X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=c1afbf76dd9d7a333a0c3243b5083bb3e7d754e4;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=c9e3629c586d8b35e1246fd10956a4e5a88df11d;hpb=0b266ea40bfb194f843840cd474b8b3a27e0df84;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index c9e3629..c1afbf7 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -31,7 +31,10 @@ import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer.ViewerType; 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; @@ -46,24 +49,25 @@ import java.awt.Insets; 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.JList; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; @@ -85,6 +89,8 @@ import javax.swing.event.ChangeListener; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; +import net.miginfocom.swing.MigLayout; + /** * Base class for the Preferences panel. * @@ -159,10 +165,15 @@ public class GPreferences extends JPanel 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 */ @@ -282,6 +293,23 @@ public class GPreferences extends JPanel 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(); @@ -296,9 +324,15 @@ public class GPreferences extends JPanel protected JPanel presetsPanel = new JPanel(); + protected JLabel presetsComboLabel = new JLabel(); + + protected JCheckBox customiseCheckbox = new JCheckBox(); + protected JButton revertButton = new JButton(); - protected JComboBox backupfilesPresetsCombo = new JComboBox<>(); + protected JComboBox backupfilesPresetsCombo = new JComboBox<>(); + + private int backupfilesPresetsComboLastSelected = 0; protected JPanel suffixPanel = new JPanel(); @@ -380,6 +414,8 @@ public class GPreferences extends 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. */ @@ -388,7 +424,7 @@ public class GPreferences extends JPanel /* * Handler to validate a tab before leaving it - currently only for - * Structure. + * Structure */ tabbedPane.addChangeListener(new ChangeListener() { @@ -442,6 +478,134 @@ public class GPreferences extends JPanel } /** + * 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 @@ -643,6 +807,7 @@ public class GPreferences extends JPanel 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); @@ -996,7 +1161,7 @@ public class GPreferences extends JPanel 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); @@ -1008,7 +1173,7 @@ public class GPreferences extends JPanel 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); @@ -1017,11 +1182,11 @@ public class GPreferences extends JPanel 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); @@ -1272,7 +1437,7 @@ public class GPreferences extends JPanel { if (e.getClickCount() == 2) { - String chosen = openFileChooser(); + String chosen = openFileChooser(false); if (chosen != null) { chimeraPath.setText(chosen); @@ -1327,10 +1492,14 @@ public class GPreferences extends JPanel * * @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( @@ -1346,21 +1515,6 @@ public class GPreferences extends JPanel 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; @@ -1694,22 +1848,28 @@ public class GPreferences extends JPanel 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", 1)); - suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX, - ".bak" + BackupFiles.NUM_PLACEHOLDER)); - suffixDigitsSpinner - .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3)); - suffixReverse.setSelected( - Cache.getDefault(BackupFiles.REVERSE_ORDER, false)); - backupfilesKeepAll - .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false)); - backupfilesRollMaxSpinner - .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 3)); - backupfilesConfirmDelete.setSelected( - Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true)); + Cache.getDefault(BackupFiles.NS + "_PRESET", + BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT)); + + backupsSetOptions(savedPreset); backupsOptionsSetEnabled(); updateBackupFilesExampleLabel(); @@ -1717,11 +1877,11 @@ public class GPreferences extends JPanel private boolean warnAboutSuffixReverseChange() { - boolean savedSuffixReverse = Cache.getDefault(BackupFiles.REVERSE_ORDER, - false); - int savedSuffixDigits = Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3); - String savedSuffixTemplate = Cache.getDefault(BackupFiles.SUFFIX, - ".bak" + BackupFiles.NUM_PLACEHOLDER); + 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); @@ -1798,7 +1958,6 @@ public class GPreferences extends JPanel gbc.gridy++; // row 1 backupsTab.add(presetsPanel, gbc); - // gbc.anchor = GridBagConstraints.NORTHWEST; // now using whole row gbc.gridwidth = 2; gbc.gridheight = 1; @@ -1820,50 +1979,10 @@ public class GPreferences extends JPanel return backupsTab; } - protected static final int BACKUPFILESSCHEMECUSTOMISE = 0; - - private static 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_all_versions")), - new IntKeyStringValueEntry(4, - MessageManager.getString("label.rolled_backups")), - // ... - // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last) - new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOMISE, - MessageManager.getString("label.customise")) }; - - private