From dbd89a2f85503279ad57c1d8a073a4b8394fa235 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 27 Apr 2017 17:34:47 +0100 Subject: [PATCH] JAL-1933 desktop preferences for occupancy --- src/jalview/gui/Preferences.java | 6 ++++++ src/jalview/jbgui/GPreferences.java | 29 ++++++++++++++++++++++++----- 2 files changed, 30 insertions(+), 5 deletions(-) diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index cf80a6d..cccdd2e 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -107,6 +107,8 @@ public class Preferences extends GPreferences public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; + private static final int MIN_FONT_SIZE = 1; private static final int MAX_FONT_SIZE = 30; @@ -210,6 +212,7 @@ public class Preferences extends GPreferences openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); showUnconserved .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); + showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false)); showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false)); showGroupConservation.setSelected(Cache.getDefault( @@ -572,6 +575,8 @@ public class Preferences extends GPreferences Boolean.toString(idItalics.isSelected())); Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean.toString(showUnconserved.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, + Boolean.toString(showOccupancy.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean.toString(showGroupConsensus.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", @@ -851,6 +856,7 @@ public class Preferences extends GPreferences conservation.setEnabled(annotations.isSelected()); quality.setEnabled(annotations.isSelected()); identity.setEnabled(annotations.isSelected()); + showOccupancy.setEnabled(annotations.isSelected()); showGroupConsensus.setEnabled(annotations.isSelected()); showGroupConservation.setEnabled(annotations.isSelected()); showConsensHistogram.setEnabled(annotations.isSelected() diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index dda06b4..1ad95dd 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -101,6 +101,8 @@ public class GPreferences extends JPanel protected JComboBox fontNameCB = new JComboBox(); + protected JCheckBox showOccupancy = new JCheckBox(); + protected JCheckBox showUnconserved = new JCheckBox(); protected JCheckBox idItalics = new JCheckBox(); @@ -1174,6 +1176,13 @@ public class GPreferences extends JPanel identity.setHorizontalTextPosition(SwingConstants.LEFT); identity.setSelected(true); identity.setText(MessageManager.getString("label.consensus")); + showOccupancy.setFont(LABEL_FONT); + showOccupancy.setEnabled(false); + showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT); + showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT); + showOccupancy.setSelected(true); + showOccupancy.setText(MessageManager.getString("label.occupancy")); + JLabel showGroupbits = new JLabel(); showGroupbits.setFont(LABEL_FONT); showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); @@ -1228,10 +1237,10 @@ public class GPreferences extends JPanel .getString("label.database_references")); annotations.setFont(LABEL_FONT); annotations.setHorizontalAlignment(SwingConstants.RIGHT); - annotations.setHorizontalTextPosition(SwingConstants.LEADING); + annotations.setHorizontalTextPosition(SwingConstants.LEFT); annotations.setSelected(true); annotations.setText(MessageManager.getString("label.show_annotations")); - annotations.setBounds(new Rectangle(169, 12, 200, 23)); + // annotations.setBounds(new Rectangle(169, 12, 200, 23)); annotations.addActionListener(new ActionListener() { @Override @@ -1358,11 +1367,13 @@ public class GPreferences extends JPanel sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21)); JPanel annsettingsPanel = new JPanel(); - annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75)); + annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96)); annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0)); annsettingsPanel.setBorder(new EtchedBorder()); visualTab.add(annsettingsPanel); Border jb = new EmptyBorder(1, 1, 4, 5); + annotations.setBorder(jb); + showOccupancy.setBorder(jb); quality.setBorder(jb); conservation.setBorder(jb); identity.setBorder(jb); @@ -1374,17 +1385,26 @@ public class GPreferences extends JPanel showConsensLogo.setBorder(jb); JPanel autoAnnotSettings = new JPanel(); - autoAnnotSettings.setLayout(new GridLayout(3, 3)); annsettingsPanel.add(autoAnnotSettings); + autoAnnotSettings.setLayout(new GridLayout(0, 2)); + autoAnnotSettings.add(annotations); autoAnnotSettings.add(quality); + // second row of autoannotation box + autoAnnotSettings = new JPanel(); + annsettingsPanel.add(autoAnnotSettings); + + autoAnnotSettings.setLayout(new GridLayout(0, 3)); autoAnnotSettings.add(conservation); autoAnnotSettings.add(identity); + autoAnnotSettings.add(showOccupancy); autoAnnotSettings.add(showGroupbits); autoAnnotSettings.add(showGroupConservation); autoAnnotSettings.add(showGroupConsensus); autoAnnotSettings.add(showConsensbits); autoAnnotSettings.add(showConsensHistogram); autoAnnotSettings.add(showConsensLogo); + + JPanel tooltipSettings = new JPanel(); tooltipSettings.setBorder(new TitledBorder(MessageManager @@ -1433,7 +1453,6 @@ public class GPreferences extends JPanel jPanel2.add(sortAnnLabel); jPanel2.add(startupCheckbox); visualTab.add(jPanel2); - visualTab.add(annotations); visualTab.add(startupFileTextfield); visualTab.add(sortby); visualTab.add(sortAnnBy); -- 1.7.10.2