X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ad3c072907489b090876befd4c0958e85cc28c77;hpb=1aa21d01e983854e9dbb1628350ac6976c52430a;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index ad3c072..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 2.8.2) - * Copyright (C) 2014 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. * @@ -22,7 +22,8 @@ package jalview.gui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; -import jalview.gui.StructureViewer.Viewer; +import jalview.gui.Help.HelpId; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GPreferences; @@ -39,15 +40,19 @@ import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.io.File; import java.util.Collection; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; +import javax.help.HelpSetException; import javax.swing.JColorChooser; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JOptionPane; import javax.swing.JPanel; +import ext.edu.ucsf.rbvi.strucviz2.StructureManager; + /** * DOCUMENT ME! * @@ -56,6 +61,15 @@ import javax.swing.JPanel; */ 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"; + + public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; + + public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; @@ -160,11 +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, @@ -220,6 +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)); @@ -247,8 +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 @@ -262,10 +277,14 @@ public class Preferences extends GPreferences */ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++) { - colour.addItem(ColourSchemeProperty.getColourName(i)); + protColour.addItem(ColourSchemeProperty.getColourName(i)); + nucColour.addItem(ColourSchemeProperty.getColourName(i)); } - String string = Cache.getDefault("DEFAULT_COLOUR", "None"); - colour.setSelectedItem(string); + String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None"); + String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); + protColour.setSelectedItem(newProp != null ? newProp : oldProp); + newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); + nucColour.setSelectedItem(newProp != null ? newProp : oldProp); minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", @@ -278,13 +297,12 @@ 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); structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY, - Viewer.JMOL.name())); + ViewerType.JMOL.name())); chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); chimeraPath.addActionListener(new ActionListener() { @@ -333,8 +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)); @@ -345,6 +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 @@ -415,6 +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", @@ -441,13 +463,15 @@ 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 */ - Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour + .getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour .getSelectedItem().toString()); Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground()); @@ -565,6 +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", @@ -585,9 +611,8 @@ public class Preferences extends GPreferences dasSource.saveProperties(Cache.applicationProperties); wsPrefs.updateAndRefreshWsMenuConfig(false); - Cache.saveProperties(); - + Desktop.instance.doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -597,7 +622,8 @@ public class Preferences extends GPreferences } /** - * Do any necessary validation before saving settings. + * Do any necessary validation before saving settings. Return focus to the + * first tab which fails validation. * * @return */ @@ -617,20 +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); @@ -772,7 +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); @@ -805,7 +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); @@ -817,7 +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); @@ -842,12 +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(""); } } @@ -880,4 +908,52 @@ public class Preferences extends GPreferences return true; } + /** + * If Chimera is selected, check it can be found on default or user-specified + * path, if not show a warning/help dialog. + */ + @Override + protected void structureViewer_actionPerformed(String selectedItem) + { + if (!selectedItem.equals(ViewerType.CHIMERA.name())) + { + return; + } + boolean found = false; + + /* + * Try user-specified and standard paths for Chimera executable. + */ + List paths = StructureManager.getChimeraPaths(); + paths.add(0, chimeraPath.getText()); + for (String path : paths) + { + if (new File(path.trim()).canExecute()) + { + found = true; + break; + } + } + if (!found) + { + 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]); + if (showHelp == JOptionPane.NO_OPTION) + { + try + { + Help.showHelpWindow(HelpId.StructureViewer); + } catch (HelpSetException e) + { + e.printStackTrace(); + } + } + } + } + }