*/
package jalview.jbgui;
+import jalview.bin.Cache;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.Desktop;
import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.BackupFilenameFilter;
+import jalview.io.BackupFilenameParts;
import jalview.io.BackupFiles;
+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.awt.event.MouseEvent;
-import java.util.HashMap;
-import java.util.Map;
+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 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 presetsPanel = new JPanel();
- protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+ protected JLabel presetsComboLabel = new JLabel();
+
+ protected JCheckBox customiseCheckbox = new JCheckBox();
+
+ protected JButton revertButton = new JButton();
+
+ protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
+
+ private int backupfilesPresetsComboLastSelected = 0;
protected JPanel suffixPanel = new JPanel();
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
/*
* 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.isWindows())
+ {
+ 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
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
- TitledBorder backupFilesBorder = new TitledBorder(
- MessageManager.getString("label.backup_files"));
-
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
jPanel11.add(clustaljv);
linkTab.setLayout(new GridBagLayout());
// Set up table for Url links
+ linkUrlTable.getTableHeader().setReorderingAllowed(false);
linkUrlTable.setFillsViewportHeight(true);
linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
linkUrlTable.setAutoCreateRowSorter(true);
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);
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
*
* @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;
}
/**
+ * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
+ */
+
+ protected void loadLastSavedBackupsOptions()
+ {
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ enableBackupFiles
+ .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+
+ BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(Cache
+ .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+ if (backupfilesCustomEntry == null)
+ {
+ backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+ }
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+ backupfilesCustomEntry);
+
+ setComboIntStringKey(backupfilesPresetsCombo,
+ Cache.getDefault(BackupFiles.NS + "_PRESET",
+ BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
+
+ backupsSetOptions(savedPreset);
+
+ backupsOptionsSetEnabled();
+ updateBackupFilesExampleLabel();
+ }
+
+ private boolean warnAboutSuffixReverseChange()
+ {
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ boolean savedSuffixReverse = bfpe.reverse;
+ int savedSuffixDigits = bfpe.digits;
+ String savedSuffixTemplate = bfpe.suffix;
+
+ boolean nowSuffixReverse = suffixReverse.isSelected();
+ int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
+ String nowSuffixTemplate = suffixTemplate.getText();
+ return nowSuffixReverse != savedSuffixReverse
+ && nowSuffixDigits == savedSuffixDigits
+ && nowSuffixTemplate != null
+ && nowSuffixTemplate.equals(savedSuffixTemplate);
+ }
+
+ /**
* Initialises the Backups tabbed panel.
*
* @return
backupsTab.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
- gbc.weightx = 1.0;
+ gbc.weightx = 0.0;
gbc.weighty = 0.0;
- gbc.anchor = GridBagConstraints.NORTHWEST;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
gbc.fill = GridBagConstraints.NONE;
initBackupsTabPresetsPanel();
initBackupsTabKeepFilesPanel();
initBackupsTabFilenameExamplesPanel();
- gbc.weightx = 0.5;
enableBackupFiles.setFont(LABEL_FONT_BOLD);
enableBackupFiles
.setText(MessageManager.getString("label.enable_backupfiles"));
@Override
public void actionPerformed(ActionEvent e)
{
- boolean selected = enableBackupFiles.isSelected();
// enable other options only when the first is checked
- backupsOptionsSetEnabled(selected);
+ backupsOptionsSetEnabled();
}
});
- // enable checkbox 1 row
+
+ // enable checkbox 1 col
gbc.gridwidth = 1;
+ gbc.gridheight = 1;
gbc.gridx = 0;
- gbc.gridy = 0;
+ gbc.gridy = 0; // row 0
backupsTab.add(enableBackupFiles, gbc);
+ // summary of scheme box (over two rows)
