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;
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 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 STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String HMMER_PATH = "HMMER_PATH";
+
+ public static final String CYGWIN_PATH = "CYGWIN_PATH";
+
+ public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ 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
*/
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
showConsensLogo
.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
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.
/*
* Set Backups tab defaults
*/
- enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
- suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
- "-v" + 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, 4));
- backupfilesConfirmDelete.setSelected(
- Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
- backupsOptionsSetEnabled(enableBackupFiles.isSelected());
- updateBackupFilesExampleLabel();
- /*
- suffixPanel.setPreferredSize(
- new Dimension(width, suffixPanel.getHeight()));
- keepfilesPanel.setPreferredSize(
- new Dimension(width, keepfilesPanel.getHeight()));
- exampleFilesPanel.setPreferredSize(
- new Dimension(width, exampleFilesPanel.getHeight()));
- */
-
+ loadLastSavedBackupsOptions();
}
/**
Boolean.toString(showConsensHistogram.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+ Boolean.toString(showHMMLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
maxColour.getBackground());
/*
+ * Save HMMER settings
+ */
+ 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();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
* Save Overview settings
*/
Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
/*
* Save Backups settings
*/
- Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
- Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
- Boolean.toString(suffixReverse.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
- suffixTemplate.getText());
- Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
- Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+ 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();
&& (identity.isSelected() || showGroupConsensus.isSelected()));
showConsensLogo.setEnabled(annotations.isSelected()
&& (identity.isSelected() || showGroupConsensus.isSelected()));
+ showInformationHistogram.setEnabled(annotations.isSelected());
+ showHMMLogo.setEnabled(annotations.isSelected());
}
@Override
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
}
return true;
}
+
+ /**
+ * 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
+ */
+ protected boolean validateExecutablePath(JTextField textField, String executable)
+ {
+ String folder = textField.getText().trim();
+
+ if (FileUtils.getExecutable(executable, folder) != null)
+ {
+ return true;
+ }
+ if (folder.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.executable_not_found",
+ executable),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+
+ /**
+ * Checks if a file can be executed
+ *
+ * @param path
+ * the path to the file
+ * @return
+ */
+ public boolean canExecute(String path)
+ {
+ File file = new File(path);
+ if (!file.canExecute())
+ {
+ file = new File(path + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
}
}
+ @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