X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2a24491ebd4d88e31f7a7893d6b3ea9d2e132d2b;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 2a24491..78a21c8 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -61,6 +61,9 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; */ public class Preferences extends GPreferences { + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; @@ -171,11 +174,11 @@ public class Preferences extends GPreferences dasTab.add(dasSource, BorderLayout.CENTER); wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); - int width = 500, height = 420; + int width = 500, height = 450; if (new jalview.util.Platform().isAMac()) { width = 570; - height = 460; + height = 480; } Desktop.addInternalFrame(frame, @@ -231,6 +234,8 @@ public class Preferences extends GPreferences + "")); smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); + scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, + false)); idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); @@ -258,8 +263,7 @@ public class Preferences extends GPreferences sortAutocalc.addItem("Autocalculated first"); sortAutocalc.addItem("Autocalculated last"); - final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, - true); + final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true); sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0) : sortAutocalc.getItemAt(1)); startupCheckbox @@ -293,8 +297,7 @@ public class Preferences extends GPreferences structFromPdb.setSelected(structSelected); useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false)); useRnaView.setEnabled(structSelected); - addSecondaryStructure - .setSelected(Cache.getDefault(ADD_SS_ANN, false)); + addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false)); addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); addTempFactor.setEnabled(structSelected); @@ -348,8 +351,8 @@ public class Preferences extends GPreferences epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", "Prompt each time")); autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); - userIdWidth.setEnabled(autoIdWidth.isSelected()); - userIdWidthlabel.setEnabled(autoIdWidth.isSelected()); + userIdWidth.setEnabled(!autoIdWidth.isSelected()); + userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH"); userIdWidth.setText(wi == null ? "" : wi.toString()); blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true)); @@ -360,6 +363,8 @@ 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 @@ -430,6 +435,8 @@ public class Preferences extends GPreferences Boolean.toString(showConsensLogo.isSelected())); Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected())); + Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, + Boolean.toString(scaleProteinToCdna.isSelected())); Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected())); Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", @@ -456,8 +463,8 @@ public class Preferences extends GPreferences } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, - Boolean.valueOf(showAutocalcFirst).toString()); + Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean + .valueOf(showAutocalcFirst).toString()); /* * Save Colours settings @@ -582,6 +589,8 @@ 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", @@ -634,20 +643,21 @@ public class Preferences extends GPreferences return validateChimeraPath(); } + /** * DOCUMENT ME! */ public void startupFileTextfield_mouseClicked() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] - { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" }, - new String[] - { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" }, + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { + "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", + "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF", + "PIR", "BLC", "Jalview" }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.select_startup_file")); + chooser.setDialogTitle(MessageManager + .getString("label.select_startup_file")); int value = chooser.showOpenDialog(this); @@ -789,7 +799,8 @@ public class Preferences extends GPreferences public void defaultBrowser_mouseClicked(MouseEvent e) { JFileChooser chooser = new JFileChooser("."); - chooser.setDialogTitle(MessageManager.getString("label.select_default_browser")); + chooser.setDialogTitle(MessageManager + .getString("label.select_default_browser")); int value = chooser.showOpenDialog(this); @@ -822,7 +833,8 @@ public class Preferences extends GPreferences public void minColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground()); + MessageManager.getString("label.select_colour_minimum_value"), + minColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -834,7 +846,8 @@ public class Preferences extends GPreferences public void maxColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground()); + MessageManager.getString("label.select_colour_maximum_value"), + maxColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -859,12 +872,10 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("warn.user_defined_width_requirements"), - MessageManager.getString("label.invalid_id_column_width"), - JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); } } @@ -925,14 +936,13 @@ public class Preferences extends GPreferences } if (!found) { - String[] options = - { "OK", "Help" }; + String[] options = { "OK", "Help" }; int showHelp = JOptionPane.showInternalOptionDialog( Desktop.desktop, JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, - JOptionPane.WARNING_MESSAGE, null, options, options[0]); + "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, + null, options, options[0]); if (showHelp == JOptionPane.NO_OPTION) { try