import jalview.io.BackupFilesPresetEntry;
import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseAdapter;
import java.util.Arrays;
import java.util.List;
+import javax.swing.AbstractButton;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JComponent;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import net.miginfocom.swing.MigLayout;
+
/**
* Base class for the Preferences panel.
*
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
+
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
+
/*
* Structure tab and components
*/
*/
protected JComboBox<Object> epsRendering = new JComboBox<>();
+ protected JComboBox<Object> htmlRendering = new JComboBox<>();
+
+ protected JComboBox<Object> svgRendering = new JComboBox<>();
+
protected JLabel userIdWidthlabel = new JLabel();
protected JCheckBox autoIdWidth = new JCheckBox();
protected JCheckBox sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab;
+
+ protected JCheckBox hmmrTrimTermini;
+
+ protected AbstractButton hmmerBackgroundUniprot;
+
+ protected AbstractButton hmmerBackgroundAlignment;
+
+ protected JTextField hmmerSequenceCount;
+
+ protected JTextField hmmerPath;
+
+ protected JTextField cygwinPath;
+
+ /*
* Web Services tab
*/
protected JPanel wsTab = new JPanel();
+ protected JPanel slivkaTab = new JPanel();
+
/*
* Backups tab components
* a lot of these are member variables instead of local variables only so that they
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
- wsTab.setLayout(new BorderLayout());
- tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ if (!Platform.isJS())
+ {
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ }
+
+ slivkaTab.setLayout(new BorderLayout());
+ tabbedPane.add(slivkaTab, "Slivka Services");
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
/**
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab = new JPanel();
+ hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+ hmmerTab.setLayout(new MigLayout("flowy"));
+
+ /*
+ * path to hmmer binaries folder
+ */
+ JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(installationPanel,
+ MessageManager.getString("label.installation"), true);
+ hmmerTab.add(installationPanel);
+ JLabel hmmerLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ hmmerLocation.setFont(LABEL_FONT);
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ validateHmmerPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
+
+ /*
+ * path to Cygwin binaries folder (for Windows)
+ */
+ if (Platform.isWindowsAndNotJS())
+ {
+ JLabel cygwinLocation = new JLabel(
+ MessageManager.getString("label.cygwin_location"));
+ cygwinLocation.setFont(LABEL_FONT);
+ cygwinPath = new JTextField(pathFieldLength);
+ cygwinPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ cygwinPath.setText(chosen);
+ validateCygwinPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
+ }
+
+ /*
+ * preferences for hmmalign
+ */
+ JPanel alignOptionsPanel = new JPanel(new MigLayout());
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(alignOptionsPanel,
+ MessageManager.getString("label.hmmalign_options"), true);
+ hmmerTab.add(alignOptionsPanel);
+ hmmrTrimTermini = new JCheckBox();
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ alignOptionsPanel.add(hmmrTrimTermini);
+
+ /*
+ * preferences for hmmsearch
+ */
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(searchOptions,
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
+ searchOptions.add(hmmerSequenceCount);
+
+ /*
+ * preferences for Information Content annotation
+ */
+ // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel annotationOptions = new JPanel(new MigLayout("left"));
+ JvSwingUtils.createTitledBorder(annotationOptions,
+ MessageManager.getString("label.information_annotation"), true);
+ // dummy.add(annotationOptions);
+ hmmerTab.add(annotationOptions);
+ ButtonGroup backgroundOptions = new ButtonGroup();
+ hmmerBackgroundUniprot = new JRadioButton(
+ MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ backgroundOptions.add(hmmerBackgroundUniprot);
+ backgroundOptions.add(hmmerBackgroundAlignment);
+ backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+ // disable buttons for now as annotation only uses Uniprot background
+ hmmerBackgroundAlignment.setEnabled(false);
+ hmmerBackgroundUniprot.setEnabled(false);
+ annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+ annotationOptions.add(hmmerBackgroundAlignment);
+
+ return hmmerTab;
+ }
+
+ /**
* Initialises the Output tabbed panel.
