X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=c921331dba2806ded88253ff064e42c078a7989f;hb=refs%2Fheads%2Ffeature%2FJAL-3515-slivka-preferences;hp=e55acf97ddfc776d5298ab8e71cf104f0af558e2;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index e55acf9..c921331 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -25,6 +25,8 @@ import jalview.bin.Cache; import jalview.gui.Help.HelpId; import jalview.gui.StructureViewer.ViewerType; import jalview.hmmer.HmmerCommand; +import jalview.io.BackupFiles; +import jalview.io.BackupFilesPresetEntry; import jalview.io.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -37,6 +39,7 @@ import jalview.urls.UrlLinkTableModel; import jalview.urls.api.UrlProviderFactoryI; import jalview.urls.api.UrlProviderI; import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.FileUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; @@ -61,6 +64,7 @@ import javax.swing.JColorChooser; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; +import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.RowFilter; import javax.swing.RowSorter; @@ -84,6 +88,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; */ public class Preferences extends GPreferences { + // suggested list delimiter character + public static final String COMMA = ","; + + public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT"; + + public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND"; + + public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI"; + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; @@ -108,7 +121,7 @@ public class Preferences extends GPreferences public static final String HMMER_PATH = "HMMER_PATH"; - public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS"; + public static final String CYGWIN_PATH = "CYGWIN_PATH"; public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS"; @@ -177,10 +190,10 @@ public class Preferences extends GPreferences JInternalFrame frame; - DasSourceBrowser dasSource; - private WsPreferences wsPrefs; + private SlivkaPreferences slivkaPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( MessageManager.getString("label.prompt_each_time"), "Prompt each time"); @@ -199,10 +212,10 @@ public class Preferences extends GPreferences super(); frame = new JInternalFrame(); frame.setContentPane(this); - dasSource = new DasSourceBrowser(); - dasTab.add(dasSource, BorderLayout.CENTER); wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); + slivkaTab.add(slivkaPrefs = new SlivkaPreferences(), + BorderLayout.CENTER); int width = 500, height = 450; new jalview.util.Platform(); if (Platform.isAMac()) @@ -218,8 +231,8 @@ public class Preferences extends GPreferences /* * Set HMMER tab defaults */ - hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false)); - if (Cache.getDefault("USE_UNIPROT", false)) + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) { hmmerBackgroundUniprot.setSelected(true); } @@ -228,14 +241,14 @@ public class Preferences extends GPreferences hmmerBackgroundAlignment.setSelected(true); } hmmerSequenceCount - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); hmmerPath.setText(Cache.getProperty(HMMER_PATH)); hmmerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - validateHMMERPath(true); + validateHmmerPath(); } }); hmmerPath.addFocusListener(new FocusAdapter() @@ -243,9 +256,34 @@ public class Preferences extends GPreferences @Override public void focusLost(FocusEvent e) { - validateHMMERPath(true); + validateHmmerPath(); } }); + if (cygwinPath != null) + { + String path = Cache.getProperty(CYGWIN_PATH); + if (path == null) + { + path = FileUtils.getPathTo("bash"); + } + cygwinPath.setText(path); + cygwinPath.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + validateCygwinPath(); + } + }); + cygwinPath.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + validateCygwinPath(); + } + }); + } /* * Set Visual tab defaults @@ -373,7 +411,7 @@ public class Preferences extends GPreferences gapLabel.setEnabled(!useLegacyGap.isSelected()); gapColour.setEnabled(!useLegacyGap.isSelected()); showHiddenAtStart - .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true)); + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); /* * Set Structure tab defaults. @@ -447,7 +485,7 @@ public class Preferences extends GPreferences doReset.addActionListener(onReset); // filter to display only custom urls - final RowFilter customUrlFilter = new RowFilter() + final RowFilter customUrlFilter = new RowFilter<>() { @Override public boolean include( @@ -569,7 +607,7 @@ public class Preferences extends GPreferences autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); userIdWidth.setEnabled(!autoIdWidth.isSelected()); userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); - Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH"); + Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); userIdWidth.setText(wi == null ? "" : wi.toString()); // TODO: refactor to use common enum via FormatAdapter and allow extension // for new flat file formats @@ -594,6 +632,12 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings + + + /* + * Set Backups tab defaults + */ + loadLastSavedBackupsOptions(); } /** @@ -706,14 +750,17 @@ public class Preferences extends GPreferences /* * Save HMMER settings */ - Cache.applicationProperties.setProperty("TRIM_TERMINI", + Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI, Boolean.toString(hmmrTrimTermini.isSelected())); - Cache.applicationProperties.setProperty("USE_UNIPROT", + Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND, Boolean.toString(hmmerBackgroundUniprot.isSelected())); - Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP", + Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT, hmmerSequenceCount.getText()); - Cache.applicationProperties.setProperty(HMMER_PATH, - hmmerPath.getText()); + Cache.setOrRemove(HMMER_PATH, hmmerPath.getText()); + if (cygwinPath != null) + { + Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText()); + } AlignFrame[] frames = Desktop.getAlignFrames(); if (frames != null && frames.length > 0) { @@ -723,8 +770,8 @@ public class Preferences extends GPreferences } } - hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false)); - if (Cache.getDefault("USE_UNIPROT", false)) + hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false)); + if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false)) { hmmerBackgroundUniprot.setSelected(true); } @@ -733,7 +780,7 @@ public class Preferences extends GPreferences hmmerBackgroundAlignment.setSelected(true); } hmmerSequenceCount - .setText(Cache.getProperty("SEQUENCES_TO_KEEP")); + .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT)); hmmerPath.setText(Cache.getProperty(HMMER_PATH)); /* @@ -865,7 +912,7 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH", + Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* @@ -878,8 +925,31 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - dasSource.saveProperties(Cache.applicationProperties); wsPrefs.updateAndRefreshWsMenuConfig(false); + + /* + * Save Backups settings + */ + Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Boolean.toString(enableBackupFiles.isSelected())); + int preset = getComboIntStringKey(backupfilesPresetsCombo); + Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); + + if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) + { + BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); + BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( + BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); + Cache.applicationProperties + .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG, + customBFPE.toString()); + } + + BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(preset); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -1204,7 +1274,7 @@ public class Preferences extends GPreferences { useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); - showHiddenAtStart.setSelected(true); + showHiddenAtStart.setSelected(false); hiddenColour.setBackground( jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @@ -1264,23 +1334,27 @@ public class Preferences extends GPreferences } /** - * Returns true if hmmer path is to a folder that contains an executable - * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning - * dialog) + * Returns true if the given text field contains a path to a folder that + * contains an executable with the given name, else false (after showing a + * warning dialog). The executable name will be tried with .exe appended if not + * found. + * + * @param textField + * @param executable */ - @Override - protected boolean validateHMMERPath(boolean showWarning) + protected boolean validateExecutablePath(JTextField textField, String executable) { - String folder = hmmerPath.getText().trim(); + String folder = textField.getText().trim(); - if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null) + if (FileUtils.getExecutable(executable, folder) != null) { return true; } - if (showWarning && folder.length() > 0) + if (folder.length() > 0) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.hmmbuild_not_found"), + MessageManager.formatMessage("label.executable_not_found", + executable), MessageManager.getString("label.invalid_folder"), JvOptionPane.ERROR_MESSAGE); } @@ -1357,6 +1431,18 @@ public class Preferences extends GPreferences } } + @Override + protected void validateHmmerPath() + { + validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD); + } + + @Override + protected void validateCygwinPath() + { + validateExecutablePath(cygwinPath, "run"); + } + public class OptionsParam { private String name;