static final Map backupfilesPresetEntriesValues = new HashMap() - { - /** - * - */ - private static final long serialVersionUID = 125L; - - { - put(1, new BackupFilesPresetEntry( - ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3, - 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() { String title = MessageManager.getString("label.schemes"); - // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title); - // TitledBorder tb = new TitledBorder(title); - // tb.setTitleFont(LABEL_FONT); - // presetsPanel.setBorder(tb); presetsPanel.setLayout(new GridBagLayout()); @@ -1878,24 +1997,53 @@ public class GPreferences extends JPanel // "Scheme: " gbc.gridx = 0; gbc.gridy = 0; - presetsPanel.add(new JLabel(title + ":"), gbc); - for (int i = 0; i < backupfilesPresetEntries.length; i++) + presetsComboLabel = new JLabel(title + ":"); + presetsPanel.add(presetsComboLabel, gbc); + + List entries = Arrays + .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries); + List 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]); } + */ - // put "Previously saved scheme" item in italics (it's not really - // selectable, as such -- it deselects itself when selected) and - // "Customise" in bold - backupfilesPresetsCombo - .setRenderer(new BackupFilesPresetsComboBoxRenderer()); 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(); + } } }); @@ -1904,20 +2052,55 @@ public class GPreferences extends JPanel 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) { - loadLastSavedBackupsOptions(); + 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; - gbc.gridy++; presetsPanel.add(revertButton, gbc); return presetsPanel; @@ -1926,7 +2109,7 @@ public class GPreferences extends JPanel private JPanel initBackupsTabFilenameExamplesPanel() { String title = MessageManager - .getString("label.summary_of_backups_scheme"); + .getString("label.scheme_examples"); TitledBorder tb = new TitledBorder(title); exampleFilesPanel.setBorder(tb); exampleFilesPanel.setLayout(new GridBagLayout()); @@ -1952,45 +2135,68 @@ public class GPreferences extends JPanel { IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo .getSelectedItem(); - int key = entry.getKey(); - String value = entry.getValue(); + int key = entry.k; + String value = entry.v; - // BACKUPFILESSCHEMECUSTOMISE (==0) reserved for "Custom" - if (key != BACKUPFILESSCHEMECUSTOMISE) + if (BackupFilesPresetEntry.backupfilesPresetEntriesValues + .containsKey(key)) { - if (backupfilesPresetEntriesValues.containsKey(key)) - { - backupsSetOptions(backupfilesPresetEntriesValues.get(key)); - } - else - { - System.out.println("Preset '" + value + "' not implemented"); - } + backupsSetOptions( + BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(key)); + } + else + { + Cache.log.error( + "Preset '" + value + "' [key:" + key + "] not implemented"); } - backupfilesCustomOptionsSetEnabled(); + // Custom options will now be enabled when the customiseCheckbox is checked + // (performed above) + // backupfilesCustomOptionsSetEnabled(); updateBackupFilesExampleLabel(); } - protected int getComboIntStringKey(JComboBox c) + protected int getComboIntStringKey( + JComboBox 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 c, + protected void setComboIntStringKey( + JComboBox backupfilesPresetsCombo2, int key) { - for (int i = 0; i < c.getItemCount(); i++) + for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++) { - IntKeyStringValueEntry e = c.getItemAt(i); - if (e.getKey() == key) + IntKeyStringValueEntry e; + try + { + e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i); + } catch (Exception ex) { - c.setSelectedIndex(i); + 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() @@ -2014,16 +2220,18 @@ public class GPreferences extends JPanel { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); + backupfilesRevertButtonSetEnabled(true); } }); - KeyListener kl = new KeyListener() + suffixTemplate.addKeyListener(new KeyListener() { @Override public void keyReleased(KeyEvent e) { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); + backupfilesRevertButtonSetEnabled(true); } @Override @@ -2043,26 +2251,25 @@ public class GPreferences extends JPanel } } - }; - 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")); @@ -2079,12 +2286,13 @@ public class GPreferences extends JPanel } if (okay) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } else { - boolean savedSuffixReverse = Cache - .getDefault(BackupFiles.REVERSE_ORDER, false); + boolean savedSuffixReverse = BackupFilesPresetEntry + .getSavedBackupEntry().reverse; suffixReverse.setSelected(savedSuffixReverse); } } @@ -2160,6 +2368,7 @@ public class GPreferences extends JPanel @Override public void actionPerformed(ActionEvent e) { + backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }); @@ -2168,6 +2377,7 @@ public class GPreferences