHidden = value;
+            }
+
+            /**
+             * Gets the value of the residueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getResidueColour() {
+                return residueColour;
+            }
+
+            /**
+             * Sets the value of the residueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setResidueColour(Integer value) {
+                this.residueColour = value;
+            }
+
+            /**
+             * Gets the value of the gapColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getGapColour() {
+                return gapColour;
+            }
+
+            /**
+             * Sets the value of the gapColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setGapColour(Integer value) {
+                this.gapColour = value;
+            }
+
+            /**
+             * Gets the value of the hiddenColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHiddenColour() {
+                return hiddenColour;
+            }
+
+            /**
+             * Sets the value of the hiddenColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHiddenColour(Integer value) {
+                this.hiddenColour = value;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
 
-    }
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java
deleted file mode 100644
index 0541d7a..0000000
--- a/src/jalview/xml/binding/jalview/JalviewModelType.java
+++ /dev/null
@@ -1,5233 +0,0 @@
-//
-// 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: 2018.09.18 at 01:33:02 PM BST 
-//
-
-package jalview.xml.binding.jalview;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlID;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
-import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-import javax.xml.datatype.XMLGregorianCalendar;
-
-/**
- * 
    
- * Java class for JalviewModelType complex type.
- * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
- * 
- * 
    - * <complexType name="JalviewModelType">
- *   <complexContent>
- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       <sequence>
- *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         <sequence>
- *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org}pdbentry">
- *                             <sequence>
- *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 <complexType>
- *                                   <simpleContent>
- *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
- *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </extension>
- *                                   </simpleContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <sequence>
- *                               <element name="secondaryStructure" maxOccurs="unbounded">
- *                                 <complexType>
- *                                   <complexContent>
- *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </restriction>
- *                                   </complexContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                             <attGroup ref="{www.jalview.org}swingwindow"/>
- *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   </sequence>
- *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- *                   </sequence>
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence minOccurs="0">
- *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                   </sequence>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="FeatureSettings" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <sequence>
- *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- *                             </sequence>
- *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *         </sequence>
- *       </sequence>
- *     </restriction>
- *   </complexContent>
- * </complexType>
- * 
    
- * 
- * 
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewModelType",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
-      "userColours", "tree", "featureSettings" })
-public class JalviewModelType
-{
-
-  @XmlElement(required = true)
-  @XmlSchemaType(name = "dateTime")
-  protected XMLGregorianCalendar creationDate;
-
-  @XmlElement(required = true)
-  protected String version;
-
-  @XmlElement(required = true)
-  protected VAMSAS vamsasModel;
-
-  @XmlElement(name = "JSeq")
-  protected List jSeq;
-
-  @XmlElement(name = "JGroup")
-  protected List jGroup;
-
-  @XmlElement(name = "Viewport")
-  protected List viewport;
-
-  @XmlElement(name = "UserColours")
-  protected List userColours;
-
-  protected List tree;
-
-  @XmlElement(name = "FeatureSettings")
-  protected JalviewModelType.FeatureSettings featureSettings;
-
-  /**
-   * Gets the value of the creationDate property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreationDate()
-  {
-    return creationDate;
-  }
-
-  /**
-   * Sets the value of the creationDate property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreationDate(XMLGregorianCalendar value)
-  {
-    this.creationDate = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the vamsasModel property.
-   * 
-   * @return possible object is {@link VAMSAS }
-   * 
-   */
-  public VAMSAS getVamsasModel()
-  {
-    return vamsasModel;
-  }
-
-  /**
-   * Sets the value of the vamsasModel property.
-   * 
-   * @param value
-   *          allowed object is {@link VAMSAS }
-   * 
-   */
-  public void setVamsasModel(VAMSAS value)
-  {
-    this.vamsasModel = value;
-  }
-
-  /**
-   * Gets the value of the jSeq 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 jSeq property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getJSeq().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.JSeq }
-   * 
-   * 
-   */
-  public List getJSeq()
-  {
-    if (jSeq == null)
-    {
-      jSeq = new ArrayList();
-    }
-    return this.jSeq;
-  }
-
-  /**
-   * Gets the value of the jGroup 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 jGroup property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getJGroup().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.JGroup }
-   * 
-   * 
-   */
-  public List getJGroup()
-  {
-    if (jGroup == null)
-    {
-      jGroup = new ArrayList();
-    }
-    return this.jGroup;
-  }
-
-  /**
-   * Gets the value of the viewport 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 viewport property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getViewport().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.Viewport }
-   * 
-   * 
-   */
-  public List getViewport()
-  {
-    if (viewport == null)
-    {
-      viewport = new ArrayList();
-    }
-    return this.viewport;
-  }
-
-  /**
-   * Gets the value of the userColours 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 userColours property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getUserColours().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.UserColours }
-   * 
-   * 
-   */
-  public List getUserColours()
-  {
-    if (userColours == null)
-    {
-      userColours = new ArrayList();
-    }
-    return this.userColours;
-  }
-
-  /**
-   * Gets the value of the tree 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 tree property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getTree().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModelType.Tree }
-   * 
-   * 
-   */
-  public List getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList();
-    }
-    return this.tree;
-  }
-
-  /**
-   * Gets the value of the featureSettings property.
-   * 
-   * @return possible object is {@link JalviewModelType.FeatureSettings }
-   * 
-   */
-  public JalviewModelType.FeatureSettings getFeatureSettings()
-  {
-    return featureSettings;
-  }
-
-  /**
-   * Sets the value of the featureSettings property.
-   * 
-   * @param value
-   *          allowed object is {@link JalviewModelType.FeatureSettings }
-   * 
-   */
-  public void setFeatureSettings(JalviewModelType.FeatureSettings value)
-  {
-    this.featureSettings = value;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-   *                 </sequence>
-   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "setting", "group" })
-  public static class FeatureSettings
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List setting;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List group;
-
-    /**
-     * Gets the value of the setting 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 setting property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getSetting().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.FeatureSettings.Setting }
-     * 
-     * 
-     */
-    public List getSetting()
-    {
-      if (setting == null)
-      {
-        setting = new ArrayList();
-      }
-      return this.setting;
-    }
-
-    /**
-     * Gets the value of the group 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 group property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getGroup().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.FeatureSettings.Group }
-     * 
-     * 
-     */
-    public List getGroup()
-    {
-      if (group == null)
-      {
-        group = new ArrayList();
-      }
-      return this.group;
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Group
-    {
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
-    public static class Setting
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List attributeName;
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected FeatureMatcherSet matcherSet;
-
-      @XmlAttribute(name = "type", required = true)
-      protected String type;
-
-      @XmlAttribute(name = "colour", required = true)
-      protected int colour;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      @XmlAttribute(name = "order")
-      protected Float order;
-
-      @XmlAttribute(name = "mincolour")
-      protected Integer mincolour;
-
-      @XmlAttribute(name = "noValueColour")
-      protected NoValueColour noValueColour;
-
-      @XmlAttribute(name = "threshold")
-      protected Float threshold;
-
-      @XmlAttribute(name = "threshstate")
-      protected Integer threshstate;
-
-      @XmlAttribute(name = "max")
-      protected Float max;
-
-      @XmlAttribute(name = "min")
-      protected Float min;
-
-      @XmlAttribute(name = "colourByLabel")
-      protected Boolean colourByLabel;
-
-      @XmlAttribute(name = "autoScale")
-      protected Boolean autoScale;
-
-      /**
-       * Gets the value of the attributeName 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 attributeName property.
-       * 
-       * 
    
-       * For example, to add a new item, do as follows:
-       * 
-       * 
    -       * getAttributeName().add(newItem);
-       * 
    
-       * 
-       * 
-       * 
    
-       * Objects of the following type(s) are allowed in the list {@link String
-       * }
-       * 
-       * 
-       */
-      public List getAttributeName()
-      {
-        if (attributeName == null)
-        {
-          attributeName = new ArrayList();
-        }
-        return this.attributeName;
-      }
-
-      /**
-       * Gets the value of the matcherSet property.
-       * 
-       * @return possible object is {@link FeatureMatcherSet }
-       * 
-       */
-      public FeatureMatcherSet getMatcherSet()
-      {
-        return matcherSet;
-      }
-
-      /**
-       * Sets the value of the matcherSet property.
-       * 
-       * @param value
-       *          allowed object is {@link FeatureMatcherSet }
-       * 
-       */
-      public void setMatcherSet(FeatureMatcherSet value)
-      {
-        this.matcherSet = value;
-      }
-
-      /**
-       * Gets the value of the type property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getType()
-      {
-        return type;
-      }
-
-      /**
-       * Sets the value of the type property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setType(String value)
-      {
-        this.type = value;
-      }
-
-      /**
-       * Gets the value of the colour property.
-       * 
-       */
-      public int getColour()
-      {
-        return colour;
-      }
-
-      /**
-       * Sets the value of the colour property.
-       * 
-       */
-      public void setColour(int value)
-      {
-        this.colour = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-      /**
-       * Gets the value of the order property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getOrder()
-      {
-        return order;
-      }
-
-      /**
-       * Sets the value of the order property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setOrder(Float value)
-      {
-        this.order = value;
-      }
-
-      /**
-       * Gets the value of the mincolour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getMincolour()
-      {
-        return mincolour;
-      }
-
-      /**
-       * Sets the value of the mincolour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setMincolour(Integer value)
-      {
-        this.mincolour = value;
-      }
-
-      /**
-       * Gets the value of the noValueColour property.
-       * 
-       * @return possible object is {@link NoValueColour }
-       * 
-       */
-      public NoValueColour getNoValueColour()
-      {
-        if (noValueColour == null)
-        {
-          return NoValueColour.MIN;
-        }
-        else
-        {
-          return noValueColour;
-        }
-      }
-
-      /**
-       * Sets the value of the noValueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link NoValueColour }
-       * 
-       */
-      public void setNoValueColour(NoValueColour value)
-      {
-        this.noValueColour = value;
-      }
-
-      /**
-       * Gets the value of the threshold property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getThreshold()
-      {
-        return threshold;
-      }
-
-      /**
-       * Sets the value of the threshold property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setThreshold(Float value)
-      {
-        this.threshold = value;
-      }
-
-      /**
-       * Gets the value of the threshstate property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getThreshstate()
-      {
-        return threshstate;
-      }
-
-      /**
-       * Sets the value of the threshstate property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setThreshstate(Integer value)
-      {
-        this.threshstate = value;
-      }
-
-      /**
-       * Gets the value of the max property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMax()
-      {
-        return max;
-      }
-
-      /**
-       * Sets the value of the max property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMax(Float value)
-      {
-        this.max = value;
-      }
-
-      /**
-       * Gets the value of the min property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMin()
-      {
-        return min;
-      }
-
-      /**
-       * Sets the value of the min property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMin(Float value)
-      {
-        this.min = value;
-      }
-
-      /**
-       * Gets the value of the colourByLabel property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isColourByLabel()
-      {
-        return colourByLabel;
-      }
-
-      /**
-       * Sets the value of the colourByLabel property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setColourByLabel(Boolean value)
-      {
-        this.colourByLabel = value;
-      }
-
-      /**
-       * Gets the value of the autoScale property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isAutoScale()
-      {
-        return autoScale;
-      }
-
-      /**
-       * Sets the value of the autoScale property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setAutoScale(Boolean value)
-      {
-        this.autoScale = value;
-      }
-
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
-  public static class JGroup
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List seq;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlAttribute(name = "start")
-    protected Integer start;
-
-    @XmlAttribute(name = "end")
-    protected Integer end;
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "colour")
-    protected String colour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "outlineColour")
-    protected Integer outlineColour;
-
-    @XmlAttribute(name = "displayBoxes")
-    protected Boolean displayBoxes;
-
-    @XmlAttribute(name = "displayText")
-    protected Boolean displayText;
-
-    @XmlAttribute(name = "colourText")
-    protected Boolean colourText;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the seq 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 seq property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getSeq().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
-     */
-    public List getSeq()
-    {
-      if (seq == null)
-      {
-        seq = new ArrayList();
-      }
-      return this.seq;
-    }
-
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStart(Integer value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setEnd(Integer value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setColour(String value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
-
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the outlineColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getOutlineColour()
-    {
-      return outlineColour;
-    }
-
-    /**
-     * Sets the value of the outlineColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setOutlineColour(Integer value)
-    {
-      this.outlineColour = value;
-    }
-
-    /**
-     * Gets the value of the displayBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayBoxes()
-    {
-      return displayBoxes;
-    }
-
-    /**
-     * Sets the value of the displayBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayBoxes(Boolean value)
-    {
-      this.displayBoxes = value;
-    }
-
-    /**
-     * Gets the value of the displayText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayText()
-    {
-      return displayText;
-    }
-
-    /**
-     * Sets the value of the displayText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayText(Boolean value)
-    {
-      this.displayText = value;
-    }
-
-    /**
-     * Gets the value of the colourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isColourText()
-    {
-      return colourText;
-    }
-
-    /**
-     * Sets the value of the colourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColourText(Boolean value)
-    {
-      this.colourText = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
-
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
-
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
-
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
-
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowUnconserved()
-    {
-      return showUnconserved;
-    }
-
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
-
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
-
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
-
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <extension base="{www.jalview.org}pdbentry">
-   *                 <sequence>
-   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-   *                     <complexType>
-   *                       <simpleContent>
-   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </extension>
-   *                       </simpleContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *               </extension>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="secondaryStructure" maxOccurs="unbounded">
-   *                     <complexType>
-   *                       <complexContent>
-   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </restriction>
-   *                       </complexContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
-  public static class JSeq
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List features;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List pdbids;
-
-    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-    protected List hiddenSequences;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List rnaViewer;
-
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-
-    @XmlAttribute(name = "hidden")
-    protected Boolean hidden;
-
-    @XmlAttribute(name = "viewreference")
-    protected Boolean viewreference;
-
-    /**
-     * Gets the value of the features 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 features property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getFeatures().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link Feature }
-     * 
-     * 
-     */
-    public List getFeatures()
-    {
-      if (features == null)
-      {
-        features = new ArrayList();
-      }
-      return this.features;
-    }
-
-    /**
-     * Gets the value of the pdbids 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 pdbids property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getPdbids().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.JSeq.Pdbids }
-     * 
-     * 
-     */
-    public List getPdbids()
-    {
-      if (pdbids == null)
-      {
-        pdbids = new ArrayList();
-      }
-      return this.pdbids;
-    }
-
-    /**
-     * Gets the value of the hiddenSequences 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 hiddenSequences property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getHiddenSequences().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
-     */
-    public List getHiddenSequences()
-    {
-      if (hiddenSequences == null)
-      {
-        hiddenSequences = new ArrayList();
-      }
-      return this.hiddenSequences;
-    }
-
-    /**
-     * Gets the value of the rnaViewer 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 rnaViewer property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getRnaViewer().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.JSeq.RnaViewer }
-     * 
-     * 
-     */
-    public List getRnaViewer()
-    {
-      if (rnaViewer == null)
-      {
-        rnaViewer = new ArrayList();
-      }
-      return this.rnaViewer;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     */
-    public int getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     */
-    public void setStart(int value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the hidden property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isHidden()
-    {
-      return hidden;
-    }
-
-    /**
-     * Sets the value of the hidden property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setHidden(Boolean value)
-    {
-      this.hidden = value;
-    }
-
-    /**
-     * Gets the value of the viewreference property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isViewreference()
-    {
-      return viewreference;
-    }
-
-    /**
-     * Sets the value of the viewreference property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setViewreference(Boolean value)
-    {
-      this.viewreference = value;
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org}pdbentry">
-     *       <sequence>
-     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <simpleContent>
-     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </extension>
-     *             </simpleContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "structureState" })
-    public static class Pdbids extends Pdbentry
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List structureState;
-
-      /**
-       * Gets the value of the structureState 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 structureState property.
-       * 
-       * 
    
-       * For example, to add a new item, do as follows:
-       * 
-       * 
    -       * getStructureState().add(newItem);
-       * 
    
-       * 
-       * 
-       * 
    
-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModelType.JSeq.Pdbids.StructureState }
-       * 
-       * 
-       */
-      public List getStructureState()
-      {
-        if (structureState == null)
-        {
-          structureState = new ArrayList();
-        }
-        return this.structureState;
-      }
-
-      /**
-       * 
    
-       * Java class for anonymous complex type.
-       * 
-       * 
    
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * 
    -       * <complexType>
-       *   <simpleContent>
-       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-       *       <attGroup ref="{www.jalview.org}swingwindow"/>
-       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </extension>
-       *   </simpleContent>
-       * </complexType>
-       * 
    
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "value" })
-      public static class StructureState
-      {
-
-        @XmlValue
-        protected String value;
-
-        @XmlAttribute(name = "visible")
-        protected Boolean visible;
-
-        @XmlAttribute(name = "viewId")
-        protected String viewId;
-
-        @XmlAttribute(name = "alignwithAlignPanel")
-        protected Boolean alignwithAlignPanel;
-
-        @XmlAttribute(name = "colourwithAlignPanel")
-        protected Boolean colourwithAlignPanel;
-
-        @XmlAttribute(name = "colourByJmol")
-        protected Boolean colourByJmol;
-
-        @XmlAttribute(name = "type")
-        protected String type;
-
-        @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 value property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getValue()
-        {
-          return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setValue(String value)
-        {
-          this.value = value;
-        }
-
-        /**
-         * Gets the value of the visible property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public Boolean isVisible()
-        {
-          return visible;
-        }
-
-        /**
-         * Sets the value of the visible property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setVisible(Boolean value)
-        {
-          this.visible = value;
-        }
-
-        /**
-         * Gets the value of the viewId property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getViewId()
-        {
-          return viewId;
-        }
-
-        /**
-         * Sets the value of the viewId property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setViewId(String value)
-        {
-          this.viewId = value;
-        }
-
-        /**
-         * Gets the value of the alignwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isAlignwithAlignPanel()
-        {
-          if (alignwithAlignPanel == null)
-          {
-            return true;
-          }
-          else
-          {
-            return alignwithAlignPanel;
-          }
-        }
-
-        /**
-         * Sets the value of the alignwithAlignPanel property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setAlignwithAlignPanel(Boolean value)
-        {
-          this.alignwithAlignPanel = value;
-        }
-
-        /**
-         * Gets the value of the colourwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isColourwithAlignPanel()
-        {
-          if (colourwithAlignPanel == null)
-          {
-            return false;
-          }
-          else
-          {
-            return colourwithAlignPanel;
-          }
-        }
-
-        /**
-         * Sets the value of the colourwithAlignPanel property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setColourwithAlignPanel(Boolean value)
-        {
-          this.colourwithAlignPanel = value;
-        }
-
-        /**
-         * Gets the value of the colourByJmol property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public boolean isColourByJmol()
-        {
-          if (colourByJmol == null)
-          {
-            return true;
-          }
-          else
-          {
-            return colourByJmol;
-          }
-        }
-
-        /**
-         * Sets the value of the colourByJmol property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setColourByJmol(Boolean value)
-        {
-          this.colourByJmol = value;
-        }
-
-        /**
-         * Gets the value of the type property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getType()
-        {
-          return type;
-        }
-
-        /**
-         * Sets the value of the type property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setType(String value)
-        {
-          this.type = value;
-        }
-
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getWidth()
-        {
-          return width;
-        }
-
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setWidth(Integer value)
-        {
-          this.width = value;
-        }
-
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getHeight()
-        {
-          return height;
-        }
-
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setHeight(Integer value)
-        {
-          this.height = value;
-        }
-
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getXpos()
-        {
-          return xpos;
-        }
-
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setXpos(Integer value)
-        {
-          this.xpos = value;
-        }
-
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return possible object is {@link Integer }
-         * 
-         */
-        public Integer getYpos()
-        {
-          return ypos;
-        }
-
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *          allowed object is {@link Integer }
-         * 
-         */
-        public void setYpos(Integer value)
-        {
-          this.ypos = value;
-        }
-
-      }
-
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="secondaryStructure" maxOccurs="unbounded">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "secondaryStructure" })
-    public static class RnaViewer
-    {
-
-      @XmlElement(namespace = "www.jalview.org", required = true)
-      protected List secondaryStructure;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "viewId")
-      protected String viewId;
-
-      @XmlAttribute(name = "dividerLocation")
-      protected Integer dividerLocation;
-
-      @XmlAttribute(name = "selectedRna")
-      protected Integer selectedRna;
-
-      @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 secondaryStructure 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 secondaryStructure property.
-       * 
-       * 
    
-       * For example, to add a new item, do as follows:
-       * 
-       * 
    -       * getSecondaryStructure().add(newItem);
-       * 
    
-       * 
-       * 
-       * 
    
-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
-       * 
-       * 
-       */
-      public List getSecondaryStructure()
-      {
-        if (secondaryStructure == null)
-        {
-          secondaryStructure = new ArrayList();
-        }
-        return this.secondaryStructure;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the viewId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getViewId()
-      {
-        return viewId;
-      }
-
-      /**
-       * Sets the value of the viewId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setViewId(String value)
-      {
-        this.viewId = value;
-      }
-
-      /**
-       * Gets the value of the dividerLocation property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getDividerLocation()
-      {
-        return dividerLocation;
-      }
-
-      /**
-       * Sets the value of the dividerLocation property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setDividerLocation(Integer value)
-      {
-        this.dividerLocation = value;
-      }
-
-      /**
-       * Gets the value of the selectedRna property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getSelectedRna()
-      {
-        return selectedRna;
-      }
-
-      /**
-       * Sets the value of the selectedRna property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setSelectedRna(Integer value)
-      {
-        this.selectedRna = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
-
-      /**
-       * 
    
-       * Java class for anonymous complex type.
-       * 
-       * 
    
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * 
    -       * <complexType>
-       *   <complexContent>
-       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </restriction>
-       *   </complexContent>
-       * </complexType>
-       * 
    
-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "")
-      public static class SecondaryStructure
-      {
-
-        @XmlAttribute(name = "title")
-        protected String title;
-
-        @XmlAttribute(name = "annotationId", required = true)
-        protected String annotationId;
-
-        @XmlAttribute(name = "gapped")
-        protected Boolean gapped;
-
-        @XmlAttribute(name = "viewerState")
-        protected String viewerState;
-
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getTitle()
-        {
-          return title;
-        }
-
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setTitle(String value)
-        {
-          this.title = value;
-        }
-
-        /**
-         * Gets the value of the annotationId property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getAnnotationId()
-        {
-          return annotationId;
-        }
-
-        /**
-         * Sets the value of the annotationId property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setAnnotationId(String value)
-        {
-          this.annotationId = value;
-        }
-
-        /**
-         * Gets the value of the gapped property.
-         * 
-         * @return possible object is {@link Boolean }
-         * 
-         */
-        public Boolean isGapped()
-        {
-          return gapped;
-        }
-
-        /**
-         * Sets the value of the gapped property.
-         * 
-         * @param value
-         *          allowed object is {@link Boolean }
-         * 
-         */
-        public void setGapped(Boolean value)
-        {
-          this.gapped = value;
-        }
-
-        /**
-         * Gets the value of the viewerState property.
-         * 
-         * @return possible object is {@link String }
-         * 
-         */
-        public String getViewerState()
-        {
-          return viewerState;
-        }
-
-        /**
-         * Sets the value of the viewerState property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
-         * 
-         */
-        public void setViewerState(String value)
-        {
-          this.viewerState = value;
-        }
-
-      }
-
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence minOccurs="0">
-   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <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="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "title", "newick" })
-  public static class Tree
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String title;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String newick;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "showBootstrap")
-    protected Boolean showBootstrap;
-
-    @XmlAttribute(name = "showDistances")
-    protected Boolean showDistances;
-
-    @XmlAttribute(name = "markUnlinked")
-    protected Boolean markUnlinked;
-
-    @XmlAttribute(name = "fitToWindow")
-    protected Boolean fitToWindow;
-
-    @XmlAttribute(name = "currentTree")
-    protected Boolean currentTree;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @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 title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
-
-    /**
-     * Gets the value of the newick property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getNewick()
-    {
-      return newick;
-    }
-
-    /**
-     * Sets the value of the newick property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setNewick(String value)
-    {
-      this.newick = value;
-    }
-
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
-
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
-
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
-
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
-
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
-
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getThreshold()
-    {
-      return threshold;
-    }
-
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the showBootstrap property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBootstrap()
-    {
-      return showBootstrap;
-    }
-
-    /**
-     * Sets the value of the showBootstrap property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBootstrap(Boolean value)
-    {
-      this.showBootstrap = value;
-    }
-
-    /**
-     * Gets the value of the showDistances property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDistances()
-    {
-      return showDistances;
-    }
-
-    /**
-     * Sets the value of the showDistances property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDistances(Boolean value)
-    {
-      this.showDistances = value;
-    }
-
-    /**
-     * Gets the value of the markUnlinked property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMarkUnlinked()
-    {
-      return markUnlinked;
-    }
-
-    /**
-     * Sets the value of the markUnlinked property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMarkUnlinked(Boolean value)
-    {
-      this.markUnlinked = value;
-    }
-
-    /**
-     * Gets the value of the fitToWindow property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isFitToWindow()
-    {
-      return fitToWindow;
-    }
-
-    /**
-     * Sets the value of the fitToWindow property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFitToWindow(Boolean value)
-    {
-      this.fitToWindow = value;
-    }
-
-    /**
-     * Gets the value of the currentTree property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isCurrentTree()
-    {
-      return currentTree;
-    }
-
-    /**
-     * Sets the value of the currentTree property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCurrentTree(Boolean value)
-    {
-      this.currentTree = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
-
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
-
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
-
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
-
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
-
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
-
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-   *       </sequence>
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "userColourScheme" })
-  public static class UserColours
-  {
-
-    @XmlElement(
-      name = "UserColourScheme",
-      namespace = "www.jalview.org",
-      required = true)
-    protected JalviewUserColours userColourScheme;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the userColourScheme property.
-     * 
-     * @return possible object is {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours getUserColourScheme()
-    {
-      return userColourScheme;
-    }
-
-    /**
-     * Sets the value of the userColourScheme property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewUserColours }
-     * 
-     */
-    public void setUserColourScheme(JalviewUserColours value)
-    {
-      this.userColourScheme = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </extension>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "annotationColours", "hiddenColumns", "calcIdParam" })
-  public static class Viewport
-  {
-
-    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List hiddenColumns;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List calcIdParam;
-
-    @XmlAttribute(name = "conservationSelected")
-    protected Boolean conservationSelected;
-
-    @XmlAttribute(name = "pidSelected")
-    protected Boolean pidSelected;
-
-    @XmlAttribute(name = "bgColour")
-    protected String bgColour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "showFullId")
-    protected Boolean showFullId;
-
-    @XmlAttribute(name = "rightAlignIds")
-    protected Boolean rightAlignIds;
-
-    @XmlAttribute(name = "showText")
-    protected Boolean showText;
-
-    @XmlAttribute(name = "showColourText")
-    protected Boolean showColourText;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "showBoxes")
-    protected Boolean showBoxes;
-
-    @XmlAttribute(name = "wrapAlignment")
-    protected Boolean wrapAlignment;
-
-    @XmlAttribute(name = "renderGaps")
-    protected Boolean renderGaps;
-
-    @XmlAttribute(name = "showSequenceFeatures")
-    protected Boolean showSequenceFeatures;
-
-    @XmlAttribute(name = "showNPfeatureTooltip")
-    protected Boolean showNPfeatureTooltip;
-
-    @XmlAttribute(name = "showDbRefTooltip")
-    protected Boolean showDbRefTooltip;
-
-    @XmlAttribute(name = "followHighlight")
-    protected Boolean followHighlight;
-
-    @XmlAttribute(name = "followSelection")
-    protected Boolean followSelection;
-
-    @XmlAttribute(name = "showAnnotation")
-    protected Boolean showAnnotation;
-
-    @XmlAttribute(name = "centreColumnLabels")
-    protected Boolean centreColumnLabels;
-
-    @XmlAttribute(name = "showGroupConservation")
-    protected Boolean showGroupConservation;
-
-    @XmlAttribute(name = "showGroupConsensus")
-    protected Boolean showGroupConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "startRes")
-    protected Integer startRes;
-
-    @XmlAttribute(name = "startSeq")
-    protected Integer startSeq;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "scaleProteinAsCdna")
-    protected Boolean scaleProteinAsCdna;
-
-    @XmlAttribute(name = "viewName")
-    protected String viewName;
-
-    @XmlAttribute(name = "sequenceSetId")
-    protected String sequenceSetId;
-
-    @XmlAttribute(name = "gatheredViews")
-    protected Boolean gatheredViews;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @XmlAttribute(name = "complementId")
-    protected String complementId;
-
-    @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 annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
-
-    /**
-     * Gets the value of the hiddenColumns 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 hiddenColumns property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getHiddenColumns().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.Viewport.HiddenColumns }
-     * 
-     * 
-     */
-    public List getHiddenColumns()
-    {
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList();
-      }
-      return this.hiddenColumns;
-    }
-
-    /**
-     * Gets the value of the calcIdParam 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 calcIdParam property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getCalcIdParam().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModelType.Viewport.CalcIdParam }
-     * 
-     * 
-     */
-    public List getCalcIdParam()
-    {
-      if (calcIdParam == null)
-      {
-        calcIdParam = new ArrayList();
-      }
-      return this.calcIdParam;
-    }
-
-    /**
-     * Gets the value of the conservationSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isConservationSelected()
-    {
-      return conservationSelected;
-    }
-
-    /**
-     * Sets the value of the conservationSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setConservationSelected(Boolean value)
-    {
-      this.conservationSelected = value;
-    }
-
-    /**
-     * Gets the value of the pidSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isPidSelected()
-    {
-      return pidSelected;
-    }
-
-    /**
-     * Sets the value of the pidSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setPidSelected(Boolean value)
-    {
-      this.pidSelected = value;
-    }
-
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getBgColour()
-    {
-      return bgColour;
-    }
-
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setBgColour(String value)
-    {
-      this.bgColour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
-
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
-
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
-
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
-
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
-
-    /**
-     * Gets the value of the showFullId property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowFullId()
-    {
-      return showFullId;
-    }
-
-    /**
-     * Sets the value of the showFullId property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowFullId(Boolean value)
-    {
-      this.showFullId = value;
-    }
-
-    /**
-     * Gets the value of the rightAlignIds property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRightAlignIds()
-    {
-      return rightAlignIds;
-    }
-
-    /**
-     * Sets the value of the rightAlignIds property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRightAlignIds(Boolean value)
-    {
-      this.rightAlignIds = value;
-    }
-
-    /**
-     * Gets the value of the showText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowText()
-    {
-      return showText;
-    }
-
-    /**
-     * Sets the value of the showText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowText(Boolean value)
-    {
-      this.showText = value;
-    }
-
-    /**
-     * Gets the value of the showColourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowColourText()
-    {
-      return showColourText;
-    }
-
-    /**
-     * Sets the value of the showColourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowColourText(Boolean value)
-    {
-      this.showColourText = value;
-    }
-
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowUnconserved()
-    {
-      if (showUnconserved == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showUnconserved;
-      }
-    }
-
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
-
-    /**
-     * Gets the value of the showBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBoxes()
-    {
-      return showBoxes;
-    }
-
-    /**
-     * Sets the value of the showBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBoxes(Boolean value)
-    {
-      this.showBoxes = value;
-    }
-
-    /**
-     * Gets the value of the wrapAlignment property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isWrapAlignment()
-    {
-      return wrapAlignment;
-    }
-
-    /**
-     * Sets the value of the wrapAlignment property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setWrapAlignment(Boolean value)
-    {
-      this.wrapAlignment = value;
-    }
-
-    /**
-     * Gets the value of the renderGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRenderGaps()
-    {
-      return renderGaps;
-    }
-
-    /**
-     * Sets the value of the renderGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRenderGaps(Boolean value)
-    {
-      this.renderGaps = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
-
-    /**
-     * Sets the value of the showSequenceFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceFeatures(Boolean value)
-    {
-      this.showSequenceFeatures = value;
-    }
-
-    /**
-     * Gets the value of the showNPfeatureTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowNPfeatureTooltip()
-    {
-      return showNPfeatureTooltip;
-    }
-
-    /**
-     * Sets the value of the showNPfeatureTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowNPfeatureTooltip(Boolean value)
-    {
-      this.showNPfeatureTooltip = value;
-    }
-
-    /**
-     * Gets the value of the showDbRefTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDbRefTooltip()
-    {
-      return showDbRefTooltip;
-    }
-
-    /**
-     * Sets the value of the showDbRefTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDbRefTooltip(Boolean value)
-    {
-      this.showDbRefTooltip = value;
-    }
-
-    /**
-     * Gets the value of the followHighlight property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowHighlight()
-    {
-      if (followHighlight == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followHighlight;
-      }
-    }
-
-    /**
-     * Sets the value of the followHighlight property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowHighlight(Boolean value)
-    {
-      this.followHighlight = value;
-    }
-
-    /**
-     * Gets the value of the followSelection property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowSelection()
-    {
-      if (followSelection == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followSelection;
-      }
-    }
-
-    /**
-     * Sets the value of the followSelection property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowSelection(Boolean value)
-    {
-      this.followSelection = value;
-    }
-
-    /**
-     * Gets the value of the showAnnotation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowAnnotation()
-    {
-      return showAnnotation;
-    }
-
-    /**
-     * Sets the value of the showAnnotation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowAnnotation(Boolean value)
-    {
-      this.showAnnotation = value;
-    }
-
-    /**
-     * Gets the value of the centreColumnLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isCentreColumnLabels()
-    {
-      if (centreColumnLabels == null)
-      {
-        return false;
-      }
-      else
-      {
-        return centreColumnLabels;
-      }
-    }
-
-    /**
-     * Sets the value of the centreColumnLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCentreColumnLabels(Boolean value)
-    {
-      this.centreColumnLabels = value;
-    }
-
-    /**
-     * Gets the value of the showGroupConservation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConservation()
-    {
-      if (showGroupConservation == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConservation;
-      }
-    }
-
-    /**
-     * Sets the value of the showGroupConservation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConservation(Boolean value)
-    {
-      this.showGroupConservation = value;
-    }
-
-    /**
-     * Gets the value of the showGroupConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConsensus()
-    {
-      if (showGroupConsensus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the showGroupConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConsensus(Boolean value)
-    {
-      this.showGroupConsensus = value;
-    }
-
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
-
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
-
-    /**
-     * Gets the value of the startRes property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartRes()
-    {
-      return startRes;
-    }
-
-    /**
-     * Sets the value of the startRes property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartRes(Integer value)
-    {
-      this.startRes = value;
-    }
-
-    /**
-     * Gets the value of the startSeq property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartSeq()
-    {
-      return startSeq;
-    }
-
-    /**
-     * Sets the value of the startSeq property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartSeq(Integer value)
-    {
-      this.startSeq = value;
-    }
-
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
-
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
-
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
-
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
-
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
-
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
-
-    /**
-     * Gets the value of the scaleProteinAsCdna property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isScaleProteinAsCdna()
-    {
-      if (scaleProteinAsCdna == null)
-      {
-        return true;
-      }
-      else
-      {
-        return scaleProteinAsCdna;
-      }
-    }
-
-    /**
-     * Sets the value of the scaleProteinAsCdna property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setScaleProteinAsCdna(Boolean value)
-    {
-      this.scaleProteinAsCdna = value;
-    }
-
-    /**
-     * Gets the value of the viewName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getViewName()
-    {
-      return viewName;
-    }
-
-    /**
-     * Sets the value of the viewName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setViewName(String value)
-    {
-      this.viewName = value;
-    }
-
-    /**
-     * Gets the value of the sequenceSetId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getSequenceSetId()
-    {
-      return sequenceSetId;
-    }
-
-    /**
-     * Sets the value of the sequenceSetId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setSequenceSetId(String value)
-    {
-      this.sequenceSetId = value;
-    }
-
-    /**
-     * Gets the value of the gatheredViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isGatheredViews()
-    {
-      return gatheredViews;
-    }
-
-    /**
-     * Sets the value of the gatheredViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setGatheredViews(Boolean value)
-    {
-      this.gatheredViews = value;
-    }
-
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
-
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
-
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
-
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the complementId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComplementId()
-    {
-      return complementId;
-    }
-
-    /**
-     * Sets the value of the complementId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComplementId(String value)
-    {
-      this.complementId = value;
-    }
-
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
-
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
-
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
-
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
-
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
-
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
-
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
-
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class CalcIdParam extends WebServiceParameterSet
-    {
-
-      @XmlAttribute(name = "calcId", required = true)
-      protected String calcId;
-
-      @XmlAttribute(name = "needsUpdate")
-      protected Boolean needsUpdate;
-
-      @XmlAttribute(name = "autoUpdate", required = true)
-      protected boolean autoUpdate;
-
-      /**
-       * Gets the value of the calcId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCalcId()
-      {
-        return calcId;
-      }
-
-      /**
-       * Sets the value of the calcId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCalcId(String value)
-      {
-        this.calcId = value;
-      }
-
-      /**
-       * Gets the value of the needsUpdate property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isNeedsUpdate()
-      {
-        if (needsUpdate == null)
-        {
-          return false;
-        }
-        else
-        {
-          return needsUpdate;
-        }
-      }
-
-      /**
-       * Sets the value of the needsUpdate property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setNeedsUpdate(Boolean value)
-      {
-        this.needsUpdate = value;
-      }
-
-      /**
-       * Gets the value of the autoUpdate property.
-       * 
-       */
-      public boolean isAutoUpdate()
-      {
-        return autoUpdate;
-      }
-
-      /**
-       * Sets the value of the autoUpdate property.
-       * 
-       */
-      public void setAutoUpdate(boolean value)
-      {
-        this.autoUpdate = value;
-      }
-
-    }
-
-    /**
-     * 
    
