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;
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;
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;
*/
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";
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";
JInternalFrame frame;
- DasSourceBrowser dasSource;
-
private WsPreferences wsPrefs;
private OptionsParam promptEachTimeOpt = new OptionsParam(
super();
frame = new JInternalFrame();
frame.setContentPane(this);
- dasSource = new DasSourceBrowser();
- dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
int width = 500, height = 450;
/*
* 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);
}
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()
@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
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.
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
}
/**
/*
* 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)
{
}
}
- 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);
}
hmmerBackgroundAlignment.setSelected(true);
}
hmmerSequenceCount
- .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
hmmerPath.setText(Cache.getProperty(HMMER_PATH));
/*
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
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
}
/**
- * 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);
}
}
}
+ @Override
+ protected void validateHmmerPath()
+ {
+ validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
+ }
+
+ @Override
+ protected void validateCygwinPath()
+ {
+ validateExecutablePath(cygwinPath, "run");
+ }
+
public class OptionsParam
{
private String name;
git://source.jalview.org / jalview.git / blobdiff