From: Jim Procter Date: Thu, 25 Jul 2024 15:45:15 +0000 (+0100) Subject: JAL-4441 new menu option to show or hide structure providers in secondary structure... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f60b4a3ba645eec0525a400a525d3bc9dd247c4d;p=jalview.git JAL-4441 new menu option to show or hide structure providers in secondary structure annotation rows --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index cb1ffb0..b5afb2a 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1309,6 +1309,7 @@ label.conservation_descr = Conservation of total alignment less than {0}% gaps label.consensus_descr = PID label.ssconsensus_label = Secondary Structure Consensus label.ssconsensus_descr = Secondary Structure Consensus +label.show_structure_provider = Show Structure Providers option.ss_providers_all = All option.ss_providers_none = None label.complement_consensus_descr = PID for cDNA diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index c80eab6..c988555 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -471,6 +471,7 @@ + whether a new group has secondary structure consensus displayed by default + diff --git a/src/jalview/api/ViewStyleI.java b/src/jalview/api/ViewStyleI.java index 8942477..bed31c4 100644 --- a/src/jalview/api/ViewStyleI.java +++ b/src/jalview/api/ViewStyleI.java @@ -68,6 +68,10 @@ public interface ViewStyleI void setAbovePIDThreshold(boolean b); void setByConsensusSecondaryStructureSelected(boolean b); + + void setShowStructureProvider(boolean b); + + boolean isShowStructureProvider(); void setThreshold(int thresh); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index febcd0c..7a06638 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -895,7 +895,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, modifyConservation .setEnabled(!nucleotide && conservationMenuItem.isSelected()); byConsensusSecondaryStructureMenuItem.setEnabled(!nucleotide); - modifyConsensusSecondaryStructureThreshold.setEnabled(!nucleotide + modifyConsensusSecondaryStructureThreshold.setEnabled(!nucleotide && byConsensusSecondaryStructureMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); @@ -930,10 +930,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); modifyConservation.setEnabled(conservationMenuItem.isSelected()); - byConsensusSecondaryStructureMenuItem.setSelected( - av.getByConsensusSecondaryStructureSelected()); - modifyConsensusSecondaryStructureThreshold.setEnabled( - byConsensusSecondaryStructureMenuItem.isSelected()); + byConsensusSecondaryStructureMenuItem + .setSelected(av.getByConsensusSecondaryStructureSelected()); + modifyConsensusSecondaryStructureThreshold + .setEnabled(byConsensusSecondaryStructureMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -955,6 +955,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showNonconservedMenuItem.setSelected(av.getShowUnconserved()); showGroupConsensus.setSelected(av.isShowGroupConsensus()); showGroupSSConsensus.setSelected(av.isShowGroupSSConsensus()); + showStrucProvider.setSelected(av.isShowStructureProvider()); showGroupConservation.setSelected(av.isShowGroupConservation()); showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); @@ -3723,7 +3724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } - + @Override protected void modifyConsensusSecondaryStructureThreshold_actionPerformed() { @@ -3752,13 +3753,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SliderPanel.hideConservationSlider(); } } - + @Override - public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(boolean selected) + public void colourByConsensusSecondaryStructureMenuItem_actionPerformed( + boolean selected) { modifyConsensusSecondaryStructureThreshold.setEnabled(selected); - viewport.setByConsensusSecondaryStructureSelected(selected); - viewport.getResidueShading().setConsensusSecondaryStructureColouring(selected); + viewport.setByConsensusSecondaryStructureSelected(selected); + viewport.getResidueShading() + .setConsensusSecondaryStructureColouring(selected); changeColour(viewport.getGlobalColourScheme()); if (selected) @@ -3894,19 +3897,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - new Thread(new Runnable() { + new Thread(new Runnable() + { @Override public void run() { - JInternalFrame frame = new JInternalFrame(); - frame.setFrameIcon(null); - frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, - MessageManager.getString("action.pairwise_alignment"), 600, - 500); + JInternalFrame frame = new JInternalFrame(); + frame.setFrameIcon(null); + frame.setContentPane(new PairwiseAlignPanel(viewport)); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), + 600, 500); } }).start(); - + } } @@ -5733,145 +5737,186 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setShowUnconserved(showNonconservedMenuItem.getState()); alignPanel.paintAlignment(false, false); } - + @Override - protected void updateShowSecondaryStructureMenu(JMenu showSS, ButtonGroup ssButtonGroup){ - + protected void showStructureProvider_actionPerformed(ActionEvent e) + { + viewport.setShowStructureProvider(showStrucProvider.getState()); + alignPanel.paintAlignment(false, false); + + } + @Override + protected void updateShowSecondaryStructureMenu(JMenu showSS, + ButtonGroup ssButtonGroup) + { + List ssSources = new ArrayList(); AlignmentAnnotation[] anns = alignPanel.getAlignment() .getAlignmentAnnotation(); - Map checkboxMap = getCheckboxesInMenu(showSS); - + Map checkboxMap = getCheckboxesInMenu( + showSS); + ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(anns); - - if(ssSources == null) { + + if (ssSources == null) + { showSS.removeAll(); ssButtonGroup.clearSelection(); return; } - + List selectedCheckBoxes = getSelectedOptions(checkboxMap); - + // Add checkboxes for categories - for (String ssSource : ssSources) { - - if(checkboxMap.get(ssSource)== null) { + for (String ssSource : ssSources) + { + + if (checkboxMap.get(ssSource) == null) + { JCheckBoxMenuItem checkBox = new JCheckBoxMenuItem(ssSource); checkBox.setSelected(false); - + checkBox.addItemListener(e -> { - if (e.getStateChange() == ItemEvent.SELECTED) { - - showOrHideSecondaryStructureForSource(ssSource, true); - - } else { - - showOrHideSecondaryStructureForSource(ssSource, false); - - } + if (e.getStateChange() == ItemEvent.SELECTED) + { + + showOrHideSecondaryStructureForSource(ssSource, true); + + } + else + { + + showOrHideSecondaryStructureForSource(ssSource, false); + + } }); showSS.add(checkBox); } } // Iterate over the keys of checkboxMap - for (String key : checkboxMap.keySet()) { - // Check if the key is not in ssSources - if (!ssSources.contains(key)) { - showSS.remove(checkboxMap.get(key)); - checkboxMap.remove(key); - selectedCheckBoxes.remove(key); - } - if(selectedCheckBoxes.contains(key)){ - checkboxMap.get(key).setSelected(true); - } - else { - checkboxMap.get(key).setSelected(false); - } + for (String key : checkboxMap.keySet()) + { + // Check if the key is not in ssSources + if (!ssSources.contains(key)) + { + showSS.remove(checkboxMap.get(key)); + checkboxMap.remove(key); + selectedCheckBoxes.remove(key); + } + if (selectedCheckBoxes.contains(key)) + { + checkboxMap.get(key).setSelected(true); + } + else + { + checkboxMap.get(key).setSelected(false); + } - ssButtonGroup.clearSelection(); + ssButtonGroup.clearSelection(); } } - - private List getSelectedOptions(Map checkboxMap) { + + private List getSelectedOptions( + Map checkboxMap) + { List selectedOptions = new ArrayList<>(); - for (String key : checkboxMap.keySet()) { - JCheckBoxMenuItem checkbox = checkboxMap.get(key); - if (checkbox.isSelected()) { - selectedOptions.add(key); - } + for (String key : checkboxMap.keySet()) + { + JCheckBoxMenuItem checkbox = checkboxMap.get(key); + if (checkbox.isSelected()) + { + selectedOptions.add(key); + } } return selectedOptions; } - - private Map getCheckboxesInMenu(JMenu menu) { + + private Map getCheckboxesInMenu(JMenu menu) + { Map checkboxMap = new HashMap<>(); - for (Component component : menu.getMenuComponents()) { - if (component instanceof JCheckBoxMenuItem) { - JCheckBoxMenuItem checkbox = (JCheckBoxMenuItem) component; - checkboxMap.put(checkbox.getText(), checkbox); - } + for (Component component : menu.getMenuComponents()) + { + if (component instanceof JCheckBoxMenuItem) + { + JCheckBoxMenuItem checkbox = (JCheckBoxMenuItem) component; + checkboxMap.put(checkbox.getText(), checkbox); + } } return checkboxMap; -} - + } + @Override - protected void showOrHideSecondaryStructureForSource(String ssSourceSelection, boolean visible){ - - String noneOption = MessageManager.getString("option.ss_providers_none"); + protected void showOrHideSecondaryStructureForSource( + String ssSourceSelection, boolean visible) + { + + String noneOption = MessageManager + .getString("option.ss_providers_none"); String allOption = MessageManager.getString("option.ss_providers_all"); - + AlignmentAnnotation[] annotations = alignPanel.getAlignment() .getAlignmentAnnotation(); - - for (AlignmentAnnotation aa: annotations) { - - if(aa.groupRef!=null) { + + for (AlignmentAnnotation aa : annotations) + { + + if (aa.groupRef != null) + { continue; } - - boolean isSSConsensus = aa.label.startsWith(MessageManager.getString("label.ssconsensus_label")); - boolean matchesSSSourceSelection = aa.description.startsWith(ssSourceSelection); - - if(isSSConsensus && (matchesSSSourceSelection || ssSourceSelection.equals(noneOption))) { - - if (ssSourceSelection.equals(allOption)) { - aa.visible = true; + + boolean isSSConsensus = aa.label.startsWith( + MessageManager.getString("label.ssconsensus_label")); + boolean matchesSSSourceSelection = aa.description + .startsWith(ssSourceSelection); + + if (isSSConsensus && (matchesSSSourceSelection + || ssSourceSelection.equals(noneOption))) + { + + if (ssSourceSelection.equals(allOption)) + { + aa.visible = true; break; } - - if(!aa.description.startsWith(allOption)) - aa.visible = visible; + + if (!aa.description.startsWith(allOption)) + aa.visible = visible; } - - for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) { - - if (label.equals(aa.label)) { - String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa); + for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) + { - if(ssSource != null && (ssSource.equals(ssSourceSelection) || ssSourceSelection.equals(noneOption))) { - aa.visible = visible; - } + if (label.equals(aa.label)) + { + + String ssSource = AlignmentUtils + .extractSSSourceFromAnnotationDescription(aa); + + if (ssSource != null && (ssSource.equals(ssSourceSelection) + || ssSourceSelection.equals(noneOption))) + { + aa.visible = visible; + } } } - + } - - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true, true); - + + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true, true); + } - + protected void showSSConsensus_actionPerformed(ActionEvent e) { viewport.setShowSSConsensus(showSSConsensus.