-     * Java class for anonymous complex type.
-     * 
-     * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class HiddenColumns
-    {
-
-      @XmlAttribute(name = "start")
-      protected Integer start;
-
-      @XmlAttribute(name = "end")
-      protected Integer end;
-
-      /**
-       * Gets the value of the start property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getStart()
-      {
-        return start;
-      }
-
-      /**
-       * Sets the value of the start property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setStart(Integer value)
-      {
-        this.start = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setEnd(Integer value)
-      {
-        this.end = value;
-      }
-
-    }
-
-  }
-
-}
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index be68266..21abacb 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,585 +16,597 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for JalviewUserColours complex type.
+ * 
    Java class for JalviewUserColours complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="JalviewUserColours"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType"
- * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="featureType" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="schemeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="JalviewUserColours">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="colour" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                 </sequence>
+ *                 <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                 <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="filter" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ *                 </sequence>
+ *                 <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewUserColours",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "version", "colour", "filter" })
-public class JalviewUserColours
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected List colour;
-
-  @XmlElement(namespace = "")
-  protected List filter;
-
-  @XmlAttribute(name = "schemeName")
-  protected String schemeName;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the colour property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getColour().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Colour }
-   * 
-   * 
-   */
-  public List getColour()
-  {
-    if (colour == null)
-    {
-      colour = new ArrayList();
-    }
-    return this.colour;
-  }
-
-  /**
-   * Gets the value of the filter property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the filter property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getFilter().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Filter }
-   * 
-   * 
-   */
-  public List getFilter()
-  {
-    if (filter == null)
-    {
-      filter = new ArrayList();
-    }
-    return this.filter;
-  }
-
-  /**
-   * Gets the value of the schemeName property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSchemeName()
-  {
-    return schemeName;
-  }
-
-  /**
-   * Sets the value of the schemeName property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSchemeName(String value)
-  {
-    this.schemeName = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="attributeName"
-   * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
-   * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
-   * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="RGB" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="noValueColour"
-   * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
-   * &lt;attribute name="threshType"
-   * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
-   * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
-   * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
-   * /&gt; &lt;attribute name="min"
-   * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
-   * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * /&gt; &lt;attribute name="autoScale"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "attributeName" })
-  public static class Colour
-  {
-
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+    "version",
+    "colour",
+    "filter"
+})
+public class JalviewUserColours {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
     @XmlElement(namespace = "")
-    protected List attributeName;
-
-    @XmlAttribute(name = "Name")
-    protected String name;
-
-    @XmlAttribute(name = "RGB", required = true)
-    protected String rgb;
-
-    @XmlAttribute(name = "minRGB")
-    protected String minRGB;
-
-    @XmlAttribute(name = "noValueColour")
-    protected NoValueColour noValueColour;
-
-    @XmlAttribute(name = "threshType")
-    protected ThresholdType threshType;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "max")
-    protected Float max;
-
-    @XmlAttribute(name = "min")
-    protected Float min;
-
-    @XmlAttribute(name = "colourByLabel")
-    protected Boolean colourByLabel;
-
-    @XmlAttribute(name = "autoScale")
-    protected Boolean autoScale;
-
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * <p> 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
-     * <CODE>set</CODE> method for the attributeName property.
-     * 
-     * <p> For example, to add a new item, do as follows: <pre>
-     * getAttributeName().add(newItem); </pre>
-     * 
-     * 
-     * <p> Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getAttributeName()
-    {
-      if (attributeName == null)
-      {
-        attributeName = new ArrayList();
-      }
-      return this.attributeName;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the rgb property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getRGB()
-    {
-      return rgb;
-    }
-
-    /**
-     * Sets the value of the rgb property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setRGB(String value)
-    {
-      this.rgb = value;
-    }
-
-    /**
-     * Gets the value of the minRGB property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getMinRGB()
-    {
-      return minRGB;
-    }
-
-    /**
-     * Sets the value of the minRGB property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setMinRGB(String value)
-    {
-      this.minRGB = value;
-    }
+    protected List colour;
+    @XmlElement(namespace = "")
+    protected List filter;
+    @XmlAttribute(name = "schemeName")
+    protected String schemeName;
 
     /**
-     * Gets the value of the noValueColour property.
-     * 
-     * @return possible object is {@link NoValueColour }
+     * Gets the value of the version property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public NoValueColour getNoValueColour()
-    {
-      if (noValueColour == null)
-      {
-        return NoValueColour.MIN;
-      }
-      else
-      {
-        return noValueColour;
-      }
+    public String getVersion() {
+        return version;
     }
 
     /**
-     * Sets the value of the noValueColour property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *          allowed object is {@link NoValueColour }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setNoValueColour(NoValueColour value)
-    {
-      this.noValueColour = value;
+    public void setVersion(String value) {
+        this.version = value;
     }
 
     /**
-     * Gets the value of the threshType property.
+     * Gets the value of the colour property.
      * 
-     * @return possible object is {@link ThresholdType }
+     * 
    
+     * 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 colour property.
      * 
-     */
-    public ThresholdType getThreshType()
-    {
-      return threshType;
-    }
-
-    /**
-     * Sets the value of the threshType property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getColour().add(newItem);
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link ThresholdType }
      * 
-     */
-    public void setThreshType(ThresholdType value)
-    {
-      this.threshType = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Colour }
      * 
-     * @return possible object is {@link Float }
      * 
      */
-    public Float getThreshold()
-    {
-      return threshold;
+    public List getColour() {
+        if (colour == null) {
+            colour = new ArrayList();
+        }
+        return this.colour;
     }
 
     /**
-     * Sets the value of the threshold property.
+     * Gets the value of the filter property.
      * 
-     * @param value
-     *          allowed object is {@link Float }
+     * 
    
+     * 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 filter property.
      * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the max property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getFilter().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link Float }
      * 
-     */
-    public Float getMax()
-    {
-      return max;
-    }
-
-    /**
-     * Sets the value of the max property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Filter }
      * 
-     * @param value
-     *          allowed object is {@link Float }
      * 
      */
-    public void setMax(Float value)
-    {
-      this.max = value;
+    public List getFilter() {
+        if (filter == null) {
+            filter = new ArrayList();
+        }
+        return this.filter;
     }
 
     /**
-     * Gets the value of the min property.
-     * 
-     * @return possible object is {@link Float }
+     * Gets the value of the schemeName property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Float getMin()
-    {
-      return min;
+    public String getSchemeName() {
+        return schemeName;
     }
 
     /**
-     * Sets the value of the min property.
+     * Sets the value of the schemeName property.
      * 
      * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setMin(Float value)
-    {
-      this.min = value;
-    }
-
-    /**
-     * Gets the value of the colourByLabel property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public Boolean isColourByLabel()
-    {
-      return colourByLabel;
+    public void setSchemeName(String value) {
+        this.schemeName = value;
     }
 
-    /**
-     * Sets the value of the colourByLabel property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColourByLabel(Boolean value)
-    {
-      this.colourByLabel = value;
-    }
 
     /**
-     * Gets the value of the autoScale property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public Boolean isAutoScale()
-    {
-      return autoScale;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "attributeName"
+    })
+    public static class Colour {
+
+        @XmlElement(namespace = "")
+        protected List attributeName;
+        @XmlAttribute(name = "Name")
+        protected String name;
+        @XmlAttribute(name = "RGB", required = true)
+        protected String rgb;
+        @XmlAttribute(name = "minRGB")
+        protected String minRGB;
+        @XmlAttribute(name = "noValueColour")
+        protected NoValueColour noValueColour;
+        @XmlAttribute(name = "threshType")
+        protected ThresholdType threshType;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "max")
+        protected Float max;
+        @XmlAttribute(name = "min")
+        protected Float min;
+        @XmlAttribute(name = "colourByLabel")
+        protected Boolean colourByLabel;
+        @XmlAttribute(name = "autoScale")
+        protected Boolean autoScale;
+
+        /**
+         * Gets the value of the attributeName 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 attributeName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getAttributeName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getAttributeName() {
+            if (attributeName == null) {
+                attributeName = new ArrayList();
+            }
+            return this.attributeName;
+        }
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the rgb property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRGB() {
+            return rgb;
+        }
+
+        /**
+         * Sets the value of the rgb property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRGB(String value) {
+            this.rgb = value;
+        }
+
+        /**
+         * Gets the value of the minRGB property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getMinRGB() {
+            return minRGB;
+        }
+
+        /**
+         * Sets the value of the minRGB property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setMinRGB(String value) {
+            this.minRGB = value;
+        }
+
+        /**
+         * Gets the value of the noValueColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public NoValueColour getNoValueColour() {
+            if (noValueColour == null) {
+                return NoValueColour.MIN;
+            } else {
+                return noValueColour;
+            }
+        }
+
+        /**
+         * Sets the value of the noValueColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public void setNoValueColour(NoValueColour value) {
+            this.noValueColour = value;
+        }
+
+        /**
+         * Gets the value of the threshType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public ThresholdType getThreshType() {
+            return threshType;
+        }
+
+        /**
+         * Sets the value of the threshType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public void setThreshType(ThresholdType value) {
+            this.threshType = value;
+        }
+
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
+
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
+
+        /**
+         * Gets the value of the max property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMax() {
+            return max;
+        }
+
+        /**
+         * Sets the value of the max property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMax(Float value) {
+            this.max = value;
+        }
+
+        /**
+         * Gets the value of the min property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMin() {
+            return min;
+        }
+
+        /**
+         * Sets the value of the min property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMin(Float value) {
+            this.min = value;
+        }
+
+        /**
+         * Gets the value of the colourByLabel property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isColourByLabel() {
+            return colourByLabel;
+        }
+
+        /**
+         * Sets the value of the colourByLabel property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setColourByLabel(Boolean value) {
+            this.colourByLabel = value;
+        }
+
+        /**
+         * Gets the value of the autoScale property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isAutoScale() {
+            return autoScale;
+        }
+
+        /**
+         * Sets the value of the autoScale property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setAutoScale(Boolean value) {
+            this.autoScale = value;
+        }
 
-    /**
-     * Sets the value of the autoScale property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setAutoScale(Boolean value)
-    {
-      this.autoScale = value;
     }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element name="matcherSet"
-   * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="featureType"
-   * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class Filter
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected FeatureMatcherSet matcherSet;
-
-    @XmlAttribute(name = "featureType", required = true)
-    protected String featureType;
 
     /**
-     * Gets the value of the matcherSet property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @return possible object is {@link FeatureMatcherSet }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public FeatureMatcherSet getMatcherSet()
-    {
-      return matcherSet;
-    }
-
-    /**
-     * Sets the value of the matcherSet property.
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+     *       </sequence>
+     *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link FeatureMatcherSet }
      * 
      */
-    public void setMatcherSet(FeatureMatcherSet value)
-    {
-      this.matcherSet = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class Filter {
+
+        @XmlElement(namespace = "", required = true)
+        protected FeatureMatcherSet matcherSet;
+        @XmlAttribute(name = "featureType", required = true)
+        protected String featureType;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public FeatureMatcherSet getMatcherSet() {
+            return matcherSet;
+        }
+
+        /**
+         * Sets the value of the matcherSet property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public void setMatcherSet(FeatureMatcherSet value) {
+            this.matcherSet = value;
+        }
+
+        /**
+         * Gets the value of the featureType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFeatureType() {
+            return featureType;
+        }
+
+        /**
+         * Sets the value of the featureType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFeatureType(String value) {
+            this.featureType = value;
+        }
 
-    /**
-     * Gets the value of the featureType property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFeatureType()
-    {
-      return featureType;
     }
 
-    /**
-     * Sets the value of the featureType property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFeatureType(String value)
-    {
-      this.featureType = value;
-    }
-
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index edc69b4..99c5b4b 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,291 +18,298 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * This effectively represents a java.util.MapList object
+ * 				This effectively represents a java.util.MapList object
+ * 			
  * 
+ * 
    Java class for mapListType complex type.
  * 
- * <p>Java class for mapListType complex type.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- * 
- * <pre> &lt;complexType name="mapListType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="mapListFrom"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="mapFromUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;attribute name="mapToUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="mapListType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *       <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
-@XmlSeeAlso({ Mapping.class })
-public class MapListType
-{
-
-  protected List mapListFrom;
-
-  protected List mapListTo;
-
-  @XmlAttribute(name = "mapFromUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapFromUnit;
-
-  @XmlAttribute(name = "mapToUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapToUnit;
-
-  /**
-   * Gets the value of the mapListFrom property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the mapListFrom property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getMapListFrom().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListFrom }
-   * 
-   * 
-   */
-  public List getMapListFrom()
-  {
-    if (mapListFrom == null)
-    {
-      mapListFrom = new ArrayList();
-    }
-    return this.mapListFrom;
-  }
-
-  /**
-   * Gets the value of the mapListTo property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the mapListTo property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getMapListTo().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListTo }
-   * 
-   * 
-   */
-  public List getMapListTo()
-  {
-    if (mapListTo == null)
-    {
-      mapListTo = new ArrayList();
-    }
-    return this.mapListTo;
-  }
-
-  /**
-   * Gets the value of the mapFromUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapFromUnit()
-  {
-    return mapFromUnit;
-  }
-
-  /**
-   * Sets the value of the mapFromUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapFromUnit(BigInteger value)
-  {
-    this.mapFromUnit = value;
-  }
+@XmlType(name = "mapListType", propOrder = {
+    "mapListFrom",
+    "mapListTo"
+})
+@XmlSeeAlso({
+    Mapping.class
+})
+public class MapListType {
 
-  /**
-   * Gets the value of the mapToUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapToUnit()
-  {
-    return mapToUnit;
-  }
-
-  /**
-   * Sets the value of the mapToUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapToUnit(BigInteger value)
-  {
-    this.mapToUnit = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListFrom
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
+    protected List mapListFrom;
+    protected List mapListTo;
+    @XmlAttribute(name = "mapFromUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapFromUnit;
+    @XmlAttribute(name = "mapToUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapToUnit;
 
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapListFrom 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 mapListFrom property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getMapListFrom().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListFrom }
+     * 
      * 
      */
-    public int getStart()
-    {
-      return start;
+    public List getMapListFrom() {
+        if (mapListFrom == null) {
+            mapListFrom = new ArrayList();
+        }
+        return this.mapListFrom;
     }
 
     /**
-     * Sets the value of the start property.
+     * Gets the value of the mapListTo 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 mapListTo property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getMapListTo().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListTo }
+     * 
      * 
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public List getMapListTo() {
+        if (mapListTo == null) {
+            mapListTo = new ArrayList();
+        }
+        return this.mapListTo;
     }
 
     /**
-     * Gets the value of the end property.
+     * Gets the value of the mapFromUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getEnd()
-    {
-      return end;
+    public BigInteger getMapFromUnit() {
+        return mapFromUnit;
     }
 
     /**
-     * Sets the value of the end property.
+     * Sets the value of the mapFromUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
+    public void setMapFromUnit(BigInteger value) {
+        this.mapFromUnit = value;
     }
 
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
-   * /&gt; &lt;attribute name="end" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListTo
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapToUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getStart()
-    {
-      return start;
+    public BigInteger getMapToUnit() {
+        return mapToUnit;
     }
 
     /**
-     * Sets the value of the start property.
+     * Sets the value of the mapToUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public void setMapToUnit(BigInteger value) {
+        this.mapToUnit = value;
     }
 
+
     /**
-     * Gets the value of the end property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
      * 
      */
-    public int getEnd()
-    {
-      return end;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListFrom {
+
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
     }
 
+
     /**
-     * Sets the value of the end property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
      * 
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListTo {
 
-  }
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index d79bdee..e898ca2 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,115 +15,127 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * Represent the jalview.datamodel.Mapping object - it also provides a way of
- * storing sequences that are mapped 'to' without adding them to the sequence
- * set (which will mean they are then added to the alignment too).
- * 
+ * 					Represent the jalview.datamodel.Mapping object - it also provides
+ * 					a way of storing sequences that are mapped 'to' without adding them
+ * 					to the sequence set (which will mean they are then added to the alignment too).
+ * 				
  * 
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
- * &lt;sequence&gt; &lt;choice minOccurs="0"&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt; &lt;element
- * name="dseqFor"&gt; &lt;simpleType&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;/restriction&gt; &lt;/simpleType&gt;
- * &lt;/element&gt; &lt;/choice&gt; &lt;/sequence&gt;
- * &lt;attribute name="mappingType"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ *       <sequence>
+ *         <choice minOccurs="0">
+ *           <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ *           <element name="dseqFor">
+ *             <simpleType>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               </restriction>
+ *             </simpleType>
+ *           </element>
+ *         </choice>
+ *       </sequence>
+ *       <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "dseqFor"
+})
 @XmlRootElement(name = "Mapping")
-public class Mapping extends MapListType
+public class Mapping
+    extends MapListType
 {
 
-  @XmlElement(name = "Sequence")
-  protected Sequence sequence;
-
-  protected String dseqFor;
-
-  @XmlAttribute(name = "mappingType")
-  protected String mappingType;
+    @XmlElement(name = "Sequence")
+    protected Sequence sequence;
+    protected String dseqFor;
+    @XmlAttribute(name = "mappingType")
+    protected String mappingType;
 
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link Sequence }
-   * 
-   */
-  public Sequence getSequence()
-  {
-    return sequence;
-  }
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Sequence }
+     *     
+     */
+    public Sequence getSequence() {
+        return sequence;
+    }
 
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Sequence }
-   * 
-   */
-  public void setSequence(Sequence value)
-  {
-    this.sequence = value;
-  }
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Sequence }
+     *     
+     */
+    public void setSequence(Sequence value) {
+        this.sequence = value;
+    }
 
-  /**
-   * Gets the value of the dseqFor property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDseqFor()
-  {
-    return dseqFor;
-  }
+    /**
+     * Gets the value of the dseqFor property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDseqFor() {
+        return dseqFor;
+    }
 
-  /**
-   * Sets the value of the dseqFor property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDseqFor(String value)
-  {
-    this.dseqFor = value;
-  }
+    /**
+     * Sets the value of the dseqFor property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDseqFor(String value) {
+        this.dseqFor = value;
+    }
 
-  /**
-   * Gets the value of the mappingType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMappingType()
-  {
-    return mappingType;
-  }
+    /**
+     * Gets the value of the mappingType property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMappingType() {
+        return mappingType;
+    }
 
-  /**
-   * Sets the value of the mappingType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMappingType(String value)
-  {
-    this.mappingType = value;
-  }
+    /**
+     * Sets the value of the mappingType property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMappingType(String value) {
+        this.mappingType = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index b0d667c..0eb5a86 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -1,60 +1,61 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for NoValueColour.
+ * 
    Java class for NoValueColour.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="NoValueColour"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="None"/&gt; &lt;enumeration value="Min"/&gt;
- * &lt;enumeration value="Max"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * 
    The following schema fragment specifies the expected content contained within this class.
+ * 
    
+ * 
    + * <simpleType name="NoValueColour">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="None"/>
+ *     <enumeration value="Min"/>
+ *     <enumeration value="Max"/>
+ *   </restriction>
+ * </simpleType>
+ * 
    
  * 
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour
-{
-
-  @XmlEnumValue("None")
-  NONE("None"), @XmlEnumValue("Min")
-  MIN("Min"), @XmlEnumValue("Max")
-  MAX("Max");
-
-  private final String value;
-
-  NoValueColour(String v)
-  {
-    value = v;
-  }
-
-  public String value()
-  {
-    return value;
-  }
-
-  public static NoValueColour fromValue(String v)
-  {
-    for (NoValueColour c : NoValueColour.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+public enum NoValueColour {
+
+    @XmlEnumValue("None")
+    NONE("None"),
+    @XmlEnumValue("Min")
+    MIN("Min"),
+    @XmlEnumValue("Max")
+    MAX("Max");
+    private final String value;
+
+    NoValueColour(String v) {
+        value = v;
+    }
+
+    public String value() {
+        return value;
+    }
+
+    public static NoValueColour fromValue(String v) {
+        for (NoValueColour c: NoValueColour.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 46ae594..8b38877 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -12,560 +13,484 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically construct new
- * instances of the Java representation for XML content. The Java representation
- * of XML content can consist of schema derived interfaces and classes
- * representing the binding of schema type definitions, element declarations and
- * model groups. Factory methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.jalview package. 
+ * 
    An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  private final static QName _JalviewModel_QNAME = new QName(
-          "www.jalview.org", "JalviewModel");
-
-  private final static QName _JalviewUserColours_QNAME = new QName(
-          "www.jalview.org/colours", "JalviewUserColours");
-
-  private final static QName _WebServiceParameterSet_QNAME = new QName(
-          "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.jalview
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link MapListType }
-   * 
-   */
-  public MapListType createMapListType()
-  {
-    return new MapListType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence }
-   * 
-   */
-  public Sequence createSequence()
-  {
-    return new Sequence();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame }
-   * 
-   */
-  public AlcodonFrame createAlcodonFrame()
-  {
-    return new AlcodonFrame();
-  }
-
-  /**
-   * Create an instance of {@link Annotation }
-   * 
-   */
-  public Annotation createAnnotation()
-  {
-    return new Annotation();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet }
-   * 
-   */
-  public SequenceSet createSequenceSet()
-  {
-    return new SequenceSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet }
-   * 
-   */
-  public FeatureMatcherSet createFeatureMatcherSet()
-  {
-    return new FeatureMatcherSet();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours }
-   * 
-   */
-  public JalviewUserColours createJalviewUserColours()
-  {
-    return new JalviewUserColours();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry }
-   * 
-   */
-  public Pdbentry createPdbentry()
-  {
-    return new Pdbentry();
-  }
-
-  /**
-   * Create an instance of {@link Feature }
-   * 
-   */
-  public Feature createFeature()
-  {
-    return new Feature();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel }
-   * 
-   */
-  public JalviewModel createJalviewModel()
-  {
-    return new JalviewModel();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
-  {
-    return new JalviewModel.FeatureSettings();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer }
-   * 
-   */
-  public JalviewModel.PcaViewer createJalviewModelPcaViewer()
-  {
-    return new JalviewModel.PcaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport }
-   * 
-   */
-  public JalviewModel.Viewport createJalviewModelViewport()
-  {
-    return new JalviewModel.Viewport();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq }
-   * 
-   */
-  public JalviewModel.JSeq createJalviewModelJSeq()
-  {
-    return new JalviewModel.JSeq();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
-  {
-    return new JalviewModel.JSeq.RnaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
-  {
-    return new JalviewModel.JSeq.Pdbids();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationColourScheme }
-   * 
-   */
-  public AnnotationColourScheme createAnnotationColourScheme()
-  {
-    return new AnnotationColourScheme();
-  }
-
-  /**
-   * Create an instance of {@link PcaDataType }
-   * 
-   */
-  public PcaDataType createPcaDataType()
-  {
-    return new PcaDataType();
-  }
-
-  /**
-   * Create an instance of {@link DoubleVector }
-   * 
-   */
-  public DoubleVector createDoubleVector()
-  {
-    return new DoubleVector();
-  }
-
-  /**
-   * Create an instance of {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix createDoubleMatrix()
-  {
-    return new DoubleMatrix();
-  }
-
-  /**
-   * Create an instance of {@link Mapping }
-   * 
-   */
-  public Mapping createMapping()
-  {
-    return new Mapping();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListFrom }
-   * 
-   */
-  public MapListType.MapListFrom createMapListTypeMapListFrom()
-  {
-    return new MapListType.MapListFrom();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListTo }
-   * 
-   */
-  public MapListType.MapListTo createMapListTypeMapListTo()
-  {
-    return new MapListType.MapListTo();
-  }
-
-  /**
-   * Create an instance of {@link SequenceType }
-   * 
-   */
-  public SequenceType createSequenceType()
-  {
-    return new SequenceType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence.DBRef }
-   * 
-   */
-  public Sequence.DBRef createSequenceDBRef()
-  {
-    return new Sequence.DBRef();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame.Alcodon }
-   * 
-   */
-  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
-  {
-    return new AlcodonFrame.Alcodon();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame.AlcodMap }
-   * 
-   */
-  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
-  {
-    return new AlcodonFrame.AlcodMap();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationElement }
-   * 
-   */
-  public AnnotationElement createAnnotationElement()
-  {
-    return new AnnotationElement();
-  }
-
-  /**
-   * Create an instance of {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine createAnnotationThresholdLine()
-  {
-    return new Annotation.ThresholdLine();
-  }
-
-  /**
-   * Create an instance of {@link Annotation.Property }
-   * 
-   */
-  public Annotation.Property createAnnotationProperty()
-  {
-    return new Annotation.Property();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet.SequenceSetProperties }
-   * 
-   */
-  public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
-  {
-    return new SequenceSet.SequenceSetProperties();
-  }
-
-  /**
-   * Create an instance of {@link VAMSAS }
-   * 
-   */
-  public VAMSAS createVAMSAS()
-  {
-    return new VAMSAS();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher createFeatureMatcher()
-  {
-    return new FeatureMatcher();
-  }
-
-  /**
-   * Create an instance of {@link WebServiceParameterSet }
-   * 
-   */
-  public WebServiceParameterSet createWebServiceParameterSet()
-  {
-    return new WebServiceParameterSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
-  {
-    return new FeatureMatcherSet.CompoundMatcher();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Colour }
-   * 
-   */
-  public JalviewUserColours.Colour createJalviewUserColoursColour()
-  {
-    return new JalviewUserColours.Colour();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Filter }
-   * 
-   */
-  public JalviewUserColours.Filter createJalviewUserColoursFilter()
-  {
-    return new JalviewUserColours.Filter();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry.Property }
-   * 
-   */
-  public Pdbentry.Property createPdbentryProperty()
-  {
-    return new Pdbentry.Property();
-  }
-
-  /**
-   * Create an instance of {@link Feature.OtherData }
-   * 
-   */
-  public Feature.OtherData createFeatureOtherData()
-  {
-    return new Feature.OtherData();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JGroup }
-   * 
-   */
-  public JalviewModel.JGroup createJalviewModelJGroup()
-  {
-    return new JalviewModel.JGroup();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.UserColours }
-   * 
-   */
-  public JalviewModel.UserColours createJalviewModelUserColours()
-  {
-    return new JalviewModel.UserColours();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Tree }
-   * 
-   */
-  public JalviewModel.Tree createJalviewModelTree()
-  {
-    return new JalviewModel.Tree();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
-  {
-    return new JalviewModel.FeatureSettings.Setting();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Group }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
-  {
-    return new JalviewModel.FeatureSettings.Group();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
-   * 
-   */
-  public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
-  {
-    return new JalviewModel.PcaViewer.SequencePoint();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.Axis }
-   * 
-   */
-  public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
-  {
-    return new JalviewModel.PcaViewer.Axis();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMin();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMax();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
-   * 
-   */
-  public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
-  {
-    return new JalviewModel.Viewport.HiddenColumns();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
-   * 
-   */
-  public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
-  {
-    return new JalviewModel.Viewport.CalcIdParam();
-  }
-
-  /**
-   * Create an instance of
-   * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
-  {
-    return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
-  {
-    return new JalviewModel.JSeq.Pdbids.StructureState();
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
-   * }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link JalviewModel }{@code >}
-   */
-  @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
-  public JAXBElement createJalviewModel(JalviewModel value)
-  {
-    return new JAXBElement(_JalviewModel_QNAME,
-            JalviewModel.class, null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link JalviewUserColours }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link JalviewUserColours }{@code >}
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/colours",
-    name = "JalviewUserColours")
-  public JAXBElement createJalviewUserColours(
-          JalviewUserColours value)
-  {
-    return new JAXBElement(_JalviewUserColours_QNAME,
-            JalviewUserColours.class, null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link WebServiceParameterSet }{@code >}
-   * 
-   * @param value
-   *          Java instance representing xml element's value.
-   * @return the new instance of {@link JAXBElement
-   *         }{@code <}{@link WebServiceParameterSet }{@code >}
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/xml/wsparamset",
-    name = "WebServiceParameterSet")
-  public JAXBElement createWebServiceParameterSet(
-          WebServiceParameterSet value)
-  {
-    return new JAXBElement(
-            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
-            null, value);
-  }
+public class ObjectFactory {
+
+    private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+    private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+    private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame }
+     * 
+     */
+    public AlcodonFrame createAlcodonFrame() {
+        return new AlcodonFrame();
+    }
+
+    /**
+     * Create an instance of {@link MapListType }
+     * 
+     */
+    public MapListType createMapListType() {
+        return new MapListType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence }
+     * 
+     */
+    public Sequence createSequence() {
+        return new Sequence();
+    }
+
+    /**
+     * Create an instance of {@link Annotation }
+     * 
+     */
+    public Annotation createAnnotation() {
+        return new Annotation();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet }
+     * 
+     */
+    public SequenceSet createSequenceSet() {
+        return new SequenceSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet }
+     * 
+     */
+    public FeatureMatcherSet createFeatureMatcherSet() {
+        return new FeatureMatcherSet();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours }
+     * 
+     */
+    public JalviewUserColours createJalviewUserColours() {
+        return new JalviewUserColours();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry }
+     * 
+     */
+    public Pdbentry createPdbentry() {
+        return new Pdbentry();
+    }
+
+    /**
+     * Create an instance of {@link Feature }
+     * 
+     */
+    public Feature createFeature() {
+        return new Feature();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel }
+     * 
+     */
+    public JalviewModel createJalviewModel() {
+        return new JalviewModel();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings }
+     * 
+     */
+    public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+        return new JalviewModel.FeatureSettings();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer }
+     * 
+     */
+    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+        return new JalviewModel.PcaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport }
+     * 
+     */
+    public JalviewModel.Viewport createJalviewModelViewport() {
+        return new JalviewModel.Viewport();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq }
+     * 
+     */
+    public JalviewModel.JSeq createJalviewModelJSeq() {
+        return new JalviewModel.JSeq();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+        return new JalviewModel.JSeq.RnaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+        return new JalviewModel.JSeq.Pdbids();
+    }
+
+    /**
+     * Create an instance of {@link DoubleMatrix }
+     * 
+     */
+    public DoubleMatrix createDoubleMatrix() {
+        return new DoubleMatrix();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme createAnnotationColourScheme() {
+        return new AnnotationColourScheme();
+    }
+
+    /**
+     * Create an instance of {@link PcaDataType }
+     * 
+     */
+    public PcaDataType createPcaDataType() {
+        return new PcaDataType();
+    }
+
+    /**
+     * Create an instance of {@link DoubleVector }
+     * 
+     */
+    public DoubleVector createDoubleVector() {
+        return new DoubleVector();
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame.Alcodon }
+     * 
+     */
+    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+        return new AlcodonFrame.Alcodon();
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame.AlcodMap }
+     * 
+     */
+    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+        return new AlcodonFrame.AlcodMap();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationElement }
+     * 
+     */
+    public AnnotationElement createAnnotationElement() {
+        return new AnnotationElement();
+    }
+
+    /**
+     * Create an instance of {@link Mapping }
+     * 
+     */
+    public Mapping createMapping() {
+        return new Mapping();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListFrom }
+     * 
+     */
+    public MapListType.MapListFrom createMapListTypeMapListFrom() {
+        return new MapListType.MapListFrom();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListTo }
+     * 
+     */
+    public MapListType.MapListTo createMapListTypeMapListTo() {
+        return new MapListType.MapListTo();
+    }
+
+    /**
+     * Create an instance of {@link SequenceType }
+     * 
+     */
+    public SequenceType createSequenceType() {
+        return new SequenceType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence.DBRef }
+     * 
+     */
+    public Sequence.DBRef createSequenceDBRef() {
+        return new Sequence.DBRef();
+    }
+
+    /**
+     * Create an instance of {@link Annotation.ThresholdLine }
+     * 
+     */
+    public Annotation.ThresholdLine createAnnotationThresholdLine() {
+        return new Annotation.ThresholdLine();
+    }
+
+    /**
+     * Create an instance of {@link Annotation.Property }
+     * 
+     */
+    public Annotation.Property createAnnotationProperty() {
+        return new Annotation.Property();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet.SequenceSetProperties }
+     * 
+     */
+    public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+        return new SequenceSet.SequenceSetProperties();
+    }
+
+    /**
+     * Create an instance of {@link VAMSAS }
+     * 
+     */
+    public VAMSAS createVAMSAS() {
+        return new VAMSAS();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcher }
+     * 
+     */
+    public FeatureMatcher createFeatureMatcher() {
+        return new FeatureMatcher();
+    }
+
+    /**
+     * Create an instance of {@link WebServiceParameterSet }
+     * 
+     */
+    public WebServiceParameterSet createWebServiceParameterSet() {
+        return new WebServiceParameterSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+     * 
+     */
+    public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+        return new FeatureMatcherSet.CompoundMatcher();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Colour }
+     * 
+     */
+    public JalviewUserColours.Colour createJalviewUserColoursColour() {
+        return new JalviewUserColours.Colour();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Filter }
+     * 
+     */
+    public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+        return new JalviewUserColours.Filter();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry.Property }
+     * 
+     */
+    public Pdbentry.Property createPdbentryProperty() {
+        return new Pdbentry.Property();
+    }
+
+    /**
+     * Create an instance of {@link Feature.OtherData }
+     * 
+     */
+    public Feature.OtherData createFeatureOtherData() {
+        return new Feature.OtherData();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JGroup }
+     * 
+     */
+    public JalviewModel.JGroup createJalviewModelJGroup() {
+        return new JalviewModel.JGroup();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.UserColours }
+     * 
+     */
+    public JalviewModel.UserColours createJalviewModelUserColours() {
+        return new JalviewModel.UserColours();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Tree }
+     * 
+     */
+    public JalviewModel.Tree createJalviewModelTree() {
+        return new JalviewModel.Tree();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+        return new JalviewModel.FeatureSettings.Setting();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+        return new JalviewModel.FeatureSettings.Group();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
+     */
+    public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+        return new JalviewModel.PcaViewer.SequencePoint();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+     * 
+     */
+    public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+        return new JalviewModel.PcaViewer.Axis();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+        return new JalviewModel.PcaViewer.SeqPointMin();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+        return new JalviewModel.PcaViewer.SeqPointMax();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+     * 
+     */
+    public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+        return new JalviewModel.Viewport.HiddenColumns();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+     * 
+     */
+    public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+        return new JalviewModel.Viewport.CalcIdParam();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.Overview }
+     * 
+     */
+    public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
+        return new JalviewModel.Viewport.Overview();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+        return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+        return new JalviewModel.JSeq.Pdbids.StructureState();
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+    public JAXBElement createWebServiceParameterSet(WebServiceParameterSet value) {
+        return new JAXBElement(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+    public JAXBElement createJalviewModel(JalviewModel value) {
+        return new JAXBElement(_JalviewModel_QNAME, JalviewModel.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+    public JAXBElement createJalviewUserColours(JalviewUserColours value) {
+        return new JAXBElement(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index 0717541..b261199 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,114 +13,117 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * The results of a PCA calculation
- * 
+ * 				The results of a PCA calculation
+ * 			
  * 
- * <p>Java class for PcaDataType complex type.
+ * 
    Java class for PcaDataType complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="PcaDataType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="pairwiseMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;element
- * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="eigenMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;/sequence&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="PcaDataType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "PcaDataType",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
-public class PcaDataType
-{
-
-  @XmlElement(required = true)
-  protected DoubleMatrix pairwiseMatrix;
-
-  @XmlElement(required = true)
-  protected DoubleMatrix tridiagonalMatrix;
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+    "pairwiseMatrix",
+    "tridiagonalMatrix",
+    "eigenMatrix"
+})
+public class PcaDataType {
 
-  @XmlElement(required = true)
-  protected DoubleMatrix eigenMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix pairwiseMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix tridiagonalMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix eigenMatrix;
 
-  /**
-   * Gets the value of the pairwiseMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getPairwiseMatrix()
-  {
-    return pairwiseMatrix;
-  }
+    /**
+     * Gets the value of the pairwiseMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getPairwiseMatrix() {
+        return pairwiseMatrix;
+    }
 
-  /**
-   * Sets the value of the pairwiseMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setPairwiseMatrix(DoubleMatrix value)
-  {
-    this.pairwiseMatrix = value;
-  }
+    /**
+     * Sets the value of the pairwiseMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setPairwiseMatrix(DoubleMatrix value) {
+        this.pairwiseMatrix = value;
+    }
 
-  /**
-   * Gets the value of the tridiagonalMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getTridiagonalMatrix()
-  {
-    return tridiagonalMatrix;
-  }
+    /**
+     * Gets the value of the tridiagonalMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getTridiagonalMatrix() {
+        return tridiagonalMatrix;
+    }
 
-  /**
-   * Sets the value of the tridiagonalMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setTridiagonalMatrix(DoubleMatrix value)
-  {
-    this.tridiagonalMatrix = value;
-  }
+    /**
+     * Sets the value of the tridiagonalMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setTridiagonalMatrix(DoubleMatrix value) {
+        this.tridiagonalMatrix = value;
+    }
 
-  /**
-   * Gets the value of the eigenMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getEigenMatrix()
-  {
-    return eigenMatrix;
-  }
+    /**
+     * Gets the value of the eigenMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getEigenMatrix() {
+        return eigenMatrix;
+    }
 
-  /**
-   * Sets the value of the eigenMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setEigenMatrix(DoubleMatrix value)
-  {
-    this.eigenMatrix = value;
-  }
+    /**
+     * Sets the value of the eigenMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setEigenMatrix(DoubleMatrix value) {
+        this.eigenMatrix = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 7d5447b..fd2e336 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,223 +16,232 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for pdbentry complex type.
+ * 
    Java class for pdbentry complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="pdbentry"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;element name="property"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="value" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="id" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="pdbentry">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence maxOccurs="unbounded" minOccurs="0">
+ *         <element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "pdbentry",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "property" })
-@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
-public class Pdbentry
-{
-
-  protected List property;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
-
-  @XmlAttribute(name = "type")
-  protected String type;
-
-  @XmlAttribute(name = "file")
-  protected String file;
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the property property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getProperty().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Pdbentry.Property }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the file property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFile()
-  {
-    return file;
-  }
-
-  /**
-   * Sets the value of the file property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFile(String value)
-  {
-    this.file = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
-   * /&gt; &lt;attribute name="value" use="required"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+    "property"
+})
+@XmlSeeAlso({
+    jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+    protected List property;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "type")
+    protected String type;
+    @XmlAttribute(name = "file")
+    protected String file;
 
     /**
-     * Gets the value of the name property.
+     * Gets the value of the property 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 property property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getProperty().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Pdbentry.Property }
+     * 
      * 
-     * @return possible object is {@link String }
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public String getId() {
+        return id;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the file property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFile() {
+        return file;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the file property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setFile(String value) {
+        this.file = value;
     }
 
