*/
package jalview.bin;
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.util.Platform;
-import jalview.ws.sifts.SiftsSettings;
-
import java.awt.Color;
import java.awt.Dimension;
import java.io.BufferedReader;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
* panel in web service preferences</li>
* </ul>
*
+ * @author $author$
+ * @version $Revision$
*/
public class Cache implements ApplicationSingletonI
{
};
/** Default file is ~/.jalview_properties */
+ // BH 2020 private, not static
private String propertiesFile;
- /**
- * flag to possibly allow properties to be written to a property file
- */
- private boolean propsAreReadOnly = Platform.isJS();
+ private static boolean propsAreReadOnly = Platform.isJS();
private final static String JS_PROPERTY_PREFIX = "jalview_";
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
laxis.setLevel(Level.toLevel(
- getDefault("logs.Axis.Level", Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(
- getDefault("logs.Castor.Level", Level.INFO.toString())));
+ Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
lcastor = Logger.getLogger("org.exolab.castor.xml");
- lcastor.setLevel(Level.toLevel(
- getDefault("logs.Castor.Level", Level.INFO.toString())));
+ lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
+ Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
+ // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
.getDefault("logs.Jalview.level", Level.INFO.toString())));
private void loadPropertiesImpl(String propsFile)
{
propertiesFile = propsFile;
- if (!propsAreReadOnly)
+ if (propsFile == null && !propsAreReadOnly)
{
- // Java only
- if (propsFile == null)
- {
- propertiesFile = System.getProperty("user.home")
- + File.separatorChar + ".jalview_properties";
+ propertiesFile = System.getProperty("user.home") + File.separatorChar
+ + ".jalview_properties";
}
else
{
// don't corrupt the file we've been given.
propsAreReadOnly = true;
}
- }
if (propertiesFile == null)
- { // BH 2019 read properties from the Info object associated with this
- // applet
+ { // BH 2019
Platform.readInfoProperties(JS_PROPERTY_PREFIX,
applicationProperties);
}
// LOAD THE AUTHORS FROM THE authors.props file
String authorDetails = (Platform.isJS() ? null
- : "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/authors.props")));
+ : resolveResourceURLFor("/authors.props"));
try
{
if (authorDetails != null)
{
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+ URL localJarFileURL = new URL(authorDetails);
InputStream in = localJarFileURL.openStream();
applicationProperties.load(in);
in.close();
applicationProperties.remove("YEAR");
}
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- String buildDetails = (Platform.isJS() ? null
- : "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties")));
- if (buildDetails != null)
- {
- try
- {
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- buildDetails = null;
- }
- }
- if (buildDetails == null)
- {
- applicationProperties.remove("VERSION");
- }
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
- String codeInstallation = getProperty("INSTALLATION");
- if (codeVersion == null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- codeInstallation = "";
- }
- else
- {
- codeInstallation = " (" + codeInstallation + ")";
- }
- new BuildDetails(codeVersion, null, codeInstallation);
+ loadBuildProperties(false);
- SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false));
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- getDefault("sifts_fail_safe_pid_threshold",
+ jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- getDefault("sifts_cache_threshold_in_days",
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
-
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.getDefault(
+ // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
- // jnlpVersion will be null if we're using InstallAnywhere
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // jnlpVersion will be null if a latest version check for the channel needs to
+ // be done
// Dont do this check if running in headless mode
- if (jnlpVersion == null && !Jalview.isHeadlessMode()
- && getDefault("VERSION_CHECK", true))
- {
- class VersionChecker extends Thread
+ if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
+ && (System.getProperty("java.awt.headless") == null || System
+ .getProperty("java.awt.headless").equals("false")))
+ {
+ new Thread()
{
@Override
public void run()
setProperty("LATEST_VERSION", remoteVersion);
}
- }
-
- VersionChecker vc = new VersionChecker();
- vc.start();
+ }.start();
}
else
{
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
- initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS));
+ Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+ false);
