From 2526066acdc3faf3a178e50672c78e428287e9ef Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 18 Aug 2015 14:24:32 +0100 Subject: [PATCH] JAL-1835 added UI for BioJSON embbeding preference --- resources/lang/Messages.properties | 3 ++- src/jalview/gui/Preferences.java | 26 +++++++++++++++----------- src/jalview/io/HtmlSvgOutput.java | 6 +----- src/jalview/jbgui/GPreferences.java | 25 ++++++++++++++++--------- 4 files changed, 34 insertions(+), 26 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 59562aa..cf11670 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1246,4 +1246,5 @@ info.enter_search_text_to_enable = Enter Search Text to Enable info.search_in_annotation_label = Search in {0} Label info.search_in_annotation_description = Search in {0} Description info.change_threshold_mode_to_enable = Change Threshold Mode to Enable -label.couldnt_read_data = Couldn't read data \ No newline at end of file +label.couldnt_read_data = Couldn't read data +label.embbed_biojson = Embbed BioJSON to HTML export \ No newline at end of file diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 67e0f83..1b274a8 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,6 +20,17 @@ */ package jalview.gui; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.Cache; +import jalview.gui.Help.HelpId; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GPreferences; +import jalview.jbgui.GSequenceLink; +import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -42,17 +53,6 @@ import javax.swing.JPanel; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.bin.Cache; -import jalview.gui.Help.HelpId; -import jalview.gui.StructureViewer.ViewerType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GPreferences; -import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; -import jalview.util.MessageManager; - /** * DOCUMENT ME! * @@ -365,6 +365,8 @@ public class Preferences extends GPreferences pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true)); pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true)); modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false)); + embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", + true)); /* * Set Editing tab defaults @@ -589,6 +591,8 @@ public class Preferences extends GPreferences Boolean.toString(pirjv.isSelected())); Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected())); + Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Boolean.toString(embbedBioJSON.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 7fcf629..16b2647 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -40,11 +40,7 @@ public class HtmlSvgOutput { try { - if (file == null /* - * && !(System.getProperty("java.awt.headless") != null - * && System - * .getProperty("java.awt.headless").equals("true")) - */) + if (file == null) { JalviewFileChooser chooser = getHTMLChooser(); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 97edb36..4f4afb0 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -20,6 +20,11 @@ */ package jalview.jbgui; +import jalview.gui.JvSwingUtils; +import jalview.gui.StructureViewer.ViewerType; +import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -61,11 +66,6 @@ import javax.swing.event.ChangeListener; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; -import jalview.gui.JvSwingUtils; -import jalview.gui.StructureViewer.ViewerType; -import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource; -import jalview.util.MessageManager; - /** * Base class for the Preferences panel. * @@ -216,6 +216,8 @@ public class GPreferences extends JPanel protected JCheckBox modellerOutput = new JCheckBox(); + protected JCheckBox embbedBioJSON = new JCheckBox(); + /* * Editing tab components */ @@ -432,6 +434,14 @@ public class GPreferences extends JPanel userIdWidth_actionPerformed(); } }); + modellerOutput.setFont(LABEL_FONT); + modellerOutput.setText(MessageManager + .getString("label.use_modeller_output")); + modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); + embbedBioJSON.setFont(LABEL_FONT); + embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson")); + embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23)); + jPanel11.add(jLabel1); jPanel11.add(blcjv); jPanel11.add(clustaljv); @@ -444,13 +454,10 @@ public class GPreferences extends JPanel outputTab.add(userIdWidth); outputTab.add(userIdWidthlabel); outputTab.add(modellerOutput); + outputTab.add(embbedBioJSON); outputTab.add(epsLabel); outputTab.add(epsRendering); outputTab.add(jPanel11); - modellerOutput.setFont(LABEL_FONT); - modellerOutput.setText(MessageManager - .getString("label.use_modeller_output")); - modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); return outputTab; } -- 1.7.10.2