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - - } + } /* * (non-Javadoc) @@ -5895,6 +5940,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + /* * (non-Javadoc) * @@ -5922,7 +5968,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } - + /* * (non-Javadoc) * diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 36812f1..9430a8b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -242,6 +242,7 @@ public class AlignViewport extends AlignmentViewport .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); viewStyle.setScaleProteinAsCdna( Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); + viewStyle.setShowStructureProvider(Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false)); } void init() diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index d7b950b..9478c6f 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1375,6 +1375,7 @@ public class AnnotationLabels extends JPanel SequenceI lastSeqRef = null; String lastLabel = null; AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + boolean isShowStructureProvider = av.isShowStructureProvider(); int fontHeight = g != null ? g.getFont().getSize() : fm.getFont().getSize(); int y = 0; @@ -1494,7 +1495,7 @@ public class AnnotationLabels extends JPanel } } - if(Constants.SECONDARY_STRUCTURE_LABELS.keySet().contains(aa[i].label)) { + if(isShowStructureProvider && aa[i].hasIcons && Constants.SECONDARY_STRUCTURE_LABELS.keySet().contains(aa[i].label)) { String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa[i]); if(ssSource != null && ssSource.length()>0) label += " (" + ssSource + ")"; diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 4fb013f..612bf26 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -133,6 +133,8 @@ public class Preferences extends GPreferences private static final int MAX_FONT_SIZE = 30; + public static final String SHOW_STRUC_PROVIDER = "SHOW_STRUCTURE_PROVIDER"; + private String previousProxyType; private static Preferences INSTANCE = null; // add "final" diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index d1d56ed..fa9626b 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -200,6 +200,8 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem expandViews = new JMenuItem(); + protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupSSConsensus = new JCheckBoxMenuItem(); @@ -680,6 +682,16 @@ public class GAlignFrame extends JInternalFrame sortAnnotations_actionPerformed(); } }); + showStrucProvider = new JCheckBoxMenuItem( + MessageManager.getString("label.show_structure_provider")); + showStrucProvider.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + showStructureProvider_actionPerformed(e); + } + + }); colourTextMenuItem = new JCheckBoxMenuItem( MessageManager.getString("label.colour_text")); colourTextMenuItem.addActionListener(new ActionListener() @@ -1977,6 +1989,7 @@ public class GAlignFrame extends JInternalFrame annotationsMenu.add(sortAnnByLabel); annotationsMenu.addSeparator(); annotationsMenu.add(showSS); + annotationsMenu.add(showStrucProvider); annotationsMenu.addSeparator(); autoAnnMenu.add(showAutoFirst); autoAnnMenu.add(showAutoLast); @@ -2071,6 +2084,12 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + protected void showStructureProvider_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + protected void showSSConsensus_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 061583c..2a2225e 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1679,6 +1679,7 @@ public class Jalview2XML view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna()); view.setRenderGaps(av.isRenderGaps()); view.setShowAnnotation(av.isShowAnnotation()); + view.setShowStructureProviders(av.isShowStructureProvider()); view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); @@ -5346,6 +5347,7 @@ public class Jalview2XML // recover view properties and display parameters viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); + viewport.setShowStructureProvider(safeBoolean(view.isShowStructureProviders())); viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected())); final int pidThreshold = safeInt(view.getPidThreshold()); viewport.setThreshold(pidThreshold); diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 1e81891..94a1424 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -259,6 +259,16 @@ public abstract class