-  }
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @XmlAttribute(name = "name", required = true)
+        protected String name;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 2001845..6a199a2 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,325 +17,332 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
- * &lt;sequence&gt; &lt;element name="DBRef" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="source"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="canonical"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="dsseqid"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ *       <sequence>
+ *         <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ *                 </sequence>
+ *                 <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+    "dbRef"
+})
 @XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+    extends SequenceType
 {
 
-  @XmlElement(name = "DBRef")
-  protected List dbRef;
-
-  @XmlAttribute(name = "dsseqid")
-  protected String dsseqid;
-
-  @XmlAttribute(name = "biotype")
-  protected String biotype;
-
-  /**
-   * Gets the value of the dbRef property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the dbRef property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getDBRef().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Sequence.DBRef }
-   * 
-   * 
-   */
-  public List getDBRef()
-  {
-    if (dbRef == null)
-    {
-      dbRef = new ArrayList();
-    }
-    return this.dbRef;
-  }
-
-  /**
-   * Gets the value of the dsseqid property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDsseqid()
-  {
-    return dsseqid;
-  }
-
-  /**
-   * Sets the value of the dsseqid property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDsseqid(String value)
-  {
-    this.dsseqid = value;
-  }
-
-  /**
-   * Gets the value of the biotype property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getBiotype()
-  {
-    return biotype;
-  }
-
-  /**
-   * Sets the value of the biotype property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setBiotype(String value)
-  {
-    this.biotype = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
-   * &lt;sequence&gt; &lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
-   * &lt;/sequence&gt; &lt;attribute name="source"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="accessionId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
-   * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="false" /&gt; &lt;attribute name="canonical"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class DBRef
-  {
-
-    @XmlElement(name = "Mapping")
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "source")
-    protected String source;
-
-    @XmlAttribute(name = "version")
-    protected String version;
-
-    @XmlAttribute(name = "accessionId")
-    protected String accessionId;
-
-    @XmlAttribute(name = "locus")
-    protected Boolean locus;
-
-    @XmlAttribute(name = "canonical")
-    protected Boolean canonical;
+    @XmlElement(name = "DBRef")
+    protected List dbRef;
+    @XmlAttribute(name = "dsseqid")
+    protected String dsseqid;
+    @XmlAttribute(name = "biotype")
+    protected String biotype;
 
     /**
-     * Gets the value of the mapping property.
+     * Gets the value of the dbRef property.
      * 
-     * @return possible object is {@link Mapping }
+     * 
    
+     * 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 dbRef property.
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *          allowed object is {@link Mapping }
-     * 
-     */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
-    }
-
-    /**
-     * Gets the value of the source property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getDBRef().add(newItem);
+     * 
    
      * 
-     * @return possible object is {@link String }
      * 
-     */
-    public String getSource()
-    {
-      return source;
-    }
-
-    /**
-     * Sets the value of the source property.
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence.DBRef }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setSource(String value)
-    {
-      this.source = value;
+    public List getDBRef() {
+        if (dbRef == null) {
+            dbRef = new ArrayList();
+        }
+        return this.dbRef;
     }
 
     /**
-     * Gets the value of the version property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the dsseqid property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getVersion()
-    {
-      return version;
+    public String getDsseqid() {
+        return dsseqid;
     }
 
     /**
-     * Sets the value of the version property.
+     * Sets the value of the dsseqid property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setVersion(String value)
-    {
-      this.version = value;
+    public void setDsseqid(String value) {
+        this.dsseqid = value;
     }
 
     /**
-     * Gets the value of the accessionId property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the biotype property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getAccessionId()
-    {
-      return accessionId;
+    public String getBiotype() {
+        return biotype;
     }
 
     /**
-     * Sets the value of the accessionId property.
+     * Sets the value of the biotype property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setAccessionId(String value)
-    {
-      this.accessionId = value;
+    public void setBiotype(String value) {
+        this.biotype = value;
     }
 
-    /**
-     * Gets the value of the locus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLocus()
-    {
-      if (locus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return locus;
-      }
-    }
 
     /**
-     * Sets the value of the locus property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setLocus(Boolean value)
-    {
-      this.locus = value;
-    }
-
-    /**
-     * Gets the value of the canonical property.
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public boolean isCanonical()
-    {
-      if (canonical == null)
-      {
-        return false;
-      }
-      else
-      {
-        return canonical;
-      }
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class DBRef {
+
+        @XmlElement(name = "Mapping")
+        protected Mapping mapping;
+        @XmlAttribute(name = "source")
+        protected String source;
+        @XmlAttribute(name = "version")
+        protected String version;
+        @XmlAttribute(name = "accessionId")
+        protected String accessionId;
+        @XmlAttribute(name = "locus")
+        protected Boolean locus;
+        @XmlAttribute(name = "canonical")
+        protected Boolean canonical;
+
+        /**
+         * Gets the value of the mapping property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
+
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
+
+        /**
+         * Gets the value of the source property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSource() {
+            return source;
+        }
+
+        /**
+         * Sets the value of the source property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSource(String value) {
+            this.source = value;
+        }
+
+        /**
+         * Gets the value of the version property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVersion() {
+            return version;
+        }
+
+        /**
+         * Sets the value of the version property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVersion(String value) {
+            this.version = value;
+        }
+
+        /**
+         * Gets the value of the accessionId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAccessionId() {
+            return accessionId;
+        }
+
+        /**
+         * Sets the value of the accessionId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAccessionId(String value) {
+            this.accessionId = value;
+        }
+
+        /**
+         * Gets the value of the locus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLocus() {
+            if (locus == null) {
+                return false;
+            } else {
+                return locus;
+            }
+        }
+
+        /**
+         * Sets the value of the locus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLocus(Boolean value) {
+            this.locus = value;
+        }
+
+        /**
+         * Gets the value of the canonical property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCanonical() {
+            if (canonical == null) {
+                return false;
+            } else {
+                return canonical;
+            }
+        }
+
+        /**
+         * Sets the value of the canonical property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCanonical(Boolean value) {
+            this.canonical = value;
+        }
 
-    /**
-     * Sets the value of the canonical property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCanonical(Boolean value)
-    {
-      this.canonical = value;
     }
 
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index d6464b3..ed2c120 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,287 +17,302 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="sequenceSetProperties"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="datasetId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "annotation",
+    "sequenceSetProperties",
+    "alcodonFrame"
+})
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
-  @XmlElement(name = "Sequence")
-  protected List sequence;
-
-  @XmlElement(name = "Annotation")
-  protected List annotation;
+public class SequenceSet {
 
-  protected List sequenceSetProperties;
+    @XmlElement(name = "Sequence")
+    protected List sequence;
+    @XmlElement(name = "Annotation")
+    protected List annotation;
+    protected List sequenceSetProperties;
+    @XmlElement(name = "AlcodonFrame")
+    protected List alcodonFrame;
+    @XmlAttribute(name = "gapChar", required = true)
+    protected String gapChar;
+    @XmlAttribute(name = "datasetId")
+    protected String datasetId;
 
-  @XmlElement(name = "AlcodonFrame")
-  protected List alcodonFrame;
-
-  @XmlAttribute(name = "gapChar", required = true)
-  protected String gapChar;
-
-  @XmlAttribute(name = "datasetId")
-  protected String datasetId;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the sequence property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getSequence().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Sequence }
-   * 
-   * 
-   */
-  public List getSequence()
-  {
-    if (sequence == null)
-    {
-      sequence = new ArrayList();
+    /**
+     * Gets the value of the sequence 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 sequence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getSequence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence }
+     * 
+     * 
+     */
+    public List getSequence() {
+        if (sequence == null) {
+            sequence = new ArrayList();
+        }
+        return this.sequence;
     }
-    return this.sequence;
-  }
 
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the annotation property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAnnotation().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link Annotation }
-   * 
-   * 
-   */
-  public List getAnnotation()
-  {
-    if (annotation == null)
-    {
-      annotation = new ArrayList();
+    /**
+     * Gets the value of the annotation 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 annotation property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAnnotation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation }
+     * 
+     * 
+     */
+    public List getAnnotation() {
+        if (annotation == null) {
+            annotation = new ArrayList();
+        }
+        return this.annotation;
     }
-    return this.annotation;
-  }
 
-  /**
-   * Gets the value of the sequenceSetProperties property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the sequenceSetProperties property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getSequenceSetProperties().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet.SequenceSetProperties }
-   * 
-   * 
-   */
-  public List getSequenceSetProperties()
-  {
-    if (sequenceSetProperties == null)
-    {
-      sequenceSetProperties = new ArrayList();
+    /**
+     * Gets the value of the sequenceSetProperties 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 sequenceSetProperties property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getSequenceSetProperties().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet.SequenceSetProperties }
+     * 
+     * 
+     */
+    public List getSequenceSetProperties() {
+        if (sequenceSetProperties == null) {
+            sequenceSetProperties = new ArrayList();
+        }
+        return this.sequenceSetProperties;
     }
-    return this.sequenceSetProperties;
-  }
 
-  /**
-   * Gets the value of the alcodonFrame property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the alcodonFrame property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getAlcodonFrame().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame }
-   * 
-   * 
-   */
-  public List getAlcodonFrame()
-  {
-    if (alcodonFrame == null)
-    {
-      alcodonFrame = new ArrayList();
+    /**
+     * Gets the value of the alcodonFrame 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 alcodonFrame property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAlcodonFrame().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame }
+     * 
+     * 
+     */
+    public List getAlcodonFrame() {
+        if (alcodonFrame == null) {
+            alcodonFrame = new ArrayList();
+        }
+        return this.alcodonFrame;
     }
-    return this.alcodonFrame;
-  }
-
-  /**
-   * Gets the value of the gapChar property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGapChar()
-  {
-    return gapChar;
-  }
-
-  /**
-   * Sets the value of the gapChar property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGapChar(String value)
-  {
-    this.gapChar = value;
-  }
-
-  /**
-   * Gets the value of the datasetId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDatasetId()
-  {
-    return datasetId;
-  }
-
-  /**
-   * Sets the value of the datasetId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDatasetId(String value)
-  {
-    this.datasetId = value;
-  }
-
-  /**
-   * <p>Java class for anonymous complex type.
-   * 
-   * <p>The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * <pre> &lt;complexType&gt; &lt;complexContent&gt;
-   * &lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
-   * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
-   * &lt;/restriction&gt; &lt;/complexContent&gt;
-   * &lt;/complexType&gt; </pre>
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class SequenceSetProperties
-  {
-
-    @XmlAttribute(name = "key")
-    protected String key;
-
-    @XmlAttribute(name = "value")
-    protected String value;
 
     /**
-     * Gets the value of the key property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the gapChar property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getKey()
-    {
-      return key;
+    public String getGapChar() {
+        return gapChar;
     }
 
     /**
-     * Sets the value of the key property.
+     * Sets the value of the gapChar property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public void setGapChar(String value) {
+        this.gapChar = value;
     }
 
     /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the datasetId property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getDatasetId() {
+        return datasetId;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the datasetId property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setDatasetId(String value) {
+        this.datasetId = value;
     }
 
-  }
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SequenceSetProperties {
+
+        @XmlAttribute(name = "key")
+        protected String key;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index 2e378da..cb7fa05 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,132 +14,140 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for SequenceType complex type.
+ * 
    Java class for SequenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="SequenceType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequence"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="SequenceType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
-@XmlSeeAlso({ Sequence.class })
-public class SequenceType
-{
-
-  protected String sequence;
-
-  protected String name;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
+@XmlType(name = "SequenceType", propOrder = {
+    "sequence",
+    "name"
+})
+@XmlSeeAlso({
+    Sequence.class
+})
+public class SequenceType {
+
+    protected String sequence;
+    protected String name;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "description")
+    protected String description;
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 501c729..49c2dd2 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -1,42 +1,47 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for ThresholdType.
+ * 
    Java class for ThresholdType.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="ThresholdType"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="NONE"/&gt; &lt;enumeration value="ABOVE"/&gt;
- * &lt;enumeration value="BELOW"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * 
    The following schema fragment specifies the expected content contained within this class.
+ * 
    
+ * 
    + * <simpleType name="ThresholdType">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="NONE"/>
+ *     <enumeration value="ABOVE"/>
+ *     <enumeration value="BELOW"/>
+ *   </restriction>
+ * </simpleType>
+ * 
    
  * 
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum ThresholdType
-{
+public enum ThresholdType {
 
-  NONE, ABOVE, BELOW;
+    NONE,
+    ABOVE,
+    BELOW;
 
-  public String value()
-  {
-    return name();
-  }
+    public String value() {
+        return name();
+    }
 
-  public static ThresholdType fromValue(String v)
-  {
-    return valueOf(v);
-  }
+    public static ThresholdType fromValue(String v) {
+        return valueOf(v);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 932ba3b..d697534 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,85 +15,95 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for VAMSAS complex type.
+ * 
    Java class for VAMSAS complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="VAMSAS"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Tree"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="VAMSAS">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
-public class VAMSAS
-{
-
-  @XmlElement(name = "Tree")
-  protected List tree;
+@XmlType(name = "VAMSAS", propOrder = {
+    "tree",
+    "sequenceSet"
+})
+public class VAMSAS {
 
-  @XmlElement(name = "SequenceSet")
-  protected List sequenceSet;
+    @XmlElement(name = "Tree")
+    protected List tree;
+    @XmlElement(name = "SequenceSet")
+    protected List sequenceSet;
 
-  /**
-   * Gets the value of the tree property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the tree property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getTree().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList();
+    /**
+     * Gets the value of the tree 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 tree property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getTree().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getTree() {
+        if (tree == null) {
+            tree = new ArrayList();
+        }
+        return this.tree;
     }
-    return this.tree;
-  }
 
-  /**
-   * Gets the value of the sequenceSet property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the sequenceSet property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getSequenceSet().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet }
-   * 
-   * 
-   */
-  public List getSequenceSet()
-  {
-    if (sequenceSet == null)
-    {
-      sequenceSet = new ArrayList();
+    /**
+     * Gets the value of the sequenceSet 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 sequenceSet property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getSequenceSet().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet }
+     * 
+     * 
+     */
+    public List getSequenceSet() {
+        if (sequenceSet == null) {
+            sequenceSet = new ArrayList();
+        }
+        return this.sequenceSet;
     }
-    return this.sequenceSet;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index 44d5829..1935391 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -1,10 +1,11 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,173 +18,177 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * <p>Java class for WebServiceParameterSet complex type.
+ * 
    Java class for WebServiceParameterSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> &lt;complexType name="WebServiceParameterSet"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="serviceURL"
- * type="{http://www.w3.org/2001/XMLSchema}anyURI"
- * maxOccurs="unbounded"/&gt; &lt;element name="parameters"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * 
    + * <complexType name="WebServiceParameterSet">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ *         <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       </sequence>
+ *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 
    
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "WebServiceParameterSet",
-  namespace = "www.jalview.org/xml/wsparamset",
-  propOrder =
-  { "version", "description", "serviceURL", "parameters" })
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+    "version",
+    "description",
+    "serviceURL",
+    "parameters"
+})
 @XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
-public class WebServiceParameterSet
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected String description;
-
-  @XmlElement(namespace = "", required = true)
-  @XmlSchemaType(name = "anyURI")
-  protected List serviceURL;
-
-  @XmlElement(namespace = "", required = true)
-  protected String parameters;
-
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the serviceURL property.
-   * 
-   * <p> 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
-   * <CODE>set</CODE> method for the serviceURL property.
-   * 
-   * <p> For example, to add a new item, do as follows: <pre>
-   * getServiceURL().add(newItem); </pre>
-   * 
-   * 
-   * <p> Objects of the following type(s) are allowed in the list
-   * {@link String }
-   * 
-   * 
-   */
-  public List getServiceURL()
-  {
-    if (serviceURL == null)
-    {
-      serviceURL = new ArrayList();
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
+    @XmlElement(namespace = "")
+    protected String description;
+    @XmlElement(namespace = "", required = true)
+    @XmlSchemaType(name = "anyURI")
+    protected List serviceURL;
+    @XmlElement(namespace = "", required = true)
+    protected String parameters;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
+
+    /**
+     * Gets the value of the version property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVersion(String value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the serviceURL 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 serviceURL property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getServiceURL().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getServiceURL() {
+        if (serviceURL == null) {
+            serviceURL = new ArrayList();
+        }
+        return this.serviceURL;
+    }
+
+    /**
+     * Gets the value of the parameters property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getParameters() {
+        return parameters;
+    }
+
+    /**
+     * Sets the value of the parameters property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setParameters(String value) {
+        this.parameters = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
     }
-    return this.serviceURL;
-  }
-
-  /**
-   * Gets the value of the parameters property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getParameters()
-  {
-    return parameters;
-  }
-
-  /**
-   * Sets the value of the parameters property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setParameters(String value)
-  {
-    this.parameters = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index aa2ab9e..338e645 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -1,11 +1,9 @@
 //
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
-// See https://eclipse-ee4j.github.io/jaxb-ri 
+// 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.01.31 at 04:07:08 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(
-  namespace = "www.vamsas.ac.uk/jalview/version2",
-  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.jalview;
diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java
index b38df87..b07b8e2 100644
--- a/src/jalview/xml/binding/uniprot/CitationType.java
+++ b/src/jalview/xml/binding/uniprot/CitationType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of citations. Equivalent to the flat file RX-, RG-,
- * RA-, RT- and RL-lines.
+ * Describes different types of citations.
+ *             Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
  * 
- * 
    
- * Java class for citationType complex type.
+ * 
    Java class for citationType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="citationType">
@@ -73,457 +72,456 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "citationType",
-  propOrder =
-  { "title", "editorList", "authorList", "locator", "dbReference" })
-public class CitationType
-{
-
-  protected String title;
-
-  protected NameListType editorList;
-
-  protected NameListType authorList;
-
-  protected String locator;
-
-  protected List dbReference;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "date")
-  protected String date;
-
-  @XmlAttribute(name = "name")
-  protected String name;
-
-  @XmlAttribute(name = "volume")
-  protected String volume;
-
-  @XmlAttribute(name = "first")
-  protected String first;
-
-  @XmlAttribute(name = "last")
-  protected String last;
-
-  @XmlAttribute(name = "publisher")
-  protected String publisher;
-
-  @XmlAttribute(name = "city")
-  protected String city;
-
-  @XmlAttribute(name = "db")
-  protected String db;
-
-  @XmlAttribute(name = "number")
-  protected String number;
-
-  @XmlAttribute(name = "institute")
-  protected String institute;
-
-  @XmlAttribute(name = "country")
-  protected String country;
-
-  /**
-   * Gets the value of the title property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTitle()
-  {
-    return title;
-  }
-
-  /**
-   * Sets the value of the title property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTitle(String value)
-  {
-    this.title = value;
-  }
-
-  /**
-   * Gets the value of the editorList property.
-   * 
-   * @return possible object is {@link NameListType }
-   * 
-   */
-  public NameListType getEditorList()
-  {
-    return editorList;
-  }
-
-  /**
-   * Sets the value of the editorList property.
-   * 
-   * @param value
-   *          allowed object is {@link NameListType }
-   * 
-   */
-  public void setEditorList(NameListType value)
-  {
-    this.editorList = value;
-  }
-
-  /**
-   * Gets the value of the authorList property.
-   * 
-   * @return possible object is {@link NameListType }
-   * 
-   */
-  public NameListType getAuthorList()
-  {
-    return authorList;
-  }
-
-  /**
-   * Sets the value of the authorList property.
-   * 
-   * @param value
-   *          allowed object is {@link NameListType }
-   * 
-   */
-  public void setAuthorList(NameListType value)
-  {
-    this.authorList = value;
-  }
-
-  /**
-   * Gets the value of the locator property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLocator()
-  {
-    return locator;
-  }
-
-  /**
-   * Sets the value of the locator property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLocator(String value)
-  {
-    this.locator = value;
-  }
-
-  /**
-   * Gets the value of the dbReference 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 dbReference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getDbReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList();
-    }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the date property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDate()
-  {
-    return date;
-  }
-
-  /**
-   * Sets the value of the date property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDate(String value)
-  {
-    this.date = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the volume property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVolume()
-  {
-    return volume;
-  }
-
-  /**
-   * Sets the value of the volume property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVolume(String value)
-  {
-    this.volume = value;
-  }
-
-  /**
-   * Gets the value of the first property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFirst()
-  {
-    return first;
-  }
-
-  /**
-   * Sets the value of the first property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFirst(String value)
-  {
-    this.first = value;
-  }
-
-  /**
-   * Gets the value of the last property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLast()
-  {
-    return last;
-  }
-
-  /**
-   * Sets the value of the last property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLast(String value)
-  {
-    this.last = value;
-  }
-
-  /**
-   * Gets the value of the publisher property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getPublisher()
-  {
-    return publisher;
-  }
-
-  /**
-   * Sets the value of the publisher property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setPublisher(String value)
-  {
-    this.publisher = value;
-  }
-
-  /**
-   * Gets the value of the city property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCity()
-  {
-    return city;
-  }
-
-  /**
-   * Sets the value of the city property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCity(String value)
-  {
-    this.city = value;
-  }
-
-  /**
-   * Gets the value of the db property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDb()
-  {
-    return db;
-  }
-
-  /**
-   * Sets the value of the db property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDb(String value)
-  {
-    this.db = value;
-  }
-
-  /**
-   * Gets the value of the number property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getNumber()
-  {
-    return number;
-  }
-
-  /**
-   * Sets the value of the number property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setNumber(String value)
-  {
-    this.number = value;
-  }
-
-  /**
-   * Gets the value of the institute property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getInstitute()
-  {
-    return institute;
-  }
-
-  /**
-   * Sets the value of the institute property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setInstitute(String value)
-  {
-    this.institute = value;
-  }
-
-  /**
-   * Gets the value of the country property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCountry()
-  {
-    return country;
-  }
-
-  /**
-   * Sets the value of the country property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCountry(String value)
-  {
-    this.country = value;
-  }
+@XmlType(name = "citationType", propOrder = {
+    "title",
+    "editorList",
+    "authorList",
+    "locator",
+    "dbReference"
+})
+public class CitationType {
+
+    protected String title;
+    protected NameListType editorList;
+    protected NameListType authorList;
+    protected String locator;
+    protected List dbReference;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "date")
+    protected String date;
+    @XmlAttribute(name = "name")
+    protected String name;
+    @XmlAttribute(name = "volume")
+    protected String volume;
+    @XmlAttribute(name = "first")
+    protected String first;
+    @XmlAttribute(name = "last")
+    protected String last;
+    @XmlAttribute(name = "publisher")
+    protected String publisher;
+    @XmlAttribute(name = "city")
+    protected String city;
+    @XmlAttribute(name = "db")
+    protected String db;
+    @XmlAttribute(name = "number")
+    protected String number;
+    @XmlAttribute(name = "institute")
+    protected String institute;
+    @XmlAttribute(name = "country")
+    protected String country;
+
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTitle() {
+        return title;
+    }
+
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTitle(String value) {
+        this.title = value;
+    }
+
+    /**
+     * Gets the value of the editorList property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link NameListType }
+     *     
+     */
+    public NameListType getEditorList() {
+        return editorList;
+    }
+
+    /**
+     * Sets the value of the editorList property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link NameListType }
+     *     
+     */
+    public void setEditorList(NameListType value) {
+        this.editorList = value;
+    }
+
+    /**
+     * Gets the value of the authorList property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link NameListType }
+     *     
+     */
+    public NameListType getAuthorList() {
+        return authorList;
+    }
+
+    /**
+     * Sets the value of the authorList property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link NameListType }
+     *     
+     */
+    public void setAuthorList(NameListType value) {
+        this.authorList = value;
+    }
+
+    /**
+     * Gets the value of the locator property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLocator() {
+        return locator;
+    }
+
+    /**
+     * Sets the value of the locator property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLocator(String value) {
+        this.locator = value;
+    }
+
+    /**
+     * Gets the value of the dbReference 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 dbReference property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getDbReference().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList();
+        }
+        return this.dbReference;
+    }
+
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
+
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the date property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDate() {
+        return date;
+    }
+
+    /**
+     * Sets the value of the date property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDate(String value) {
+        this.date = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the volume property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVolume() {
+        return volume;
+    }
+
+    /**
+     * Sets the value of the volume property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVolume(String value) {
+        this.volume = value;
+    }
+
+    /**
+     * Gets the value of the first property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getFirst() {
+        return first;
+    }
+
+    /**
+     * Sets the value of the first property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFirst(String value) {
+        this.first = value;
+    }
+
+    /**
+     * Gets the value of the last property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLast() {
+        return last;
+    }
+
+    /**
+     * Sets the value of the last property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLast(String value) {
+        this.last = value;
+    }
+
+    /**
+     * Gets the value of the publisher property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getPublisher() {
+        return publisher;
+    }
+
+    /**
+     * Sets the value of the publisher property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setPublisher(String value) {
+        this.publisher = value;
+    }
+
+    /**
+     * Gets the value of the city property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCity() {
+        return city;
+    }
+
+    /**
+     * Sets the value of the city property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCity(String value) {
+        this.city = value;
+    }
+
+    /**
+     * Gets the value of the db property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDb() {
+        return db;
+    }
+
+    /**
+     * Sets the value of the db property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDb(String value) {
+        this.db = value;
+    }
+
+    /**
+     * Gets the value of the number property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getNumber() {
+        return number;
+    }
+
+    /**
+     * Sets the value of the number property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setNumber(String value) {
+        this.number = value;
+    }
+
+    /**
+     * Gets the value of the institute property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getInstitute() {
+        return institute;
+    }
+
+    /**
+     * Sets the value of the institute property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setInstitute(String value) {
+        this.institute = value;
+    }
+
+    /**
+     * Gets the value of the country property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCountry() {
+        return country;
+    }
+
+    /**
+     * Sets the value of the country property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCountry(String value) {
+        this.country = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java
index 424bcff..7dc9df3 100644
--- a/src/jalview/xml/binding/uniprot/CofactorType.java
+++ b/src/jalview/xml/binding/uniprot/CofactorType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a cofactor.
  * 
- * 
    
- * Java class for cofactorType complex type.
+ * 
    Java class for cofactorType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="cofactorType">
@@ -42,94 +41,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
-public class CofactorType
-{
-
-  @XmlElement(required = true)
-  protected String name;
-
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
+@XmlType(name = "cofactorType", propOrder = {
+    "name",
+    "dbReference"
+})
+public class CofactorType {
 
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+    @XmlElement(required = true)
+    protected String name;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java
index afd1da1..8766f7a 100644
--- a/src/jalview/xml/binding/uniprot/CommentType.java
+++ b/src/jalview/xml/binding/uniprot/CommentType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,16 +17,14 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of general annotations. Equivalent to the flat file
- * CC-line.
+ * Describes different types of general annotations.
+ *             Equivalent to the flat file CC-line.
  * 
- * 
    
- * Java class for commentType complex type.
+ * 
    Java class for commentType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="commentType">
@@ -174,1673 +173,1619 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "commentType",
-  propOrder =
-  { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
-      "temperatureDependence", "reaction", "physiologicalReaction",
-      "cofactor", "subcellularLocation", "conflict", "link", "event",
-      "isoform", "interactant", "organismsDiffer", "experiments", "disease",
-      "location", "text" })
-public class CommentType
-{
-
-  protected MoleculeType molecule;
-
-  protected CommentType.Absorption absorption;
-
-  protected CommentType.Kinetics kinetics;
-
-  protected CommentType.PhDependence phDependence;
-
-  protected CommentType.RedoxPotential redoxPotential;
-
-  protected CommentType.TemperatureDependence temperatureDependence;
-
-  protected ReactionType reaction;
-
-  protected List physiologicalReaction;
-
-  protected List cofactor;
-
-  protected List subcellularLocation;
-
-  protected CommentType.Conflict conflict;
-
-  protected List link;
+@XmlType(name = "commentType", propOrder = {
+    "molecule",
+    "absorption",
+    "kinetics",
+    "phDependence",
+    "redoxPotential",
+    "temperatureDependence",
+    "reaction",
+    "physiologicalReaction",
+    "cofactor",
+    "subcellularLocation",
+    "conflict",
+    "link",
+    "event",
+    "isoform",
+    "interactant",
+    "organismsDiffer",
+    "experiments",
+    "disease",
+    "location",
+    "text"
+})
+public class CommentType {
+
+    protected MoleculeType molecule;
+    protected CommentType.Absorption absorption;
+    protected CommentType.Kinetics kinetics;
+    protected CommentType.PhDependence phDependence;
+    protected CommentType.RedoxPotential redoxPotential;
+    protected CommentType.TemperatureDependence temperatureDependence;
+    protected ReactionType reaction;
+    protected List physiologicalReaction;
+    protected List cofactor;
+    protected List subcellularLocation;
+    protected CommentType.Conflict conflict;
+    protected List link;
+    protected List event;
+    protected List isoform;
+    protected List interactant;
+    @XmlElement(defaultValue = "false")
+    protected Boolean organismsDiffer;
+    protected Integer experiments;
+    protected CommentType.Disease disease;
+    protected List location;
+    protected List text;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "locationType")
+    protected String locationType;
+    @XmlAttribute(name = "name")
+    protected String name;
+    @XmlAttribute(name = "mass")
+    protected Float mass;
+    @XmlAttribute(name = "error")
+    protected String error;
+    @XmlAttribute(name = "method")
+    protected String method;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  protected List event;
-
-  protected List isoform;
-
-  protected List interactant;
-
-  @XmlElement(defaultValue = "false")
-  protected Boolean organismsDiffer;
-
-  protected Integer experiments;
-
-  protected CommentType.Disease disease;
-
-  protected List location;
-
-  protected List text;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "locationType")
-  protected String locationType;
-
-  @XmlAttribute(name = "name")
-  protected String name;
-
-  @XmlAttribute(name = "mass")
-  protected Float mass;
-
-  @XmlAttribute(name = "error")
-  protected String error;
-
-  @XmlAttribute(name = "method")
-  protected String method;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  /**
-   * Gets the value of the molecule property.
-   * 
-   * @return possible object is {@link MoleculeType }
-   * 
-   */
-  public MoleculeType getMolecule()
-  {
-    return molecule;
-  }
-
-  /**
-   * Sets the value of the molecule property.
-   * 
-   * @param value
-   *          allowed object is {@link MoleculeType }
-   * 
-   */
-  public void setMolecule(MoleculeType value)
-  {
-    this.molecule = value;
-  }
-
-  /**
-   * Gets the value of the absorption property.
-   * 
-   * @return possible object is {@link CommentType.Absorption }
-   * 
-   */
-  public CommentType.Absorption getAbsorption()
-  {
-    return absorption;
-  }
-
-  /**
-   * Sets the value of the absorption property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Absorption }
-   * 
-   */
-  public void setAbsorption(CommentType.Absorption value)
-  {
-    this.absorption = value;
-  }
-
-  /**
-   * Gets the value of the kinetics property.
-   * 
-   * @return possible object is {@link CommentType.Kinetics }
-   * 
-   */
-  public CommentType.Kinetics getKinetics()
-  {
-    return kinetics;
-  }
-
-  /**
-   * Sets the value of the kinetics property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Kinetics }
-   * 
-   */
-  public void setKinetics(CommentType.Kinetics value)
-  {
-    this.kinetics = value;
-  }
-
-  /**
-   * Gets the value of the phDependence property.
-   * 
-   * @return possible object is {@link CommentType.PhDependence }
-   * 
-   */
-  public CommentType.PhDependence getPhDependence()
-  {
-    return phDependence;
-  }
-
-  /**
-   * Sets the value of the phDependence property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.PhDependence }
-   * 
-   */
-  public void setPhDependence(CommentType.PhDependence value)
-  {
-    this.phDependence = value;
-  }
-
-  /**
-   * Gets the value of the redoxPotential property.
-   * 
-   * @return possible object is {@link CommentType.RedoxPotential }
-   * 
-   */
-  public CommentType.RedoxPotential getRedoxPotential()
-  {
-    return redoxPotential;
-  }
-
-  /**
-   * Sets the value of the redoxPotential property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.RedoxPotential }
-   * 
-   */
-  public void setRedoxPotential(CommentType.RedoxPotential value)
-  {
-    this.redoxPotential = value;
-  }
-
-  /**
-   * Gets the value of the temperatureDependence property.
-   * 
-   * @return possible object is {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public CommentType.TemperatureDependence getTemperatureDependence()
-  {
-    return temperatureDependence;
-  }
-
-  /**
-   * Sets the value of the temperatureDependence property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public void setTemperatureDependence(
-          CommentType.TemperatureDependence value)
-  {
-    this.temperatureDependence = value;
-  }
-
-  /**
-   * Gets the value of the reaction property.
-   * 
-   * @return possible object is {@link ReactionType }
-   * 
-   */
-  public ReactionType getReaction()
-  {
-    return reaction;
-  }
-
-  /**
-   * Sets the value of the reaction property.
-   * 
-   * @param value
-   *          allowed object is {@link ReactionType }
-   * 
-   */
-  public void setReaction(ReactionType value)
-  {
-    this.reaction = value;
-  }
-
-  /**
-   * Gets the value of the physiologicalReaction 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 physiologicalReaction property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getPhysiologicalReaction().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link PhysiologicalReactionType }
-   * 
-   * 
-   */
-  public List getPhysiologicalReaction()
-  {
-    if (physiologicalReaction == null)
-    {
-      physiologicalReaction = new ArrayList();
+    /**
+     * Gets the value of the molecule property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public MoleculeType getMolecule() {
+        return molecule;
     }
-    return this.physiologicalReaction;
-  }
-
-  /**
-   * Gets the value of the cofactor 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 cofactor property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getCofactor().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link CofactorType }
-   * 
-   * 
-   */
-  public List getCofactor()
-  {
-    if (cofactor == null)
-    {
-      cofactor = new ArrayList();
+
+    /**
+     * Sets the value of the molecule property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public void setMolecule(MoleculeType value) {
+        this.molecule = value;
     }
-    return this.cofactor;
-  }
-
-  /**
-   * Gets the value of the subcellularLocation 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 subcellularLocation property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getSubcellularLocation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link SubcellularLocationType }
-   * 
-   * 
-   */
-  public List getSubcellularLocation()
-  {
-    if (subcellularLocation == null)
-    {
-      subcellularLocation = new ArrayList();
+
+    /**
+     * Gets the value of the absorption property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Absorption }
+     *     
+     */
+    public CommentType.Absorption getAbsorption() {
+        return absorption;
     }
-    return this.subcellularLocation;
-  }
-
-  /**
-   * Gets the value of the conflict property.
-   * 
-   * @return possible object is {@link CommentType.Conflict }
-   * 
-   */
-  public CommentType.Conflict getConflict()
-  {
-    return conflict;
-  }
-
-  /**
-   * Sets the value of the conflict property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Conflict }
-   * 
-   */
-  public void setConflict(CommentType.Conflict value)
-  {
-    this.conflict = value;
-  }
-
-  /**
-   * Gets the value of the link 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 link property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getLink().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link CommentType.Link }
-   * 
-   * 
-   */
-  public List getLink()
-  {
-    if (link == null)
-    {
-      link = new ArrayList();
+
+    /**
+     * Sets the value of the absorption property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.Absorption }
+     *     
+     */
+    public void setAbsorption(CommentType.Absorption value) {
+        this.absorption = value;
     }
-    return this.link;
-  }
-
-  /**
-   * Gets the value of the event 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 event property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvent().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link EventType }
-   * 
-   * 
-   */
-  public List getEvent()
-  {
-    if (event == null)
-    {
-      event = new ArrayList();
+
+    /**
+     * Gets the value of the kinetics property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Kinetics }
+     *     
+     */
+    public CommentType.Kinetics getKinetics() {
+        return kinetics;
     }
-    return this.event;
-  }
-
-  /**
-   * Gets the value of the isoform 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 isoform property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getIsoform().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link IsoformType
-   * }
-   * 
-   * 
-   */
-  public List getIsoform()
-  {
-    if (isoform == null)
-    {
-      isoform = new ArrayList();
+
+    /**
+     * Sets the value of the kinetics property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.Kinetics }
+     *     
+     */
+    public void setKinetics(CommentType.Kinetics value) {
+        this.kinetics = value;
     }
-    return this.isoform;
-  }
-
-  /**
-   * Gets the value of the interactant 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 interactant property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getInteractant().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link InteractantType }
-   * 
-   * 
-   */
-  public List getInteractant()
-  {
-    if (interactant == null)
-    {
-      interactant = new ArrayList();
+
+    /**
+     * Gets the value of the phDependence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.PhDependence }
+     *     
+     */
+    public CommentType.PhDependence getPhDependence() {
+        return phDependence;
     }
-    return this.interactant;
-  }
-
-  /**
-   * Gets the value of the organismsDiffer property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isOrganismsDiffer()
-  {
-    return organismsDiffer;
-  }
-
-  /**
-   * Sets the value of the organismsDiffer property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setOrganismsDiffer(Boolean value)
-  {
-    this.organismsDiffer = value;
-  }
-
-  /**
-   * Gets the value of the experiments property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getExperiments()
-  {
-    return experiments;
-  }
-
-  /**
-   * Sets the value of the experiments property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setExperiments(Integer value)
-  {
-    this.experiments = value;
-  }
-
-  /**
-   * Gets the value of the disease property.
-   * 
-   * @return possible object is {@link CommentType.Disease }
-   * 
-   */
-  public CommentType.Disease getDisease()
-  {
-    return disease;
-  }
-
-  /**
-   * Sets the value of the disease property.
-   * 
-   * @param value
-   *          allowed object is {@link CommentType.Disease }
-   * 
-   */
-  public void setDisease(CommentType.Disease value)
-  {
-    this.disease = value;
-  }
-
-  /**
-   * Gets the value of the location 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 location property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getLocation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link LocationType }
-   * 
-   * 
-   */
-  public List getLocation()
-  {
-    if (location == null)
-    {
-      location = new ArrayList();
+
+    /**
+     * Sets the value of the phDependence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.PhDependence }
+     *     
+     */
+    public void setPhDependence(CommentType.PhDependence value) {
+        this.phDependence = value;
     }
-    return this.location;
-  }
-
-  /**
-   * Gets the value of the text 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 text property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getText().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getText()
-  {
-    if (text == null)
-    {
-      text = new ArrayList();
+
+    /**
+     * Gets the value of the redoxPotential property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.RedoxPotential }
+     *     
+     */
+    public CommentType.RedoxPotential getRedoxPotential() {
+        return redoxPotential;
     }
-    return this.text;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the locationType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLocationType()
-  {
-    return locationType;
-  }
-
-  /**
-   * Sets the value of the locationType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLocationType(String value)
-  {
-    this.locationType = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the mass property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getMass()
-  {
-    return mass;
-  }
-
-  /**
-   * Sets the value of the mass property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setMass(Float value)
-  {
-    this.mass = value;
-  }
-
-  /**
-   * Gets the value of the error property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getError()
-  {
-    return error;
-  }
-
-  /**
-   * Sets the value of the error property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setError(String value)
-  {
-    this.error = value;
-  }
-
-  /**
-   * Gets the value of the method property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMethod()
-  {
-    return method;
-  }
-
-  /**
-   * Sets the value of the method property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMethod(String value)
-  {
-    this.method = value;
-  }
-
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+
+    /**
+     * Sets the value of the redoxPotential property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.RedoxPotential }
+     *     
+     */
+    public void setRedoxPotential(CommentType.RedoxPotential value) {
+        this.redoxPotential = value;
     }
-    return this.evidence;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "max", "text" })
-  public static class Absorption
-  {
-
-    protected EvidencedStringType max;
 