}
+ /**
+ * construct a resource URL for the given absolute resource pathname
+ *
+ * @param resourcePath
+ * @return
+ */
+ private static String resolveResourceURLFor(String resourcePath)
+ {
+ String url = null;
+ if (Platform.isJS() || !Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString().endsWith(".jar"))
+ {
+ try
+ {
+ url = Cache.class.getResource(resourcePath).toString();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to resolve resource " + resourcePath + ": "
+ + ex.getMessage());
+ }
+ }
+ else
+ {
+ url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!" + resourcePath));
+ }
+ return url;
+ }
+
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printVersion = codeInstallation == null;
+
+ /*
+ * read build properties - from the Jalview jar for a Java distribution,
+ * or from codebase file in test or JalviewJS context
+ */
+ try
+ {
+ String buildDetails = resolveResourceURLFor("/.build_properties");
+ URL localJarFileURL = new URL(buildDetails);
+ InputStream in = localJarFileURL.openStream();
+ getInstance().applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ getInstance().applicationProperties.remove("VERSION");
+ }
+ String codeVersion = getProperty("VERSION");
+ codeInstallation = getProperty("INSTALLATION");
+
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ setProperty("VERSION", codeVersion);
+ new BuildDetails(codeVersion, null, codeInstallation);
+ if (printVersion && reportVersion)
+ {
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
+ // BH 2020 was static
private void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
public static String getProperty(String key)
{
return getInstance().applicationProperties.getProperty(key);
+
+// old, original idea:
+// String prop = applicationProperties.getProperty(key);
+// if (prop == null && Platform.isJS())
+// {
+// prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+// + "_" + JS_PROPERTY_PREFIX + key);
+// }
+// return prop;
+
}
+
+ //These methods are used when checking if the saved preference is different
+ // to the default setting
+
/**
* Returns the boolean property value for the given property name. If the
* value is absent then the default value is returned instead.
* @param def
* @return
*/
- public static boolean getDefault(String property, final boolean def)
+ public static boolean getDefault(String property, boolean def)
{
String string = getProperty(property);
+ // BH simplification only
return string == null ? def : Boolean.parseBoolean(string);
}
* @param def
* @return
*/
- public static int getDefault(String property, final int def)
+ public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
try
{
+ // BH simplification only
+
return Integer.parseInt(string);
} catch (NumberFormatException e)
{
}
/**
- * retrieve a dimension, such as for Jmol
- *
- * @param property
- * @param def
- * @return
- */
- public static Dimension getDefaultDim(String property, Dimension def)
- {
- String s = getProperty(property);
- if (s != null)
- {
- if (s.indexOf(',') < 0)
- {
- s = s.trim().replace(' ', ',');
- if (s.indexOf(',') < 0)
- {
- s += "," + s;
- }
- }
- try
- {
- int pt = s.indexOf(",");
- return new Dimension(Integer.parseInt(s.substring(0, pt)),
- Integer.parseInt(s.substring(pt + 1)));
- } catch (NumberFormatException e)
- {
- System.out.println("Error parsing Dimension property '" + property
- + "' with value '" + s + "'");
- }
- }
- return def;
- }
-
- /**
* Returns the value of the given property, or the supplied default value if
* the property is not set
*
* @param def
* @return
*/
- public static String getDefault(String property, final String def)
+ public static String getDefault(String property, String def)
{
String value = getProperty(property);
return value == null ? def : value;
/**
* Sets a property value for the running application, without saving it to the
- * properties file
+ * properties file.
+ *
+ * Used extensively in AppletParams and Preferences.ok_actionPerformed
+ *
*
* @param key
* @param obj
getInstance().setPropertyImpl(key, obj, false);
}
+
/**
* Sets a property value, and optionally also saves the current properties to
* file
/**
* Removes the named property for the running application, without saving the
- * properties file
+ * properties file.
+ *
+ * Called by Preferences.ok_actionPerformed specifically for SEQUENCE_LINKS and STORED_LINKS.
+ *
*
* @param key
*/
.newInstance(new Object[]
{ "Jalview Desktop",
(vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + getDefault("BUILD_DATE", "unknown")),
+ + jalview.bin.Cache.getDefault("BUILD_DATE",
+ "unknown")),
"UA-9060947-1" });
jgoogleanalyticstracker
.getMethod("trackAsynchronously", new Class[]
* parseable.