AlignmentViewport return viewStyle.getByConsensusSecondaryStructureSelected(); } + public void setShowStructureProvider(boolean b) + { + viewStyle.setShowStructureProvider(b); + } + + public boolean isShowStructureProvider() + { + return viewStyle.isShowStructureProvider(); + } + /** * @param inc * @see jalview.api.ViewStyleI#setIncrement(int) diff --git a/src/jalview/viewmodel/styles/ViewStyle.java b/src/jalview/viewmodel/styles/ViewStyle.java index 502d0fc..0726517 100644 --- a/src/jalview/viewmodel/styles/ViewStyle.java +++ b/src/jalview/viewmodel/styles/ViewStyle.java @@ -390,6 +390,8 @@ public class ViewStyle implements ViewStyleI */ private List secondaryStructureSources = List.of( new String[0] ); + private boolean showStructureProvider; + /** * GUI state * @@ -1203,4 +1205,15 @@ public class ViewStyle implements ViewStyleI { this.secondaryStructureSources = secondaryStructureSources; } + + @Override + public void setShowStructureProvider(boolean showStructureProvider) + { + this.showStructureProvider=showStructureProvider; + } + @Override + public boolean isShowStructureProvider() + { + return showStructureProvider; + } } diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 06fab20..ab8fbf5 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index a906543..4c2a9a3 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index de46d74..4df374f 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index d074219..ac12f03 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index aad7c25..29cb972 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index f1ba7ee..5d5e444 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 17b5c9f..7982504 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 5c1cdeb..730cb71 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index 22f938d..9656aad 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index fa80470..5704bf9 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 0300df2..3f8185c 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // @@ -195,6 +195,7 @@ import javax.xml.datatype.XMLGregorianCalendar; * <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="showStructureProviders" 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" /> @@ -5542,6 +5543,7 @@ public class JalviewModel { * <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="showStructureProviders" 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" /> @@ -5625,6 +5627,8 @@ public class JalviewModel { protected Boolean followSelection; @XmlAttribute(name = "showAnnotation") protected Boolean showAnnotation; + @XmlAttribute(name = "showStructureProviders") + protected Boolean showStructureProviders; @XmlAttribute(name = "centreColumnLabels") protected Boolean centreColumnLabels; /** @@ -6286,6 +6290,30 @@ public class JalviewModel { } /** + * Gets the value of the showStructureProviders property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowStructureProviders() { + return showStructureProviders; + } + + /** + * Sets the value of the showStructureProviders property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowStructureProviders(Boolean value) { + this.showStructureProviders = value; + } + + /** * Gets the value of the centreColumnLabels property. * * @return diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 5a97ac8..b48ca13 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index f25dcf5..72fada5 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java index ece5d33..b4b1105 100644 --- a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java +++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index 4f28ae3..fcfd7e4 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java index 714b3f3..0fd8ef5 100644 --- a/src/jalview/xml/binding/jalview/MatrixType.java +++ b/src/jalview/xml/binding/jalview/MatrixType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 5fe4041..baa9eed 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index b86ebdb..8ac2701 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index a0dd653..b807190 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 1093e94..f7e4d73 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java index f6da4ad..d63c051 100644 --- a/src/jalview/xml/binding/jalview/Property.java +++ b/src/jalview/xml/binding/jalview/Property.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index fc07dbb..3b9e3f5 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index db9aea9..8629a7e 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index 2bbbdc3..590ea6d 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index c213d18..345ede6 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index beacdce..bd17cc2 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 29732de..78833f6 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index 496652f..cdebe06 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -2,7 +2,7 @@ // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2024.07.25 at 02:29:22 PM BST +// Generated on: 2024.07.25 at 04:43:38 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)