-    protected List text;
+    /**
+     * Gets the value of the temperatureDependence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.TemperatureDependence }
+     *     
+     */
+    public CommentType.TemperatureDependence getTemperatureDependence() {
+        return temperatureDependence;
+    }
 
     /**
-     * Gets the value of the max property.
+     * Sets the value of the temperatureDependence property.
      * 
-     * @return possible object is {@link EvidencedStringType }
+     * @param value
+     *     allowed object is
+     *     {@link CommentType.TemperatureDependence }
+     *     
+     */
+    public void setTemperatureDependence(CommentType.TemperatureDependence value) {
+        this.temperatureDependence = value;
+    }
+
+    /**
+     * Gets the value of the reaction property.
      * 
+     * @return
+     *     possible object is
+     *     {@link ReactionType }
+     *     
      */
-    public EvidencedStringType getMax()
-    {
-      return max;
+    public ReactionType getReaction() {
+        return reaction;
     }
 
     /**
-     * Sets the value of the max property.
+     * Sets the value of the reaction property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link ReactionType }
+     *     
      */
-    public void setMax(EvidencedStringType value)
-    {
-      this.max = value;
+    public void setReaction(ReactionType value) {
+        this.reaction = value;
     }
 
     /**
-     * Gets the value of the text property.
+     * Gets the value of the physiologicalReaction 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 text 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 physiologicalReaction property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getText().add(newItem);
+     *    getPhysiologicalReaction().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * {@link PhysiologicalReactionType }
      * 
      * 
      */
-    public List getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList();
-      }
-      return this.text;
+    public List getPhysiologicalReaction() {
+        if (physiologicalReaction == null) {
+            physiologicalReaction = new ArrayList();
+        }
+        return this.physiologicalReaction;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="sequence" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="resource" use="required">
-   *                   <simpleType>
-   *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *                       <enumeration value="EMBL-CDS"/>
-   *                       <enumeration value="EMBL"/>
-   *                     </restriction>
-   *                   </simpleType>
-   *                 </attribute>
-   *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attribute name="type" use="required">
-   *         <simpleType>
-   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             <enumeration value="frameshift"/>
-   *             <enumeration value="erroneous initiation"/>
-   *             <enumeration value="erroneous termination"/>
-   *             <enumeration value="erroneous gene model prediction"/>
-   *             <enumeration value="erroneous translation"/>
-   *             <enumeration value="miscellaneous discrepancy"/>
-   *           </restriction>
-   *         </simpleType>
-   *       </attribute>
-   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "sequence" })
-  public static class Conflict
-  {
-
-    protected CommentType.Conflict.Sequence sequence;
-
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-
-    @XmlAttribute(name = "ref")
-    protected String ref;
-
     /**
-     * Gets the value of the sequence property.
+     * Gets the value of the cofactor 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 cofactor property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getCofactor().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link CofactorType }
      * 
-     * @return possible object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public CommentType.Conflict.Sequence getSequence()
-    {
-      return sequence;
+    public List getCofactor() {
+        if (cofactor == null) {
+            cofactor = new ArrayList();
+        }
+        return this.cofactor;
     }
 
     /**
-     * Sets the value of the sequence property.
+     * Gets the value of the subcellularLocation 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 subcellularLocation property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getSubcellularLocation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link SubcellularLocationType }
      * 
-     * @param value
-     *          allowed object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public void setSequence(CommentType.Conflict.Sequence value)
-    {
-      this.sequence = value;
+    public List getSubcellularLocation() {
+        if (subcellularLocation == null) {
+            subcellularLocation = new ArrayList();
+        }
+        return this.subcellularLocation;
     }
 
     /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the conflict property.
      * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Conflict }
+     *     
      */
-    public String getType()
-    {
-      return type;
+    public CommentType.Conflict getConflict() {
+        return conflict;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the conflict property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link CommentType.Conflict }
+     *     
      */
-    public void setType(String value)
-    {
-      this.type = value;
+    public void setConflict(CommentType.Conflict value) {
+        this.conflict = value;
     }
 
     /**
-     * Gets the value of the ref property.
+     * Gets the value of the link 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 link property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getLink().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link CommentType.Link }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getRef()
-    {
-      return ref;
+    public List getLink() {
+        if (link == null) {
+            link = new ArrayList();
+        }
+        return this.link;
     }
 
     /**
-     * Sets the value of the ref property.
+     * Gets the value of the event 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 event property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvent().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EventType }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setRef(String value)
-    {
-      this.ref = value;
+    public List getEvent() {
+        if (event == null) {
+            event = new ArrayList();
+        }
+        return this.event;
     }
 
     /**
-     * 
    
-     * Java class for anonymous complex type.
+     * Gets the value of the isoform property.
      * 
      * 
    
-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 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 isoform property.
      * 
+     * 
    
+     * For example, to add a new item, do as follows:
      * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="resource" use="required">
-     *         <simpleType>
-     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             <enumeration value="EMBL-CDS"/>
-     *             <enumeration value="EMBL"/>
-     *           </restriction>
-     *         </simpleType>
-     *       </attribute>
-     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     *    getIsoform().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link IsoformType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Sequence
-    {
-
-      @XmlAttribute(name = "resource", required = true)
-      protected String resource;
-
-      @XmlAttribute(name = "id", required = true)
-      protected String id;
-
-      @XmlAttribute(name = "version")
-      protected Integer version;
-
-      /**
-       * Gets the value of the resource property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getResource()
-      {
-        return resource;
-      }
-
-      /**
-       * Sets the value of the resource property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setResource(String value)
-      {
-        this.resource = value;
-      }
-
-      /**
-       * Gets the value of the id property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getId()
-      {
-        return id;
-      }
-
-      /**
-       * Sets the value of the id property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setId(String value)
-      {
-        this.id = value;
-      }
-
-      /**
-       * Gets the value of the version property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getVersion()
-      {
-        return version;
-      }
-
-      /**
-       * Sets the value of the version property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setVersion(Integer value)
-      {
-        this.version = value;
-      }
-
+    public List getIsoform() {
+        if (isoform == null) {
+            isoform = new ArrayList();
+        }
+        return this.isoform;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-   *       </sequence>
-   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "name", "acronym", "description", "dbReference" })
-  public static class Disease
-  {
-
-    @XmlElement(required = true)
-    protected String name;
-
-    @XmlElement(required = true)
-    protected String acronym;
+    /**
+     * Gets the value of the interactant 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 interactant property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getInteractant().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link InteractantType }
+     * 
+     * 
+     */
+    public List getInteractant() {
+        if (interactant == null) {
+            interactant = new ArrayList();
+        }
+        return this.interactant;
+    }
 
-    @XmlElement(required = true)
-    protected String description;
+    /**
+     * Gets the value of the organismsDiffer property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isOrganismsDiffer() {
+        return organismsDiffer;
+    }
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
+    /**
+     * Sets the value of the organismsDiffer property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setOrganismsDiffer(Boolean value) {
+        this.organismsDiffer = value;
+    }
 
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
+    /**
+     * Gets the value of the experiments property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getExperiments() {
+        return experiments;
+    }
 
     /**
-     * Gets the value of the name property.
+     * Sets the value of the experiments property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setExperiments(Integer value) {
+        this.experiments = value;
+    }
+
+    /**
+     * Gets the value of the disease property.
      * 
+     * @return
+     *     possible object is
+     *     {@link CommentType.Disease }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public CommentType.Disease getDisease() {
+        return disease;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the disease property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link CommentType.Disease }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public void setDisease(CommentType.Disease value) {
+        this.disease = value;
     }
 
     /**
-     * Gets the value of the acronym property.
+     * Gets the value of the location 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 location property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getLocation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link LocationType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getAcronym()
-    {
-      return acronym;
+    public List getLocation() {
+        if (location == null) {
+            location = new ArrayList();
+        }
+        return this.location;
     }
 
     /**
-     * Sets the value of the acronym property.
+     * Gets the value of the text 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 text property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getText().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setAcronym(String value)
-    {
-      this.acronym = value;
+    public List getText() {
+        if (text == null) {
+            text = new ArrayList();
+        }
+        return this.text;
     }
 
     /**
-     * Gets the value of the description property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getDescription()
-    {
-      return description;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Sets the value of the description property.
+     * Sets the value of the type property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the locationType property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setDescription(String value)
-    {
-      this.description = value;
+    public String getLocationType() {
+        return locationType;
     }
 
     /**
-     * Gets the value of the dbReference property.
+     * Sets the value of the locationType property.
      * 
-     * @return possible object is {@link DbReferenceType }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLocationType(String value) {
+        this.locationType = value;
+    }
+
+    /**
+     * Gets the value of the name property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public DbReferenceType getDbReference()
-    {
-      return dbReference;
+    public String getName() {
+        return name;
     }
 
     /**
-     * Sets the value of the dbReference property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *          allowed object is {@link DbReferenceType }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the mass property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
      */
-    public void setDbReference(DbReferenceType value)
-    {
-      this.dbReference = value;
+    public Float getMass() {
+        return mass;
     }
 
     /**
-     * Gets the value of the id property.
+     * Sets the value of the mass property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setMass(Float value) {
+        this.mass = value;
+    }
+
+    /**
+     * Gets the value of the error property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getId()
-    {
-      return id;
+    public String getError() {
+        return error;
     }
 
     /**
-     * Sets the value of the id property.
+     * Sets the value of the error property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setId(String value)
-    {
-      this.id = value;
+    public void setError(String value) {
+        this.error = value;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "km", "vmax", "text" })
-  public static class Kinetics
-  {
-
-    @XmlElement(name = "KM")
-    protected List km;
-
-    @XmlElement(name = "Vmax")
-    protected List vmax;
+    /**
+     * Gets the value of the method property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMethod() {
+        return method;
+    }
 
-    protected List text;
+    /**
+     * Sets the value of the method property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMethod(String value) {
+        this.method = value;
+    }
 
     /**
-     * Gets the value of the km property.
+     * Gets the value of the evidence 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 km 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 evidence property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getKM().add(newItem);
+     *    getEvidence().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * {@link Integer }
      * 
      * 
      */
-    public List getKM()
-    {
-      if (km == null)
-      {
-        km = new ArrayList();
-      }
-      return this.km;
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
 
+
     /**
-     * Gets the value of the vmax property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 vmax property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getVmax().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getVmax()
-    {
-      if (vmax == null)
-      {
-        vmax = new ArrayList();
-      }
-      return this.vmax;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "max",
+        "text"
+    })
+    public static class Absorption {
+
+        protected EvidencedStringType max;
+        protected List text;
+
+        /**
+         * Gets the value of the max property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getMax() {
+            return max;
+        }
+
+        /**
+         * Sets the value of the max property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setMax(EvidencedStringType value) {
+            this.max = value;
+        }
+
+        /**
+         * Gets the value of the text 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 text property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getText().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getText() {
+            if (text == null) {
+                text = new ArrayList();
+            }
+            return this.text;
+        }
+
     }
 
+
     /**
-     * Gets the value of the text property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 text property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getText().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="sequence" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="resource" use="required">
+     *                   <simpleType>
+     *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *                       <enumeration value="EMBL-CDS"/>
+     *                       <enumeration value="EMBL"/>
+     *                     </restriction>
+     *                   </simpleType>
+     *                 </attribute>
+     *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attribute name="type" use="required">
+     *         <simpleType>
+     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             <enumeration value="frameshift"/>
+     *             <enumeration value="erroneous initiation"/>
+     *             <enumeration value="erroneous termination"/>
+     *             <enumeration value="erroneous gene model prediction"/>
+     *             <enumeration value="erroneous translation"/>
+     *             <enumeration value="miscellaneous discrepancy"/>
+     *           </restriction>
+     *         </simpleType>
+     *       </attribute>
+     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "sequence"
+    })
+    public static class Conflict {
+
+        protected CommentType.Conflict.Sequence sequence;
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "ref")
+        protected String ref;
+
+        /**
+         * Gets the value of the sequence property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link CommentType.Conflict.Sequence }
+         *     
+         */
+        public CommentType.Conflict.Sequence getSequence() {
+            return sequence;
+        }
+
+        /**
+         * Sets the value of the sequence property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link CommentType.Conflict.Sequence }
+         *     
+         */
+        public void setSequence(CommentType.Conflict.Sequence value) {
+            this.sequence = value;
+        }
+
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
+
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
+
+        /**
+         * Gets the value of the ref property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRef() {
+            return ref;
+        }
+
+        /**
+         * Sets the value of the ref property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRef(String value) {
+            this.ref = value;
+        }
+
+
+        /**
+         * 
    Java class for anonymous complex type.
+         * 
+         * 
    The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
    +         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="resource" use="required">
+         *         <simpleType>
+         *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+         *             <enumeration value="EMBL-CDS"/>
+         *             <enumeration value="EMBL"/>
+         *           </restriction>
+         *         </simpleType>
+         *       </attribute>
+         *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 
    
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Sequence {
+
+            @XmlAttribute(name = "resource", required = true)
+            protected String resource;
+            @XmlAttribute(name = "id", required = true)
+            protected String id;
+            @XmlAttribute(name = "version")
+            protected Integer version;
+
+            /**
+             * Gets the value of the resource property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getResource() {
+                return resource;
+            }
+
+            /**
+             * Sets the value of the resource property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setResource(String value) {
+                this.resource = value;
+            }
+
+            /**
+             * Gets the value of the id property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getId() {
+                return id;
+            }
+
+            /**
+             * Sets the value of the id property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setId(String value) {
+                this.id = value;
+            }
+
+            /**
+             * Gets the value of the version property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getVersion() {
+                return version;
+            }
+
+            /**
+             * Sets the value of the version property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setVersion(Integer value) {
+                this.version = value;
+            }
+
+        }
+
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Link
-  {
-
-    @XmlAttribute(name = "uri", required = true)
-    @XmlSchemaType(name = "anyURI")
-    protected String uri;
 
     /**
-     * Gets the value of the uri property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+     *       </sequence>
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getUri()
-    {
-      return uri;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "name",
+        "acronym",
+        "description",
+        "dbReference"
+    })
+    public static class Disease {
+
+        @XmlElement(required = true)
+        protected String name;
+        @XmlElement(required = true)
+        protected String acronym;
+        @XmlElement(required = true)
+        protected String description;
+        @XmlElement(required = true)
+        protected DbReferenceType dbReference;
+        @XmlAttribute(name = "id", required = true)
+        protected String id;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the acronym property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAcronym() {
+            return acronym;
+        }
+
+        /**
+         * Sets the value of the acronym property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAcronym(String value) {
+            this.acronym = value;
+        }
+
+        /**
+         * Gets the value of the description property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDescription() {
+            return description;
+        }
+
+        /**
+         * Sets the value of the description property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDescription(String value) {
+            this.description = value;
+        }
+
+        /**
+         * Gets the value of the dbReference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link DbReferenceType }
+         *     
+         */
+        public DbReferenceType getDbReference() {
+            return dbReference;
+        }
+
+        /**
+         * Sets the value of the dbReference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link DbReferenceType }
+         *     
+         */
+        public void setDbReference(DbReferenceType value) {
+            this.dbReference = value;
+        }
+
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
+
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
+
     }
 
+
     /**
-     * Sets the value of the uri property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setUri(String value)
-    {
-      this.uri = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "km",
+        "vmax",
+        "text"
+    })
+    public static class Kinetics {
+
+        @XmlElement(name = "KM")
+        protected List km;
+        @XmlElement(name = "Vmax")
+        protected List vmax;
+        protected List text;
+
+        /**
+         * Gets the value of the km 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 km property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getKM().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getKM() {
+            if (km == null) {
+                km = new ArrayList();
+            }
+            return this.km;
+        }
+
+        /**
+         * Gets the value of the vmax 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 vmax property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getVmax().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getVmax() {
+            if (vmax == null) {
+                vmax = new ArrayList();
+            }
+            return this.vmax;
+        }
+
+        /**
+         * Gets the value of the text 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 text property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getText().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getText() {
+            if (text == null) {
+                text = new ArrayList();
+            }
+            return this.text;
+        }
+
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class PhDependence
-  {
-
-    @XmlElement(required = true)
-    protected List text;
 
     /**
-     * Gets the value of the text property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 text property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getText().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Link {
+
+        @XmlAttribute(name = "uri", required = true)
+        @XmlSchemaType(name = "anyURI")
+        protected String uri;
+
+        /**
+         * Gets the value of the uri property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getUri() {
+            return uri;
+        }
+
+        /**
+         * Sets the value of the uri property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setUri(String value) {
+            this.uri = value;
+        }
+
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class RedoxPotential
-  {
-
-    @XmlElement(required = true)
-    protected List text;
 
     /**
-     * Gets the value of the text property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 text property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getText().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList();
-      }
-      return this.text;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class PhDependence {
+
+        @XmlElement(required = true)
+        protected List text;
+
+        /**
+         * Gets the value of the text 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 text property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getText().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getText() {
+            if (text == null) {
+                text = new ArrayList();
+            }
+            return this.text;
+        }
+
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "text" })
-  public static class TemperatureDependence
-  {
-
-    @XmlElement(required = true)
-    protected List text;
 
     /**
-     * Gets the value of the text property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 text property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getText().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class RedoxPotential {
+
+        @XmlElement(required = true)
+        protected List text;
+
+        /**
+         * Gets the value of the text 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 text property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getText().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getText() {
+            if (text == null) {
+                text = new ArrayList();
+            }
+            return this.text;
+        }
+
+    }
+
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
      * 
      * 
      */
-    public List getText()
-    {
-      if (text == null)
-      {
-        text = new ArrayList();
-      }
-      return this.text;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "text"
+    })
+    public static class TemperatureDependence {
+
+        @XmlElement(required = true)
+        protected List text;
+
+        /**
+         * Gets the value of the text 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 text property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getText().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getText() {
+            if (text == null) {
+                text = new ArrayList();
+            }
+            return this.text;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java
index 1b98b9b..e1b1db1 100644
--- a/src/jalview/xml/binding/uniprot/ConsortiumType.java
+++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the authors of a citation when these are represented by a
- * consortium. Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a consortium.
+ *             Equivalent to the flat file RG-line.
  * 
- * 
    
- * Java class for consortiumType complex type.
+ * 
    Java class for consortiumType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="consortiumType">
@@ -37,33 +36,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "consortiumType")
-public class ConsortiumType
-{
+public class ConsortiumType {
 
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java
index 84cbba7..9bfde39 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a database cross-reference. Equivalent to the flat file DR-line.
+ * Describes a database cross-reference.
+ *             Equivalent to the flat file DR-line.
+ *             
  * 
+ * 
    Java class for dbReferenceType complex type.
  * 
- * 
    
- * Java class for dbReferenceType complex type.
- * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="dbReferenceType">
@@ -44,153 +44,149 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
-public class DbReferenceType
-{
-
-  protected MoleculeType molecule;
-
-  protected List property;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  /**
-   * Gets the value of the molecule property.
-   * 
-   * @return possible object is {@link MoleculeType }
-   * 
-   */
-  public MoleculeType getMolecule()
-  {
-    return molecule;
-  }
+@XmlType(name = "dbReferenceType", propOrder = {
+    "molecule",
+    "property"
+})
+public class DbReferenceType {
+
+    protected MoleculeType molecule;
+    protected List property;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+
+    /**
+     * Gets the value of the molecule property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public MoleculeType getMolecule() {
+        return molecule;
+    }
 
-  /**
-   * Sets the value of the molecule property.
-   * 
-   * @param value
-   *          allowed object is {@link MoleculeType }
-   * 
-   */
-  public void setMolecule(MoleculeType value)
-  {
-    this.molecule = value;
-  }
+    /**
+     * Sets the value of the molecule property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MoleculeType }
+     *     
+     */
+    public void setMolecule(MoleculeType value) {
+        this.molecule = value;
+    }
 
-  /**
-   * Gets the value of the property 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 property property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getProperty().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link PropertyType }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
+    /**
+     * Gets the value of the property 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 property property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getProperty().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link PropertyType }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
     }
-    return this.property;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java
index 65bbd88..8ca1da7 100644
--- a/src/jalview/xml/binding/uniprot/Entry.java
+++ b/src/jalview/xml/binding/uniprot/Entry.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -18,13 +19,11 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * 
    
- * Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType>
@@ -66,594 +65,561 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "accession", "name", "protein", "gene", "organism", "organismHost",
-      "geneLocation", "reference", "comment", "dbReference",
-      "proteinExistence", "keyword", "feature", "evidence", "sequence" })
+@XmlType(name = "", propOrder = {
+    "accession",
+    "name",
+    "protein",
+    "gene",
+    "organism",
+    "organismHost",
+    "geneLocation",
+    "reference",
+    "comment",
+    "dbReference",
+    "proteinExistence",
+    "keyword",
+    "feature",
+    "evidence",
+    "sequence"
+})
 @XmlRootElement(name = "entry")
-public class Entry
-{
-
-  @XmlElement(required = true)
-  protected List accession;
-
-  @XmlElement(required = true)
-  protected List name;
-
-  @XmlElement(required = true)
-  protected ProteinType protein;
-
-  protected List gene;
+public class Entry {
+
+    @XmlElement(required = true)
+    protected List accession;
+    @XmlElement(required = true)
+    protected List name;
+    @XmlElement(required = true)
+    protected ProteinType protein;
+    protected List gene;
+    @XmlElement(required = true)
+    protected OrganismType organism;
+    protected List organismHost;
+    protected List geneLocation;
+    @XmlElement(required = true)
+    protected List reference;
+    @XmlElement(nillable = true)
+    protected List comment;
+    protected List dbReference;
+    @XmlElement(required = true)
+    protected ProteinExistenceType proteinExistence;
+    protected List keyword;
+    protected List feature;
+    protected List evidence;
+    @XmlElement(required = true)
+    protected SequenceType sequence;
+    @XmlAttribute(name = "dataset", required = true)
+    protected String dataset;
+    @XmlAttribute(name = "created", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar created;
+    @XmlAttribute(name = "modified", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar modified;
+    @XmlAttribute(name = "version", required = true)
+    protected int version;
+
+    /**
+     * Gets the value of the accession 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 accession property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getAccession().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getAccession() {
+        if (accession == null) {
+            accession = new ArrayList();
+        }
+        return this.accession;
+    }
 
-  @XmlElement(required = true)
-  protected OrganismType organism;
+    /**
+     * Gets the value of the name 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 name property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getName().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getName() {
+        if (name == null) {
+            name = new ArrayList();
+        }
+        return this.name;
+    }
 
-  protected List organismHost;
+    /**
+     * Gets the value of the protein property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinType }
+     *     
+     */
+    public ProteinType getProtein() {
+        return protein;
+    }
 
-  protected List geneLocation;
+    /**
+     * Sets the value of the protein property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ProteinType }
+     *     
+     */
+    public void setProtein(ProteinType value) {
+        this.protein = value;
+    }
 
-  @XmlElement(required = true)
-  protected List reference;
+    /**
+     * Gets the value of the gene 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 gene property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getGene().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneType }
+     * 
+     * 
+     */
+    public List getGene() {
+        if (gene == null) {
+            gene = new ArrayList();
+        }
+        return this.gene;
+    }
 
-  @XmlElement(nillable = true)
-  protected List comment;
+    /**
+     * Gets the value of the organism property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link OrganismType }
+     *     
+     */
+    public OrganismType getOrganism() {
+        return organism;
+    }
 
-  protected List dbReference;
+    /**
+     * Sets the value of the organism property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link OrganismType }
+     *     
+     */
+    public void setOrganism(OrganismType value) {
+        this.organism = value;
+    }
 
-  @XmlElement(required = true)
-  protected ProteinExistenceType proteinExistence;
+    /**
+     * Gets the value of the organismHost 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 organismHost property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getOrganismHost().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link OrganismType }
+     * 
+     * 
+     */
+    public List getOrganismHost() {
+        if (organismHost == null) {
+            organismHost = new ArrayList();
+        }
+        return this.organismHost;
+    }
 
-  protected List keyword;
+    /**
+     * Gets the value of the geneLocation 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 geneLocation property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getGeneLocation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneLocationType }
+     * 
+     * 
+     */
+    public List getGeneLocation() {
+        if (geneLocation == null) {
+            geneLocation = new ArrayList();
+        }
+        return this.geneLocation;
+    }
 
-  protected List feature;
+    /**
+     * Gets the value of the reference 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 reference property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getReference().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link ReferenceType }
+     * 
+     * 
+     */
+    public List getReference() {
+        if (reference == null) {
+            reference = new ArrayList();
+        }
+        return this.reference;
+    }
 
-  protected List evidence;
+    /**
+     * Gets the value of the comment 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 comment property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getComment().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link CommentType }
+     * 
+     * 
+     */
+    public List getComment() {
+        if (comment == null) {
+            comment = new ArrayList();
+        }
+        return this.comment;
+    }
 
-  @XmlElement(required = true)
-  protected SequenceType sequence;
+    /**
+     * Gets the value of the dbReference 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 dbReference property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getDbReference().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList();
+        }
+        return this.dbReference;
+    }
 
-  @XmlAttribute(name = "dataset", required = true)
-  protected String dataset;
+    /**
+     * Gets the value of the proteinExistence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinExistenceType }
+     *     
+     */
+    public ProteinExistenceType getProteinExistence() {
+        return proteinExistence;
+    }
 
-  @XmlAttribute(name = "created", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar created;
+    /**
+     * Sets the value of the proteinExistence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ProteinExistenceType }
+     *     
+     */
+    public void setProteinExistence(ProteinExistenceType value) {
+        this.proteinExistence = value;
+    }
 
-  @XmlAttribute(name = "modified", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar modified;
+    /**
+     * Gets the value of the keyword 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 keyword property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getKeyword().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link KeywordType }
+     * 
+     * 
+     */
+    public List getKeyword() {
+        if (keyword == null) {
+            keyword = new ArrayList();
+        }
+        return this.keyword;
+    }
 
-  @XmlAttribute(name = "version", required = true)
-  protected int version;
+    /**
+     * Gets the value of the feature 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 feature property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getFeature().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link FeatureType }
+     * 
+     * 
+     */
+    public List getFeature() {
+        if (feature == null) {
+            feature = new ArrayList();
+        }
+        return this.feature;
+    }
 
-  /**
-   * Gets the value of the accession 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 accession property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getAccession().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getAccession()
-  {
-    if (accession == null)
-    {
-      accession = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidenceType }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.accession;
-  }
-
-  /**
-   * Gets the value of the name 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 name property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList();
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SequenceType }
+     *     
+     */
+    public SequenceType getSequence() {
+        return sequence;
     }
-    return this.name;
-  }
-
-  /**
-   * Gets the value of the protein property.
-   * 
-   * @return possible object is {@link ProteinType }
-   * 
-   */
-  public ProteinType getProtein()
-  {
-    return protein;
-  }
-
-  /**
-   * Sets the value of the protein property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinType }
-   * 
-   */
-  public void setProtein(ProteinType value)
-  {
-    this.protein = value;
-  }
-
-  /**
-   * Gets the value of the gene 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 gene property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getGene().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link GeneType }
-   * 
-   * 
-   */
-  public List getGene()
-  {
-    if (gene == null)
-    {
-      gene = new ArrayList();
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SequenceType }
+     *     
+     */
+    public void setSequence(SequenceType value) {
+        this.sequence = value;
     }
-    return this.gene;
-  }
-
-  /**
-   * Gets the value of the organism property.
-   * 
-   * @return possible object is {@link OrganismType }
-   * 
-   */
-  public OrganismType getOrganism()
-  {
-    return organism;
-  }
-
-  /**
-   * Sets the value of the organism property.
-   * 
-   * @param value
-   *          allowed object is {@link OrganismType }
-   * 
-   */
-  public void setOrganism(OrganismType value)
-  {
-    this.organism = value;
-  }
-
-  /**
-   * Gets the value of the organismHost 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 organismHost property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getOrganismHost().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link OrganismType }
-   * 
-   * 
-   */
-  public List getOrganismHost()
-  {
-    if (organismHost == null)
-    {
-      organismHost = new ArrayList();
+
+    /**
+     * Gets the value of the dataset property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDataset() {
+        return dataset;
     }
-    return this.organismHost;
-  }
-
-  /**
-   * Gets the value of the geneLocation 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 geneLocation property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getGeneLocation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link GeneLocationType }
-   * 
-   * 
-   */
-  public List getGeneLocation()
-  {
-    if (geneLocation == null)
-    {
-      geneLocation = new ArrayList();
+
+    /**
+     * Sets the value of the dataset property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDataset(String value) {
+        this.dataset = value;
     }
-    return this.geneLocation;
-  }
-
-  /**
-   * Gets the value of the reference 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 reference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ReferenceType }
-   * 
-   * 
-   */
-  public List getReference()
-  {
-    if (reference == null)
-    {
-      reference = new ArrayList();
+
+    /**
+     * Gets the value of the created property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getCreated() {
+        return created;
     }
-    return this.reference;
-  }
-
-  /**
-   * Gets the value of the comment 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 comment property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getComment().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link CommentType
-   * }
-   * 
-   * 
-   */
-  public List getComment()
-  {
-    if (comment == null)
-    {
-      comment = new ArrayList();
+
+    /**
+     * Sets the value of the created property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setCreated(XMLGregorianCalendar value) {
+        this.created = value;
     }
-    return this.comment;
-  }
-
-  /**
-   * Gets the value of the dbReference 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 dbReference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getDbReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList();
+
+    /**
+     * Gets the value of the modified property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getModified() {
+        return modified;
     }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the proteinExistence property.
-   * 
-   * @return possible object is {@link ProteinExistenceType }
-   * 
-   */
-  public ProteinExistenceType getProteinExistence()
-  {
-    return proteinExistence;
-  }
-
-  /**
-   * Sets the value of the proteinExistence property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinExistenceType }
-   * 
-   */
-  public void setProteinExistence(ProteinExistenceType value)
-  {
-    this.proteinExistence = value;
-  }
-
-  /**
-   * Gets the value of the keyword 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 keyword property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getKeyword().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link KeywordType
-   * }
-   * 
-   * 
-   */
-  public List getKeyword()
-  {
-    if (keyword == null)
-    {
-      keyword = new ArrayList();
+
+    /**
+     * Sets the value of the modified property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setModified(XMLGregorianCalendar value) {
+        this.modified = value;
     }
-    return this.keyword;
-  }
-
-  /**
-   * Gets the value of the feature 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 feature property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getFeature().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link FeatureType
-   * }
-   * 
-   * 
-   */
-  public List getFeature()
-  {
-    if (feature == null)
-    {
-      feature = new ArrayList();
+
+    /**
+     * Gets the value of the version property.
+     * 
+     */
+    public int getVersion() {
+        return version;
     }
-    return this.feature;
-  }
-
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidenceType }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+
+    /**
+     * Sets the value of the version property.
+     * 
+     */
+    public void setVersion(int value) {
+        this.version = value;
     }
-    return this.evidence;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link SequenceType }
-   * 
-   */
-  public SequenceType getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link SequenceType }
-   * 
-   */
-  public void setSequence(SequenceType value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the dataset property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDataset()
-  {
-    return dataset;
-  }
-
-  /**
-   * Sets the value of the dataset property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDataset(String value)
-  {
-    this.dataset = value;
-  }
-
-  /**
-   * Gets the value of the created property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreated()
-  {
-    return created;
-  }
-
-  /**
-   * Sets the value of the created property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreated(XMLGregorianCalendar value)
-  {
-    this.created = value;
-  }
-
-  /**
-   * Gets the value of the modified property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getModified()
-  {
-    return modified;
-  }
-
-  /**
-   * Sets the value of the modified property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setModified(XMLGregorianCalendar value)
-  {
-    this.modified = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   */
-  public int getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   */
-  public void setVersion(int value)
-  {
-    this.version = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java
index d3fe7f9..44566fe 100644
--- a/src/jalview/xml/binding/uniprot/EventType.java
+++ b/src/jalview/xml/binding/uniprot/EventType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,15 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes the type of events that cause alternative products.
  * 
- * 
    
- * Java class for eventType complex type.
+ * 
    Java class for eventType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="eventType">
@@ -45,33 +44,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "eventType")
-public class EventType
-{
+public class EventType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java
index 6e0ff99..371a778 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -13,15 +14,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the evidence for an annotation. No flat file equivalent.
+ * Describes the evidence for an annotation.
+ *             No flat file equivalent.
  * 
- * 
    
- * Java class for evidenceType complex type.
+ * 
    Java class for evidenceType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="evidenceType">
@@ -41,110 +41,113 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
-public class EvidenceType
-{
-
-  protected SourceType source;
-
-  protected ImportedFromType importedFrom;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "key", required = true)
-  protected BigInteger key;
-
-  /**
-   * Gets the value of the source property.
-   * 
-   * @return possible object is {@link SourceType }
-   * 
-   */
-  public SourceType getSource()
-  {
-    return source;
-  }
-
-  /**
-   * Sets the value of the source property.
-   * 
-   * @param value
-   *          allowed object is {@link SourceType }
-   * 
-   */
-  public void setSource(SourceType value)
-  {
-    this.source = value;
-  }
-
-  /**
-   * Gets the value of the importedFrom property.
-   * 
-   * @return possible object is {@link ImportedFromType }
-   * 
-   */
-  public ImportedFromType getImportedFrom()
-  {
-    return importedFrom;
-  }
-
-  /**
-   * Sets the value of the importedFrom property.
-   * 
-   * @param value
-   *          allowed object is {@link ImportedFromType }
-   * 
-   */
-  public void setImportedFrom(ImportedFromType value)
-  {
-    this.importedFrom = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the key property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getKey()
-  {
-    return key;
-  }
-
-  /**
-   * Sets the value of the key property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setKey(BigInteger value)
-  {
-    this.key = value;
-  }
+@XmlType(name = "evidenceType", propOrder = {
+    "source",
+    "importedFrom"
+})
+public class EvidenceType {
+
+    protected SourceType source;
+    protected ImportedFromType importedFrom;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "key", required = true)
+    protected BigInteger key;
+
+    /**
+     * Gets the value of the source property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SourceType }
+     *     
+     */
+    public SourceType getSource() {
+        return source;
+    }
+
+    /**
+     * Sets the value of the source property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SourceType }
+     *     
+     */
+    public void setSource(SourceType value) {
+        this.source = value;
+    }
+
+    /**
+     * Gets the value of the importedFrom property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link ImportedFromType }
+     *     
+     */
+    public ImportedFromType getImportedFrom() {
+        return importedFrom;
+    }
+
+    /**
+     * Sets the value of the importedFrom property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link ImportedFromType }
+     *     
+     */
+    public void setImportedFrom(ImportedFromType value) {
+        this.importedFrom = value;
+    }
+
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
+
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the key property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getKey() {
+        return key;
+    }
+
+    /**
+     * Sets the value of the key property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setKey(BigInteger value) {
+        this.key = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
index 33e8c53..def955e 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * 
    
- * Java class for evidencedStringType complex type.
+ * 
    Java class for evidencedStringType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="evidencedStringType">
@@ -45,94 +44,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = { "value" })
-public class EvidencedStringType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+@XmlType(name = "evidencedStringType", propOrder = {
+    "value"
+})
+public class EvidencedStringType {
 
-  @XmlAttribute(name = "status")
-  protected String status;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+    @XmlAttribute(name = "status")
+    protected String status;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        return status;
+    }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java
index fe9f4c4..0a6f7fe 100644
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes different types of sequence annotations. Equivalent to the flat
- * file FT-line.
+ * Describes different types of sequence annotations.
+ *             Equivalent to the flat file FT-line.
  * 
- * 
    
- * Java class for featureType complex type.
+ * 
    Java class for featureType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="featureType">
@@ -101,259 +100,254 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "featureType",
-  propOrder =
-  { "original", "variation", "location" })
-public class FeatureType
-{
-
-  protected String original;
-
-  protected List variation;
-
-  @XmlElement(required = true)
-  protected LocationType location;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+@XmlType(name = "featureType", propOrder = {
+    "original",
+    "variation",
+    "location"
+})
+public class FeatureType {
 
-  @XmlAttribute(name = "status")
-  protected String status;
+    protected String original;
+    protected List variation;
+    @XmlElement(required = true)
+    protected LocationType location;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "description")
+    protected String description;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+    @XmlAttribute(name = "ref")
+    protected String ref;
 
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  @XmlAttribute(name = "ref")
-  protected String ref;
-
-  /**
-   * Gets the value of the original property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getOriginal()
-  {
-    return original;
-  }
+    /**
+     * Gets the value of the original property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getOriginal() {
+        return original;
+    }
 
-  /**
-   * Sets the value of the original property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setOriginal(String value)
-  {
-    this.original = value;
-  }
+    /**
+     * Sets the value of the original property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setOriginal(String value) {
+        this.original = value;
+    }
 
-  /**
-   * Gets the value of the variation 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 variation property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getVariation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getVariation()
-  {
-    if (variation == null)
-    {
-      variation = new ArrayList();
+    /**
+     * Gets the value of the variation 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 variation property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getVariation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getVariation() {
+        if (variation == null) {
+            variation = new ArrayList();
+        }
+        return this.variation;
     }
-    return this.variation;
-  }
 
-  /**
-   * Gets the value of the location property.
-   * 
-   * @return possible object is {@link LocationType }
-   * 
-   */
-  public LocationType getLocation()
-  {
-    return location;
-  }
+    /**
+     * Gets the value of the location property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link LocationType }
+     *     
+     */
+    public LocationType getLocation() {
+        return location;
+    }
 