*
* @param property
- * @param defaultColour
+ * @param defcolour
* @return
- * @see Cache#setColourPropertyNoSave(String, Color)
- * @see ColorUtils#parseColourString(String)
*/
- public static Color getDefaultColour(String property,
- final Color defaultColour)
+ public static Color getDefaultColour(String property, Color defcolour)
{
String colprop = getProperty(property);
if (colprop == null)
{
- return defaultColour;
+ return defcolour;
}
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ property);
}
- return (col == null) ? defaultColour : col;
+ return (col == null) ? defcolour : col;
}
/**
* Stores a colour as a Jalview property, converted to hex values for rgb.
* Properties are not saved to file.
*
+ *
+ *
+ * Used extensively in Preferences.ok_actionPerformed
+ *
* @param property
* @param colour
*/
}
/**
+ * store a colour as a Jalview user default property
+ *
+ * @param property
+ * @param colour
+ */
+ public static void setColourProperty(String property, Color colour)
+ {
+ setProperty(property, jalview.util.Format.getHexString(colour));
+ }
+
+ /**
* Stores a formatted date in a jalview property, using a fixed locale.
* Updated properties are written out to the properties file.
*
{
if (coloursFound.toString().length() > 1)
{
+ // BH moved to Preferences for consistency
setProperty(Preferences.USER_DEFINED_COLOURS,
coloursFound.toString());
}
else
{
+ // BH moved to Preferences for consistency
getInstance().applicationProperties
.remove(Preferences.USER_DEFINED_COLOURS);
}
}
}
+ /**
+ * Initial logging information helper for various versions output
+ *
+ * @param prefix
+ * @param value
+ * @param defaultValue
+ */
+ private static void appendIfNotNull(StringBuilder sb, String prefix,
+ String value, String suffix, String defaultValue)
+ {
+ if (value == null && defaultValue == null)
+ {
+ return;
+ }
+ String line = prefix + (value != null ? value : defaultValue) + suffix;
+ sb.append(line);
+ }
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: " + System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
+ sb.append("\n");
+ appendIfNotNull(sb, "Install4j version: ",
+ System.getProperty("sys.install4jVersion"), "\n", null);
+ appendIfNotNull(sb, "Install4j template version: ",
+ System.getProperty("installer_template_version"), "\n", null);
+ appendIfNotNull(sb, "Launcher version: ",
+ System.getProperty("launcher_version"), "\n", null);
+ if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
+ }
+ return sb.toString();
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
+
+ /**
+ * retrieve a dimension, such as for Jmol
+ *
+ * @param property
+ * @param def
+ * @return
+ */
+ public static Dimension getDefaultDim(String property, Dimension def)
+ {
+ String s = getProperty(property);
+ if (s != null)
+ {
+ if (s.indexOf(',') < 0)
+ {
+ s = s.trim().replace(' ', ',');
+ if (s.indexOf(',') < 0)
+ {
+ s += "," + s;
+ }
+ }
+ try
+ {
+ int pt = s.indexOf(",");
+ return new Dimension(Integer.parseInt(s.substring(0, pt)),
+ Integer.parseInt(s.substring(pt + 1)));
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing Dimension property '" + property
+ + "' with value '" + s + "'");
+ }
+ }
+ return def;
+ }
+
+
}
"Tootip text to format must not be null!");
ttext = ttext.trim();
boolean maxLengthExceeded = false;
- boolean isHTML = ttext.startsWith("<html>");
- if (isHTML)
- {
- ttext = ttext.substring(6);
- }
- if (ttext.endsWith("</html>"))
- {
- isHTML = true;
- ttext = ttext.substring(0, ttext.length() - 7);
- }
- boolean hasBR = ttext.contains("<br>");
- enclose |= isHTML || hasBR;
- if (hasBR)
+
+ if (ttext.contains("<br>"))
{
String[] htmllines = ttext.split("<br>");
for (String line : htmllines)
* @param entries
* @param tooltips
*/
- public static JComboBox<String> buildComboWithTooltips(
- List<String> entries, List<String> tooltips)
+ public static JComboBox<Object> buildComboWithTooltips(
+ List<Object> entries, List<String> tooltips)
{
- JComboBox<String> combo = new JComboBox<>();
+ JComboBox<Object> combo = new JComboBox<>();
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
combo.setRenderer(renderer);
- for (String attName : entries)
+ for (Object attName : entries)
{
combo.addItem(attName);
}
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
@SuppressWarnings("serial")
public class Preferences extends GPreferences
{
- public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ // original to develop
+
+ 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 DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ 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;
+
+ // new for applet
+
public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
- public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
- public static final String CHIMERA_PATH = "CHIMERA_PATH";
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
- public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
-
- public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
-
- public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
-
- public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
-
public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
public static final String FONT_STYLE = "FONT_STYLE";