gbc.gridx = 1;
- gbc.weightx = 1.0;
+ gbc.weightx = 0.0;
gbc.gridheight = 2;
- // gbc.anchor = GridBagConstraints.NORTHEAST;
- // gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_END;
+ gbc.fill = GridBagConstraints.BOTH;
backupsTab.add(exampleFilesPanel, gbc);
+ gbc.gridheight = 1;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+ // fill empty space on right
+ gbc.gridx++;
+ gbc.weightx = 1.0;
+ backupsTab.add(new JPanel(), gbc);
+
+ // schemes box
+ gbc.weightx = 0.0;
gbc.gridx = 0;
- gbc.gridy = 1;
+ gbc.gridy++; // row 1
backupsTab.add(presetsPanel, gbc);
- gbc.anchor = GridBagConstraints.NORTHWEST;
- gbc.fill = GridBagConstraints.NONE;
+ // now using whole row
gbc.gridwidth = 2;
gbc.gridheight = 1;
- // whole suffix panel next row
+ // keep files box
gbc.gridx = 0;
- gbc.gridy = 2;
- backupsTab.add(suffixPanel, gbc);
-
- // keep files panel
- gbc.gridy = 3;
+ gbc.gridy++; // row 2
backupsTab.add(keepfilesPanel, gbc);
- /*
- // whole examples panel next row
- gbc.gridy = 3;
- backupsTab.add(exampleFilesPanel, gbc);
-
+ // filename strategy box
+ gbc.gridy++; // row 3
+ backupsTab.add(suffixPanel, gbc);
+
// fill empty space
- gbc.gridy = 4;
+ gbc.gridy++; // row 4
gbc.weighty = 1.0;
backupsTab.add(new JPanel(), gbc);
- */
- backupsOptionsSetEnabled(enableBackupFiles.isSelected());
+ backupsOptionsSetEnabled();
return backupsTab;
}
- private final IntKeyStringValueEntry[] backupfilesPresetEntries = {
- new IntKeyStringValueEntry(1,
- MessageManager.getString("label.default")),
- new IntKeyStringValueEntry(2,
- MessageManager.getString("label.single_file")),
- new IntKeyStringValueEntry(3,
- MessageManager.getString("label.keep_everything")),
- new IntKeyStringValueEntry(4,
- MessageManager.getString("label.rolled_backups")),
- // ...
- // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
- new IntKeyStringValueEntry(0,
- MessageManager.getString("label.custom")) };
-
- private final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
- {
- {
- put(1, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
- 3, false, false, 4, false));
- put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
- put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
- 3, false, true, 10, true));
- put(4, new BackupFilesPresetEntry(
- "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
- false));
- }
- };
-
private JPanel initBackupsTabPresetsPanel()
{
- presetsPanel.setBorder(
- new TitledBorder(MessageManager.getString("label.presets")));
- for (int i = 0; i < backupfilesPresetEntries.length; i++)
+ String title = MessageManager.getString("label.schemes");
+
+ presetsPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.BASELINE_LEADING;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+
+ // "Scheme: "
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+
+ presetsComboLabel = new JLabel(title + ":");
+ presetsPanel.add(presetsComboLabel, gbc);
+
+ List<Object> entries = Arrays
+ .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<String> tooltips = Arrays.asList(
+ BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+ backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+ tooltips);
+ /*
+ for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
{
- backupfilesPresetsCombo.addItem(backupfilesPresetEntries[i]);
+ backupfilesPresetsCombo
+ .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
}
+ */
backupfilesPresetsCombo.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- backupsTabUpdatePresets();
+ int key = getComboIntStringKey(backupfilesPresetsCombo);
+ if (!customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = key;
+ }
+ if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ if (customiseCheckbox.isSelected())
+ {
+ // got here by clicking on customiseCheckbox so don't change the values
+ backupfilesCustomOptionsSetEnabled();
+ }
+ else
+ {
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
+ }
+ else
+ {
+ customiseCheckbox.setSelected(false);
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
}
});
- presetsPanel.add(backupfilesPresetsCombo);
+ // dropdown list of preset schemes
+ gbc.gridx = 1;
+ presetsPanel.add(backupfilesPresetsCombo, gbc);
+
+ revertButton.setText(MessageManager.getString("label.cancel_changes"));