-  /**
-   * Sets the value of the location property.
-   * 
-   * @param value
-   *          allowed object is {@link LocationType }
-   * 
-   */
-  public void setLocation(LocationType value)
-  {
-    this.location = value;
-  }
+    /**
+     * Sets the value of the location property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link LocationType }
+     *     
+     */
+    public void setLocation(LocationType value) {
+        this.location = value;
+    }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        return status;
+    }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
 
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the ref property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getRef()
-  {
-    return ref;
-  }
+    /**
+     * Gets the value of the ref property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getRef() {
+        return ref;
+    }
 
-  /**
-   * Sets the value of the ref property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setRef(String value)
-  {
-    this.ref = value;
-  }
+    /**
+     * Sets the value of the ref property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setRef(String value) {
+        this.ref = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java
index 33f0bfd..9a04acc 100644
--- a/src/jalview/xml/binding/uniprot/GeneLocationType.java
+++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
- * the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids).
+ *             Equivalent to the flat file OG-line.
  * 
- * 
    
- * Java class for geneLocationType complex type.
+ * 
    Java class for geneLocationType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="geneLocationType">
@@ -57,102 +56,97 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = { "name" })
-public class GeneLocationType
-{
-
-  protected List name;
+@XmlType(name = "geneLocationType", propOrder = {
+    "name"
+})
+public class GeneLocationType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    protected List name;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  /**
-   * Gets the value of the name 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 name property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link StatusType
-   * }
-   * 
-   * 
-   */
-  public List getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList();
+    /**
+     * Gets the value of the name 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 name property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getName().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link StatusType }
+     * 
+     * 
+     */
+    public List getName() {
+        if (name == null) {
+            name = new ArrayList();
+        }
+        return this.name;
     }
-    return this.name;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java
index 84850d3..8b69d3d 100644
--- a/src/jalview/xml/binding/uniprot/GeneNameType.java
+++ b/src/jalview/xml/binding/uniprot/GeneNameType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * Describes different types of gene designations. Equivalent to the flat file
- * GN-line.
+ * Describes different types of gene designations.
+ *             Equivalent to the flat file GN-line.
  * 
- * 
    
- * Java class for geneNameType complex type.
+ * 
    Java class for geneNameType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="geneNameType">
@@ -49,94 +48,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = { "value" })
-public class GeneNameType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+@XmlType(name = "geneNameType", propOrder = {
+    "value"
+})
+public class GeneNameType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java
index 0b0a19e..24285cb 100644
--- a/src/jalview/xml/binding/uniprot/GeneType.java
+++ b/src/jalview/xml/binding/uniprot/GeneType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,15 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a gene. Equivalent to the flat file GN-line.
+ * Describes a gene.
+ *             Equivalent to the flat file GN-line.
  * 
- * 
    
- * Java class for geneType complex type.
+ * 
    Java class for geneType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="geneType">
@@ -39,43 +39,41 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = { "name" })
-public class GeneType
-{
+@XmlType(name = "geneType", propOrder = {
+    "name"
+})
+public class GeneType {
 
-  @XmlElement(required = true)
-  protected List name;
+    @XmlElement(required = true)
+    protected List name;
 
-  /**
-   * Gets the value of the name 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 name property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link GeneNameType }
-   * 
-   * 
-   */
-  public List getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList();
+    /**
+     * Gets the value of the name 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 name property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getName().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link GeneNameType }
+     * 
+     * 
+     */
+    public List getName() {
+        if (name == null) {
+            name = new ArrayList();
+        }
+        return this.name;
     }
-    return this.name;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java
index f46afb5..070e48e 100644
--- a/src/jalview/xml/binding/uniprot/ImportedFromType.java
+++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the source of the evidence, when it is not assigned by UniProt, but
- * imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
  * 
- * 
    
- * Java class for importedFromType complex type.
+ * 
    Java class for importedFromType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="importedFromType">
@@ -38,34 +36,36 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = { "dbReference" })
-public class ImportedFromType
-{
+@XmlType(name = "importedFromType", propOrder = {
+    "dbReference"
+})
+public class ImportedFromType {
 
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java
index 0e59c4b..9a0e97a 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for interactantType complex type.
+ * 
    Java class for interactantType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="interactantType">
@@ -34,84 +33,87 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = { "id", "label" })
-public class InteractantType
-{
-
-  protected String id;
-
-  protected String label;
+@XmlType(name = "interactantType", propOrder = {
+    "id",
+    "label"
+})
+public class InteractantType {
 
-  @XmlAttribute(name = "intactId", required = true)
-  protected String intactId;
+    protected String id;
+    protected String label;
+    @XmlAttribute(name = "intactId", required = true)
+    protected String intactId;
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
-  /**
-   * Gets the value of the label property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLabel()
-  {
-    return label;
-  }
+    /**
+     * Gets the value of the label property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLabel() {
+        return label;
+    }
 
-  /**
-   * Sets the value of the label property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLabel(String value)
-  {
-    this.label = value;
-  }
+    /**
+     * Sets the value of the label property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLabel(String value) {
+        this.label = value;
+    }
 
-  /**
-   * Gets the value of the intactId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getIntactId()
-  {
-    return intactId;
-  }
+    /**
+     * Gets the value of the intactId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getIntactId() {
+        return intactId;
+    }
 
-  /**
-   * Sets the value of the intactId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setIntactId(String value)
-  {
-    this.intactId = value;
-  }
+    /**
+     * Sets the value of the intactId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setIntactId(String value) {
+        this.intactId = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java
index 631ab01..33710ef 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,15 +17,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes isoforms in 'alternative products' annotations.
  * 
- * 
    
- * Java class for isoformType complex type.
+ * 
    Java class for isoformType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="isoformType">
@@ -70,316 +69,302 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "isoformType",
-  propOrder =
-  { "id", "name", "sequence", "text" })
-public class IsoformType
-{
-
-  @XmlElement(required = true)
-  protected List id;
-
-  @XmlElement(required = true)
-  protected List name;
-
-  @XmlElement(required = true)
-  protected IsoformType.Sequence sequence;
-
-  protected List text;
-
-  /**
-   * Gets the value of the id 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 id property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getId().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getId()
-  {
-    if (id == null)
-    {
-      id = new ArrayList();
-    }
-    return this.id;
-  }
-
-  /**
-   * Gets the value of the name 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 name property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link IsoformType.Name }
-   * 
-   * 
-   */
-  public List getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList();
-    }
-    return this.name;
-  }
+@XmlType(name = "isoformType", propOrder = {
+    "id",
+    "name",
+    "sequence",
+    "text"
+})
+public class IsoformType {
 
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link IsoformType.Sequence }
-   * 
-   */
-  public IsoformType.Sequence getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link IsoformType.Sequence }
-   * 
-   */
-  public void setSequence(IsoformType.Sequence value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the text 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 text property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getText().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getText()
-  {
-    if (text == null)
-    {
-      text = new ArrayList();
-    }
-    return this.text;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <simpleContent>
-   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     </extension>
-   *   </simpleContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Name
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+    @XmlElement(required = true)
+    protected List id;
+    @XmlElement(required = true)
+    protected List name;
+    @XmlElement(required = true)
+    protected IsoformType.Sequence sequence;
+    protected List text;
 
     /**
-     * Gets the value of the value property.
+     * Gets the value of the id property.
      * 
-     * @return possible object is {@link String }
+     * 
    
+     * 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 id property.
      * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
-
-    /**
-     * Sets the value of the value property.
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getId().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public List getId() {
+        if (id == null) {
+            id = new ArrayList();
+        }
+        return this.id;
     }
 
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the name 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 evidence 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 name property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getEvidence().add(newItem);
+     *    getName().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * Objects of the following type(s) are allowed in the list
+     * {@link IsoformType.Name }
      * 
      * 
      */
-    public List getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList();
-      }
-      return this.evidence;
+    public List getName() {
+        if (name == null) {
+            name = new ArrayList();
+        }
+        return this.name;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="type" use="required">
-   *         <simpleType>
-   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-   *             <enumeration value="not described"/>
-   *             <enumeration value="described"/>
-   *             <enumeration value="displayed"/>
-   *             <enumeration value="external"/>
-   *           </restriction>
-   *         </simpleType>
-   *       </attribute>
-   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Sequence
-  {
-
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-
-    @XmlAttribute(name = "ref")
-    protected String ref;
-
     /**
-     * Gets the value of the type property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the sequence property.
      * 
+     * @return
+     *     possible object is
+     *     {@link IsoformType.Sequence }
+     *     
      */
-    public String getType()
-    {
-      return type;
+    public IsoformType.Sequence getSequence() {
+        return sequence;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the sequence property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link IsoformType.Sequence }
+     *     
      */
-    public void setType(String value)
-    {
-      this.type = value;
+    public void setSequence(IsoformType.Sequence value) {
+        this.sequence = value;
     }
 
     /**
-     * Gets the value of the ref property.
+     * Gets the value of the text 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 text property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getText().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getRef()
-    {
-      return ref;
+    public List getText() {
+        if (text == null) {
+            text = new ArrayList();
+        }
+        return this.text;
     }
 
+
     /**
-     * Sets the value of the ref property.
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <simpleContent>
+     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     </extension>
+     *   </simpleContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setRef(String value)
-    {
-      this.ref = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Name {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence 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 evidence property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEvidence().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList();
+            }
+            return this.evidence;
+        }
+
     }
 
-  }
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="type" use="required">
+     *         <simpleType>
+     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             <enumeration value="not described"/>
+     *             <enumeration value="described"/>
+     *             <enumeration value="displayed"/>
+     *             <enumeration value="external"/>
+     *           </restriction>
+     *         </simpleType>
+     *       </attribute>
+     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Sequence {
+
+        @XmlAttribute(name = "type", required = true)
+        protected String type;
+        @XmlAttribute(name = "ref")
+        protected String ref;
+
+        /**
+         * Gets the value of the type property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getType() {
+            return type;
+        }
+
+        /**
+         * Sets the value of the type property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setType(String value) {
+            this.type = value;
+        }
+
+        /**
+         * Gets the value of the ref property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRef() {
+            return ref;
+        }
+
+        /**
+         * Sets the value of the ref property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRef(String value) {
+            this.ref = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java
index ac58dfd..3f1a75f 100644
--- a/src/jalview/xml/binding/uniprot/KeywordType.java
+++ b/src/jalview/xml/binding/uniprot/KeywordType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * 
    
- * Java class for keywordType complex type.
+ * 
    Java class for keywordType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="keywordType">
@@ -37,94 +36,93 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = { "value" })
-public class KeywordType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+@XmlType(name = "keywordType", propOrder = {
+    "value"
+})
+public class KeywordType {
 
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java
index d1d1457..5d7e7e9 100644
--- a/src/jalview/xml/binding/uniprot/LocationType.java
+++ b/src/jalview/xml/binding/uniprot/LocationType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,17 +13,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a sequence location as either a range with a begin and end or as a
- * position. The 'sequence' attribute is only used when the location is not on
- * the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
  * 
- * 
    
- * Java class for locationType complex type.
+ * 
    Java class for locationType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="locationType">
@@ -44,109 +41,113 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
-public class LocationType
-{
-
-  protected PositionType begin;
-
-  protected PositionType end;
-
-  protected PositionType position;
-
-  @XmlAttribute(name = "sequence")
-  protected String sequence;
-
-  /**
-   * Gets the value of the begin property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getBegin()
-  {
-    return begin;
-  }
-
-  /**
-   * Sets the value of the begin property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setBegin(PositionType value)
-  {
-    this.begin = value;
-  }
-
-  /**
-   * Gets the value of the end property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getEnd()
-  {
-    return end;
-  }
-
-  /**
-   * Sets the value of the end property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setEnd(PositionType value)
-  {
-    this.end = value;
-  }
-
-  /**
-   * Gets the value of the position property.
-   * 
-   * @return possible object is {@link PositionType }
-   * 
-   */
-  public PositionType getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   * @param value
-   *          allowed object is {@link PositionType }
-   * 
-   */
-  public void setPosition(PositionType value)
-  {
-    this.position = value;
-  }
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
+@XmlType(name = "locationType", propOrder = {
+    "begin",
+    "end",
+    "position"
+})
+public class LocationType {
+
+    protected PositionType begin;
+    protected PositionType end;
+    protected PositionType position;
+    @XmlAttribute(name = "sequence")
+    protected String sequence;
+
+    /**
+     * Gets the value of the begin property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getBegin() {
+        return begin;
+    }
+
+    /**
+     * Sets the value of the begin property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setBegin(PositionType value) {
+        this.begin = value;
+    }
+
+    /**
+     * Gets the value of the end property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getEnd() {
+        return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setEnd(PositionType value) {
+        this.end = value;
+    }
+
+    /**
+     * Gets the value of the position property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link PositionType }
+     *     
+     */
+    public PositionType getPosition() {
+        return position;
+    }
+
+    /**
+     * Sets the value of the position property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link PositionType }
+     *     
+     */
+    public void setPosition(PositionType value) {
+        this.position = value;
+    }
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java
index 72f6c4f..b7657f8 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes a molecule by name or unique identifier.
  * 
- * 
    
- * Java class for moleculeType complex type.
+ * 
    Java class for moleculeType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="moleculeType">
@@ -36,60 +35,62 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = { "value" })
-public class MoleculeType
-{
-
-  @XmlValue
-  protected String value;
+@XmlType(name = "moleculeType", propOrder = {
+    "value"
+})
+public class MoleculeType {
 
-  @XmlAttribute(name = "id")
-  protected String id;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "id")
+    protected String id;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java
index 947f2f4..c316941 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for nameListType complex type.
+ * 
    Java class for nameListType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="nameListType">
@@ -39,45 +38,45 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
-public class NameListType
-{
+@XmlType(name = "nameListType", propOrder = {
+    "consortiumOrPerson"
+})
+public class NameListType {
 
-  @XmlElements({
-      @XmlElement(name = "consortium", type = ConsortiumType.class),
-      @XmlElement(name = "person", type = PersonType.class) })
-  protected List consortiumOrPerson;
+    @XmlElements({
+        @XmlElement(name = "consortium", type = ConsortiumType.class),
+        @XmlElement(name = "person", type = PersonType.class)
+    })
+    protected List consortiumOrPerson;
 
-  /**
-   * Gets the value of the consortiumOrPerson 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 consortiumOrPerson property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getConsortiumOrPerson().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ConsortiumType } {@link PersonType }
-   * 
-   * 
-   */
-  public List getConsortiumOrPerson()
-  {
-    if (consortiumOrPerson == null)
-    {
-      consortiumOrPerson = new ArrayList();
+    /**
+     * Gets the value of the consortiumOrPerson 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 consortiumOrPerson property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getConsortiumOrPerson().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link ConsortiumType }
+     * {@link PersonType }
+     * 
+     * 
+     */
+    public List getConsortiumOrPerson() {
+        if (consortiumOrPerson == null) {
+            consortiumOrPerson = new ArrayList();
+        }
+        return this.consortiumOrPerson;
     }
-    return this.consortiumOrPerson;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java
index a647bd0..324ef9f 100644
--- a/src/jalview/xml/binding/uniprot/ObjectFactory.java
+++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.JAXBElement;
@@ -12,558 +13,496 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
+
 /**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.uniprot package.
- * 
    
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.uniprot package. 
+ * 
    An ObjectFactory allows you to programatically 
+ * construct new instances of the Java representation 
+ * for XML content. The Java representation of XML 
+ * content can consist of schema derived interfaces 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory
-{
-
-  private final static QName _Copyright_QNAME = new QName(
-          "http://uniprot.org/uniprot", "copyright");
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.uniprot
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType }
-   * 
-   */
-  public SourceDataType createSourceDataType()
-  {
-    return new SourceDataType();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType }
-   * 
-   */
-  public IsoformType createIsoformType()
-  {
-    return new IsoformType();
-  }
-
-  /**
-   * Create an instance of {@link CommentType }
-   * 
-   */
-  public CommentType createCommentType()
-  {
-    return new CommentType();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Conflict }
-   * 
-   */
-  public CommentType.Conflict createCommentTypeConflict()
-  {
-    return new CommentType.Conflict();
-  }
-
-  /**
-   * Create an instance of {@link OrganismType }
-   * 
-   */
-  public OrganismType createOrganismType()
-  {
-    return new OrganismType();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType }
-   * 
-   */
-  public ProteinType createProteinType()
-  {
-    return new ProteinType();
-  }
-
-  /**
-   * Create an instance of {@link Entry }
-   * 
-   */
-  public Entry createEntry()
-  {
-    return new Entry();
-  }
-
-  /**
-   * Create an instance of {@link GeneType }
-   * 
-   */
-  public GeneType createGeneType()
-  {
-    return new GeneType();
-  }
-
-  /**
-   * Create an instance of {@link GeneLocationType }
-   * 
-   */
-  public GeneLocationType createGeneLocationType()
-  {
-    return new GeneLocationType();
-  }
-
-  /**
-   * Create an instance of {@link ReferenceType }
-   * 
-   */
-  public ReferenceType createReferenceType()
-  {
-    return new ReferenceType();
-  }
-
-  /**
-   * Create an instance of {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType createDbReferenceType()
-  {
-    return new DbReferenceType();
-  }
-
-  /**
-   * Create an instance of {@link ProteinExistenceType }
-   * 
-   */
-  public ProteinExistenceType createProteinExistenceType()
-  {
-    return new ProteinExistenceType();
-  }
-
-  /**
-   * Create an instance of {@link KeywordType }
-   * 
-   */
-  public KeywordType createKeywordType()
-  {
-    return new KeywordType();
-  }
-
-  /**
-   * Create an instance of {@link FeatureType }
-   * 
-   */
-  public FeatureType createFeatureType()
-  {
-    return new FeatureType();
-  }
-
-  /**
-   * Create an instance of {@link EvidenceType }
-   * 
-   */
-  public EvidenceType createEvidenceType()
-  {
-    return new EvidenceType();
-  }
-
-  /**
-   * Create an instance of {@link SequenceType }
-   * 
-   */
-  public SequenceType createSequenceType()
-  {
-    return new SequenceType();
-  }
-
-  /**
-   * Create an instance of {@link Uniprot }
-   * 
-   */
-  public Uniprot createUniprot()
-  {
-    return new Uniprot();
-  }
-
-  /**
-   * Create an instance of {@link StatusType }
-   * 
-   */
-  public StatusType createStatusType()
-  {
-    return new StatusType();
-  }
-
-  /**
-   * Create an instance of {@link PositionType }
-   * 
-   */
-  public PositionType createPositionType()
-  {
-    return new PositionType();
-  }
-
-  /**
-   * Create an instance of {@link ConsortiumType }
-   * 
-   */
-  public ConsortiumType createConsortiumType()
-  {
-    return new ConsortiumType();
-  }
-
-  /**
-   * Create an instance of {@link GeneNameType }
-   * 
-   */
-  public GeneNameType createGeneNameType()
-  {
-    return new GeneNameType();
-  }
-
-  /**
-   * Create an instance of {@link LocationType }
-   * 
-   */
-  public LocationType createLocationType()
-  {
-    return new LocationType();
-  }
-
-  /**
-   * Create an instance of {@link CitationType }
-   * 
-   */
-  public CitationType createCitationType()
-  {
-    return new CitationType();
-  }
-
-  /**
-   * Create an instance of {@link PropertyType }
-   * 
-   */
-  public PropertyType createPropertyType()
-  {
-    return new PropertyType();
-  }
-
-  /**
-   * Create an instance of {@link PhysiologicalReactionType }
-   * 
-   */
-  public PhysiologicalReactionType createPhysiologicalReactionType()
-  {
-    return new PhysiologicalReactionType();
-  }
-
-  /**
-   * Create an instance of {@link CofactorType }
-   * 
-   */
-  public CofactorType createCofactorType()
-  {
-    return new CofactorType();
-  }
-
-  /**
-   * Create an instance of {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType createEvidencedStringType()
-  {
-    return new EvidencedStringType();
-  }
-
-  /**
-   * Create an instance of {@link PersonType }
-   * 
-   */
-  public PersonType createPersonType()
-  {
-    return new PersonType();
-  }
-
-  /**
-   * Create an instance of {@link ImportedFromType }
-   * 
-   */
-  public ImportedFromType createImportedFromType()
-  {
-    return new ImportedFromType();
-  }
-
-  /**
-   * Create an instance of {@link EventType }
-   * 
-   */
-  public EventType createEventType()
-  {
-    return new EventType();
-  }
-
-  /**
-   * Create an instance of {@link InteractantType }
-   * 
-   */
-  public InteractantType createInteractantType()
-  {
-    return new InteractantType();
-  }
-
-  /**
-   * Create an instance of {@link NameListType }
-   * 
-   */
-  public NameListType createNameListType()
-  {
-    return new NameListType();
-  }
-
-  /**
-   * Create an instance of {@link ReactionType }
-   * 
-   */
-  public ReactionType createReactionType()
-  {
-    return new ReactionType();
-  }
-
-  /**
-   * Create an instance of {@link SourceType }
-   * 
-   */
-  public SourceType createSourceType()
-  {
-    return new SourceType();
-  }
-
-  /**
-   * Create an instance of {@link MoleculeType }
-   * 
-   */
-  public MoleculeType createMoleculeType()
-  {
-    return new MoleculeType();
-  }
-
-  /**
-   * Create an instance of {@link OrganismNameType }
-   * 
-   */
-  public OrganismNameType createOrganismNameType()
-  {
-    return new OrganismNameType();
-  }
-
-  /**
-   * Create an instance of {@link SubcellularLocationType }
-   * 
-   */
-  public SubcellularLocationType createSubcellularLocationType()
-  {
-    return new SubcellularLocationType();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Strain }
-   * 
-   */
-  public SourceDataType.Strain createSourceDataTypeStrain()
-  {
-    return new SourceDataType.Strain();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Plasmid }
-   * 
-   */
-  public SourceDataType.Plasmid createSourceDataTypePlasmid()
-  {
-    return new SourceDataType.Plasmid();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Transposon }
-   * 
-   */
-  public SourceDataType.Transposon createSourceDataTypeTransposon()
-  {
-    return new SourceDataType.Transposon();
-  }
-
-  /**
-   * Create an instance of {@link SourceDataType.Tissue }
-   * 
-   */
-  public SourceDataType.Tissue createSourceDataTypeTissue()
-  {
-    return new SourceDataType.Tissue();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType.Name }
-   * 
-   */
-  public IsoformType.Name createIsoformTypeName()
-  {
-    return new IsoformType.Name();
-  }
-
-  /**
-   * Create an instance of {@link IsoformType.Sequence }
-   * 
-   */
-  public IsoformType.Sequence createIsoformTypeSequence()
-  {
-    return new IsoformType.Sequence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Absorption }
-   * 
-   */
-  public CommentType.Absorption createCommentTypeAbsorption()
-  {
-    return new CommentType.Absorption();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Kinetics }
-   * 
-   */
-  public CommentType.Kinetics createCommentTypeKinetics()
-  {
-    return new CommentType.Kinetics();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.PhDependence }
-   * 
-   */
-  public CommentType.PhDependence createCommentTypePhDependence()
-  {
-    return new CommentType.PhDependence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.RedoxPotential }
-   * 
-   */
-  public CommentType.RedoxPotential createCommentTypeRedoxPotential()
-  {
-    return new CommentType.RedoxPotential();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.TemperatureDependence }
-   * 
-   */
-  public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
-  {
-    return new CommentType.TemperatureDependence();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Link }
-   * 
-   */
-  public CommentType.Link createCommentTypeLink()
-  {
-    return new CommentType.Link();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Disease }
-   * 
-   */
-  public CommentType.Disease createCommentTypeDisease()
-  {
-    return new CommentType.Disease();
-  }
-
-  /**
-   * Create an instance of {@link CommentType.Conflict.Sequence }
-   * 
-   */
-  public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
-  {
-    return new CommentType.Conflict.Sequence();
-  }
-
-  /**
-   * Create an instance of {@link OrganismType.Lineage }
-   * 
-   */
-  public OrganismType.Lineage createOrganismTypeLineage()
-  {
-    return new OrganismType.Lineage();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.RecommendedName }
-   * 
-   */
-  public ProteinType.RecommendedName createProteinTypeRecommendedName()
-  {
-    return new ProteinType.RecommendedName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.AlternativeName }
-   * 
-   */
-  public ProteinType.AlternativeName createProteinTypeAlternativeName()
-  {
-    return new ProteinType.AlternativeName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.SubmittedName }
-   * 
-   */
-  public ProteinType.SubmittedName createProteinTypeSubmittedName()
-  {
-    return new ProteinType.SubmittedName();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.Domain }
-   * 
-   */
-  public ProteinType.Domain createProteinTypeDomain()
-  {
-    return new ProteinType.Domain();
-  }
-
-  /**
-   * Create an instance of {@link ProteinType.Component }
-   * 
-   */
-  public ProteinType.Component createProteinTypeComponent()
-  {
-    return new ProteinType.Component();
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement }{@code <}{@link String
-   * }{@code >}}
-   * 
-   */
-  @XmlElementDecl(
-    namespace = "http://uniprot.org/uniprot",
-    name = "copyright")
-  public JAXBElement createCopyright(String value)
-  {
-    return new JAXBElement(_Copyright_QNAME, String.class, null,
-            value);
-  }
+public class ObjectFactory {
+
+    private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType }
+     * 
+     */
+    public SourceDataType createSourceDataType() {
+        return new SourceDataType();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType }
+     * 
+     */
+    public IsoformType createIsoformType() {
+        return new IsoformType();
+    }
+
+    /**
+     * Create an instance of {@link CommentType }
+     * 
+     */
+    public CommentType createCommentType() {
+        return new CommentType();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Conflict }
+     * 
+     */
+    public CommentType.Conflict createCommentTypeConflict() {
+        return new CommentType.Conflict();
+    }
+
+    /**
+     * Create an instance of {@link OrganismType }
+     * 
+     */
+    public OrganismType createOrganismType() {
+        return new OrganismType();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType }
+     * 
+     */
+    public ProteinType createProteinType() {
+        return new ProteinType();
+    }
+
+    /**
+     * Create an instance of {@link Entry }
+     * 
+     */
+    public Entry createEntry() {
+        return new Entry();
+    }
+
+    /**
+     * Create an instance of {@link GeneType }
+     * 
+     */
+    public GeneType createGeneType() {
+        return new GeneType();
+    }
+
+    /**
+     * Create an instance of {@link GeneLocationType }
+     * 
+     */
+    public GeneLocationType createGeneLocationType() {
+        return new GeneLocationType();
+    }
+
+    /**
+     * Create an instance of {@link ReferenceType }
+     * 
+     */
+    public ReferenceType createReferenceType() {
+        return new ReferenceType();
+    }
+
+    /**
+     * Create an instance of {@link DbReferenceType }
+     * 
+     */
+    public DbReferenceType createDbReferenceType() {
+        return new DbReferenceType();
+    }
+
+    /**
+     * Create an instance of {@link ProteinExistenceType }
+     * 
+     */
+    public ProteinExistenceType createProteinExistenceType() {
+        return new ProteinExistenceType();
+    }
+
+    /**
+     * Create an instance of {@link KeywordType }
+     * 
+     */
+    public KeywordType createKeywordType() {
+        return new KeywordType();
+    }
+
+    /**
+     * Create an instance of {@link FeatureType }
+     * 
+     */
+    public FeatureType createFeatureType() {
+        return new FeatureType();
+    }
+
+    /**
+     * Create an instance of {@link EvidenceType }
+     * 
+     */
+    public EvidenceType createEvidenceType() {
+        return new EvidenceType();
+    }
+
+    /**
+     * Create an instance of {@link SequenceType }
+     * 
+     */
+    public SequenceType createSequenceType() {
+        return new SequenceType();
+    }
+
+    /**
+     * Create an instance of {@link Uniprot }
+     * 
+     */
+    public Uniprot createUniprot() {
+        return new Uniprot();
+    }
+
+    /**
+     * Create an instance of {@link StatusType }
+     * 
+     */
+    public StatusType createStatusType() {
+        return new StatusType();
+    }
+
+    /**
+     * Create an instance of {@link PositionType }
+     * 
+     */
+    public PositionType createPositionType() {
+        return new PositionType();
+    }
+
+    /**
+     * Create an instance of {@link ConsortiumType }
+     * 
+     */
+    public ConsortiumType createConsortiumType() {
+        return new ConsortiumType();
+    }
+
+    /**
+     * Create an instance of {@link GeneNameType }
+     * 
+     */
+    public GeneNameType createGeneNameType() {
+        return new GeneNameType();
+    }
+
+    /**
+     * Create an instance of {@link LocationType }
+     * 
+     */
+    public LocationType createLocationType() {
+        return new LocationType();
+    }
+
+    /**
+     * Create an instance of {@link CitationType }
+     * 
+     */
+    public CitationType createCitationType() {
+        return new CitationType();
+    }
+
+    /**
+     * Create an instance of {@link PropertyType }
+     * 
+     */
+    public PropertyType createPropertyType() {
+        return new PropertyType();
+    }
+
+    /**
+     * Create an instance of {@link PhysiologicalReactionType }
+     * 
+     */
+    public PhysiologicalReactionType createPhysiologicalReactionType() {
+        return new PhysiologicalReactionType();
+    }
+
+    /**
+     * Create an instance of {@link CofactorType }
+     * 
+     */
+    public CofactorType createCofactorType() {
+        return new CofactorType();
+    }
+
+    /**
+     * Create an instance of {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType createEvidencedStringType() {
+        return new EvidencedStringType();
+    }
+
+    /**
+     * Create an instance of {@link PersonType }
+     * 
+     */
+    public PersonType createPersonType() {
+        return new PersonType();
+    }
+
+    /**
+     * Create an instance of {@link ImportedFromType }
+     * 
+     */
+    public ImportedFromType createImportedFromType() {
+        return new ImportedFromType();
+    }
+
+    /**
+     * Create an instance of {@link EventType }
+     * 
+     */
+    public EventType createEventType() {
+        return new EventType();
+    }
+
+    /**
+     * Create an instance of {@link InteractantType }
+     * 
+     */
+    public InteractantType createInteractantType() {
+        return new InteractantType();
+    }
+
+    /**
+     * Create an instance of {@link NameListType }
+     * 
+     */
+    public NameListType createNameListType() {
+        return new NameListType();
+    }
+
+    /**
+     * Create an instance of {@link ReactionType }
+     * 
+     */
+    public ReactionType createReactionType() {
+        return new ReactionType();
+    }
+
+    /**
+     * Create an instance of {@link SourceType }
+     * 
+     */
+    public SourceType createSourceType() {
+        return new SourceType();
+    }
+
+    /**
+     * Create an instance of {@link MoleculeType }
+     * 
+     */
+    public MoleculeType createMoleculeType() {
+        return new MoleculeType();
+    }
+
+    /**
+     * Create an instance of {@link OrganismNameType }
+     * 
+     */
+    public OrganismNameType createOrganismNameType() {
+        return new OrganismNameType();
+    }
+
+    /**
+     * Create an instance of {@link SubcellularLocationType }
+     * 
+     */
+    public SubcellularLocationType createSubcellularLocationType() {
+        return new SubcellularLocationType();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Strain }
+     * 
+     */
+    public SourceDataType.Strain createSourceDataTypeStrain() {
+        return new SourceDataType.Strain();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Plasmid }
+     * 
+     */
+    public SourceDataType.Plasmid createSourceDataTypePlasmid() {
+        return new SourceDataType.Plasmid();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Transposon }
+     * 
+     */
+    public SourceDataType.Transposon createSourceDataTypeTransposon() {
+        return new SourceDataType.Transposon();
+    }
+
+    /**
+     * Create an instance of {@link SourceDataType.Tissue }
+     * 
+     */
+    public SourceDataType.Tissue createSourceDataTypeTissue() {
+        return new SourceDataType.Tissue();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType.Name }
+     * 
+     */
+    public IsoformType.Name createIsoformTypeName() {
+        return new IsoformType.Name();
+    }
+
+    /**
+     * Create an instance of {@link IsoformType.Sequence }
+     * 
+     */
+    public IsoformType.Sequence createIsoformTypeSequence() {
+        return new IsoformType.Sequence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Absorption }
+     * 
+     */
+    public CommentType.Absorption createCommentTypeAbsorption() {
+        return new CommentType.Absorption();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Kinetics }
+     * 
+     */
+    public CommentType.Kinetics createCommentTypeKinetics() {
+        return new CommentType.Kinetics();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.PhDependence }
+     * 
+     */
+    public CommentType.PhDependence createCommentTypePhDependence() {
+        return new CommentType.PhDependence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.RedoxPotential }
+     * 
+     */
+    public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
+        return new CommentType.RedoxPotential();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.TemperatureDependence }
+     * 
+     */
+    public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
+        return new CommentType.TemperatureDependence();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Link }
+     * 
+     */
+    public CommentType.Link createCommentTypeLink() {
+        return new CommentType.Link();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Disease }
+     * 
+     */
+    public CommentType.Disease createCommentTypeDisease() {
+        return new CommentType.Disease();
+    }
+
+    /**
+     * Create an instance of {@link CommentType.Conflict.Sequence }
+     * 
+     */
+    public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
+        return new CommentType.Conflict.Sequence();
+    }
+
+    /**
+     * Create an instance of {@link OrganismType.Lineage }
+     * 
+     */
+    public OrganismType.Lineage createOrganismTypeLineage() {
+        return new OrganismType.Lineage();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.RecommendedName }
+     * 
+     */
+    public ProteinType.RecommendedName createProteinTypeRecommendedName() {
+        return new ProteinType.RecommendedName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.AlternativeName }
+     * 
+     */
+    public ProteinType.AlternativeName createProteinTypeAlternativeName() {
+        return new ProteinType.AlternativeName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.SubmittedName }
+     * 
+     */
+    public ProteinType.SubmittedName createProteinTypeSubmittedName() {
+        return new ProteinType.SubmittedName();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.Domain }
+     * 
+     */
+    public ProteinType.Domain createProteinTypeDomain() {
+        return new ProteinType.Domain();
+    }
+
+    /**
+     * Create an instance of {@link ProteinType.Component }
+     * 
+     */
+    public ProteinType.Component createProteinTypeComponent() {
+        return new ProteinType.Component();
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
+    public JAXBElement createCopyright(String value) {
+        return new JAXBElement(_Copyright_QNAME, String.class, null, value);
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java
index 5668759..5e82f4f 100644
--- a/src/jalview/xml/binding/uniprot/OrganismNameType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Describes different types of source organism names.
  * 
- * 
    
- * Java class for organismNameType complex type.
+ * 
    Java class for organismNameType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="organismNameType">
@@ -46,60 +45,62 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = { "value" })
-public class OrganismNameType
-{
-
-  @XmlValue
-  protected String value;
+@XmlType(name = "organismNameType", propOrder = {
+    "value"
+})
+public class OrganismNameType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java
index e53de4c..ca8ad97 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes the source organism.
  * 
- * 
    
- * Java class for organismType complex type.
+ * 
    Java class for organismType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="organismType">
@@ -53,203 +52,190 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "organismType",
-  propOrder =
-  { "name", "dbReference", "lineage" })
-public class OrganismType
-{
-
-  @XmlElement(required = true)
-  protected List name;
-
-  @XmlElement(required = true)
-  protected List dbReference;
-
-  protected OrganismType.Lineage lineage;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  /**
-   * Gets the value of the name 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 name property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link OrganismNameType }
-   * 
-   * 
-   */
-  public List getName()
-  {
-    if (name == null)
-    {
-      name = new ArrayList();
+@XmlType(name = "organismType", propOrder = {
+    "name",
+    "dbReference",
+    "lineage"
+})
+public class OrganismType {
+
+    @XmlElement(required = true)
+    protected List name;
+    @XmlElement(required = true)
+    protected List dbReference;
+    protected OrganismType.Lineage lineage;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+
+    /**
+     * Gets the value of the name 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 name property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getName().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link OrganismNameType }
+     * 
+     * 
+     */
+    public List getName() {
+        if (name == null) {
+            name = new ArrayList();
+        }
+        return this.name;
     }
-    return this.name;
-  }
-
-  /**
-   * Gets the value of the dbReference 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 dbReference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getDbReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList();
+
+    /**
+     * Gets the value of the dbReference 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 dbReference property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getDbReference().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList();
+        }
+        return this.dbReference;
     }
-    return this.dbReference;
-  }
-
-  /**
-   * Gets the value of the lineage property.
-   * 
-   * @return possible object is {@link OrganismType.Lineage }
-   * 
-   */
-  public OrganismType.Lineage getLineage()
-  {
-    return lineage;
-  }
-
-  /**
-   * Sets the value of the lineage property.
-   * 
-   * @param value
-   *          allowed object is {@link OrganismType.Lineage }
-   * 
-   */
-  public void setLineage(OrganismType.Lineage value)
-  {
-    this.lineage = value;
-  }
-
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+
+    /**
+     * Gets the value of the lineage property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link OrganismType.Lineage }
+     *     
+     */
+    public OrganismType.Lineage getLineage() {
+        return lineage;
     }
-    return this.evidence;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "taxon" })
-  public static class Lineage
-  {
 
-    @XmlElement(required = true)
-    protected List taxon;
+    /**
+     * Sets the value of the lineage property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link OrganismType.Lineage }
+     *     
+     */
+    public void setLineage(OrganismType.Lineage value) {
+        this.lineage = value;
+    }
 
     /**
-     * Gets the value of the taxon property.
+     * Gets the value of the evidence 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 taxon 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 evidence property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getTaxon().add(newItem);
+     *    getEvidence().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list {@link String }
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
      * 
      * 
      */
-    public List getTaxon()
-    {
-      if (taxon == null)
-      {
-        taxon = new ArrayList();
-      }
-      return this.taxon;
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
 
-  }
+
+    /**
+     * 
    Java class for anonymous complex type.
+     * 
+     * 
    The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
    
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "taxon"
+    })
+    public static class Lineage {
+
+        @XmlElement(required = true)
+        protected List taxon;
+
+        /**
+         * Gets the value of the taxon 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 taxon property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getTaxon().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getTaxon() {
+            if (taxon == null) {
+                taxon = new ArrayList();
+            }
+            return this.taxon;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java
index ebbb691..4639054 100644
--- a/src/jalview/xml/binding/uniprot/PersonType.java
+++ b/src/jalview/xml/binding/uniprot/PersonType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for personType complex type.
+ * 
    Java class for personType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="personType">
@@ -34,33 +33,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "personType")
-public class PersonType
-{
+public class PersonType {
 