- public static final String GAP_COLOUR = "GAP_COLOUR";
-
public static final String GAP_SYMBOL = "GAP_SYMBOL";
- public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
-
public static final String HIDE_INTRONS = "HIDE_INTRONS";
public static final String ID_ITALICS = "ID_ITALICS";
public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
- public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
-
public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
- public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
-
public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
- public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+ public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
- public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+ public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
- public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
- public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
- public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
-
public static final String SORT_BY_TREE = "SORT_BY_TREE";
- public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
-
- public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
-
public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
public static final String USE_FULL_SO = "USE_FULL_SO";
- public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
-
- public static final String USE_RNAVIEW = "USE_RNAVIEW";
-
public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
- private static final int MIN_FONT_SIZE = 1;
-
- private static final int MAX_FONT_SIZE = 30;
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
/**
* Holds name and link separated with | character. Sequence ID must be
public static final List<String> groupURLLinks; // not implemented
- public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
-
- public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
-
- public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
-
- public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
- 600, 600);
-
static
{
// get links selected to be in the menu (SEQUENCE_LINKS)
Boolean.toString(modellerOutput.isSelected()));
Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
- Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH,
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText());
if (!Platform.isJS())
{
wsPrefs.updateAndRefreshWsMenuConfig(false);
+ }
+
/*
* Save Backups settings
*/
- Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.ENABLED,
+ Cache.setPropertyNoSave(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.NO_MAX,
- Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
- Boolean.toString(suffixReverse.isSelected()));
- Cache.setPropertyNoSave(BackupFiles.SUFFIX, suffixTemplate.getText());
- Cache.setPropertyNoSave(BackupFiles.ROLL_MAX, Integer
- .toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
- Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer
- .toString(getComboIntStringKey(backupfilesPresetsCombo)));
+ int preset = getComboIntStringKey(backupfilesPresetsCombo);
+ Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
+ Integer.toString(preset));
+ if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
+ customBFPE.toString());
}
+ BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(preset);
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.SAVEDCONFIG,
+ savedBFPE.toString());
+
Cache.saveProperties();
Desktop.getInstance().doConfigureStructurePrefs();
try
{
ListSelectionModel lsm = (ListSelectionModel) e.getSource();
- int index = lsm.getMinSelectionIndex();
- if (index == -1)
- {
- // no selection, so disable delete/edit buttons
- editLink.setEnabled(false);
- deleteLink.setEnabled(false);
- return;
- }
- int modelIndex = linkUrlTable.convertRowIndexToModel(index);
+ updateValueChanged(lsm.getMinSelectionIndex());
+ }
+ }
- // enable/disable edit and delete link buttons
- if (((UrlLinkTableModel) linkUrlTable.getModel())
- .isRowDeletable(modelIndex))
- {
- deleteLink.setEnabled(true);
- }
- else
- {
- deleteLink.setEnabled(false);
- }
+ public void updateValueChanged(int index)
+ {
+ if (index == -1)
+ {
+ // no selection, so disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+ return;
+ }
+ int modelIndex = linkUrlTable.convertRowIndexToModel(index);
- if (((UrlLinkTableModel) linkUrlTable.getModel())
- .isRowEditable(modelIndex))
- {
- editLink.setEnabled(true);
- }
- else
- {
- editLink.setEnabled(false);
- }
+ // enable/disable edit and delete link buttons
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isRowDeletable(modelIndex))
+ {
+ deleteLink.setEnabled(true);
+ }
+ else
+ {
+ deleteLink.setEnabled(false);
+ }
+
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isRowEditable(modelIndex))
+ {
+ editLink.setEnabled(true);
+ }
+ else
+ {
+ editLink.setEnabled(false);
}
}
}
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
* BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
- * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
- * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
- * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
- * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
- * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files.
- * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
+ * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
+ * (see BackupFilesPresetEntry)
*/
public class BackupFiles
public static final String ENABLED = NS + "_ENABLED";
- public static final String SUFFIX = NS + "_SUFFIX";
-
- public static final String NO_MAX = NS + "_NO_MAX";
-
- public static final String ROLL_MAX = NS + "_ROLL_MAX";
-
- public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
-
public static final String NUM_PLACEHOLDER = "%n";
- public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER";
-
- public static final String CONFIRM_DELETE_OLD = NS
- + "_CONFIRM_DELETE_OLD";
-
private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
private static final String TEMP_FILE_EXT = ".tmp";
// REVERSE_ORDER
public BackupFiles(File file)
{
- this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
- }
-
- public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
- int defaultMax, int defaultDigits, boolean defaultReverseOrder)
- {
classInit();
this.file = file;
- this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
- this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
- this.max = Cache.getDefault(ROLL_MAX, defaultMax);
- this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
- this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
- defaultReverseOrder);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+ this.suffix = bfpe.suffix;
+ this.noMax = bfpe.keepAll;
+ this.max = bfpe.rollMax;
+ this.digits = bfpe.digits;
+ this.reverseOrder = bfpe.reverse;
// create a temp file to save new data in
File temp = null;
public static void classInit()
{
setEnabled(Cache.getDefault(ENABLED, !Platform.isJS()));
- setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ setConfirmDelete(bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+public class BackupFilesPresetEntry
+{
+
+ public String suffix;
+
+ public static final int DIGITSMIN = 1;
+
+ public static final int DIGITSMAX = 6;
+
+ public int digits;
+
+ public boolean reverse;
+
+ public boolean keepAll;
+
+ public static final int ROLLMAXMIN = 1;
+
+ public static final int ROLLMAXMAX = 999;
+
+ public int rollMax;
+
+ public boolean confirmDelete;
+
+ public static final String SAVEDCONFIG = BackupFiles.NS + "_SAVED";
+
+ public static final String CUSTOMCONFIG = BackupFiles.NS + "_CUSTOM";
+
+ private static final String stringDelim = "\t";
+
+ public static final int BACKUPFILESSCHEMECUSTOM = 0;
+
+ public static final int BACKUPFILESSCHEMEDEFAULT = 1;
+
+ public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
+ boolean keepAll, int rollMax, boolean confirmDelete)
+ {
+ this.suffix = suffix == null ? "" : suffix;
+ this.digits = digits < DIGITSMIN ? DIGITSMIN
+ : (digits > DIGITSMAX ? DIGITSMAX : digits);
+ this.reverse = reverse;
+ this.keepAll = keepAll;
+ this.rollMax = rollMax < ROLLMAXMIN ? ROLLMAXMIN
+ : (rollMax > ROLLMAXMAX ? ROLLMAXMAX : rollMax);
+ this.confirmDelete = confirmDelete;
+ }
+
+ public boolean equals(BackupFilesPresetEntry compare)
+ {
+ return suffix.equals(compare.suffix) && digits == compare.digits
+ && reverse == compare.reverse && keepAll == compare.keepAll
+ && rollMax == compare.rollMax
+ && confirmDelete == compare.confirmDelete;
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append(suffix);
+ sb.append(stringDelim);
+ sb.append(digits);
+ sb.append(stringDelim);
+ sb.append(reverse);
+ sb.append(stringDelim);
+ sb.append(keepAll);
+ sb.append(stringDelim);
+ sb.append(rollMax);
+ sb.append(stringDelim);
+ sb.append(confirmDelete);
+ return sb.toString();
+ }
+
+ public static BackupFilesPresetEntry createBackupFilesPresetEntry(
+ String line)
+ {
+ if (line == null)
+ {
+ return null;
+ }
+ StringTokenizer st = new StringTokenizer(line, stringDelim);
+ String suffix = null;
+ int digits = 0;
+ boolean reverse = false;
+ boolean keepAll = false;
+ int rollMax = 0;
+ boolean confirmDelete = false;
+
+ try
+ {
+ suffix = st.nextToken();
+ digits = Integer.valueOf(st.nextToken());
+ reverse = Boolean.valueOf(st.nextToken());
+ keepAll = Boolean.valueOf(st.nextToken());
+ rollMax = Integer.valueOf(st.nextToken());
+ confirmDelete = Boolean.valueOf(st.nextToken());
+ } catch (Exception e)
+ {
+ Cache.log.error("Error parsing backupfiles scheme '" + line + "'");
+ }
+
+ return new BackupFilesPresetEntry(suffix, digits, reverse, keepAll,
+ rollMax, confirmDelete);
+ }
+
+ public static BackupFilesPresetEntry getSavedBackupEntry()
+ {