+ revertButton.setToolTipText(
+ MessageManager.getString("label.cancel_changes_description"));
+ revertButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ });
+ revertButton.setFont(LABEL_FONT);
+
+ customiseCheckbox.setFont(LABEL_FONT);
+ customiseCheckbox.setText(MessageManager.getString("label.customise"));
+ customiseCheckbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ int currently = getComboIntStringKey(backupfilesPresetsCombo);
+ if (customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = currently;
+ setComboIntStringKey(backupfilesPresetsCombo,
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ }
+ else
+ {
+ setComboIntStringKey(backupfilesPresetsCombo,
+ backupfilesPresetsComboLastSelected);
+
+ }
+ backupfilesCustomOptionsSetEnabled();
+ }
+ });
+ customiseCheckbox.setToolTipText(
+ MessageManager.getString("label.customise_description"));
+
+ // customise checkbox
+ gbc.gridx = 0;
+ gbc.gridy++;
+ presetsPanel.add(customiseCheckbox, gbc);
+
+ // "Cancel changes" button (aligned with combo box above)
+ gbc.gridx = 1;
+ presetsPanel.add(revertButton, gbc);
+
return presetsPanel;
}
+ private JPanel initBackupsTabFilenameExamplesPanel()
+ {
+ String title = MessageManager
+ .getString("label.scheme_examples");
+ TitledBorder tb = new TitledBorder(title);
+ exampleFilesPanel.setBorder(tb);
+ exampleFilesPanel.setLayout(new GridBagLayout());
+
+
+ backupfilesExampleLabel.setEditable(false);
+ backupfilesExampleLabel
+ .setBackground(exampleFilesPanel.getBackground());
+
+ updateBackupFilesExampleLabel();
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 1.0;
+ gbc.weighty = 1.0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+
+ exampleFilesPanel.add(backupfilesExampleLabel, gbc);
+ return exampleFilesPanel;
+ }
+
private void backupsTabUpdatePresets()
{
IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
.getSelectedItem();
- int key = entry.getKey();
- String value = entry.getValue();
- boolean custom = key == 0;
+ int key = entry.k;
+ String value = entry.v;
- if (custom)
+ if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .containsKey(key))
{
- // backupsSetCustomOptions();
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(key));
}
else
{
- if (backupfilesPresetEntriesValues.containsKey(key))
- {
- backupsSetOptions(backupfilesPresetEntriesValues.get(key));
- }
- else
- {
- System.out.println("Preset '" + value + "' not implemented yet");
- }
+ Cache.log.error(
+ "Preset '" + value + "' [key:" + key + "] not implemented");
}
+ // Custom options will now be enabled when the customiseCheckbox is checked
+ // (performed above)
+ // backupfilesCustomOptionsSetEnabled();
updateBackupFilesExampleLabel();
- backupsCustomOptionsSetEnabled(custom);
}
- protected int getComboIntStringKey(JComboBox c)
+ protected int getComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2)
{
- IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem();
- return e != null ? e.getKey() : 0;
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+ .getSelectedItem();
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry.");
+ e = null;
+ }
+ return e != null ? e.k : 0;
}
- protected void setComboIntStringKey(JComboBox<IntKeyStringValueEntry> c,
+ protected void setComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2,
int key)
{
- for (int i = 0; i < c.getItemCount(); i++)
+ for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
{
- IntKeyStringValueEntry e = c.getItemAt(i);
- int k = e.getKey();
- String v = e.getValue();
- if (e.getKey() == key)
+ IntKeyStringValueEntry e;
+ try
{
- c.setSelectedIndex(i);
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+ continue;
+ }
+ if (e.k == key)
+ {
+ backupfilesPresetsCombo2.setSelectedIndex(i);
break;
}
}
- backupsTabUpdatePresets();
+ // backupsTabUpdatePresets();
}
private JPanel initBackupsTabSuffixPanel()
{
suffixPanel.setBorder(new TitledBorder(
- MessageManager.getString("label.suffix_format")));
+ MessageManager.getString("label.backup_filename_strategy")));
suffixPanel.setLayout(new GridBagLayout());
suffixTemplateLabel
- .setText(MessageManager.getString("label.suffix_template"));
+ .setText(MessageManager.getString("label.append_to_filename"));
suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
suffixTemplateLabel.setFont(LABEL_FONT);
final String tooltip = JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.suffix_template_tooltip"));
+ MessageManager.getString("label.append_to_filename_tooltip"));
suffixTemplate.setToolTipText(tooltip);
suffixTemplate.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
});
- KeyListener kl = new KeyListener()
+ suffixTemplate.addKeyListener(new KeyListener()
{
@Override
public void keyReleased(KeyEvent e)
{
updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
@Override
{
}
- // disable use of ':'
+ // disable use of ':' or '/' or '\'
@Override
public void keyTyped(KeyEvent e)
{
char c = e.getKeyChar();
- if (c == ':')
+ if (c == ':' || c == '/' || c == '\\')
{
- // don't process ':'
+ // don't process ':' or '/' or '\'
e.consume();
}
}
- };
- suffixTemplate.addKeyListener(kl);
+ });
// digits spinner
suffixDigitsLabel
.setText(MessageManager.getString("label.index_digits"));
suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
suffixDigitsLabel.setFont(LABEL_FONT);
- int defaultmin = 1;
- int defaultmax = 6;
ChangeListener c = new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c);
+ setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+ BackupFilesPresetEntry.DIGITSMAX, 3, c);
suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
MessageManager.getString("label.increment_index"));
@Override
public void actionPerformed(ActionEvent e)
{
- updateBackupFilesExampleLabel();
+ boolean okay = true;
+ if (warnAboutSuffixReverseChange())
+ {
+ // Warning popup
+ okay = confirmSuffixReverseChange();
+ }
+ if (okay)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ updateBackupFilesExampleLabel();
+ }
+ else
+ {
+ boolean savedSuffixReverse = BackupFilesPresetEntry
+ .getSavedBackupEntry().reverse;
+ suffixReverse.setSelected(savedSuffixReverse);
+ }
}
});
return suffixPanel;
}
- private void backupfilesKeepAllEnabled(boolean enabled)
+ private boolean confirmSuffixReverseChange()
{
- backupfilesKeepAll.setEnabled(enabled);
- keepRollMaxOptionsEnabled();
+ boolean ret = false;
+ String warningMessage = MessageManager
+ .getString("label.warning_confirm_change_reverse");
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ warningMessage,
+ MessageManager.getString("label.change_increment_decrement"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+ ret = (confirm == JvOptionPane.YES_OPTION);
+ return ret;
}
private JPanel initBackupsTabKeepFilesPanel()
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- boolean selected = backupfilesKeepAll.isSelected();
+ backupfilesRevertButtonSetEnabled(true);
keepRollMaxOptionsEnabled();
updateBackupFilesExampleLabel();
}
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
+ setIntegerSpinner(backupfilesRollMaxSpinner,
+ BackupFilesPresetEntry.ROLLMAXMIN,
+ BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
backupfilesConfirmDelete.setLabels(
- MessageManager.getString("label.confirm_delete"),
+ MessageManager.getString("label.always_ask"),
MessageManager.getString("label.auto_delete"));
+ backupfilesConfirmDelete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ }
+ });
// update the enabled section
keepRollMaxOptionsEnabled();
kgbc.gridwidth = GridBagConstraints.REMAINDER;
kgbc.fill = GridBagConstraints.HORIZONTAL;
kgbc.weightx = 1.0;
- /*
- keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc);
-
- // fourth row (indented)
- kgbc.gridy = 3;
- keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc);
- */
JPanel jp = new JPanel();
jp.setLayout(new FlowLayout());
oldBackupFilesLabel
- .setText(MessageManager.getString("label.old_backup_files"));
+ .setText(MessageManager
+ .getString("label.autodelete_old_backup_files"));
oldBackupFilesLabel.setFont(LABEL_FONT);
oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
jp.add(oldBackupFilesLabel);
return keepfilesPanel;
}
- private JPanel initBackupsTabFilenameExamplesPanel()
- {
- String title = MessageManager.getString("label.example_filenames");
- TitledBorder tb = new TitledBorder(title);
- // tb.setTitleFont(LABEL_FONT);
- exampleFilesPanel.setBorder(tb);
- exampleFilesPanel.setLayout(new GridBagLayout());