extends JPanel @Override public void actionPerformed(ActionEvent e) { + backupfilesRevertButtonSetEnabled(true); keepRollMaxOptionsEnabled(); updateBackupFilesExampleLabel(); } @@ -2178,15 +2388,26 @@ public class GPreferences extends JPanel @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(); @@ -2222,13 +2443,6 @@ public class GPreferences extends JPanel 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()); @@ -2284,6 +2498,7 @@ public class GPreferences extends JPanel int uppersurround = 0; StringBuilder exampleSB = new StringBuilder(); boolean firstLine = true; + int lineNumber = 0; if (reverse) { @@ -2294,6 +2509,7 @@ public class GPreferences extends JPanel if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); + lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { @@ -2308,6 +2524,7 @@ public class GPreferences extends JPanel else { exampleSB.append("\n"); + lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); @@ -2347,6 +2564,7 @@ public class GPreferences extends JPanel if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); + lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { @@ -2361,6 +2579,7 @@ public class GPreferences extends JPanel else { exampleSB.append("\n"); + lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); @@ -2389,6 +2608,18 @@ public class GPreferences extends JPanel } + // 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()); } @@ -2403,7 +2634,7 @@ public class GPreferences extends JPanel i = Integer.parseInt((String) s.getValue()); } catch (Exception e) { - System.out.println( + Cache.log.error( "Exception casting the initial value of s.getValue()"); } } @@ -2435,7 +2666,7 @@ public class GPreferences extends JPanel 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; } @@ -2452,7 +2683,7 @@ public class GPreferences extends JPanel private void backupfilesKeepAllSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() - && getComboIntStringKey(backupfilesPresetsCombo) == 0 + && customiseCheckbox.isSelected() && suffixTemplate.getText() .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1; keepfilesPanel.setEnabled(enabled); @@ -2473,18 +2704,48 @@ public class GPreferences extends JPanel private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() - && getComboIntStringKey(backupfilesPresetsCombo) == 0; + && customiseCheckbox.isSelected(); suffixPanel.setEnabled(enabled); suffixTemplateLabel.setEnabled(enabled); suffixTemplate.setEnabled(enabled); backupfilesSuffixTemplateDigitsSetEnabled(); } + private void backupfilesRevertButtonSetEnabled(boolean tryEnabled) + { + boolean enabled = tryEnabled && enableBackupFiles.isSelected() + && customiseCheckbox.isSelected() && backupfilesCustomChanged(); + revertButton.setEnabled(enabled); + } + + private boolean backupfilesCustomChanged() + { + BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM); + BackupFilesPresetEntry current = getBackupfilesCurrentEntry(); + return !custom.equals(current); + } + + 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(); + + BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits, + reverse, keepAll, rollMax, confirmDelete); + + return bfpe; + } + protected void backupfilesCustomOptionsSetEnabled() { - int scheme = getComboIntStringKey(backupfilesPresetsCombo); - boolean enabled = scheme == 0 && enableBackupFiles.isSelected(); + boolean enabled = customiseCheckbox.isSelected(); + backupfilesRevertButtonSetEnabled(enabled); backupfilesSuffixTemplateSetEnabled(enabled); backupfilesKeepAllSetEnabled(enabled); } @@ -2500,7 +2761,10 @@ public class GPreferences extends JPanel { boolean enabled = enableBackupFiles.isSelected(); presetsPanel.setEnabled(enabled); + presetsComboLabel.setEnabled(enabled); backupfilesPresetsCombo.setEnabled(enabled); + customiseCheckbox.setEnabled(enabled); + revertButton.setEnabled(enabled); } protected void backupsOptionsSetEnabled() @@ -2712,87 +2976,41 @@ public class GPreferences extends JPanel } } -} - -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; - } -} - -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; - } -} - -class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer -{ /** + * A helper method to add a panel containing a label and a component to a + * panel * + * @param panel + * @param tooltip + * @param label + * @param valBox */ - private static final long serialVersionUID = 88L; - - @Override - public Component getListCellRendererComponent(JList list, Object value, - int index, boolean isSelected, boolean cellHasFocus) - { - super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus); - - try { - IntKeyStringValueEntry e = (IntKeyStringValueEntry) value; - if (e.getKey() == GPreferences.BACKUPFILESSCHEMECUSTOMISE) - { - // "Customise" item - this.setFont(this.getFont().deriveFont(Font.BOLD)); - } - } catch (Exception e) { - return this; - } - - return this; + 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(); } -} \ No newline at end of file +} +