+ String savedPresetString = Cache
+ .getDefault(BackupFilesPresetEntry.SAVEDCONFIG, null);
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(savedPresetString);
+ if (savedPreset == null)
+ {
+ savedPreset = backupfilesPresetEntriesValues
+ .get(BACKUPFILESSCHEMEDEFAULT);
+ }
+ return savedPreset;
+ }
+
+ public static final IntKeyStringValueEntry[] backupfilesPresetEntries = {
+ new IntKeyStringValueEntry(BACKUPFILESSCHEMEDEFAULT,
+ 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(BACKUPFILESSCHEMECUSTOM,
+ MessageManager.getString("label.custom")) };
+
+ public static final String[] backupfilesPresetEntryDescriptions = {
+ MessageManager.getString("label.default_description"),
+ MessageManager.getString("label.single_file_description"),
+ MessageManager.getString("label.keep_all_versions_description"),
+ MessageManager.getString("label.rolled_backups_description"),
+ MessageManager.getString("label.custom_description") };
+
+ public static final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
+ {
+ /**
+ *
+ */
+ 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));
+
+ // This gets replaced by GPreferences
+ put(BACKUPFILESSCHEMECUSTOM,
+ new BackupFilesPresetEntry("", 0, false, false, 0, false));
+ }
+ };
+
+}
--- /dev/null
+package jalview.io;
+
+public class IntKeyStringValueEntry
+{
+ public final int k;
+
+ public final String v;
+
+ public IntKeyStringValueEntry(int k, String v)
+ {
+ this.k = k;
+ this.v = v;
+ }
+
+ @Override
+ public String toString()
+ {
+ return v;
+ }
+
+}
*/
package jalview.io;
-import jalview.bin.Cache;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.io.IOException;
+import java.util.Vector;
public class PIRFile extends AlignFile
{
- // Vector words = new Vector(); // Stores the words in a line after splitting
+ public static boolean useModellerOutput = false;
+
+ Vector words = new Vector(); // Stores the words in a line after splitting
public PIRFile()
{
StringBuffer out = new StringBuffer();
int i = 0;
ModellerDescription md;
- boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
}
else
{
+
if (useModellerOutput)
{
out.append(">P1;" + s[i].getName());
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.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.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
-import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
* @author $author$
* @version $Revision$
*/
-@SuppressWarnings("serial")
public class GPreferences extends JPanel
{
private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
/*
* Connections tab components
*/
- public JTable linkUrlTable = new JTable();
+ protected JTable linkUrlTable = new JTable();
- public JButton editLink = new JButton();
+ protected JButton editLink = new JButton();
- public JButton deleteLink = new JButton();
+ protected JButton deleteLink = new JButton();
- public JTextField filterTB = new JTextField();
+ protected JTextField filterTB = new JTextField();
protected JButton doReset = new JButton();
protected JPanel presetsPanel = new JPanel();
+ protected JLabel presetsComboLabel = new JLabel();
+
+ protected JCheckBox customiseCheckbox = new JCheckBox();
+
protected JButton revertButton = new JButton();
- protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+ protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
+
+ private int backupfilesPresetsComboLastSelected = 0;
protected JPanel suffixPanel = new JPanel();
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- if (!Platform.isJS())
- {
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
- }
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
new Insets(0, 2, 5, 5), 70, 1));
+ versioncheck.setVisible(false);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
connectTab.add(spacePanel,
// in height
// on Windows
// OS
- // Was 320
+ // Was 320, 96
annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
annsettingsPanel.setBorder(new EtchedBorder());
visualTab.add(annsettingsPanel);
protected void loadLastSavedBackupsOptions()
{
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .getSavedBackupEntry();
enableBackupFiles
.setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+
+ 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();
}
- protected boolean warnAboutSuffixReverseChange()
+ 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);
gbc.gridy++; // row 1
backupsTab.add(presetsPanel, gbc);
- // gbc.anchor = GridBagConstraints.NORTHWEST;
// now using whole row
gbc.gridwidth = 2;
gbc.gridheight = 1;