-
- // inordinately difficult to get this titledborder the right size for the
- // title
-
- backupfilesExampleLabel.setEditable(false);
- backupfilesExampleLabel.setPreferredSize(new Dimension(280, 85));
- backupfilesExampleLabel.setAlignmentX(LEFT_ALIGNMENT);
- backupfilesExampleLabel.setAlignmentY(TOP_ALIGNMENT);
-
- backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
- backupfilesExampleLabel
- .setBackground(exampleFilesPanel.getBackground());
-
- updateBackupFilesExampleLabel();
- exampleFilesPanel.setMinimumSize(new Dimension(280, 85));
-
- GridBagConstraints gbc = new GridBagConstraints();
- gbc.anchor = GridBagConstraints.EAST;
-
- gbc.gridy = 0;
- exampleFilesPanel.add(backupfilesExampleLabel, gbc);
- return exampleFilesPanel;
- }
-
protected void updateBackupFilesExampleLabel()
{
int exampleindex = 12;
- String base = MessageManager.getString("label.filename");
- if (base == null || base.length() > 0)
+ String base = MessageManager.getString("label.filename") + ".fa";
+ if (base == null || base.length() == 0)
{
- base = "filename.fa";
+ base = "file_name.fa";
}
- String suffix = suffixTemplate.getText();
- int digits = 3;
- try
- {
- suffixDigitsSpinner.commitEdit();
- digits = (Integer) suffixDigitsSpinner.getValue();
- digits = digits < 1 ? 1 : digits;
- } catch (Exception e)
- {
- System.out.println(
- "Failed casting (Integer) suffixTemplateSpinner.getValue()");
- }
boolean reverse = suffixReverse.isSelected();
boolean keepAll = backupfilesKeepAll.isSelected();
int rollMax = 4;
- try
+ String suffix = suffixTemplate.getText();
+ int digits = 3;
+
+ backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
+ if (suffix == null || suffix.length() == 0)
{
- backupfilesRollMaxSpinner.commitEdit();
- rollMax = (Integer) backupfilesRollMaxSpinner.getValue();
- rollMax = rollMax < 1 ? 1 : rollMax;
- } catch (Exception e)
+ backupfilesExampleLabel
+ .setText(MessageManager.getString("label.no_backup_files"));
+ backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
+ return;
+ }
+
+ rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
+ rollMax = rollMax < 1 ? 1 : rollMax;
+
+ if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
{
- System.out.println(
- "Failed casting (Integer) backupfilesRollMaxSpinner.getValue()");
+ rollMax = 1;
}
+ digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ digits = digits < 1 ? 1 : digits;
+
int lowersurround = 2;
int uppersurround = 0;
StringBuilder exampleSB = new StringBuilder();
boolean firstLine = true;
+ int lineNumber = 0;
if (reverse)
{
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
- exampleSB.append(BackupFilenameFilter.getBackupFilename(index,
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
if (min == max)
{
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
- exampleSB.append(BackupFilenameFilter.getBackupFilename(index,
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
if (min == max)
{
}
+ // add some extra empty lines to pad out the example files box. ugh, please tell
+ // me how to do this better
+ int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
+ if (remainingLines > 0)
+ {
+ for (int i = 0; i < remainingLines; i++)
+ {
+ exampleSB.append("\n ");
+ lineNumber++;
+ }
+ }
+
backupfilesExampleLabel.setText(exampleSB.toString());
}
i = Integer.parseInt((String) s.getValue());
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- System.out.println("Failed casting (Integer) JSpinner s.getValue()");
+ Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
- protected void keepRollMaxOptionsEnabled()
+ private void keepRollMaxOptionsEnabled()
{
- keepRollMaxOptionsEnabled(backupfilesKeepAll.isEnabled());
+ boolean enabled = backupfilesKeepAll.isEnabled()
+ && !backupfilesKeepAll.isSelected();
+ oldBackupFilesLabel.setEnabled(enabled);
+ backupfilesRollMaxSpinner.setEnabled(enabled);
+ backupfilesConfirmDelete.setEnabled(enabled);
}
- protected void keepRollMaxOptionsEnabled(boolean tryEnabled)
+ private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
{
- boolean enabled = tryEnabled && !backupfilesKeepAll.isSelected();
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected()
+ && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ keepfilesPanel.setEnabled(enabled);
