import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenMarkovModel;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.hmmer.HMMBuildThread;
+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 java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.Scanner;
import javax.help.HelpSetException;
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;
*/
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";
public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
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
*/
- trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
- isHMMERInstalled
- .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
- if (Cache.getDefault("USE_UNIPROT", false))
+ hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
{
- uniprot.setSelected(true);
+ hmmerBackgroundUniprot.setSelected(true);
}
else
{
- alignment.setSelected(true);
+ hmmerBackgroundAlignment.setSelected(true);
}
- numberOfSequencesToKeepField
- .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
- installationLocation.setEnabled(isHMMERInstalled.isSelected());
- hmmerPath.setEnabled(isHMMERInstalled.isSelected());
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
hmmerPath.setText(Cache.getProperty(HMMER_PATH));
hmmerPath.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- validateHMMERPath();
+ validateHmmerPath();
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ 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
Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
/*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
+
+ /*
* Set Structure tab defaults.
*/
final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
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
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
}
/**
/*
* Save HMMER settings
*/
- Cache.applicationProperties.setProperty("TRIM_TERMINI",
- Boolean.toString(trimTermini.isSelected()));
- Cache.applicationProperties.setProperty("USE_UNIPROT",
- Boolean.toString(uniprot.isSelected()));
- Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
- numberOfSequencesToKeepField.getText());
- Cache.applicationProperties.setProperty(HMMER_PATH,
- hmmerPath.getText());
- boolean hmmerInstalled = isHMMERInstalled.isSelected();
- Cache.applicationProperties.setProperty("HMMER_INSTALLED",
- Boolean.toString(hmmerInstalled));
- boolean hmmerFunctioning = validateHMMERPath(false);
- Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
- Boolean.toString(hmmerFunctioning));
+ Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
+ hmmerSequenceCount.getText());
+ Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
+ if (cygwinPath != null)
+ {
+ Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+ }
AlignFrame[] frames = Desktop.getAlignFrames();
- boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
- for (AlignFrame frame : frames)
+ if (frames != null && frames.length > 0)
{
- frame.updateHMMERStatus(hmmerStatus);
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
}
-
- trimTermini.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))
{
- uniprot.setSelected(true);
+ hmmerBackgroundUniprot.setSelected(true);
}
else
{
- alignment.setSelected(true);
+ hmmerBackgroundAlignment.setSelected(true);
}
- numberOfSequencesToKeepField
- .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
hmmerPath.setText(Cache.getProperty(HMMER_PATH));
/*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*
* Save Structure settings
*/
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
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
structureTab.requestFocusInWindow();
return false;
}
- if (isHMMERInstalled.isSelected())
- {
- if (!validateHMMER())
- {
- hmmerTab.requestFocusInWindow();
- return false;
- }
- }
return true;
}
}
- @Override
- protected boolean validateHMMER()
- {
- return validateHMMERPath();
-
- }
-
/**
* DOCUMENT ME!
*/
}
@Override
+ public void gapColour_actionPerformed(JPanel gap)
+ {
+ if (!useLegacyGap.isSelected())
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getBackground());
+ if (col != null)
+ {
+ gap.setBackground(col);
+ }
+ gap.repaint();
+ }
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JPanel hidden)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hiddenColour.getBackground());
+ if (col != null)
+ {
+ hidden.setBackground(col);
+ }
+ hidden.repaint();
+ }
+
+ @Override
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ boolean enabled = useLegacyGap.isSelected();
+ if (enabled)
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+ }
+ else
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ }
+ gapColour.setEnabled(!enabled);
+ gapLabel.setEnabled(!enabled);
+ }
+
+ @Override
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ useLegacyGap.setSelected(false);
+ useLegacyGaps_actionPerformed(null);
+ showHiddenAtStart.setSelected(false);
+ hiddenColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+ }
+
+ @Override
protected void userIdWidth_actionPerformed()
{
try
}
/**
- * Returns true if hmmer path contains the necessary valid executables, else
- * show an error dialog (if showing 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
*/
- private boolean validateHMMERPath(boolean showDialog)
+ protected boolean validateExecutablePath(JTextField textField, String executable)
{
- int missing = 0;
- String message = "";
- String folder = hmmerPath.getText().trim();
+ String folder = textField.getText().trim();
+
+ if (FileUtils.getExecutable(executable, folder) != null)
+ {
+ return true;
+ }
if (folder.length() > 0)
{
- File f = new File(folder);
- if (!f.exists())
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.folder_not_exists"),
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
- return false;
- }
- AlignmentI alignment = new Alignment(
- new SequenceI[]
- { new Sequence("test", "WLWL", 0, 3) });
- if (canExecute(folder + "/hmmbuild"))
- {
- validateHMMBuild(alignment);
- }
- else
- {
- message += MessageManager.getString("label.hmmbuild_not_found")
- + "\n";
- missing++;
- }
-
-
- if (canExecute(folder + "/hmmalign"))
- {
-
- }
- else
- {
- message += MessageManager.getString("label.hmmalign_not_found")
- + "\n";
- missing++;
- }
-
-
- if (canExecute(folder + "/hmmsearch"))
- {
-
- }
- else
- {
- message += MessageManager.getString("label.hmmsearch_not_found")
- + "\n";
- missing++;
- }
- }
-
- if (missing > 0)
- {
- if (missing < 3)
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
- return false;
- }
- else
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_binaries"),
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
-
- return false;
- }
- }
-
- return true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.executable_not_found",
+ executable),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
}
/**
}
/**
- * Runs hmmbuild to check if it is working. While doing this it parses the
- * version of HMMER.
- *
- * @param frame
- * @return
- */
- public boolean validateHMMBuild(AlignmentI alignment)
- {
- HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
- hmmbuild.hmmbuildWaitTillComplete();
- SequenceI hmmSeq = alignment.getSequenceAt(0);
- HiddenMarkovModel hmm;
- if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
- {
- hmm = hmmSeq.getHMM();
-
- if (hmm.getNumberOfSymbols() < 1)
- {
- return false;
- }
- }
- else
- {
- return false;
- }
-
- String header = hmm.getFileHeader();
- if (header == null)
- {
- return false;
- }
- else
- {
- Scanner scanner = new Scanner(header);
- scanner.next();
- String string = scanner.next();
- String version = string.substring(1);
- Cache.setProperty("HMMER_VERSION", version);
- scanner.close();
-
- }
- return true;
- }
-
-
- private boolean validateHMMERPath()
- {
- return validateHMMERPath(true);
- }
-
- /**
* If Chimera is selected, check it can be found on default or user-specified
* path, if not show a warning/help dialog.
*/
}
}
+ @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