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
index 95298e4..b01e412 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a physiological reaction.
  * 
- * 
    
- * Java class for physiologicalReactionType complex type.
+ * 
    Java class for physiologicalReactionType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="physiologicalReactionType">
@@ -49,94 +48,93 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
-public class PhysiologicalReactionType
-{
-
-  @XmlElement(required = true)
-  protected DbReferenceType dbReference;
-
-  @XmlAttribute(name = "direction", required = true)
-  protected String direction;
+@XmlType(name = "physiologicalReactionType", propOrder = {
+    "dbReference"
+})
+public class PhysiologicalReactionType {
 
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "direction", required = true)
+    protected String direction;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the direction property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDirection()
-  {
-    return direction;
-  }
+    /**
+     * Gets the value of the direction property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDirection() {
+        return direction;
+    }
 
-  /**
-   * Sets the value of the direction property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDirection(String value)
-  {
-    this.direction = value;
-  }
+    /**
+     * Sets the value of the direction property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDirection(String value) {
+        this.direction = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java
index c3713fa..25d6030 100644
--- a/src/jalview/xml/binding/uniprot/PositionType.java
+++ b/src/jalview/xml/binding/uniprot/PositionType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -16,13 +17,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for positionType complex type.
+ * 
    Java class for positionType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="positionType">
@@ -50,101 +49,95 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "positionType")
-public class PositionType
-{
-
-  @XmlAttribute(name = "position")
-  @XmlSchemaType(name = "unsignedLong")
-  protected BigInteger position;
-
-  @XmlAttribute(name = "status")
-  protected String status;
+public class PositionType {
 
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
+    @XmlAttribute(name = "position")
+    @XmlSchemaType(name = "unsignedLong")
+    protected BigInteger position;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  /**
-   * Gets the value of the position property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setPosition(BigInteger value)
-  {
-    this.position = value;
-  }
+    /**
+     * Gets the value of the position property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getPosition() {
+        return position;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    if (status == null)
-    {
-      return "certain";
+    /**
+     * Sets the value of the position property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setPosition(BigInteger value) {
+        this.position = value;
     }
-    else
-    {
-      return status;
+
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        if (status == null) {
+            return "certain";
+        } else {
+            return status;
+        }
     }
-  }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java
index 6b43149..b1ab0f3 100644
--- a/src/jalview/xml/binding/uniprot/PropertyType.java
+++ b/src/jalview/xml/binding/uniprot/PropertyType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for propertyType complex type.
+ * 
    Java class for propertyType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="propertyType">
@@ -35,59 +34,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "propertyType")
-public class PropertyType
-{
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+public class PropertyType {
 
-  @XmlAttribute(name = "value", required = true)
-  protected String value;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
index 3d07edb..73f4c21 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,16 +13,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the evidence for the protein's existence. Equivalent to the flat
- * file PE-line.
+ * Describes the evidence for the protein's existence.
+ *             Equivalent to the flat file PE-line.
  * 
- * 
    
- * Java class for proteinExistenceType complex type.
+ * 
    Java class for proteinExistenceType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="proteinExistenceType">
@@ -47,33 +46,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType
-{
+public class ProteinExistenceType {
 
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java
index 5a7d731..f3d0e80 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,14 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the names for the protein and parts thereof. Equivalent to the flat
- * file DE-line.
+ * Describes the names for the protein and parts thereof.
+ *             Equivalent to the flat file DE-line.
  * 
- * 
    
- * Java class for proteinType complex type.
+ * 
    Java class for proteinType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="proteinType">
@@ -58,497 +57,66 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "proteinType",
-  propOrder =
-  { "recommendedName", "alternativeName", "submittedName", "allergenName",
-      "biotechName", "cdAntigenName", "innName", "domain", "component" })
-public class ProteinType
-{
-
-  protected ProteinType.RecommendedName recommendedName;
-
-  protected List alternativeName;
-
-  protected List submittedName;
-
-  protected EvidencedStringType allergenName;
-
-  protected EvidencedStringType biotechName;
-
-  protected List cdAntigenName;
-
-  protected List innName;
-
-  protected List domain;
-
-  protected List component;
-
-  /**
-   * Gets the value of the recommendedName property.
-   * 
-   * @return possible object is {@link ProteinType.RecommendedName }
-   * 
-   */
-  public ProteinType.RecommendedName getRecommendedName()
-  {
-    return recommendedName;
-  }
-
-  /**
-   * Sets the value of the recommendedName property.
-   * 
-   * @param value
-   *          allowed object is {@link ProteinType.RecommendedName }
-   * 
-   */
-  public void setRecommendedName(ProteinType.RecommendedName value)
-  {
-    this.recommendedName = value;
-  }
-
-  /**
-   * Gets the value of the alternativeName 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 alternativeName property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getAlternativeName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.AlternativeName }
-   * 
-   * 
-   */
-  public List getAlternativeName()
-  {
-    if (alternativeName == null)
-    {
-      alternativeName = new ArrayList();
-    }
-    return this.alternativeName;
-  }
-
-  /**
-   * Gets the value of the submittedName 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 submittedName property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getSubmittedName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.SubmittedName }
-   * 
-   * 
-   */
-  public List getSubmittedName()
-  {
-    if (submittedName == null)
-    {
-      submittedName = new ArrayList();
-    }
-    return this.submittedName;
-  }
-
-  /**
-   * Gets the value of the allergenName property.
-   * 
-   * @return possible object is {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType getAllergenName()
-  {
-    return allergenName;
-  }
-
-  /**
-   * Sets the value of the allergenName property.
-   * 
-   * @param value
-   *          allowed object is {@link EvidencedStringType }
-   * 
-   */
-  public void setAllergenName(EvidencedStringType value)
-  {
-    this.allergenName = value;
-  }
-
-  /**
-   * Gets the value of the biotechName property.
-   * 
-   * @return possible object is {@link EvidencedStringType }
-   * 
-   */
-  public EvidencedStringType getBiotechName()
-  {
-    return biotechName;
-  }
-
-  /**
-   * Sets the value of the biotechName property.
-   * 
-   * @param value
-   *          allowed object is {@link EvidencedStringType }
-   * 
-   */
-  public void setBiotechName(EvidencedStringType value)
-  {
-    this.biotechName = value;
-  }
-
-  /**
-   * Gets the value of the cdAntigenName 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 cdAntigenName property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getCdAntigenName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getCdAntigenName()
-  {
-    if (cdAntigenName == null)
-    {
-      cdAntigenName = new ArrayList();
-    }
-    return this.cdAntigenName;
-  }
-
-  /**
-   * Gets the value of the innName 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 innName property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getInnName().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getInnName()
-  {
-    if (innName == null)
-    {
-      innName = new ArrayList();
-    }
-    return this.innName;
-  }
-
-  /**
-   * Gets the value of the domain 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 domain property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getDomain().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.Domain }
-   * 
-   * 
-   */
-  public List getDomain()
-  {
-    if (domain == null)
-    {
-      domain = new ArrayList();
-    }
-    return this.domain;
-  }
-
-  /**
-   * Gets the value of the component 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 component property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getComponent().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link ProteinType.Component }
-   * 
-   * 
-   */
-  public List getComponent()
-  {
-    if (component == null)
-    {
-      component = new ArrayList();
-    }
-    return this.component;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
-  public static class AlternativeName
-  {
-
-    protected EvidencedStringType fullName;
-
-    protected List shortName;
-
-    protected List ecNumber;
-
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
-    }
-
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
-
-    /**
-     * Gets the value of the shortName 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 shortName property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getShortName().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List getShortName()
-    {
-      if (shortName == null)
-      {
-        shortName = new ArrayList();
-      }
-      return this.shortName;
-    }
-
-    /**
-     * Gets the value of the ecNumber 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 ecNumber property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
-     * 
    -     * getEcNumber().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList();
-      }
-      return this.ecNumber;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "recommendedName", "alternativeName", "submittedName", "allergenName",
-        "biotechName", "cdAntigenName", "innName" })
-  public static class Component
-  {
+@XmlType(name = "proteinType", propOrder = {
+    "recommendedName",
+    "alternativeName",
+    "submittedName",
+    "allergenName",
+    "biotechName",
+    "cdAntigenName",
+    "innName",
+    "domain",
+    "component"
+})
+public class ProteinType {
 
     protected ProteinType.RecommendedName recommendedName;
-
     protected List alternativeName;
-
     protected List submittedName;
-
     protected EvidencedStringType allergenName;
-
     protected EvidencedStringType biotechName;
-
     protected List cdAntigenName;
-
     protected List innName;
+    protected List domain;
+    protected List component;
 
     /**
      * Gets the value of the recommendedName property.
      * 
-     * @return possible object is {@link ProteinType.RecommendedName }
-     * 
+     * @return
+     *     possible object is
+     *     {@link ProteinType.RecommendedName }
+     *     
      */
-    public ProteinType.RecommendedName getRecommendedName()
-    {
-      return recommendedName;
+    public ProteinType.RecommendedName getRecommendedName() {
+        return recommendedName;
     }
 
     /**
      * Sets the value of the recommendedName property.
      * 
      * @param value
-     *          allowed object is {@link ProteinType.RecommendedName }
-     * 
+     *     allowed object is
+     *     {@link ProteinType.RecommendedName }
+     *     
      */
-    public void setRecommendedName(ProteinType.RecommendedName value)
-    {
-      this.recommendedName = value;
+    public void setRecommendedName(ProteinType.RecommendedName value) {
+        this.recommendedName = value;
     }
 
     /**
      * Gets the value of the alternativeName 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 alternativeName 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 alternativeName property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getAlternativeName().add(newItem);
+     *    getAlternativeName().add(newItem);
      * 
    
      * 
      * 
@@ -558,29 +126,26 @@ public class ProteinType
      * 
      * 
      */
-    public List getAlternativeName()
-    {
-      if (alternativeName == null)
-      {
-        alternativeName = new ArrayList();
-      }
-      return this.alternativeName;
+    public List getAlternativeName() {
+        if (alternativeName == null) {
+            alternativeName = new ArrayList();
+        }
+        return this.alternativeName;
     }
 
     /**
      * Gets the value of the submittedName 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 submittedName 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 submittedName property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getSubmittedName().add(newItem);
+     *    getSubmittedName().add(newItem);
      * 
    
      * 
      * 
@@ -590,75 +155,74 @@ public class ProteinType
      * 
      * 
      */
-    public List getSubmittedName()
-    {
-      if (submittedName == null)
-      {
-        submittedName = new ArrayList();
-      }
-      return this.submittedName;
+    public List getSubmittedName() {
+        if (submittedName == null) {
+            submittedName = new ArrayList();
+        }
+        return this.submittedName;
     }
 
     /**
      * Gets the value of the allergenName property.
      * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
+     * @return
+     *     possible object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public EvidencedStringType getAllergenName()
-    {
-      return allergenName;
+    public EvidencedStringType getAllergenName() {
+        return allergenName;
     }
 
     /**
      * Sets the value of the allergenName property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public void setAllergenName(EvidencedStringType value)
-    {
-      this.allergenName = value;
+    public void setAllergenName(EvidencedStringType value) {
+        this.allergenName = value;
     }
 
     /**
      * Gets the value of the biotechName property.
      * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
+     * @return
+     *     possible object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public EvidencedStringType getBiotechName()
-    {
-      return biotechName;
+    public EvidencedStringType getBiotechName() {
+        return biotechName;
     }
 
     /**
      * Sets the value of the biotechName property.
      * 
      * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
+     *     allowed object is
+     *     {@link EvidencedStringType }
+     *     
      */
-    public void setBiotechName(EvidencedStringType value)
-    {
-      this.biotechName = value;
+    public void setBiotechName(EvidencedStringType value) {
+        this.biotechName = value;
     }
 
     /**
      * Gets the value of the cdAntigenName 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 cdAntigenName 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 cdAntigenName property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getCdAntigenName().add(newItem);
+     *    getCdAntigenName().add(newItem);
      * 
    
      * 
      * 
@@ -668,29 +232,26 @@ public class ProteinType
      * 
      * 
      */
-    public List getCdAntigenName()
-    {
-      if (cdAntigenName == null)
-      {
-        cdAntigenName = new ArrayList();
-      }
-      return this.cdAntigenName;
+    public List getCdAntigenName() {
+        if (cdAntigenName == null) {
+            cdAntigenName = new ArrayList();
+        }
+        return this.cdAntigenName;
     }
 
     /**
      * Gets the value of the innName 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 innName 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 innName property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getInnName().add(newItem);
+     *    getInnName().add(newItem);
      * 
    
      * 
      * 
@@ -700,472 +261,849 @@ public class ProteinType
      * 
      * 
      */
-    public List getInnName()
-    {
-      if (innName == null)
-      {
-        innName = new ArrayList();
-      }
-      return this.innName;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "recommendedName", "alternativeName", "submittedName", "allergenName",
-        "biotechName", "cdAntigenName", "innName" })
-  public static class Domain
-  {
-
-    protected ProteinType.RecommendedName recommendedName;
-
-    protected List alternativeName;
-
-    protected List submittedName;
-
-    protected EvidencedStringType allergenName;
-
-    protected EvidencedStringType biotechName;
-
-    protected List cdAntigenName;
-
-    protected List innName;
-
-    /**
-     * Gets the value of the recommendedName property.
-     * 
-     * @return possible object is {@link ProteinType.RecommendedName }
-     * 
-     */
-    public ProteinType.RecommendedName getRecommendedName()
-    {
-      return recommendedName;
+    public List getInnName() {
+        if (innName == null) {
+            innName = new ArrayList();
+        }
+        return this.innName;
     }
 
     /**
-     * Sets the value of the recommendedName property.
-     * 
-     * @param value
-     *          allowed object is {@link ProteinType.RecommendedName }
-     * 
-     */
-    public void setRecommendedName(ProteinType.RecommendedName value)
-    {
-      this.recommendedName = value;
-    }
-
-    /**
-     * Gets the value of the alternativeName property.
+     * Gets the value of the domain 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 alternativeName 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 domain property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getAlternativeName().add(newItem);
+     *    getDomain().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.AlternativeName }
+     * {@link ProteinType.Domain }
      * 
      * 
      */
-    public List getAlternativeName()
-    {
-      if (alternativeName == null)
-      {
-        alternativeName = new ArrayList();
-      }
-      return this.alternativeName;
+    public List getDomain() {
+        if (domain == null) {
+            domain = new ArrayList();
+        }
+        return this.domain;
     }
 
     /**
-     * Gets the value of the submittedName property.
+     * Gets the value of the component 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 submittedName 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 component property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getSubmittedName().add(newItem);
+     *    getComponent().add(newItem);
      * 
    
      * 
      * 
      * 
    
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.SubmittedName }
-     * 
-     * 
-     */
-    public List getSubmittedName()
-    {
-      if (submittedName == null)
-      {
-        submittedName = new ArrayList();
-      }
-      return this.submittedName;
-    }
-
-    /**
-     * Gets the value of the allergenName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getAllergenName()
-    {
-      return allergenName;
-    }
-
-    /**
-     * Sets the value of the allergenName property.
+     * {@link ProteinType.Component }
      * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
      * 
      */
-    public void setAllergenName(EvidencedStringType value)
-    {
-      this.allergenName = value;
+    public List getComponent() {
+        if (component == null) {
+            component = new ArrayList();
+        }
+        return this.component;
     }
 
-    /**
-     * Gets the value of the biotechName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getBiotechName()
-    {
-      return biotechName;
-    }
 
     /**
-     * Sets the value of the biotechName property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setBiotechName(EvidencedStringType value)
-    {
-      this.biotechName = value;
-    }
-
-    /**
-     * Gets the value of the cdAntigenName 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 cdAntigenName property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getCdAntigenName().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getCdAntigenName()
-    {
-      if (cdAntigenName == null)
-      {
-        cdAntigenName = new ArrayList();
-      }
-      return this.cdAntigenName;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "shortName",
+        "ecNumber"
+    })
+    public static class AlternativeName {
+
+        protected EvidencedStringType fullName;
+        protected List shortName;
+        protected List ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the shortName 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 shortName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getShortName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getShortName() {
+            if (shortName == null) {
+                shortName = new ArrayList();
+            }
+            return this.shortName;
+        }
+
+        /**
+         * Gets the value of the ecNumber 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 ecNumber property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEcNumber().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList();
+            }
+            return this.ecNumber;
+        }
+
     }
 
+
     /**
-     * Gets the value of the innName property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 innName property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getInnName().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getInnName()
-    {
-      if (innName == null)
-      {
-        innName = new ArrayList();
-      }
-      return this.innName;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "recommendedName",
+        "alternativeName",
+        "submittedName",
+        "allergenName",
+        "biotechName",
+        "cdAntigenName",
+        "innName"
+    })
+    public static class Component {
+
+        protected ProteinType.RecommendedName recommendedName;
+        protected List alternativeName;
+        protected List submittedName;
+        protected EvidencedStringType allergenName;
+        protected EvidencedStringType biotechName;
+        protected List cdAntigenName;
+        protected List innName;
+
+        /**
+         * Gets the value of the recommendedName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public ProteinType.RecommendedName getRecommendedName() {
+            return recommendedName;
+        }
+
+        /**
+         * Sets the value of the recommendedName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public void setRecommendedName(ProteinType.RecommendedName value) {
+            this.recommendedName = value;
+        }
+
+        /**
+         * Gets the value of the alternativeName 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 alternativeName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getAlternativeName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.AlternativeName }
+         * 
+         * 
+         */
+        public List getAlternativeName() {
+            if (alternativeName == null) {
+                alternativeName = new ArrayList();
+            }
+            return this.alternativeName;
+        }
+
+        /**
+         * Gets the value of the submittedName 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 submittedName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getSubmittedName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.SubmittedName }
+         * 
+         * 
+         */
+        public List getSubmittedName() {
+            if (submittedName == null) {
+                submittedName = new ArrayList();
+            }
+            return this.submittedName;
+        }
+
+        /**
+         * Gets the value of the allergenName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getAllergenName() {
+            return allergenName;
+        }
+
+        /**
+         * Sets the value of the allergenName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setAllergenName(EvidencedStringType value) {
+            this.allergenName = value;
+        }
+
+        /**
+         * Gets the value of the biotechName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getBiotechName() {
+            return biotechName;
+        }
+
+        /**
+         * Sets the value of the biotechName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setBiotechName(EvidencedStringType value) {
+            this.biotechName = value;
+        }
+
+        /**
+         * Gets the value of the cdAntigenName 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 cdAntigenName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getCdAntigenName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getCdAntigenName() {
+            if (cdAntigenName == null) {
+                cdAntigenName = new ArrayList();
+            }
+            return this.cdAntigenName;
+        }
+
+        /**
+         * Gets the value of the innName 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 innName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getInnName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getInnName() {
+            if (innName == null) {
+                innName = new ArrayList();
+            }
+            return this.innName;
+        }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
-  public static class RecommendedName
-  {
-
-    @XmlElement(required = true)
-    protected EvidencedStringType fullName;
-
-    protected List shortName;
-
-    protected List ecNumber;
-
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
     }
 
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
 
     /**
-     * Gets the value of the shortName property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 shortName property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getShortName().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getShortName()
-    {
-      if (shortName == null)
-      {
-        shortName = new ArrayList();
-      }
-      return this.shortName;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "recommendedName",
+        "alternativeName",
+        "submittedName",
+        "allergenName",
+        "biotechName",
+        "cdAntigenName",
+        "innName"
+    })
+    public static class Domain {
+
+        protected ProteinType.RecommendedName recommendedName;
+        protected List alternativeName;
+        protected List submittedName;
+        protected EvidencedStringType allergenName;
+        protected EvidencedStringType biotechName;
+        protected List cdAntigenName;
+        protected List innName;
+
+        /**
+         * Gets the value of the recommendedName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public ProteinType.RecommendedName getRecommendedName() {
+            return recommendedName;
+        }
+
+        /**
+         * Sets the value of the recommendedName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ProteinType.RecommendedName }
+         *     
+         */
+        public void setRecommendedName(ProteinType.RecommendedName value) {
+            this.recommendedName = value;
+        }
+
+        /**
+         * Gets the value of the alternativeName 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 alternativeName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getAlternativeName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.AlternativeName }
+         * 
+         * 
+         */
+        public List getAlternativeName() {
+            if (alternativeName == null) {
+                alternativeName = new ArrayList();
+            }
+            return this.alternativeName;
+        }
+
+        /**
+         * Gets the value of the submittedName 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 submittedName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getSubmittedName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link ProteinType.SubmittedName }
+         * 
+         * 
+         */
+        public List getSubmittedName() {
+            if (submittedName == null) {
+                submittedName = new ArrayList();
+            }
+            return this.submittedName;
+        }
+
+        /**
+         * Gets the value of the allergenName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getAllergenName() {
+            return allergenName;
+        }
+
+        /**
+         * Sets the value of the allergenName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setAllergenName(EvidencedStringType value) {
+            this.allergenName = value;
+        }
+
+        /**
+         * Gets the value of the biotechName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getBiotechName() {
+            return biotechName;
+        }
+
+        /**
+         * Sets the value of the biotechName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setBiotechName(EvidencedStringType value) {
+            this.biotechName = value;
+        }
+
+        /**
+         * Gets the value of the cdAntigenName 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 cdAntigenName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getCdAntigenName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getCdAntigenName() {
+            if (cdAntigenName == null) {
+                cdAntigenName = new ArrayList();
+            }
+            return this.cdAntigenName;
+        }
+
+        /**
+         * Gets the value of the innName 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 innName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getInnName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getInnName() {
+            if (innName == null) {
+                innName = new ArrayList();
+            }
+            return this.innName;
+        }
+
     }
 
+
     /**
-     * Gets the value of the ecNumber 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 ecNumber property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getEcNumber().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList();
-      }
-      return this.ecNumber;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
-  public static class SubmittedName
-  {
-
-    @XmlElement(required = true)
-    protected EvidencedStringType fullName;
-
-    protected List ecNumber;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "shortName",
+        "ecNumber"
+    })
+    public static class RecommendedName {
+
+        @XmlElement(required = true)
+        protected EvidencedStringType fullName;
+        protected List shortName;
+        protected List ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the shortName 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 shortName property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getShortName().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getShortName() {
+            if (shortName == null) {
+                shortName = new ArrayList();
+            }
+            return this.shortName;
+        }
+
+        /**
+         * Gets the value of the ecNumber 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 ecNumber property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEcNumber().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList();
+            }
+            return this.ecNumber;
+        }
 
-    /**
-     * Gets the value of the fullName property.
-     * 
-     * @return possible object is {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType getFullName()
-    {
-      return fullName;
     }
 
-    /**
-     * Sets the value of the fullName property.
-     * 
-     * @param value
-     *          allowed object is {@link EvidencedStringType }
-     * 
-     */
-    public void setFullName(EvidencedStringType value)
-    {
-      this.fullName = value;
-    }
 
     /**
-     * Gets the value of the ecNumber property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 ecNumber property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getEcNumber().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
      */
-    public List getEcNumber()
-    {
-      if (ecNumber == null)
-      {
-        ecNumber = new ArrayList();
-      }
-      return this.ecNumber;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "fullName",
+        "ecNumber"
+    })
+    public static class SubmittedName {
+
+        @XmlElement(required = true)
+        protected EvidencedStringType fullName;
+        protected List ecNumber;
+
+        /**
+         * Gets the value of the fullName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public EvidencedStringType getFullName() {
+            return fullName;
+        }
+
+        /**
+         * Sets the value of the fullName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link EvidencedStringType }
+         *     
+         */
+        public void setFullName(EvidencedStringType value) {
+            this.fullName = value;
+        }
+
+        /**
+         * Gets the value of the ecNumber 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 ecNumber property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEcNumber().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link EvidencedStringType }
+         * 
+         * 
+         */
+        public List getEcNumber() {
+            if (ecNumber == null) {
+                ecNumber = new ArrayList();
+            }
+            return this.ecNumber;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java
index bc660fe..0e84d09 100644
--- a/src/jalview/xml/binding/uniprot/ReactionType.java
+++ b/src/jalview/xml/binding/uniprot/ReactionType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * Describes a chemical reaction.
  * 
- * 
    
- * Java class for reactionType complex type.
+ * 
    Java class for reactionType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="reactionType">
@@ -42,103 +41,99 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
-public class ReactionType
-{
-
-  @XmlElement(required = true)
-  protected String text;
+@XmlType(name = "reactionType", propOrder = {
+    "text",
+    "dbReference"
+})
+public class ReactionType {
 
-  @XmlElement(required = true)
-  protected List dbReference;
+    @XmlElement(required = true)
+    protected String text;
+    @XmlElement(required = true)
+    protected List dbReference;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  /**
-   * Gets the value of the text property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getText()
-  {
-    return text;
-  }
+    /**
+     * Gets the value of the text property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getText() {
+        return text;
+    }
 
-  /**
-   * Sets the value of the text property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setText(String value)
-  {
-    this.text = value;
-  }
+    /**
+     * Sets the value of the text property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setText(String value) {
+        this.text = value;
+    }
 
-  /**
-   * Gets the value of the dbReference 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 dbReference property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getDbReference().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link DbReferenceType }
-   * 
-   * 
-   */
-  public List getDbReference()
-  {
-    if (dbReference == null)
-    {
-      dbReference = new ArrayList();
+    /**
+     * Gets the value of the dbReference 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 dbReference property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getDbReference().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link DbReferenceType }
+     * 
+     * 
+     */
+    public List getDbReference() {
+        if (dbReference == null) {
+            dbReference = new ArrayList();
+        }
+        return this.dbReference;
     }
-    return this.dbReference;
-  }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java
index 729acae..afd4647 100644
--- a/src/jalview/xml/binding/uniprot/ReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/ReferenceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,16 +16,14 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes a citation and a summary of its content. Equivalent to the flat
- * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content.
+ *             Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
  * 
- * 
    
- * Java class for referenceType complex type.
+ * 
    Java class for referenceType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="referenceType">
@@ -44,156 +43,151 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "referenceType",
-  propOrder =
-  { "citation", "scope", "source" })
-public class ReferenceType
-{
-
-  @XmlElement(required = true)
-  protected CitationType citation;
-
-  @XmlElement(required = true)
-  protected List scope;
-
-  protected SourceDataType source;
-
-  @XmlAttribute(name = "evidence")
-  protected List evidence;
-
-  @XmlAttribute(name = "key", required = true)
-  protected String key;
-
-  /**
-   * Gets the value of the citation property.
-   * 
-   * @return possible object is {@link CitationType }
-   * 
-   */
-  public CitationType getCitation()
-  {
-    return citation;
-  }
+@XmlType(name = "referenceType", propOrder = {
+    "citation",
+    "scope",
+    "source"
+})
+public class ReferenceType {
+
+    @XmlElement(required = true)
+    protected CitationType citation;
+    @XmlElement(required = true)
+    protected List scope;
+    protected SourceDataType source;
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
+    @XmlAttribute(name = "key", required = true)
+    protected String key;
+
+    /**
+     * Gets the value of the citation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link CitationType }
+     *     
+     */
+    public CitationType getCitation() {
+        return citation;
+    }
 
-  /**
-   * Sets the value of the citation property.
-   * 
-   * @param value
-   *          allowed object is {@link CitationType }
-   * 
-   */
-  public void setCitation(CitationType value)
-  {
-    this.citation = value;
-  }
+    /**
+     * Sets the value of the citation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link CitationType }
+     *     
+     */
+    public void setCitation(CitationType value) {
+        this.citation = value;
+    }
 
-  /**
-   * Gets the value of the scope 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 scope property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getScope().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getScope()
-  {
-    if (scope == null)
-    {
-      scope = new ArrayList();
+    /**
+     * Gets the value of the scope 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 scope property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getScope().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getScope() {
+        if (scope == null) {
+            scope = new ArrayList();
+        }
+        return this.scope;
     }
-    return this.scope;
-  }
 
-  /**
-   * Gets the value of the source property.
-   * 
-   * @return possible object is {@link SourceDataType }
-   * 
-   */
-  public SourceDataType getSource()
-  {
-    return source;
-  }
+    /**
+     * Gets the value of the source property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link SourceDataType }
+     *     
+     */
+    public SourceDataType getSource() {
+        return source;
+    }
 
-  /**
-   * Sets the value of the source property.
-   * 
-   * @param value
-   *          allowed object is {@link SourceDataType }
-   * 
-   */
-  public void setSource(SourceDataType value)
-  {
-    this.source = value;
-  }
+    /**
+     * Sets the value of the source property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link SourceDataType }
+     *     
+     */
+    public void setSource(SourceDataType value) {
+        this.source = value;
+    }
 
-  /**
-   * Gets the value of the evidence 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 evidence property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEvidence().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Integer }
-   * 
-   * 
-   */
-  public List getEvidence()
-  {
-    if (evidence == null)
-    {
-      evidence = new ArrayList();
+    /**
+     * Gets the value of the evidence 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 evidence property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEvidence().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Integer }
+     * 
+     * 
+     */
+    public List getEvidence() {
+        if (evidence == null) {
+            evidence = new ArrayList();
+        }
+        return this.evidence;
     }
-    return this.evidence;
-  }
 
-  /**
-   * Gets the value of the key property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getKey()
-  {
-    return key;
-  }
+    /**
+     * Gets the value of the key property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getKey() {
+        return key;
+    }
 
-  /**
-   * Sets the value of the key property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setKey(String value)
-  {
-    this.key = value;
-  }
+    /**
+     * Sets the value of the key property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setKey(String value) {
+        this.key = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java
index 78ddd89..cddff7f 100644
--- a/src/jalview/xml/binding/uniprot/SequenceType.java
+++ b/src/jalview/xml/binding/uniprot/SequenceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * 
    
- * Java class for sequenceType complex type.
+ * 
    Java class for sequenceType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="sequenceType">
@@ -49,202 +48,195 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = { "value" })
-public class SequenceType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "length", required = true)
-  protected int length;
-
-  @XmlAttribute(name = "mass", required = true)
-  protected int mass;
-
-  @XmlAttribute(name = "checksum", required = true)
-  protected String checksum;
-
-  @XmlAttribute(name = "modified", required = true)
-  @XmlSchemaType(name = "date")
-  protected XMLGregorianCalendar modified;
-
-  @XmlAttribute(name = "version", required = true)
-  protected int version;
-
-  @XmlAttribute(name = "precursor")
-  protected Boolean precursor;
-
-  @XmlAttribute(name = "fragment")
-  protected String fragment;
-
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
-
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
-
-  /**
-   * Gets the value of the length property.
-   * 
-   */
-  public int getLength()
-  {
-    return length;
-  }
-
-  /**
-   * Sets the value of the length property.
-   * 
-   */
-  public void setLength(int value)
-  {
-    this.length = value;
-  }
-
-  /**
-   * Gets the value of the mass property.
-   * 
-   */
-  public int getMass()
-  {
-    return mass;
-  }
-
-  /**
-   * Sets the value of the mass property.
-   * 
-   */
-  public void setMass(int value)
-  {
-    this.mass = value;
-  }
-
-  /**
-   * Gets the value of the checksum property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getChecksum()
-  {
-    return checksum;
-  }
-
-  /**
-   * Sets the value of the checksum property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setChecksum(String value)
-  {
-    this.checksum = value;
-  }
-
-  /**
-   * Gets the value of the modified property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getModified()
-  {
-    return modified;
-  }
-
-  /**
-   * Sets the value of the modified property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setModified(XMLGregorianCalendar value)
-  {
-    this.modified = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   */
-  public int getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   */
-  public void setVersion(int value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the precursor property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPrecursor()
-  {
-    return precursor;
-  }
-
-  /**
-   * Sets the value of the precursor property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPrecursor(Boolean value)
-  {
-    this.precursor = value;
-  }
-
-  /**
-   * Gets the value of the fragment property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFragment()
-  {
-    return fragment;
-  }
-
-  /**
-   * Sets the value of the fragment property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFragment(String value)
-  {
-    this.fragment = value;
-  }
+@XmlType(name = "sequenceType", propOrder = {
+    "value"
+})
+public class SequenceType {
+
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "length", required = true)
+    protected int length;
+    @XmlAttribute(name = "mass", required = true)
+    protected int mass;
+    @XmlAttribute(name = "checksum", required = true)
+    protected String checksum;
+    @XmlAttribute(name = "modified", required = true)
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar modified;
+    @XmlAttribute(name = "version", required = true)
+    protected int version;
+    @XmlAttribute(name = "precursor")
+    protected Boolean precursor;
+    @XmlAttribute(name = "fragment")
+    protected String fragment;
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
+
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
+
+    /**
+     * Gets the value of the length property.
+     * 
+     */
+    public int getLength() {
+        return length;
+    }
+
+    /**
+     * Sets the value of the length property.
+     * 
+     */
+    public void setLength(int value) {
+        this.length = value;
+    }
+
+    /**
+     * Gets the value of the mass property.
+     * 
+     */
+    public int getMass() {
+        return mass;
+    }
+
+    /**
+     * Sets the value of the mass property.
+     * 
+     */
+    public void setMass(int value) {
+        this.mass = value;
+    }
+
+    /**
+     * Gets the value of the checksum property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getChecksum() {
+        return checksum;
+    }
+
+    /**
+     * Sets the value of the checksum property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setChecksum(String value) {
+        this.checksum = value;
+    }
+
+    /**
+     * Gets the value of the modified property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getModified() {
+        return modified;
+    }
+
+    /**
+     * Sets the value of the modified property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setModified(XMLGregorianCalendar value) {
+        this.modified = value;
+    }
+
+    /**
+     * Gets the value of the version property.
+     * 
+     */
+    public int getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
+     * 
+     */
+    public void setVersion(int value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the precursor property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPrecursor() {
+        return precursor;
+    }
+
+    /**
+     * Sets the value of the precursor property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPrecursor(Boolean value) {
+        this.precursor = value;
+    }
+
+    /**
+     * Gets the value of the fragment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getFragment() {
+        return fragment;
+    }
+
+    /**
+     * Sets the value of the fragment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFragment(String value) {
+        this.fragment = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java
index 3b71bae..f66020c 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -17,16 +18,14 @@ import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
- * Describes the source of the sequence according to the citation. Equivalent to
- * the flat file RC-line.
+ * Describes the source of the sequence according to the citation.
+ *             Equivalent to the flat file RC-line.
  * 
- * 
    
- * Java class for sourceDataType complex type.
+ * 
    Java class for sourceDataType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="sourceDataType">
@@ -78,401 +77,385 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "sourceDataType",
-  propOrder =
-  { "strainOrPlasmidOrTransposon" })
-public class SourceDataType
-{
-
-  @XmlElements({
-      @XmlElement(name = "strain", type = SourceDataType.Strain.class),
-      @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
-      @XmlElement(
-        name = "transposon",
-        type = SourceDataType.Transposon.class),
-      @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
-  protected List strainOrPlasmidOrTransposon;
-
-  /**
-   * Gets the value of the strainOrPlasmidOrTransposon 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 strainOrPlasmidOrTransposon property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getStrainOrPlasmidOrTransposon().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
-   * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
-   * 
-   * 
-   */
-  public List getStrainOrPlasmidOrTransposon()
-  {
-    if (strainOrPlasmidOrTransposon == null)
-    {
-      strainOrPlasmidOrTransposon = new ArrayList();
-    }
-    return this.strainOrPlasmidOrTransposon;
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <simpleContent>
-   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     </extension>
-   *   </simpleContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Plasmid
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
+@XmlType(name = "sourceDataType", propOrder = {
+    "strainOrPlasmidOrTransposon"
+})
+public class SourceDataType {
+
+    @XmlElements({
+        @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+        @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+        @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
+        @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
+    })
+    protected List strainOrPlasmidOrTransposon;
 
     /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
-
-    /**
-     * Gets the value of the evidence property.
+     * Gets the value of the strainOrPlasmidOrTransposon 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 evidence 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 strainOrPlasmidOrTransposon property.
      * 
      * 
    
      * For example, to add a new item, do as follows:
-     * 
      * 
    -     * getEvidence().add(newItem);
+     *    getStrainOrPlasmidOrTransposon().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * Objects of the following type(s) are allowed in the list
+     * {@link SourceDataType.Strain }
+     * {@link SourceDataType.Plasmid }
+     * {@link SourceDataType.Transposon }
+     * {@link SourceDataType.Tissue }
      * 
      * 
      */
-    public List getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList();
-      }
-      return this.evidence;
+    public List getStrainOrPlasmidOrTransposon() {
+        if (strainOrPlasmidOrTransposon == null) {
+            strainOrPlasmidOrTransposon = new ArrayList();
+        }
+        return this.strainOrPlasmidOrTransposon;
     }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <simpleContent>
-   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     </extension>
-   *   </simpleContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Strain
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
 
     /**
-     * Gets the value of the value property.
+     * 
    Java class for anonymous complex type.
      * 
-     * @return possible object is {@link String }
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
-
-    /**
-     * Sets the value of the value property.
+     * 
    +     * <complexType>
+     *   <simpleContent>
+     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     </extension>
+     *   </simpleContent>
+     * </complexType>
+     * 
    
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Plasmid {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence 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 evidence property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEvidence().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList();
+            }
+            return this.evidence;
+        }
+
     }
 
+
     /**
-     * Gets the value of the evidence property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 evidence property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getEvidence().add(newItem);
+     * <complexType>
+     *   <simpleContent>
+     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     </extension>
+     *   </simpleContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList();
-      }
-      return this.evidence;
-    }
-
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <simpleContent>
-   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     </extension>
-   *   </simpleContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Tissue
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Strain {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence 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 evidence property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEvidence().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList();
+            }
+            return this.evidence;
+        }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
     }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
 
     /**
-     * Gets the value of the evidence property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 evidence property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getEvidence().add(newItem);
+     * <complexType>
+     *   <simpleContent>
+     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     </extension>
+     *   </simpleContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList();
-      }
-      return this.evidence;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Tissue {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence 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 evidence property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEvidence().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList();
+            }
+            return this.evidence;
+        }
 
-  }
-
-  /**
-   * 
    
-   * Java class for anonymous complex type.
-   * 
-   * 
    
-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
    -   * <complexType>
-   *   <simpleContent>
-   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-   *     </extension>
-   *   </simpleContent>
-   * </complexType>
-   * 
    