*
* @return
{
JPanel outputTab = new JPanel();
outputTab.setLayout(null);
- JLabel epsLabel = new JLabel();
+
+ JLabel epsLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "EPS"));
epsLabel.setFont(LABEL_FONT);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
epsRendering.setFont(LABEL_FONT);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+ JLabel htmlLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "HTML"));
+ htmlLabel.setFont(LABEL_FONT);
+ htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+ htmlRendering.setFont(LABEL_FONT);
+ htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+ JLabel svgLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "SVG"));
+ svgLabel.setFont(LABEL_FONT);
+ svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+ svgRendering.setFont(LABEL_FONT);
+ svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
JLabel jLabel1 = new JLabel();
jLabel1.setFont(LABEL_FONT);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(MessageManager.getString("label.append_start_end"));
jLabel1.setFont(LABEL_FONT);
+
fastajv.setFont(LABEL_FONT);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
TitledBorder titledBorder2 = new TitledBorder(
MessageManager.getString("label.file_output"));
jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
GridLayout gridLayout3 = new GridLayout();
jPanel11.setLayout(gridLayout3);
gridLayout3.setRows(8);
MessageManager.getString("label.automatically_set_id_width"));
autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.adjusts_width_generated_eps_png")));
- autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
autoIdWidth.addActionListener(new ActionListener()
{
userIdWidthlabel.setToolTipText(
JvSwingUtils.wrapTooltip(true, MessageManager.getString(
"label.manually_specify_width_left_column")));
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+ userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
userIdWidth.addActionListener(new ActionListener()
{
modellerOutput.setFont(LABEL_FONT);
modellerOutput
.setText(MessageManager.getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
embbedBioJSON.setFont(LABEL_FONT);
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
- embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+ embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
outputTab.add(userIdWidth);
outputTab.add(userIdWidthlabel);
outputTab.add(modellerOutput);
- outputTab.add(embbedBioJSON);
- outputTab.add(epsLabel);
- outputTab.add(epsRendering);
+ if (!Platform.isJS())
+ {
+ /*
+ * JalviewJS doesn't support Lineart option or SVG output
+ */
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(htmlLabel);
+ outputTab.add(htmlRendering);
+ outputTab.add(svgLabel);
+ outputTab.add(svgRendering);
+ }
outputTab.add(jPanel11);
return outputTab;
}
GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
new Insets(0, 2, 5, 5), 70, 1));
+ versioncheck.setVisible(false);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
connectTab.add(spacePanel,
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(
MessageManager.getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(
MessageManager.getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
annotationShding.setBorder(new TitledBorder(
MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
structureTab.add(viewerLabel);
- structViewer.setFont(LABEL_FONT);
- structViewer.setBounds(new Rectangle(160, ypos, 120, height));
- structViewer.addItem(ViewerType.JMOL.name());
- structViewer.addItem(ViewerType.CHIMERA.name());
- structViewer.addActionListener(new ActionListener()
+ if (!Platform.isJS())
{
- @Override
- public void actionPerformed(ActionEvent e)
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
{
- structureViewer_actionPerformed(
- (String) structViewer.getSelectedItem());
- }
- });
- structureTab.add(structViewer);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
+ }
+ });
+ structureTab.add(structViewer);
+ }
ypos += lineSpacing;
JLabel pathLabel = new JLabel();
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
structureTab.add(docFieldPref);
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
+ pathLabel.setVisible(false);
+ chimeraPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }
+
return structureTab;
}
*
* @return
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
return choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
- {
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
- }
-
protected boolean validateStructure()
{
return false;
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
+
+ if (Platform.isJS())
+ {
+ startupCheckbox.setVisible(false);
+ startupFileTextfield.setVisible(false);
+ }
+
return visualTab;
}
BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
.getSavedBackupEntry();
enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+ .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
.createBackupFilesPresetEntry(Cache
boolean ret = false;
String warningMessage = MessageManager
.getString("label.warning_confirm_change_reverse");
- int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
warningMessage,
MessageManager.getString("label.change_increment_decrement"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
{
try
{
- i = Integer.parseInt((String) s.getValue());
+ i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
Cache.log.error(
{
max = def;
}
+ if (def < min)
+ {
+ def = min;
+ }
SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
s.setModel(sModel);
}
}
+
+ protected void validateHmmerPath()
+ {
+ }
+
+ protected void validateCygwinPath()
+ {
+ }
+
+ /**
+ * A helper method to add a panel containing a label and a component to a
+ * panel
+ *
+ * @param panel
+ * @param tooltip
+ * @param label
+ * @param valBox
+ */
+ protected static void addtoLayout(JPanel panel, String tooltip,
+ JComponent label, JComponent valBox)
+ {
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
+ labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+ valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+ labPanel.add(label, BorderLayout.WEST);
+ valPanel.add(valBox);
+ laypanel.add(labPanel);
+ laypanel.add(valPanel);
+ valPanel.setToolTipText(tooltip);
+ labPanel.setToolTipText(tooltip);
+ valBox.setToolTipText(tooltip);
+ panel.add(laypanel);
+ panel.validate();
+ }
}
git://source.jalview.org / jalview.git / blobdiff