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<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
- {
- /**
- *
- */
- 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());
// "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<Object> entries = Arrays.asList(
+ (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<String> 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();
+ }
}
});
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;
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());
return exampleFilesPanel;
}
- protected void backupsTabUpdatePresets()
+ private void backupsTabUpdatePresets()
{
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));
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(key));
}
else
{
- System.out.println("Preset '" + value + "' not implemented");
+ 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<IntKeyStringValueEntry> c)
+ protected int getComboIntStringKey(
+ JComboBox<Object> 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<IntKeyStringValueEntry> c,
+ protected void setComboIntStringKey(
+ JComboBox<Object> 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
{
- c.setSelectedIndex(i);
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+ } catch (Exception ex)
+ {
+ 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()
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
});
- KeyListener kl = new KeyListener()
+ suffixTemplate.addKeyListener(new KeyListener()
{
@Override
public void keyReleased(KeyEvent e)
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
@Override
}
}
- };
- 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"));
}
if (okay)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
else
{
- boolean savedSuffixReverse = Cache
- .getDefault(BackupFiles.REVERSE_ORDER, false);
+ boolean savedSuffixReverse = BackupFilesPresetEntry
+ .getSavedBackupEntry().reverse;
suffixReverse.setSelected(savedSuffixReverse);
}
}
return suffixPanel;
}
- protected boolean confirmSuffixReverseChange()
+ private boolean confirmSuffixReverseChange()
{
boolean ret = false;
String warningMessage = MessageManager
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
keepRollMaxOptionsEnabled();
updateBackupFilesExampleLabel();
}
@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.always_ask"),
MessageManager.getString("label.auto_delete"));
+ backupfilesConfirmDelete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ }
+ });
// update the enabled section
keepRollMaxOptionsEnabled();
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());
int uppersurround = 0;
StringBuilder exampleSB = new StringBuilder();
boolean firstLine = true;
+ int lineNumber = 0;
if (reverse)
{
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
}
+ // 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());
}
{
try
{
- i = Integer.parseInt((String) s.getValue());
+ i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Exception casting the initial value of s.getValue()");
}
}
{
max = def;
}
+ if (def < min)
+ {
+ def = min;
+ }
SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
s.setModel(sModel);
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;
}
- protected void keepRollMaxOptionsEnabled()
+ private void keepRollMaxOptionsEnabled()
{
boolean enabled = backupfilesKeepAll.isEnabled()
&& !backupfilesKeepAll.isSelected();
backupfilesConfirmDelete.setEnabled(enabled);
}
- protected void backupfilesKeepAllSetEnabled(boolean tryEnabled)
+ 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);
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);
}
{
boolean enabled = enableBackupFiles.isSelected();
presetsPanel.setEnabled(enabled);
+ presetsComboLabel.setEnabled(enabled);
backupfilesPresetsCombo.setEnabled(enabled);
+ customiseCheckbox.setEnabled(enabled);
+ revertButton.setEnabled(enabled);
}
protected void backupsOptionsSetEnabled()
button.setHorizontalAlignment(SwingConstants.CENTER);
this.button.addActionListener(new ActionListener()
{
- @SuppressWarnings("synthetic-access")
@Override
public void actionPerformed(ActionEvent e)
{
}
}
-class IntKeyStringValueEntry
-{
- int k;
-
- String v;
-
- public IntKeyStringValueEntry(int k, String v)
- {
- this.k = k;
- this.v = v;
- }
-
- @Override
- public String toString()
- {
- return this.getValue();
- }
-
- public int getKey()
- {
- 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
-{
- /**
- *
- */
- 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;
- }
-}
git://source.jalview.org / jalview.git / commitdiff