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "value" })
-  public static class Transposon
-  {
-
-    @XmlValue
-    protected String value;
-
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
     }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
 
     /**
-     * Gets the value of the evidence property.
+     * 
    Java class for anonymous complex type.
      * 
-     * 
    
-     * 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 evidence property.
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
+     * 
    The following schema fragment specifies the expected content contained within this class.
      * 
      * 
    -     * getEvidence().add(newItem);
+     * <complexType>
+     *   <simpleContent>
+     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+     *     </extension>
+     *   </simpleContent>
+     * </complexType>
      * 
    
      * 
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
      */
-    public List getEvidence()
-    {
-      if (evidence == null)
-      {
-        evidence = new ArrayList();
-      }
-      return this.evidence;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "value"
+    })
+    public static class Transposon {
+
+        @XmlValue
+        protected String value;
+        @XmlAttribute(name = "evidence")
+        protected List evidence;
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the evidence 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 evidence property.
+         * 
+         * 
    
+         * For example, to add a new item, do as follows:
+         * 
    +         *    getEvidence().add(newItem);
+         * 
    
+         * 
+         * 
+         * 
    
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getEvidence() {
+            if (evidence == null) {
+                evidence = new ArrayList();
+            }
+            return this.evidence;
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java
index 5d71178..012d588 100644
--- a/src/jalview/xml/binding/uniprot/SourceType.java
+++ b/src/jalview/xml/binding/uniprot/SourceType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -13,17 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the source of the data using a database cross-reference (or a 'ref'
- * attribute when the source cannot be found in a public data source, such as
- * PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
  * 
- * 
    
- * Java class for sourceType complex type.
+ * 
    Java class for sourceType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="sourceType">
@@ -41,59 +38,61 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = { "dbReference" })
-public class SourceType
-{
-
-  protected DbReferenceType dbReference;
+@XmlType(name = "sourceType", propOrder = {
+    "dbReference"
+})
+public class SourceType {
 
-  @XmlAttribute(name = "ref")
-  protected BigInteger ref;
+    protected DbReferenceType dbReference;
+    @XmlAttribute(name = "ref")
+    protected BigInteger ref;
 
-  /**
-   * Gets the value of the dbReference property.
-   * 
-   * @return possible object is {@link DbReferenceType }
-   * 
-   */
-  public DbReferenceType getDbReference()
-  {
-    return dbReference;
-  }
+    /**
+     * Gets the value of the dbReference property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public DbReferenceType getDbReference() {
+        return dbReference;
+    }
 
-  /**
-   * Sets the value of the dbReference property.
-   * 
-   * @param value
-   *          allowed object is {@link DbReferenceType }
-   * 
-   */
-  public void setDbReference(DbReferenceType value)
-  {
-    this.dbReference = value;
-  }
+    /**
+     * Sets the value of the dbReference property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DbReferenceType }
+     *     
+     */
+    public void setDbReference(DbReferenceType value) {
+        this.dbReference = value;
+    }
 
-  /**
-   * Gets the value of the ref property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getRef()
-  {
-    return ref;
-  }
+    /**
+     * Gets the value of the ref property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getRef() {
+        return ref;
+    }
 
-  /**
-   * Sets the value of the ref property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setRef(BigInteger value)
-  {
-    this.ref = value;
-  }
+    /**
+     * Sets the value of the ref property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setRef(BigInteger value) {
+        this.ref = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java
index 5f22a99..8411265 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +14,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
+
 /**
  * Indicates whether the name of a plasmid is known or unknown.
  * 
- * 
    
- * Java class for statusType complex type.
+ * 
    Java class for statusType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="statusType">
@@ -43,67 +42,66 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = { "value" })
-public class StatusType
-{
-
-  @XmlValue
-  protected String value;
-
-  @XmlAttribute(name = "status")
-  protected String status;
+@XmlType(name = "statusType", propOrder = {
+    "value"
+})
+public class StatusType {
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    @XmlValue
+    protected String value;
+    @XmlAttribute(name = "status")
+    protected String status;
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    if (status == null)
-    {
-      return "known";
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
     }
-    else
-    {
-      return status;
+
+    /**
+     * Gets the value of the status property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getStatus() {
+        if (status == null) {
+            return "known";
+        } else {
+            return status;
+        }
     }
-  }
 
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
+    /**
+     * Sets the value of the status property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
index f1a06ef..77765a7 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -14,16 +15,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * Describes the subcellular location and optionally the topology and
- * orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and orientation of a molecule.
  * 
- * 
    
- * Java class for subcellularLocationType complex type.
+ * 
    Java class for subcellularLocationType complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType name="subcellularLocationType">
@@ -42,114 +40,103 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "subcellularLocationType",
-  propOrder =
-  { "location", "topology", "orientation" })
-public class SubcellularLocationType
-{
-
-  @XmlElement(required = true)
-  protected List location;
-
-  protected List topology;
+@XmlType(name = "subcellularLocationType", propOrder = {
+    "location",
+    "topology",
+    "orientation"
+})
+public class SubcellularLocationType {
 
-  protected List orientation;
+    @XmlElement(required = true)
+    protected List location;
+    protected List topology;
+    protected List orientation;
 
-  /**
-   * Gets the value of the location 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 location property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getLocation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getLocation()
-  {
-    if (location == null)
-    {
-      location = new ArrayList();
+    /**
+     * Gets the value of the location 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 location property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getLocation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List getLocation() {
+        if (location == null) {
+            location = new ArrayList();
+        }
+        return this.location;
     }
-    return this.location;
-  }
 
-  /**
-   * Gets the value of the topology 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 topology property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getTopology().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getTopology()
-  {
-    if (topology == null)
-    {
-      topology = new ArrayList();
+    /**
+     * Gets the value of the topology 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 topology property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getTopology().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List getTopology() {
+        if (topology == null) {
+            topology = new ArrayList();
+        }
+        return this.topology;
     }
-    return this.topology;
-  }
 
-  /**
-   * Gets the value of the orientation 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 orientation property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getOrientation().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list
-   * {@link EvidencedStringType }
-   * 
-   * 
-   */
-  public List getOrientation()
-  {
-    if (orientation == null)
-    {
-      orientation = new ArrayList();
+    /**
+     * Gets the value of the orientation 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 orientation property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getOrientation().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List getOrientation() {
+        if (orientation == null) {
+            orientation = new ArrayList();
+        }
+        return this.orientation;
     }
-    return this.orientation;
-  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java
index 3383e5d..a18d58b 100644
--- a/src/jalview/xml/binding/uniprot/Uniprot.java
+++ b/src/jalview/xml/binding/uniprot/Uniprot.java
@@ -2,9 +2,10 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
+
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 
    
- * Java class for anonymous complex type.
+ * 
    Java class for anonymous complex type.
  * 
- * 
    
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
    The following schema fragment specifies the expected content contained within this class.
  * 
  * 
      * <complexType>
@@ -39,68 +38,68 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entry", "copyright" })
+@XmlType(name = "", propOrder = {
+    "entry",
+    "copyright"
+})
 @XmlRootElement(name = "uniprot")
-public class Uniprot
-{
-
-  @XmlElement(required = true)
-  protected List entry;
+public class Uniprot {
 
-  protected String copyright;
+    @XmlElement(required = true)
+    protected List entry;
+    protected String copyright;
 
-  /**
-   * Gets the value of the entry 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 entry property.
-   * 
-   * 
    
-   * For example, to add a new item, do as follows:
-   * 
-   * 
    -   * getEntry().add(newItem);
-   * 
    
-   * 
-   * 
-   * 
    
-   * Objects of the following type(s) are allowed in the list {@link Entry }
-   * 
-   * 
-   */
-  public List getEntry()
-  {
-    if (entry == null)
-    {
-      entry = new ArrayList();
+    /**
+     * Gets the value of the entry 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 entry property.
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    +     *    getEntry().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link Entry }
+     * 
+     * 
+     */
+    public List getEntry() {
+        if (entry == null) {
+            entry = new ArrayList();
+        }
+        return this.entry;
     }
-    return this.entry;
-  }
 
-  /**
-   * Gets the value of the copyright property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCopyright()
-  {
-    return copyright;
-  }
+    /**
+     * Gets the value of the copyright property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCopyright() {
+        return copyright;
+    }
 
-  /**
-   * Sets the value of the copyright property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCopyright(String value)
-  {
-    this.copyright = value;
-  }
+    /**
+     * Sets the value of the copyright property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCopyright(String value) {
+        this.copyright = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java
index 8a7c699..b8a8636 100644
--- a/src/jalview/xml/binding/uniprot/package-info.java
+++ b/src/jalview/xml/binding/uniprot/package-info.java
@@ -2,10 +2,8 @@
 // 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: 2019.04.05 at 08:01:44 AM BST 
+// Generated on: 2023.01.31 at 04:07:10 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(
-  namespace = "http://uniprot.org/uniprot",
-  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.uniprot;
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 2970e3d..e693a7c 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -28,6 +28,16 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
@@ -42,15 +52,6 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
 
 public class CrossRefTest
 {
@@ -62,6 +63,12 @@ public class CrossRefTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+  }
+
   @Test(groups = { "Functional" })
   public void testFindXDbRefs()
   {
@@ -187,6 +194,7 @@ public class CrossRefTest
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
     Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
             .findXrefSequences("UNIPROT", true);
+    System.err.println("xrefs=" + xrefs);
     assertEquals(1, xrefs.getHeight());
     assertSame(uniprotSeq, xrefs.getSequenceAt(0));
   }
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6e18324..0151a12 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.util.Locale;
-
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
@@ -30,20 +28,13 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.PDBEntry.Type;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
 
 import org.testng.Assert;
@@ -51,6 +42,13 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.bin.Cache;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
 import junit.extensions.PA;
 
 public class SequenceTest
@@ -62,6 +60,12 @@ public class SequenceTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+  }
+
   Sequence seq;
 
   @BeforeMethod(alwaysRun = true)
@@ -123,9 +127,13 @@ public class SequenceTest
     assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
     // test DNA with X
     assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+    // short sequence is nucleotide only if 50% is nucleotide and remaining N/X
+    // is either N or X only
+    assertTrue(new Sequence("prot", "ACGTACGTACGTXN").isProtein());
     // test DNA with N
     assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
     // test RNA with X
+    assertFalse(new Sequence("prot", "ACGUACGUACGUACTGACAXX").isProtein());
     assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
     assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
   }
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index a137ff6..2d7e3dc 100644
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertNotNull;
 
 import java.awt.Dimension;
 import java.awt.Font;
@@ -290,4 +291,43 @@ public class AlignmentPanelTest
     Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
     assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
   }
-}
+ 
+  @Test(groups = "Functional")
+  public void testSetOverviewTitle()
+  {
+    OverviewPanel ov1 = this.af.openOverviewPanel(true);
+    String alignFrameTitle = af.getTitle();
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+    
+    /*
+     * on New View, existing overview should get " Original" added to title
+     * and new view's overview should get " View 1" added
+     */
+    af.newView_actionPerformed(null);
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    OverviewPanel ov2 = this.af.openOverviewPanel(true);
+    assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+  }
+  
+  @Test(groups = "Functional")
+  public void testSetOverviewTitle_automaticOverview()
+  {
+    Cache.setProperty("SHOW_OVERVIEW",  "true");
+    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
+    assertNotNull(ov1);
+    String alignFrameTitle = alignFrame.getTitle();
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+    
+    /*
+     * on New View, existing overview should get " Original" added to title
+     * and new view's automatic overview should have " View 1" added
+     */
+    alignFrame.newView_actionPerformed(null);
+    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
+    assertNotNull(ov2);
+    assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+  }
+}
\ No newline at end of file
diff --git a/test/jalview/gui/QuitHandlerTest.java b/test/jalview/gui/QuitHandlerTest.java
new file mode 100644
index 0000000..b257088
--- /dev/null
+++ b/test/jalview/gui/QuitHandlerTest.java
@@ -0,0 +1,304 @@
+package jalview.gui;
+
+import static org.testng.Assert.assertNotNull;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.gui.QuitHandler.QResponse;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+import jalview.project.Jalview2XML;
+
+@Test(singleThreaded = true)
+public class QuitHandlerTest
+{
+  private static String saveProjectFile = "test-output/tempSaveFile.jvp";
+
+  private static String saveFastaFile = "test-output/tempSaveFile.fa";
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    Jalview2XML.setDebugDelaySave(3);
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
+
+    /*
+     * set news feed last read to a future time to ensure no
+     * 'unread' news item is displayed
+     */
+    Date oneHourFromNow = new Date(
+            System.currentTimeMillis() + 3600 * 1000);
+    Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+    Jalview.main(
+            new String[]
+            { "-nowebservicediscovery", "-nosplash", "-nonews" });
+  }
+
+  @AfterClass(alwaysRun = true)
+  public static void resetProps()
+  {
+    // reset quit response
+    QuitHandler.setResponse(QResponse.NULL);
+    // reset mock response
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    // close desktop windows/frames
+    Desktop.instance.closeAll_actionPerformed(null);
+    // reset debug delay
+    Jalview2XML.setDebugDelaySave(20);
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public static void tearDownAfterClass() throws Exception
+  {
+    // reset quit response
+    QuitHandler.setResponse(QResponse.NULL);
+    // reset mock response
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    // close desktop windows/frames
+    Desktop.instance.closeAll_actionPerformed(null);
+    // reset debug delay
+    Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+    Jalview2XML.setDebugDelaySave(3);
+    // set the project file
+    Desktop.instance.setProjectFile(new File(saveProjectFile));
+  }
+
+  @AfterMethod(alwaysRun = true)
+  public static void cleanup()
+  {
+    // delete save files
+    List files = new ArrayList<>();
+    files.add(saveProjectFile);
+    files.add(saveFastaFile);
+    for (String filename : files)
+    {
+      File file = new File(filename);
+      if (file.exists())
+      {
+        file.delete();
+      }
+    }
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+  public void testInstantQuit() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+
+    long start = System.currentTimeMillis();
+
+    // if a save is attempted it will delay 3s
+    Jalview2XML.setDebugDelaySave(3);
+    Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+
+    // loaded file but haven't done anything, should just quit
+    QResponse response = QuitHandler.getQuitResponse(true);
+    long end = System.currentTimeMillis();
+
+    Assert.assertEquals(response, QResponse.QUIT);
+    Assert.assertTrue(end - start < 500,
+            "Quit-with-no-save-needed took too long (" + (end - start)
+                    + "ms)");
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 10)
+  public void testWaitForSaveQuit() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+
+    long start = System.currentTimeMillis();
+
+    // start a long save (3s)
+    Jalview2XML.setDebugDelaySave(3);
+    Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+    Desktop.instance.saveState_actionPerformed(false);
+
+    // give the saveState thread time to start!
+    Thread.sleep(500);
+
+    // af.saveAlignment(saveProjectFile, FileFormat.Jalview);
+    QResponse response = QuitHandler.getQuitResponse(true);
+    long end = System.currentTimeMillis();
+
+    Assert.assertEquals(response, QResponse.QUIT);
+    Assert.assertTrue(end - start > 2900,
+            "Quit-whilst-saving was too short (" + (end - start) + "ms)");
+
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
+  public void testSavedProjectChanges() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+    AlignViewport viewport = af.getViewport();
+    // pretend something has happened
+    viewport.setSavedUpToDate(false);
+    Jalview2XML.setStateSavedUpToDate(false);
+
+    // don't want to hang around here
+    Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+    af.saveAlignment(saveProjectFile, FileFormat.Jalview);
+
+    // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION (to
+    // mean [CANCEL] -- file should already be saved so this doesn't happen and
+    // we get a QUIT response)
+    JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+    QResponse response = QuitHandler.getQuitResponse(true);
+
+    // if not saved this would be CANCEL_QUIT
+    Assert.assertEquals(response, QResponse.QUIT);
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
+  public void testSavedAlignmentChanges() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+    AlignViewport viewport = af.getViewport();
+    // pretend something has happened
+    viewport.setSavedUpToDate(false);
+    Jalview2XML.setStateSavedUpToDate(false);
+
+    // no hanging around needed here
+    Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+    af.saveAlignment(saveFastaFile, FileFormat.Fasta);
+
+    // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+    JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+    QResponse response = QuitHandler.getQuitResponse(true);
+
+    // if not saved this would be CANCEL_QUIT
+    Assert.assertEquals(response, QResponse.QUIT);
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+  public void testUnsavedChanges() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+    AlignViewport viewport = af.getViewport();
+    // pretend something has happened
+    viewport.setSavedUpToDate(false);
+    Jalview2XML.setStateSavedUpToDate(false);
+
+    // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+    JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+    QResponse response = QuitHandler.getQuitResponse(true);
+
+    Assert.assertEquals(response, QResponse.CANCEL_QUIT);
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+  public void testNoGUIUnsavedChanges() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+    AlignViewport viewport = af.getViewport();
+    // pretend something has happened
+    viewport.setSavedUpToDate(false);
+    Jalview2XML.setStateSavedUpToDate(false);
+
+    // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+    JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+    /*
+    QResponse response = QuitHandler.getQuitResponse(false,
+            QuitHandler.defaultOkQuit, () -> {
+              // set FORCE_QUIT without the force quit
+              QuitHandler.setResponse(QResponse.FORCE_QUIT);
+              return null;
+            }, QuitHandler.defaultCancelQuit);
+            */
+    QResponse response = QuitHandler.getQuitResponse(false);
+
+    Assert.assertEquals(response, QResponse.QUIT);
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @Test(groups = { "Functional" }, singleThreaded = true, priority = 11)
+  public void testForceQuit() throws Exception
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Didn't read input file " + inFile);
+
+    long start = System.currentTimeMillis();
+
+    // start a long save (10s)
+    Jalview2XML.setDebugDelaySave(10);
+    Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+    Desktop.instance.saveState_actionPerformed(false);
+
+    // give the saveState thread time to start!
+    Thread.sleep(100);
+
+    // this will select "Force Quit"
+    JvOptionPane.setMockResponse(JvOptionPane.YES_OPTION);
+    QResponse response = QuitHandler.getQuitResponse(true,
+            QuitHandler.defaultOkQuit, () -> {
+              // set FORCE_QUIT without the force quit
+              jalview.bin.Console.debug(
+                      "Setting FORCE_QUIT without actually quitting");
+              QuitHandler.setResponse(QResponse.FORCE_QUIT);
+              return null;
+            }, QuitHandler.defaultCancelQuit);
+    long end = System.currentTimeMillis();
+
+    Assert.assertEquals(response, QResponse.FORCE_QUIT);
+    // if the wait (min wait is 1s) wasn't long enough...
+    Assert.assertTrue(end - start > 1000,
+            "Force-Quit-whilst-saving was too short (" + (end - start)
+                    + "ms)");
+    // if the wait was too long (probably waited for file to save)
+    Assert.assertTrue(end - start < 9090,
+            "Force-Quit-whilst-saving was too long (" + (end - start)
+                    + "ms)");
+
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+}
diff --git a/test/jalview/gui/quitProps.jvprops b/test/jalview/gui/quitProps.jvprops
new file mode 100644
index 0000000..be2b1cb
--- /dev/null
+++ b/test/jalview/gui/quitProps.jvprops
@@ -0,0 +1,7 @@
+DEBUG_DELAY_SAVE=true
+BACKUPFILES_ENABLED=true
+BACKUPFILES_FC_INCLUDE=false
+BACKUPFILES_PRESET=1
+CONFIRM_OVERWRITE_FILE=true
+SHOW_STARTUP_FILE=false
+logs.Jalview.level=DEBUG
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 79d622c..c070edb 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -23,11 +23,13 @@ package jalview.project;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import java.awt.Color;
+import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -48,8 +50,10 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.HiddenSequences;
@@ -69,8 +73,10 @@ import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
 import jalview.gui.PopupMenu;
+import jalview.gui.Preferences;
 import jalview.gui.SliderPanel;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -233,8 +239,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     boolean diffseqcols = false, diffgseqcols = false;
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
-    for (int p = 0, pSize = af.getViewport().getAlignment()
-            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
@@ -253,8 +260,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0, pSize = af.getViewport().getAlignment()
-            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
@@ -585,6 +593,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+    /*
+     * test for patch release versions
+     */
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0","2.11.4"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.0b1","2.12.2.0"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.3","2.12.2.2"));
+
   }
 
   /**
@@ -819,6 +835,88 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * @throws IOException
    */
   @Test(groups = { "Functional" })
+  public void testStoreAndRecoverAnnotationRowElementColours()
+          throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ",
+            DataSourceType.PASTE);
+
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    SequenceI fsq;
+    fsq = al.getSequenceAt(0);
+    Annotation annots[] = new Annotation[fsq.getLength()];
+    AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots",
+            annots);
+    annots[0] = new Annotation(1.0f);
+    annots[1] = new Annotation(2.0f);
+    annots[2] = new Annotation(3.0f);
+    annots[0].colour = Color.RED;
+    annots[1].colour = Color.GREEN;
+    annots[2].colour = Color.BLUE;
+    ala.validateRangeAndDisplay();
+    al.getSequenceAt(0).addAlignmentAnnotation(ala);
+    al.addAnnotation(ala);
+    /*
+     * and colour by annotation
+     */
+    AnnotationColourGradient acg = new AnnotationColourGradient(ala,
+            af.alignPanel.av.getGlobalColourScheme(), 0);
+    acg.setSeqAssociated(true);
+    acg.setPredefinedColours(true);
+    af.changeColour(acg);
+    Color seqcol[] = new Color[3];
+    for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
+      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+    }
+    /*
+     * save project, close windows, reload project, verify
+     */
+    File tfile = File.createTempFile(
+            "testStoreAndRecoverAnnotRowElemColors", ".jvp");
+    tfile.deleteOnExit();
+    new Jalview2XML(false).saveState(tfile);
+    //Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    Assert.assertNotNull(af, "Failed to reload project");
+    /*
+     * verify alignment annotation has colors
+     */
+    av = af.getViewport();
+    
+    ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
+    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+    acg = (AnnotationColourGradient) loadedCscheme;
+    assertTrue(acg.isSeqAssociated());
+    assertTrue(acg.isPredefinedColours());
+
+    al = av.getAlignment();
+    fsq = al.getSequenceAt(0);
+    ala = fsq.getAnnotation()[0];
+    Assert.assertNotNull(ala, "No annotation row recovered");
+    Assert.assertNotNull(ala.annotations);
+    for (int iStart = al.getSequenceAt(0)
+            .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
+    {
+      Assert.assertTrue(ala.annotations[i].colour!=null);
+      Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
+      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+      Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+
+    }
+    
+  }
+
+  /**
+   * Configure an alignment and a sub-group each with distinct colour schemes,
+   * Conservation and PID thresholds, and confirm these are restored from the
+   * saved project.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
     Desktop.instance.closeAll_actionPerformed(null);
@@ -1274,4 +1372,158 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(dbRef instanceof GeneLocus);
     assertEquals(dbRef, dbref3);
   }
+
+  /**
+   * test store and recovery of Overview windows
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverOverview() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "false");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true");
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+
+    /*
+     * open and resize / reposition overview 
+     */
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov1 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov1);
+    ov1.setFrameBounds(20, 30, 200, 400);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa");
+    assertTrue(ov1.isShowHiddenRegions());
+
+    /*
+     * open a New View and its Overview and reposition it
+     */
+    af.newView_actionPerformed(null);
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov2 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov2);
+    assertNotSame(ov1, ov2);
+    ov2.setFrameBounds(25, 35, 205, 405);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    /*
+     * change preferences (should _not_ affect reloaded Overviews)
+     */
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "true");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false");
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    /*
+     * workaround: explicitly select View 1 (not in focus after restore)
+     */
+    af.tabSelectionChanged(1);
+
+    /*
+     * verify restored overview for View 1
+     */
+    ov2 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov2.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov2.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+    assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405));
+    assertTrue(ov2.isShowHiddenRegions());
+
+    /*
+     * verify restored overview for Original view
+     */
+    af.tabSelectionChanged(0);
+    ov1 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov1.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+    assertTrue(ov1.isShowHiddenRegions());
+  }
+
+  /**
+   * Test that a view with no Overview is restored with no Overview, even if
+   * 'Open Overview' is selected in Preferences
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverNoOverview() throws Exception
+  {
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    assertNull(af.alignPanel.getOverviewPanel());
+  }
+
+  /**
+   * Test that a view from an older version of Jalview is restored with Overview automatically shown when the preference is set
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testAutoShowOverviewForLegacyProjects() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile.jvp", DataSourceType.FILE);
+
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    assertNotNull(af.alignPanel.getOverviewPanel());
+  }
+
+  /**
+   * Test that loading example.jvp, doing some stuff, then hitting reload
+   * doesn't leave the modified window still open
+   * 
+   * See JAL-4127 - interactively performing the same actions and reloading
+   * works fine, but programmatically they do not
+   * 
+   * @throws Exception
+   */
+  @Test(groups = {"Functional"}, enabled=false)
+  public void testReloadActuallyReloads() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile.jvp", DataSourceType.FILE);
+    af.getViewport().getColumnSelection().addElement(3);
+    af.hideSelColumns_actionPerformed(null);
+    af.newView("new", true);
+    af.reload_actionPerformed(null);
+    Thread.sleep(30);
+    // af exists still but isn't shown
+    assertTrue(af.isClosed());
+  }
 }
diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
index c59e520..cdb69e3 100644
--- a/test/jalview/renderer/OverviewRendererTest.java
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -46,8 +46,9 @@ public class OverviewRendererTest
   @Test
   public void testGetColumnColourFromSequence()
   {
-    OverviewResColourFinder cf = new OverviewResColourFinder(false,
-            Color.PINK, Color.green); // gapColour, hiddenColour
+    // gapColour, residueColour, hiddenColour
+    OverviewResColourFinder cf = new OverviewResColourFinder(
+            Color.PINK, Color.white, Color.green); 
     Sequence seq1 = new Sequence("seq1", "PQ-RL-");
     Sequence seq2 = new Sequence("seq2", "FVE");
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 3931dbf..028777e 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -22,6 +22,12 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -30,16 +36,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewCanvas;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
-import java.awt.Color;
-import java.util.ArrayList;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class OverviewResColourFinderTest
 {
 
@@ -185,7 +186,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
 
     // use legacy colouring
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
 
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -200,7 +201,7 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
 
     // use new colouring
-    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
 
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -233,12 +234,10 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
 
     // legacy colouring set explicitly via constructor
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
     shader = new ResidueShader();
 
     // residues light gray
@@ -259,12 +258,10 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
-    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
     shader = new ResidueShader(new ZappoColourScheme());
 
     // M residue pink
@@ -276,7 +273,7 @@ public class OverviewResColourFinderTest
     assertEquals(Color.blue, c);
 
     // legacy colouring with colour scheme
-    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
 
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index 180deaf..28f39d8 100644
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -23,8 +23,6 @@ package jalview.schemes;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
 
-import jalview.gui.JvOptionPane;
-
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -32,6 +30,8 @@ import java.util.Map;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class ResiduePropertiesTest
 {
 
@@ -222,7 +222,8 @@ public class ResiduePropertiesTest
      */
     residues = ResidueProperties.getResidues(true, true);
     Collections.sort(residues);
-    assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
+    assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
+            residues.toString());
   }
 
   @Test(groups = { "Functional" })
diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index cef9ffc..99c097f 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -24,13 +24,15 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class ComparisonTest
 {
 
@@ -41,6 +43,12 @@ public class ComparisonTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+  }
+
   @Test(groups = { "Functional" })
   public void testIsGap()
   {
@@ -60,24 +68,41 @@ public class ComparisonTest
   @Test(groups = { "Functional" })
   public void testIsNucleotide_sequences()
   {
-    SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
+    SequenceI seq = new Sequence("eightypercent+fivepercent", "agctuagcPV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
     assertFalse(
             Comparison.isNucleotide(new SequenceI[][]
             { new SequenceI[] { seq } }));
 
-    seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
+    seq = new Sequence("eightyfivepercent+tenpercent",
+            "agctuagcgVagctuagcuVE");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence(">nineyfivepercent+0percent",
+            "aagctuagcgEagctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
-    seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
+    seq = new Sequence("nineyfivepercent+fivepercent",
+            "agctuagcgWagctuagcua");
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
+    seq = new Sequence("nineyfivepercent+tenpercent",
+            "agctuagcgEWWctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+    seq = new Sequence("eightyfivepercent+fifteenpercent",
+            "agctuagcgWWWctuagcua");
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
     seq = new Sequence("eightyfivepercentgapped",
             "--agc--tuA--GCPV-a---gct-uA-GC---UV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
 
-    seq = new Sequence("nineypercentgapped",
-            "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
+    seq = new Sequence("ninetyfivepercentgapped",
+            "ag--ct-u-a---gc---g----aag--c---tuagcuV");
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     seq = new Sequence("allgap", "---------");
@@ -108,8 +133,10 @@ public class ComparisonTest
                 new SequenceI[]
                 { seq, seq, seq, seq, seq2, seq2, null } }));
 
-    seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
-    // 12/14 = 85.7%
+    String seqString = "aaatatatatgEcctgagtcgt";
+    seq = new Sequence("ShortProteinThatLooksLikeDNA", seqString);
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+    seq = new Sequence("LongProteinThatLooksLikeDNA", seqString.repeat(10));
     assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
 
     assertFalse(Comparison.isNucleotide((SequenceI[]) null));
@@ -165,6 +192,25 @@ public class ComparisonTest
     assertFalse(Comparison.isNucleotide('P'));
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsNucleotideAmbiguity()
+  {
+    assertTrue(Comparison.isNucleotide('b', true));
+    assertTrue(Comparison.isNucleotide('B', true));
+    assertTrue(Comparison.isNucleotide('d', true));
+    assertTrue(Comparison.isNucleotide('V', true));
+    assertTrue(Comparison.isNucleotide('M', true));
+    assertTrue(Comparison.isNucleotide('s', true));
+    assertTrue(Comparison.isNucleotide('W', true));
+    assertTrue(Comparison.isNucleotide('x', true));
+    assertTrue(Comparison.isNucleotide('Y', true));
+    assertTrue(Comparison.isNucleotide('r', true));
+    assertTrue(Comparison.isNucleotide('i', true));
+    assertFalse(Comparison.isNucleotide('-', true));
+    assertFalse(Comparison.isNucleotide('n', true));
+    assertFalse(Comparison.isNucleotide('P', true));
+  }
+
   /**
    * Test the percentage identity calculation for two sequences
    */
@@ -206,6 +252,30 @@ public class ComparisonTest
     assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
     assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
     assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("gatactawgataca", false));
+    // including nucleotide ambiguity
+    assertTrue(
+            Comparison.isNucleotideSequence("gatacaWgataca", true, true));
+    assertFalse(
+            Comparison.isNucleotideSequence("gatacaEgataca", true, true));
+
+    // not quite all nucleotides and ambiguity codes
+    Sequence seq = new Sequence("Ambiguity DNA codes", "gatacagatacabve");
+    assertFalse(Comparison.isNucleotide(seq));
+    // all nucleotide and nucleotide ambiguity codes
+    seq = new Sequence("Ambiguity DNA codes", "gatacagatacabvt");
+    assertFalse(Comparison.isNucleotide(seq));
+    seq = new Sequence("Ambiguity DNA codes", "agatacabb");
+    assertFalse(Comparison.isNucleotide(seq));
+    // 55% nucleotide with only Xs or Ns
+    assertTrue(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacaXXXX")));
+    assertTrue(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacaNNNN")));
+    assertFalse(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacXXXXX")));
+    assertFalse(Comparison
+            .isNucleotide(new Sequence("dnaWithXs", "gatacNNNNN")));
   }
 
   @Test(groups = { "Functional" })
@@ -219,4 +289,23 @@ public class ComparisonTest
     assertFalse(Comparison.isSameResidue('a', 'A', true));
     assertFalse(Comparison.isSameResidue('A', 'a', true));
   }
+
+  @Test(groups = { "Functional" })
+  public void testNucleotideProportion()
+  {
+    assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 3));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 3));
+    assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 4));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 4));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(17, 20));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(18, 20));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(38, 50));
+    assertTrue(Comparison.myShortSequenceNucleotideProportionCount(39, 50));
+    assertFalse(
+            Comparison.myShortSequenceNucleotideProportionCount(54, 100));
+    assertTrue(
+            Comparison.myShortSequenceNucleotideProportionCount(55, 100));
+  }
 }
diff --git a/test/jalview/util/comparisonTestProps.jvprops b/test/jalview/util/comparisonTestProps.jvprops
new file mode 100644
index 0000000..55f9303
--- /dev/null
+++ b/test/jalview/util/comparisonTestProps.jvprops
@@ -0,0 +1,5 @@
+NUCLEOTIDE_AMBIGUITY_DETECTION=true
+NUCLEOTIDE_COUNT_PERCENT=55
+NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT=95
+NUCLEOTIDE_COUNT_SHORT=100
+NUCLEOTIDE_COUNT_VERY_SHORT=4
diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 7eb3b75..176cddc 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -224,9 +224,6 @@ public class UniprotTest
     res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
             DBRefSource.UNIPROT);
     assertEquals(2, res.size());
-    res = DBRefUtils.searchRefs(seq.getDBRefs(), "AAK85932");
-    assertEquals(1, res.size());
-    assertTrue("1".equals(res.get(0).getVersion()));
     /*
      * NB this test fragile - relies on ordering being preserved
      */
diff --git a/utils/download_jdks.sh b/utils/download_jdks.sh
index cf8634a..b6e8379 100755
--- a/utils/download_jdks.sh
+++ b/utils/download_jdks.sh
@@ -15,26 +15,64 @@
 ### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
 
 BASE=https://api.adoptium.net/v3/binary/latest
+ZULU_BASE=https://cdn.azul.com/zulu/bin
 RELEASE_TYPE=ga
 JVM_IMPL=hotspot
 HEAP_SIZE=normal
 VENDOR=eclipse
 IMAGE_TYPE=jdk
+TAR=tar
+ZIP=zip
+UNZIP=unzip
+
+STRIP_MAC_APP_BUNDLING=false
+# archives not needed for JDKs
+CREATE_ARCHIVES=""
+# need zip with top-level jre dir for getdown updates. need tgz without top-level jre dir for install4j bundling
 
 RM=/bin/rm
 
 # unzip-strip from https://superuser.com/questions/518347/equivalent-to-tars-strip-components-1-in-unzip
-unzip-strip() (
+unzip-strip() {
   local zip=$1
   local dest=${2:-.}
-  local temp=$(mktemp -d) && unzip -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
+  local temp=$(mktemp -d) && $UNZIP -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
   shopt -s dotglob && local f=("$temp"/*) &&
   if (( ${#f[@]} == 1 )) && [[ -d "${f[0]}" ]] ; then
     mv "$temp"/*/* "$dest"
   else
     mv "$temp"/* "$dest"
   fi && rmdir "$temp"/* "$temp"
-)
+}
+
+dl_zulu() {
+  local OS="$1"
+  local ARCH="$2"
+  local VERSION="$3"
+  local TARFILE="$4"
+  declare -A osmap
+  osmap[mac]=macosx
+  osmap[windows]=win
+  osmap[linux]=linux
+  ZOS="${osmap[$OS]}"
+  echo "- Looking for download from Azul"
+  LATEST_DL_URL_FILE=$(wget -q -O - "${ZULU_BASE}/" | perl -n -e 'm/]*href="(([^"]*\/)?zulu[^"]*-ca-'"${IMAGE_TYPE}""${VERSION}"'\.[^"]*-'"${ZOS}"'_'"${ARCH}"'.tar.gz)"[^"]*>/ && print "$1\n";' | tail -1)
+  local URL="${ZULU_BASE}/${LATEST_DL_URL_FILE}"
+  if [ -z "${LATEST_DL_URL_FILE}" ]; then
+    echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' found at Azul"
+    return 1
+  fi
+  echo "- Found at Azul. Downloading '${URL}'"
+  wget -q -O "${TARFILE}" "${URL}" "${TARFILE}"
+  echo RETURN=$?
+  if [ "$?" != 0 ]; then
+    echo "- Download from Azul failed"
+    return 1
+  fi
+  return 0
+}
+
+declare -A DOWNLOAD_SUMMARY
 
 for FEATURE_VERSION in 8 11 17; do
   for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
@@ -42,13 +80,30 @@ for FEATURE_VERSION in 8 11 17; do
     ARCH=${OS_ARCH#*:}
     NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
     TARFILE="${NAME}.tgz"
+    DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+    STRIP_COMPONENTS=1
+    MAC_STRIP_COMPONENTS=3
     echo "* Downloading ${TARFILE}"
     URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
     wget -q -O "${TARFILE}" "${URL}"
     if [ "$?" != 0 ]; then
-      echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+      echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' at Adoptium"
       $RM -f "${TARFILE}"
-      continue;
+
+      # Try Azul Zulu (not an API, a bit messier, but has Java 8 JRE for mac:aarch64
+      dl_zulu "${OS}" "${ARCH}" "${FEATURE_VERSION}" "${TARFILE}"
+
+      if [ "$?" != 0 ]; then
+        DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+        continue;
+      fi
+      STRIP_COMPONENTS=2
+      MAC_STRIP_COMPONENTS=4
+      DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Azul"
+      echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Azul"
+    else
+      DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Adoptium"
+      echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Adoptium"
     fi
     echo "Unpacking ${TARFILE}"
     JREDIR="${NAME}/${IMAGE_TYPE}"
@@ -60,14 +115,58 @@ for FEATURE_VERSION in 8 11 17; do
       RET=$?
     else
       echo "using tar"
-      tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
-      RET=$?
+      if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
+        echo "Running $TAR --strip-components=\"${MAC_STRIP_COMPONENTS}\" -C \"${JREDIR}\" -zxf \"${TARFILE}\" \"*/Contents/Home\""
+        $TAR --strip-components="${MAC_STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
+        RET=$?
+      else
+        $TAR --strip-components="${STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}"
+        RET=$?
+      fi
     fi
     if [ "$RET" != 0 ]; then
       echo "Error unpacking ${TARFILE}"
       exit 1
     fi
     $RM "${TARFILE}"
+    if [ \! -z "$CREATE_ARCHIVES" ]; then
+      for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
+        ARCHIVEDIR=$CREATEARCHIVE
+        case $CREATEARCHIVE in
+          zip)
+            EXT=${CREATEARCHIVE}
+            echo "Creating ${NAME}.${EXT} for getdown updates"
+            [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+            ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
+            ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
+            [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
+            cd ${NAME}
+            $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
+            cd -
+            ;;
+          tgz)
+            EXT=tar.gz
+            echo "Creating ${NAME}.${EXT} for install4j bundling"
+            [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+            $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
+            # make symbolic link with _ instead of - for install4j9
+            NEWNAME=${NAME//-/_}
+            echo "Linking from ${NEWNAME}.${EXT} for install4j9"
+            [ -e "${ARCHIVEDIR}/${NEWNAME}.${EXT}" ] && $RM "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+            ln -s "${NAME}.${EXT}" "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+            ;;
+          *)
+            echo "Archiving as '${CREATEARCHIVE}' file not supported"
+            ;;
+        esac
+      done
+    fi
   done
 done
 