+ backupfilesKeepAll.setEnabled(enabled);
oldBackupFilesLabel.setEnabled(enabled);
- backupfilesRollMaxSpinner.setEnabled(enabled);
- backupfilesConfirmDelete.setEnabled(enabled);
+ keepRollMaxOptionsEnabled();
}
- protected void backupsCustomOptionsSetEnabled(boolean enabled)
+ private void backupfilesSuffixTemplateDigitsSetEnabled()
{
- backupsOptionsSetEnabled(enabled, false);
+ boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ suffixDigitsLabel.setEnabled(enabled);
+ suffixDigitsSpinner.setEnabled(enabled);
+ suffixReverse.setEnabled(enabled);
}
- protected void backupsOptionsSetEnabled(boolean enabled)
+ private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
{
- backupsOptionsSetEnabled(enabled, true);
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected();
+ suffixPanel.setEnabled(enabled);
+ suffixTemplateLabel.setEnabled(enabled);
+ suffixTemplate.setEnabled(enabled);
+ backupfilesSuffixTemplateDigitsSetEnabled();
}
- protected void backupsOptionsSetEnabled(boolean enabled, boolean all)
+ private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
{
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+ revertButton.setEnabled(enabled);
+ }
- if (all)
- {
- presetsPanel.setEnabled(enabled);
- exampleFilesPanel.setEnabled(enabled);
+ private boolean backupfilesCustomChanged()
+ {
+ BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+ return !custom.equals(current);
+ }
- backupfilesPresetsCombo.setEnabled(enabled);
- backupfilesExampleLabel.setEnabled(enabled);
- }
- suffixPanel.setEnabled(enabled);
- keepfilesPanel.setEnabled(enabled);
+ protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+ {
+ String suffix = suffixTemplate.getText();
+ int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+ boolean confirmDelete = backupfilesConfirmDelete.isSelected();
- suffixTemplate.setEnabled(enabled);
- suffixTemplateLabel.setEnabled(enabled);
- suffixDigitsLabel.setEnabled(enabled);
- suffixDigitsSpinner.setEnabled(enabled);
- suffixReverse.setEnabled(enabled);
- oldBackupFilesLabel.setEnabled(enabled);
- backupfilesKeepAllEnabled(enabled);
+ BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+ reverse, keepAll, rollMax, confirmDelete);
- if (enabled && all)
- {
- backupsTabUpdatePresets();
- }
+ return bfpe;
+ }
+
+ protected void backupfilesCustomOptionsSetEnabled()
+ {
+ boolean enabled = customiseCheckbox.isSelected();
+
+ backupfilesRevertButtonSetEnabled(enabled);
+ backupfilesSuffixTemplateSetEnabled(enabled);
+ backupfilesKeepAllSetEnabled(enabled);
+ }
+
+ private void backupfilesSummarySetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ backupfilesExampleLabel.setEnabled(enabled);
+ exampleFilesPanel.setEnabled(enabled);
+ }
+
+ private void backupfilesPresetsSetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ presetsPanel.setEnabled(enabled);
+ presetsComboLabel.setEnabled(enabled);
+ backupfilesPresetsCombo.setEnabled(enabled);
+ customiseCheckbox.setEnabled(enabled);
+ revertButton.setEnabled(enabled);
+ }
+
+ protected void backupsOptionsSetEnabled()
+ {
+ backupfilesPresetsSetEnabled();
+ backupfilesSummarySetEnabled();
+ backupfilesCustomOptionsSetEnabled();
}
protected void backupsSetOptions(String suffix, int digits,
}
}
-}
-class IntKeyStringValueEntry
-{
- int k;
-
- String v;
-
- public IntKeyStringValueEntry(int k, String v)
- {
- this.k = k;
- this.v = v;
- }
-
- @Override
- public String toString()
+ protected void validateHmmerPath()
{
- return this.getValue();
}
- public int getKey()
+ protected void validateCygwinPath()
{
- return k;
}
- public String getValue()
- {
- return v;
+ /**
+ * 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();
}
}
-class BackupFilesPresetEntry
-{
- String suffix;
-
- int digits;
-
- boolean reverse;
-
- boolean keepAll;
-
- int rollMax;
-
- boolean confirmDelete;
-
- public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
- boolean keepAll, int rollMax, boolean confirmDelete)
- {
- this.suffix = suffix;
- this.digits = digits;
- this.reverse = reverse;
- this.keepAll = keepAll;
- this.rollMax = rollMax;
- this.confirmDelete = confirmDelete;
- }
-}
git://source.jalview.org / jalview.git / blobdiff