+echo ""
+echo "Download Summary"
+for OA in "${!DOWNLOAD_SUMMARY[@]}"; do
+  echo "$OA: ${DOWNLOAD_SUMMARY[$OA]}"
+done
+
diff --git a/utils/download_jres.sh b/utils/download_jres.sh
index 26442ea..c1a5a0d 100755
--- a/utils/download_jres.sh
+++ b/utils/download_jres.sh
@@ -15,6 +15,7 @@
 ### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
 
 BASE=https://api.adoptium.net/v3/binary/latest
+ZULU_BASE=https://cdn.azul.com/zulu/bin
 RELEASE_TYPE=ga
 JVM_IMPL=hotspot
 HEAP_SIZE=normal
@@ -31,7 +32,7 @@ CREATE_ARCHIVES="zip tgz"
 RM=/bin/rm
 
 # unzip-strip from https://superuser.com/questions/518347/equivalent-to-tars-strip-components-1-in-unzip
-unzip-strip() (
+unzip-strip() {
   local zip=$1
   local dest=${2:-.}
   local temp=$(mktemp -d) && $UNZIP -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
@@ -41,7 +42,36 @@ unzip-strip() (
   else
     mv "$temp"/* "$dest"
   fi && rmdir "$temp"/* "$temp"
-)
+}
+
+dl_zulu() {
+  local OS="$1"
+  local ARCH="$2"
+  local VERSION="$3"
+  local TARFILE="$4"
+  declare -A osmap
+  osmap[mac]=macosx
+  osmap[windows]=win
+  osmap[linux]=linux
+  ZOS="${osmap[$OS]}"
+  echo "- Looking for download from Azul"
+  LATEST_DL_URL_FILE=$(wget -q -O - "${ZULU_BASE}/" | perl -n -e 'm/]*href="(([^"]*\/)?zulu[^"]*-ca-'"${IMAGE_TYPE}""${VERSION}"'\.[^"]*-'"${ZOS}"'_'"${ARCH}"'.tar.gz)"[^"]*>/ && print "$1\n";' | tail -1)
+  local URL="${ZULU_BASE}/${LATEST_DL_URL_FILE}"
+  if [ -z "${LATEST_DL_URL_FILE}" ]; then
+    echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' found at Azul"
+    return 1
+  fi
+  echo "- Found at Azul. Downloading '${URL}'"
+  wget -q -O "${TARFILE}" "${URL}" "${TARFILE}"
+  echo RETURN=$?
+  if [ "$?" != 0 ]; then
+    echo "- Download from Azul failed"
+    return 1
+  fi
+  return 0
+}
+
+declare -A DOWNLOAD_SUMMARY
 
 for FEATURE_VERSION in 8 11 17; do
   for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
@@ -49,13 +79,30 @@ for FEATURE_VERSION in 8 11 17; do
     ARCH=${OS_ARCH#*:}
     NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
     TARFILE="${NAME}.tgz"
+    DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+    STRIP_COMPONENTS=1
+    MAC_STRIP_COMPONENTS=3
     echo "* Downloading ${TARFILE}"
     URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
     wget -q -O "${TARFILE}" "${URL}"
     if [ "$?" != 0 ]; then
-      echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+      echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' at Adoptium"
       $RM -f "${TARFILE}"
-      continue;
+
+      # Try Azul Zulu (not an API, a bit messier, but has Java 8 JRE for mac:aarch64
+      dl_zulu "${OS}" "${ARCH}" "${FEATURE_VERSION}" "${TARFILE}"
+
+      if [ "$?" != 0 ]; then
+        DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+        continue;
+      fi
+      STRIP_COMPONENTS=2
+      MAC_STRIP_COMPONENTS=4
+      DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Azul"
+      echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Azul"
+    else
+      DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Adoptium"
+      echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Adoptium"
     fi
     echo "Unpacking ${TARFILE}"
     JREDIR="${NAME}/${IMAGE_TYPE}"
@@ -68,10 +115,11 @@ for FEATURE_VERSION in 8 11 17; do
     else
       echo "using tar"
       if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
-        $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
+        echo "Running $TAR --strip-components=\"${MAC_STRIP_COMPONENTS}\" -C \"${JREDIR}\" -zxf \"${TARFILE}\" \"*/Contents/Home\""
+        $TAR --strip-components="${MAC_STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
         RET=$?
       else
-        $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+        $TAR --strip-components="${STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}"
         RET=$?
       fi
     fi
@@ -115,3 +163,9 @@ for FEATURE_VERSION in 8 11 17; do
   done
 done
 
+echo ""
+echo "Download Summary"
+for OA in "${!DOWNLOAD_SUMMARY[@]}"; do
+  echo "$OA: ${DOWNLOAD_SUMMARY[$OA]}"
+done
+
diff --git a/utils/install4j/auto_file_associations-i4j10.pl b/utils/install4j/auto_file_associations-i4j10.pl
new file mode 100755
index 0000000..f7e17a1
--- /dev/null
+++ b/utils/install4j/auto_file_associations-i4j10.pl
@@ -0,0 +1,227 @@
+#!/usr/bin/env perl
+
+use strict;
+
+my $i4jversion = 10;
+if ($ARGV[0] eq "-v") {
+  shift @ARGV;
+  $i4jversion = shift @ARGV;
+  die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
+}
+
+my $fileformats = $ARGV[0];
+$fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
+
+# default mimetype will be text/x-$shortname
+# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
+# TODO: look up standard mime type used for BLASTfmt matrices, etc
+my $mimetypes = {
+  rnaml => "application/rnaml+xml",
+  biojson => "application/x-jalview-biojson+json",
+  jnet => "application/x-jalview-jnet+text",
+  features => "application/x-jalview-features+text",
+  scorematrix => "application/x-jalview-scorematrix+text",
+  pdb => "chemical/x-pdb",
+  mmcif => "chemical/x-cif",
+  mmcif2 => "chemical/x-mmcif",
+  jalview => "application/x-jalview+xml+zip",
+  jvl => "application/x-jalview-jvl+text",
+  annotations => "application/x-jalview-annotations+text",
+};
+
+my @dontaddshortname = qw(features json);
+my @dontaddextension = qw(html xml json jar mfa fastq);
+my $add_associations = {
+  biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
+  gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
+  gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
+  features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
+  annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
+  mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
+  mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
+  jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
+  jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
+  scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
+};
+my $add_extensions = {
+  blc => ["blc"],
+};
+my @put_first = qw(jalview jvl);
+my @owner = @put_first;
+
+my @non_primary = qw(mmcif mmcif2 pdb);
+
+my $v = ($i4jversion >= 8)?$i4jversion:"";
+my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
+my $i4jtemplate;
+my $mactemplatefile = "file_associations_template-Info_plist.xml";
+my $mactemplate;
+
+open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
+while(){
+  $mactemplate .= $_;
+}
+close(MT);
+open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
+while(){
+  $i4jtemplate .= $_;
+}
+close(IT);
+my $macauto;
+my $i4jauto;
+
+my $macautofile = $mactemplatefile;
+$macautofile =~ s/template/auto$1/;
+
+my $i4jautofile = $i4jtemplatefile;
+$i4jautofile =~ s/template/auto$1/;
+
+for my $key (sort keys %$add_associations) {
+  my $a = $add_associations->{$key};
+  warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
+}
+
+open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
+print MA "CFBundleDocumentTypes\n\n\n";
+
+open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
+
+open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
+my $id = 10000;
+my $file_associations = {};
+while(my $line = ) {
+  $line =~ s/\s+/ /g;
+  $line =~ s/(^ | $)//g;
+  if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
+    my $shortname = lc($1);
+    next if (grep($_ eq $shortname, @dontaddshortname));
+    my $name = $2;
+    my $extensions = $3;
+    $extensions =~ s/\s+//g;
+    my @possextensions = map(lc($_),split(m/,/,$extensions));
+    my @extensions;
+    my $addext = $add_extensions->{$shortname};
+    if (ref($addext) eq "ARRAY") {
+      push(@possextensions, @$addext);
+    }
+    for my $possext (@possextensions) {
+      next if grep($_ eq $possext, @extensions);
+      next if grep($_ eq $possext, @dontaddextension);
+      push(@extensions,$possext);
+    }
+    next unless scalar(@extensions);
+    $file_associations->{$shortname} = {
+      shortname => $shortname,
+      name => $name,
+      extensions => \@extensions
+    };
+    warn("Reading file association for $shortname (".join(",",@extensions).")\n");
+  }
+}
+close(IN);
+
+my %all_associations = (%$file_associations, %$add_associations);
+
+my @ordered = (@put_first, @non_primary);
+for my $key (sort keys %all_associations) {
+  next if grep($_ eq $key, @ordered);
+  push(@ordered, $key);
+}
+my $num = $#ordered + 1;
+
+warn("--\n");
+
+my $i4jcount = 0;
+for my $shortname (@ordered) {
+  my $a = $all_associations{$shortname};
+  next if (ref($a) ne "HASH");
+
+  my $name = $a->{name};
+  my $extensions = $a->{extensions};
+  my $mimetype = $mimetypes->{$shortname};
+  $mimetype = "application/x-$shortname+txt" unless $mimetype;
+
+  my $iconfile = $a->{iconfile};
+  $iconfile = "Jalview-File" unless $iconfile;
+
+  my $owner = grep($_ eq $shortname, @owner);
+  my $primary = (! grep($_ eq $shortname, @non_primary));
+  my $primarystring = $primary?"true":"false";
+  #my $role = $owner?"Owner":($primary?"Editor":"Viewer");
+  my $role = $primary?"Editor":"Viewer";
+  my $rank = $owner?"Owner":($primary?"Default":"Alternate");
+
+  my @extensions = @$extensions;
+
+  my $xname = xml_escape($name);
+  my $xmimetype = xml_escape($mimetype);
+  my $xshortname = xml_escape($shortname);
+  my $xiconfile = xml_escape($iconfile);
+  my $xrole = xml_escape($role);
+  my $xROLE = xml_escape(uc($role));
+  my $xrank = xml_escape($rank);
+  my $xprimarystring = xml_escape($primarystring);
+
+  my $macentry = $mactemplate;
+  $macentry =~ s/\$\$NAME\$\$/$xname/g;
+  $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+  $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+  $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+  $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
+  $macentry =~ s/\$\$RANK\$\$/$xrank/g;
+  $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+  while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
+    my $pre = $1;
+    my $post = $2;
+    my $macextensions;
+    for my $ext (@extensions) {
+      my $xext = xml_escape($ext);
+      $macextensions .= $pre.$xext.$post;
+    }
+    $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+  }
+  print MA $macentry;
+
+  my $i4jentry = $i4jtemplate;
+  $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
+  $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+  $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+  $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+  $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+  $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
+
+  my $ext = join(",",sort(@extensions));
+  my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
+  my $progresspercent = int(($i4jcount/$num)*100);
+  $progresspercent = 100 if $progresspercent > 100;
+  $i4jcount++;
+  my $xext = xml_escape($ext);
+  my $addunixextension = "true";
+
+  $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
+  $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
+  $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
+  $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
+  $i4jentry =~ s/\$\$ID\$\$/$id/g;
+  $id++;
+  $i4jentry =~ s/\$\$ID1\$\$/$id/g;
+  $id++;
+  $i4jentry =~ s/\$\$ID2\$\$/$id/g;
+  $id++;
+
+  print IA $i4jentry;
+
+  delete $all_associations{$shortname};
+  warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
+}
+
+close(IA);
+print MA "\n";
+close(MA);
+
+sub xml_escape {
+  my $x = shift;
+  # stolen from Pod::Simple::XMLOutStream in base distro
+  $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
+  return $x;
+}  
diff --git a/utils/install4j/file_associations_auto-Info_plist.xml b/utils/install4j/file_associations_auto-Info_plist.xml
index 0b927a8..2e23321 100644
--- a/utils/install4j/file_associations_auto-Info_plist.xml
+++ b/utils/install4j/file_associations_auto-Info_plist.xml
@@ -12,6 +12,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Owner
 CFBundleTypeMIMETypes
 
 application/x-jalview+xml+zip
@@ -31,6 +33,8 @@
 jvl_file.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Owner
 CFBundleTypeMIMETypes
 
 application/x-jalview-jvl+text
@@ -50,6 +54,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Viewer
+LSHandlerRank
+Alternate
 CFBundleTypeMIMETypes
 
 chemical/x-cif
@@ -70,6 +76,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Viewer
+LSHandlerRank
+Alternate
 CFBundleTypeMIMETypes
 
 chemical/x-mmcif
@@ -90,6 +98,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Viewer
+LSHandlerRank
+Alternate
 CFBundleTypeMIMETypes
 
 chemical/x-pdb
@@ -109,6 +119,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-amsa+txt
@@ -129,6 +141,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-jalview-annotations+text
@@ -148,6 +162,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-jalview-biojson+json
@@ -167,6 +183,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-blc+txt
@@ -186,6 +204,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-clustal+txt
@@ -205,6 +225,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-embl+txt
@@ -225,6 +247,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-fasta+txt
@@ -245,6 +269,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-jalview-features+text
@@ -265,6 +291,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-genbank+txt
@@ -284,6 +312,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-gff2+txt
@@ -303,6 +333,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-gff3+txt
@@ -323,6 +355,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-jalview-jnet+text
@@ -342,6 +376,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-msf+txt
@@ -361,6 +397,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-pfam+txt
@@ -380,6 +418,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-phylip+txt
@@ -399,6 +439,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-pileup+txt
@@ -418,6 +460,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-pir+txt
@@ -437,6 +481,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/rnaml+xml
@@ -456,6 +502,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-jalview-scorematrix+text
@@ -476,6 +524,8 @@
 Jalview-File.icns
 CFBundleTypeRole
 Editor
+LSHandlerRank
+Default
 CFBundleTypeMIMETypes
 
 application/x-stockholm+txt
diff --git a/utils/install4j/file_associations_auto-install4j10.xml b/utils/install4j/file_associations_auto-install4j10.xml
new file mode 100644
index 0000000..ee70251
--- /dev/null
+++ b/utils/install4j/file_associations_auto-install4j10.xml
@@ -0,0 +1,1125 @@
+
+                  
+                    
+                      Jalview (.jvp)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Jalview File
+                      jvp
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview+xml+zip
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Jalview Launch (.jvl)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Jalview Launch File
+                      jvl
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          jvl_file.png
+                        
+                      
+                      application/x-jalview-jvl+text
+                      
+                        
+                          jvl_file.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      CIF (.cif)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      CIF File
+                      cif
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      chemical/x-cif
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      mmCIF (.mcif, .mmcif)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      mmCIF File
+                      mcif,mmcif
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      chemical/x-mmcif
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      PDB (.ent, .pdb)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      PDB File
+                      ent,pdb
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      chemical/x-pdb
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      AMSA (.amsa)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      AMSA File
+                      amsa
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-amsa+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Jalview Annotations (.annotations, .jvannotations)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Jalview Annotations File
+                      annotations,jvannotations
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview-annotations+text
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      BioJSON (.biojson)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      BioJSON File
+                      biojson
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview-biojson+json
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      BLC (.blc)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      BLC File
+                      blc
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-blc+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Clustal (.aln)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Clustal File
+                      aln
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-clustal+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      ENA Flatfile (.txt)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      ENA Flatfile File
+                      txt
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-embl+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Fasta (.fa, .fasta)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Fasta File
+                      fa,fasta
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-fasta+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Jalview Features (.features, .jvfeatures)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Jalview Features File
+                      features,jvfeatures
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview-features+text
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      GenBank Flatfile (.gb, .gbk)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      GenBank Flatfile File
+                      gb,gbk
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-genbank+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Generic Features Format v2 (.gff2)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Generic Features Format v2 File
+                      gff2
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-gff2+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Generic Features Format v3 (.gff3)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Generic Features Format v3 File
+                      gff3
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-gff3+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      JnetFile (.concise, .jnet)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      JnetFile File
+                      concise,jnet
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview-jnet+text
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      MSF (.msf)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      MSF File
+                      msf
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-msf+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      PFAM (.pfam)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      PFAM File
+                      pfam
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-pfam+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      PHYLIP (.phy)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      PHYLIP File
+                      phy
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-phylip+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      PileUp (.pileup)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      PileUp File
+                      pileup
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-pileup+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      PIR (.pir)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      PIR File
+                      pir
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-pir+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      RNAML (.rnaml)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      RNAML File
+                      rnaml
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/rnaml+xml
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Substitution Matrix (.mat)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Substitution Matrix File
+                      mat
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-jalview-scorematrix+text
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
+
+                  
+                    
+                      Stockholm (.stk, .sto)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      Stockholm File
+                      stk,sto
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          Jalview-File.png
+                        
+                      
+                      application/x-stockholm+txt
+                      
+                        
+                          Jalview-File.ico
+                        
+                      
+                    
+                  
+
+
diff --git a/utils/install4j/file_associations_template-Info_plist.xml b/utils/install4j/file_associations_template-Info_plist.xml
index a260658..afac20c 100644
--- a/utils/install4j/file_associations_template-Info_plist.xml
+++ b/utils/install4j/file_associations_template-Info_plist.xml
@@ -9,6 +9,8 @@ $$
 $$ICONFILE$$.icns
 CFBundleTypeRole
 $$ROLE$$
+LSHandlerRank
+$$RANK$$
 CFBundleTypeMIMETypes
 
 $$MIMETYPE$$
diff --git a/utils/install4j/file_associations_template-install4j10.xml b/utils/install4j/file_associations_template-install4j10.xml
new file mode 100644
index 0000000..8663ed9
--- /dev/null
+++ b/utils/install4j/file_associations_template-install4j10.xml
@@ -0,0 +1,45 @@
+
+                  
+                    
+                      $$NAME$$ ($$DISPLAYEXTENSION$$)
+                      Creating file associations...
+                      
+                      
+                    
+                  
+
+                  
+                    
+                      
+                    
+                  
+
+                  
+                    
+                      $$NAME$$ File
+                      $$EXTENSION$$
+                      JALVIEW
+                      
+                      
+                      
+                      
+                      
+                        
+                          $$ICONFILE$$.png
+                        
+                      
+                      $$MIMETYPE$$
+                      
+                        
+                          $$ICONFILE$$.ico
+                        
+                      
+                    
+                  
+
+
diff --git a/utils/install4j/install4j10_template.install4j b/utils/install4j/install4j10_template.install4j
new file mode 100644
index 0000000..ac2f1eb
--- /dev/null
+++ b/utils/install4j/install4j10_template.install4j
@@ -0,0 +1,1496 @@
+
+
+  
+  
+    
+      
+      
+      
+    
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        *.dylib
+        *.so
+        *.jnilib
+        unpack200
+        tnameserv
+        servertool
+        rmiregistry
+        rmid
+        policytool
+        pack200
+        orbd
+        keytool
+        jjs
+        java
+        jspawnhelper
+        libfreetype.dylib.6
+        applet
+        jaotc
+        jfr
+        jrunscript
+        libjli.dylib
+      
+    
+  
+  
+    
+      
+      
+      
+    
+    
+      
+      
+      
+    
+    
+      
+      
+      
+    
+    
+      
+        
+          
+        
+      
+      
+      
+      
+      
+    
+    
+      
+        
+          
+        
+      
+    
+  
+  
+    
+      
+        
+      
+      
+        
+          
+          
+        
+      
+      
+        
+          
+          
+        
+        
+          
+          
+        
+      
+      ${compiler:file("${compiler:INFO_PLIST_FILE_ASSOCIATIONS_FILE}")}
+      
+        
+      
+      
+        
+        
+        
+      
+    
+  
+  
+    
+      
+        
+          
+        
+        
+          
+            
+              
+                
+                  
+                    
+                      255
+                      255
+                      255
+                      255
+                    
+                    
+                      49
+                      52
+                      53
+                      255
+                    
+                  
+                
+                
+                  
+                    
+                  
+                
+                
+                  
+                    255
+                    255
+                    255
+                    255
+                  
+                
+                
+                
+                  
+                    ${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}
+                  
+                
+                
+                  
+                    5
+                    10
+                    10
+                    10
+                  
+                
+              
+              
+                imageAnchor
+                imageEdgeBackgroundColor
+                imageFile
+              
+            
+          
+          
+            
+              
+                
+              
+              
+                labelText
+              
+            
+          
+        
+        
+          
+            
+              
+                
+                  
+                
+              
+              
+                
+                  
+                    
+                      String userHome = (String)context.getVariable("sys.userHome");
+
+ArrayList<String> tryPaths = new ArrayList<> ();
+tryPaths.add(userHome + File.separator + "bin");
+tryPaths.add(userHome + File.separator + ".local" + File.separator + "bin");
+tryPaths.add(userHome + File.separator + "local" + File.separator + "bin");
+tryPaths.add(userHome + File.separator + "opt" + File.separator + "bin");
+
+if (Util.isMacOS()) { // && root permission?
+    tryPaths.add(File.separator + "usr" + File.separator + "local" + File.separator + "bin"); 
+}
+
+for (int i = 0; i < tryPaths.size(); i++) {
+    String tryPath = tryPaths.get(i);
+    File unixUserBinDir = new File(tryPath);
+    if (unixUserBinDir.exists()) {
+        return tryPath;
+    }
+}
+
+return null;
+
+                    
+                  
+                  unixUserBinDir
+                
+                Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()
+              
+              
+                
+                  
+                    
+                      String javaHome = System.getProperty("java.home");
+String appName = ((String)context.getCompilerVariable("JALVIEW_APPLICATION_NAME")) + ".app";
+int i = javaHome.indexOf(appName);
+String wrapperLink = null;
+if (i > -1) {
+    wrapperLink = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS" + File.separator + ((String)context.getCompilerVariable("WRAPPER_LINK"));
+}
+return wrapperLink;
+
+                    
+                  
+                  macWrapperLinkLocation
+                
+                Util.isMacOS()
+              
+            
+          
+        
+        
+          
+            
+              
+                
+                  
+                    
+                      
+                        
+                          255
+                          255
+                          255
+                          255
+                        
+                        
+                          49
+                          52
+                          53
+                          255
+                        
+                      
+                    
+                    
+                      
+                        
+                      
+                    
+                    
+                      
+                        
+                          25
+                          143
+                          220
+                          255
+                        
+                        
+                          0
+                          74
+                          151
+                          255
+                        
+                      
+                    
+                    
+                    
+                      
+                        ${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}
+                      
+                    
+                    
+                      
+                        5
+                        10
+                        10
+                        10
+                      
+                    
+                  
+                  
+                    imageAnchor
+                    imageEdgeBackgroundColor
+                    imageFile
+                  
+                
+              
+            
+            
+              
+                
+                  
+                    sys.installationDir
+                  
+                
+                context.getBooleanVariable("sys.confirmedUpdateInstallation")
+              
+            
+            
+              
+                
+                  ${form:welcomeMessage}
+                
+                !context.isConsole()
+              
+              
+                
+                  
+                    
+                      String message = context.getMessage("ConsoleWelcomeLabel", context.getApplicationName());
+return console.askOkCancel(message, true);
+
+                    
+                  
+                
+              
+              
+                
+                  updateCheck
+                
+              
+              
+                
+                  ${i18n:ClickNext}
+                
+              
+            
+          
+          
+            !context.getBooleanVariable("sys.confirmedUpdateInstallation")
+            
+              
+                
+                  
+                    sys.installationDir
+                  
+                
+                context.getVariable("sys.responseFile") == null
+              
+            
+            
+              
+                
+                  ${i18n:SelectDirLabel(${compiler:sys.fullName})}
+                
+              
+              
+                
+                  
+                
+                
+                  allowSpacesOnUnix
+                  checkFreeSpace
+                  checkWritable
+                  existingDirWarning
+                  manualEntryAllowed
+                  showFreeDiskSpace
+                  showRequiredDiskSpace
+                  standardValidation
+                  suggestAppDir
+                  validateApplicationId
+                  validationScript
+                
+              
+            
+          
+          
+            
+              
+                
+                  ${i18n:SelectComponentsLabel2}
+                
+                !context.isConsole()
+              
+              
+                
+                  
+                
+                
+                  selectionChangedScript
+                
+              
+            
+          
+          
+            
+              
+                
+                  ${i18n:SelectAssociationsLabel}
+                
+              
+              
+                
+                  
+                  
+                  
+                
+                
+                  showSelectionButtons
+                  selectionButtonPosition
+                
+              
+            
+          
+          
+            
+              
+              
+                
+                  
+                  ${compiler:APPLICATION_CATEGORIES}
+                  
+                    
+                      
+                        Examples
+                        
+                          
+                            examples
+                          
+                        
+                      
+                    
+                  
+                  ${compiler:JALVIEW_NAME}
+                  ${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}
+                
+                !context.getBooleanVariable("sys.programGroupDisabled")
+              
+              
+                
+                  
+                  ${compiler:APPLICATION_CATEGORIES}
+                  ${compiler:JALVIEW_NAME}
+                  ${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}
+                
+                !context.getBooleanVariable("sys.programGroupDisabled")
+              
+              
+                
+                  ${compiler:sys.fullName} ${compiler:sys.version}
+                
+              
+              
+                
+                  
+                    
+                      
+                    
+                  
+                  
+                
+                true
+              
+              
+                
+                  121
+                  
+                
+              
+              
+                
+                  
+                    
+                      Creating file associations...
+                      
+                      
+                    
+                  
+                  
+                    
+                      
+                    
+                  
+                  
+                    
+                      
+                        
+                          This action, identified by its name "EXTENSIONS_REPLACED_BY_GRADLE", will be replaced by gradle with the contents of file 'file_associations_auto_install4j.xml'.
+                          extensions_to_be_replaced_by_gradle
+                          JALVIEW
+                        
+                      
+                    
+                  
+                  
+                    
+                      Finished creating file associations
+                      
+                      
+                    
+                  
+                  
+                    
+                      
+                    
+                  
+                
+              
+              
+                
+                  JALVIEW
+                  jalview
+                
+              
+              
+                
+                  JALVIEW
+                  jalviews
+                
+              
+              
+                
+                  JALVIEW
+                  ${compiler:EXTRA_SCHEME}
+                
+              
+            
+            
+              
+                
+                  ${i18n:WizardPreparing}
+                
+              
+            
+          
+          
+            
+              
+                
+                  
+                  ${compiler:APPLICATION_CATEGORIES}
+                  ${compiler:JALVIEW_APPLICATION_NAME}
+                  
+                    
+                      ${installer:sys.contentDir}/${compiler:EXECUTABLE_NAME}
+                    
+                  
+                  
+                    
+                      ${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}
+                    
+                  
+                  ${compiler:JALVIEW_NAME}
+                  
+                    
+                      ${compiler:JALVIEW_DIR}/${compiler:PNG_ICON_FILE}
+                    
+                  
+                
+                !context.getBooleanVariable("sys.programGroupDisabled")
+              
+              
+                
+                  
+                  ${compiler:JALVIEW_APPLICATION_NAME}
+                  
+                    
+                      ${installer:sys.contentDir}/${compiler:EXECUTABLE_NAME}
+                    
+                  
+                  ${compiler:JALVIEW_APPLICATION_NAME}
+                  
+                    
+                      ${compiler:JALVIEW_DIR}/${compiler:PNG_ICON_FILE}
+                    
+                  
+                  
+                    
+                      ${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}
+                    
+                  
+                
+                context.getBooleanVariable("createDesktopLinkAction")
+              
+              
+                
+                  
+                    
+                      ${compiler:JALVIEW_APPLICATION_NAME}.app
+                    
+                  
+                
+                context.getBooleanVariable("addToDockAction")
+              
+              
+                
+                  
+                    
+                      ${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}
+                    
+                  
+                  
+                    
+                      ${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}
+                    
+                  
+                
+                Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()
+              
+              
+                
+                  
+                  ${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}
+                  Path
+                
+                context.getBooleanVariable("appendToPathAction")
+              
+              
+                
+                  
+                    
+                      ${installer:sys.contentDir}/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}
+                    
+                  
+                  
+                    
+                      ${installer:unixUserBinDir}/${compiler:WRAPPER_LINK}
+                    
+                  
+                
+                context.getBooleanVariable("makeSymbolicLinkAction") && ( Util.isLinux() || Util.isUnixInstaller() ) && ( context.getVariable("unixUserBinDir") != null )
+              
+              
+                
+                  
+                    
+                      ${installer:macWrapperLinkLocation}
+                    
+                  
+                  
+                    
+                      ${installer:unixUserBinDir}/${compiler:WRAPPER_LINK}
+                    
+                  
+                
+                context.getBooleanVariable("makeSymbolicLinkAction") && Util.isMacOS() && ( context.getVariable("unixUserBinDir") != null ) && ( context.getVariable("macWrapperLinkLocation") != null )
+              
+            
+            
+              
+                
+                  ${form:finishedMessage}
+                
+              
+              
+                
+                  ${i18n:CreateDesktopIcon}
+                  
+                  createDesktopLinkAction
+                
+                !Util.isMacOS()
+              
+              
+                
+                  ${i18n:AddToDock}
+                  
+                  addToDockAction
+                
+                Util.isMacOS()
+              
+              
+                
+                  Add ${compiler:JALVIEW_APPLICATION_NAME}'s bin folder to the Path environment variable
+                  
+                  appendToPathAction
+                
+                Util.isWindows()
+              
+              
+                
+                  Make a ${compiler:WRAPPER_LINK} symbolic link in ${installer:unixUserBinDir}
+                  
+                  makeSymbolicLinkAction
+                
+                ( Util.isLinux() || Util.isUnixInstaller() || ( Util.isMacOS() && ( context.getVariable("macWrapperLinkLocation") != null ) ) ) && ( context.getVariable("unixUserBinDir") != null )
+              
+            
+          
+        
+      
+      
+        
+          ${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}
+          
+        
+        
+          
+            
+              
+                
+                  
+                    
+                      255
+                      255
+                      255
+                      255
+                    
+                    
+                      49
+                      52
+                      53
+                      255
+                    
+                  
+                
+                
+                  
+                    
+                  
+                
+                
+                  
+                    192
+                    192
+                    192
+                    255
+                  
+                
+                
+                
+                  
+                    ${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}
+                  
+                
+                
+                  
+                    5
+                    10
+                    10
+                    10
+                  
+                
+              
+              
+                imageAnchor
+                imageEdgeBackgroundColor
+                imageFile
+              
+            
+          
+        
+        
+          
+            
+              
+              
+            
+          
+        
+        
+          
+            
+              
+                
+                  ${form:welcomeMessage}
+                
+                !context.isConsole()
+              
+              
+                
+                  
+                    
+                      String message = context.getMessage("ConfirmUninstall", context.getApplicationName());
+return console.askYesNo(message, true);
+
+                    
+                  
+                
+              
+            
+          
+          
+            
+              
+                
+                  
+                
+              
+              
+              
+                
+                  
+                
+              
+              
+                
+                  
+                    
+                      
+                        jre
+                      
+                    
+                    
+                      
+                        jre.jar
+                      
+                    
+                    
+                      
+                        .install4j
+                      
+                    
+                    
+                      
+                        getdown-launcher.jar
+                      
+                    
+                    
+                      
+                        getdown-launcher-old.jar
+                      
+                    
+                    
+                      
+                        getdown-launcher-new.jar
+                      
+                    
+                    
+                      
+                        gettingdown.lock
+                      
+                    
+                    
+                      
+                        jre.zip
+                      
+                    
+                    
+                      
+                        digest.txt
+                      
+                    
+                    
+                      
+                        digest2.txt
+                      
+                    
+                    
+                      
+                        getdown-launcher.jarv
+                      
+                    
+                    
+                      
+                        getdown-launcher-new.jarv
+                      
+                    
+                    
+                      
+                        launcher.log
+                      
+                    
+                    
+                      
+                        proxy.txt
+                      
+                    
+                    
+                      
+                        build_properties
+                      
+                    
+                    
+                      
+                        channel_launch*.jvl
+                      
+                    
+                    
+                      
+                        jalview*.jvl
+                      
+                    
+                    
+                      
+                        *.jarv
+                      
+                    
+                    
+                      
+                        *.log
+                      
+                    
+                    
+                      
+                        *.txt
+                      
+                    
+                    
+                      
+                        *_new
+                      
+                    
+                    
+                      
+                        hs_err_*.*
+                      
+                    
+                    
+                      
+                        ${compiler:GETDOWN_DIST_DIR}
+                      
+                    
+                    
+                      
+                        ${compiler:GETDOWN_ALT_DIR}
+                      
+                    
+                    
+                      
+                        ${compiler:GETDOWN_RESOURCE_DIR}
+                      
+                    
+                    
+                      
+                        META-INF
+                      
+                    
+                    
+                      
+                        install
+                      
+                    
+                    
+                      
+                        resource
+                      
+                    
+                    
+                      
+                        dist
+                      
+                    
+                    
+                      
+                        release
+                      
+                    
+                    
+                      
+                        alt
+                      
+                    
+                    
+                      
+                        dev
+                      
+                    
+                    
+                      
+                        build
+                      
+                    
+                    
+                      
+                        alt_*
+                      
+                    
+                    
+                      
+                        dev_*
+                      
+                    
+                    
+                      
+                        build_*
+                      
+                    
+                    
+                      
+                        ${compiler:WRAPPER_SCRIPT_BIN_DIR}
+                      
+                    
+                    
+                      
+                        bin
+                      
+                    
+                    
+                      
+                        channel.props
+                      
+                    
+                    
+                      
+                        channel.propsv
+                      
+                    
+                  
+                  
+                
+              
+              
+                
+                  
+                
+              
+            
+            
+              
+                
+                  ${i18n:UninstallerPreparing}
+                
+              
+            
+          
+          
+          
+            
+              
+                
+                  ${form:successMessage}
+                
+              
+            
+          
+        
+      
+      
+        
+          
+            
+              .
+            
+          
+          ${compiler:WRAPPER_LINK}_setup
+          ${compiler:sys.fullName}
+        
+        
+          
+            
+              
+              
+              
+            
+          
+        
+        
+          
+            
+              Running ${i18n:SetupAppTitle}
+            
+            
+              
+              
+            
+            
+              
+                
+                  ${i18n:FinishedLabel(${compiler:JALVIEW_APPLICATION_NAME})}
+                
+              
+              
+                
+                  ${i18n:AddToDock}
+                  
+                  addToDockAction
+                
+                Util.isMacOS()
+              
+              
+                
+                  Make a ${compiler:WRAPPER_LINK} symbolic link in ${installer:unixUserBinDir}
+                  
+                  makeSymbolicLinkAction
+                
+                ( Util.isLinux() || Util.isUnixInstaller() || ( Util.isMacOS() && ( context.getVariable("macWrapperLinkLocation") != null ) ) ) && ( context.getVariable("unixUserBinDir") != null )
+              
+              
+                
+                  
+${i18n:ClickFinish}
+
+${compiler:JALVIEW_APPLICATION_NAME} will now launch.
+                
+              
+            
+          
+        
+      
+    
+    
+      
+      
+      
+        
+          
+          
+        
+      
+    
+  
+  
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+    
+      
+        
+        
+      
+      
+      
+        
+        
+        
+        
+        
+        
+      
+    
+    
+      
+        
+        
+      
+      
+      
+        
+        
+        
+        
+        
+        
+      
+    
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+  
+  
+    
+    
+    
+    
+    
+    
+    
+  
+
diff --git a/utils/install4j/install4j9_template.install4j b/utils/install4j/install4j9_template.install4j
index 23ff9c9..979b1a9 100644
--- a/utils/install4j/install4j9_template.install4j
+++ b/utils/install4j/install4j9_template.install4j
@@ -1,5 +1,5 @@
 
-
+
   
   
     
@@ -23,18 +23,22 @@
       
       
       
-      
-      
-      
-      
-      
-      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       
       
       
       
-      
-      
+      
+      
       
       
       
@@ -86,25 +90,20 @@
   
     
       
-      
-      
-      
+      
+      
     
     
       
-      
-      
-      
+      
+      
     
     
-      
       
-      
-      
-      
+      
+      
     
     
-      
       
         
           
@@ -112,9 +111,8 @@
       
       
       
-      
-      
-      
+      
+      
     
     
       
@@ -122,26 +120,6 @@
           
         
       
-      
-        
-          
-        
-      
-      
-        
-          
-        
-      
-      
-        
-          
-        
-      
-      
-        
-          
-        
-      
     
   
   
@@ -1421,31 +1399,35 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.
   
   
     
-      
-        
-        
-        
-        
-      
+      
+        
+      
       
         
-        
-        
-        
-        
+        
+        
       
-      
+      
     
-    
-      
-        
-        
-        
-      
+    
+      
+        
+        
+      
+      
+      
+        
+        
+        
+        
+        
+        
+      
+    
+    
       
         
-        
-        
+        
       
       
       
@@ -1457,59 +1439,57 @@ ${compiler:JALVIEW_APPLICATION_NAME} will now launch.
         
       
     
-    
-      
-        
-        
-        
-        
-      
+    
+      
+        
+      
+      
+        
+        
+        
+      
+      
+    
+    
+      
+        
+      
       
         
-        
-        
-        
-        
+        
+        
       
-      
+      
     
     
-      
-        
-        
-        
-        
-      
+      
+        
+      
       
         
-        
-        
-        
-        
+        
+        
       
-      
+      
     
     
-      
-        
-        
-        
-        
-      
+      
+        
+      
       
         
-        
-        
-        
-        
+        
+        
       
-      
+      
     
   
   
     
     
+    
     
+