*/
package jalview.bin;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-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.File;
import java.io.FileInputStream;
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
* @author $author$
* @version $Revision$
*/
-public class Cache
+public class Cache implements ApplicationSingletonI
{
+
+ private Cache()
+ {
+ // private singleton
+ }
+
+ /**
+ * In Java, this will be a static field instance, which will be
+ * application-specific; in JavaScript it will be an applet-specific instance
+ * tied to the applet's ThreadGroup.
+ *
+ * @return
+ */
+ public static Cache getInstance()
+ {
+ return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
+ }
+
/**
* property giving log4j level for CASTOR loggers
*/
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties()
+ // BH 2019.05.08 was static
+ @SuppressWarnings("serial")
+ public Properties applicationProperties = new Properties()
{
// override results in properties output in alphabetical order
@Override
};
/** Default file is ~/.jalview_properties */
- static String propertiesFile;
+ // BH 2020 private, not static
+ private String propertiesFile;
private static boolean propsAreReadOnly = Platform.isJS();
*/
public static void loadProperties(String propsFile)
{
+ getInstance().loadPropertiesImpl(propsFile);
+ }
+
+ private void loadPropertiesImpl(String propsFile)
+ {
propertiesFile = propsFile;
if (propsFile == null && !propsAreReadOnly)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
- }
- else
- {
- // don't corrupt the file we've been given.
- propsAreReadOnly = true;
- }
+ }
+ else
+ {
+ // don't corrupt the file we've been given.
+ propsAreReadOnly = true;
+ }
if (propertiesFile == null)
{ // BH 2019
}
// LOAD THE AUTHORS FROM THE authors.props file
- String authorDetails = resolveResourceURLFor("/authors.props");
+ String authorDetails = (Platform.isJS() ? null
+ : resolveResourceURLFor("/authors.props"));
try
{
}
if (authorDetails == null)
{
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
loadBuildProperties(false);
jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
DEFAULT_CACHE_THRESHOLD_IN_DAYS));
- IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+ IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
- .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
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"))
+ /**
+ * construct a resource URL for the given absolute resource pathname
+ *
+ * @param resourcePath
+ * @return
+ */
+ private static String resolveResourceURLFor(String resourcePath)
{
- try
+ String url = null;
+ if (Platform.isJS() || !Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString().endsWith(".jar"))
{
- url = Cache.class.getResource(resourcePath).toString();
- } catch (Exception ex)
+ try
+ {
+ url = Cache.class.getResource(resourcePath).toString();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to resolve resource " + resourcePath + ": "
+ + ex.getMessage());
+ }
+ }
+ else
{
- System.err.println("Failed to resolve resource " + resourcePath + ": "
- + ex.getMessage());
+ url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!" + resourcePath));
}
+ return url;
}
- 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
+ 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();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
+ 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");
}
}
- private static void deleteBuildProperties()
+ // BH 2020 was static
+ private void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
applicationProperties.remove("VERSION");
*/
public static String getProperty(String key)
{
- String prop = applicationProperties.getProperty(key);
- if (prop == null && Platform.isJS())
- {
- prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
- + "_" + JS_PROPERTY_PREFIX + key);
- }
- return prop;
+ 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
+
/**
- * 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 property
+ * @param def
+ * @return
*/
-
public static boolean getDefault(String property, boolean def)
{
String string = getProperty(property);
- if (string != null)
- {
- def = Boolean.valueOf(string).booleanValue();
- }
-
- return def;
+ // BH simplification only
+ return string == null ? def : Boolean.parseBoolean(string);
}
+ /**
+ * Returns the integer property value for the given property name. If the
+ * value is absent, or malformed (not an integer), then the default value is
+ * returned instead.
+ *
+ * @param property
+ * @param def
+ * @return
+ */
public static int getDefault(String property, int def)
{
String string = getProperty(property);
{
try
{
- def = Integer.parseInt(string);
+ // BH simplification only
+
+ return Integer.parseInt(string);
} catch (NumberFormatException e)
{
System.out.println("Error parsing int property '" + property
}
/**
- * Answers the value of the given property, or the supplied default value if
+ * Returns the value of the given property, or the supplied default value if
* the property is not set
+ *
+ * @param property
+ * @param def
+ * @return
*/
public static String getDefault(String property, String def)
{
*/
public static Object setProperty(String key, String obj)
{
+ return getInstance().setPropertyImpl(key, obj, true);
+ }
+
+ /**
+ *
+ * Sets a property value for the running application, without saving it to the
+ * properties file.
+ *
+ * Replaces direct call to Cache.applicationProperties.setProperty
+ *
+ * Used extensively in AppletParams and Preferences.ok_actionPerformed
+ *
+ *
+ * @param key
+ * @param obj
+ */
+ public static void setPropertyNoSave(String key, String obj)
+ {
+ getInstance().setPropertyImpl(key, obj, false);
+ }
+
+
+ /**
+ * Sets a property value, and optionally also saves the current properties to
+ * file
+ *
+ * @param key
+ * @param obj
+ * @param andSave
+ * @return
+ */
+ private Object setPropertyImpl(String key, String obj, boolean andSave)
+ {
Object oldValue = null;
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (propertiesFile != null && !propsAreReadOnly)
+ if (andSave && !propsAreReadOnly && propertiesFile != null)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
/**
- * remove the specified property from the jalview properties file
+ * Removes the specified property from the jalview properties file
*
- * @param string
+ * @param key
*/
- public static void removeProperty(String string)
+ public static void removeProperty(String key)
{
- applicationProperties.remove(string);
- saveProperties();
+ getInstance().removePropertyImpl(key, true);
}
/**
- * save the properties to the jalview properties path
+ * Removes the named property for the running application, without saving the
+ * properties file.
+ *
+ * Called by Preferences.ok_actionPerformed specifically for SEQUENCE_LINKS and STORED_LINKS.
+ *
+ *
+ * @param key
+ */
+ public static void removePropertyNoSave(String key)
+ {
+ getInstance().removePropertyImpl(key, false);
+ }
+
+ /**
+ * Removes the named property, and optionally saves the current properties to
+ * file
+ *
+ * @param key
+ * @param andSave
+ */
+ private void removePropertyImpl(String key, boolean andSave)
+ {
+ applicationProperties.remove(key);
+ if (andSave)
+ {
+ savePropertiesImpl();
+ }
+ }
+
+ /**
+ * Saves the current properties to file
*/
public static void saveProperties()
{
+ getInstance().savePropertiesImpl();
+ }
+
+ /**
+ * save the properties to the jalview properties path
+ */
+ private void savePropertiesImpl()
+ {
if (!propsAreReadOnly)
{
try
}
}
+ private final static int UNTESTED = -1;
+
+ private final static int TRUE = 1;
+
+ private final static int FALSE = 0;
+
/**
* internal vamsas class discovery state
*/
- private static int vamsasJarsArePresent = -1;
+ private static int vamsasJarsArePresent = (Platform.isJS() ? FALSE
+ : UNTESTED);
/**
* Searches for vamsas client classes on class path.
*/
public static boolean vamsasJarsPresent()
{
- if (vamsasJarsArePresent == -1)
+ if (vamsasJarsArePresent == UNTESTED)
{
try
{
{
jalview.bin.Cache.log.debug(
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
- vamsasJarsArePresent = 1;
+ vamsasJarsArePresent = TRUE;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
lvclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Vamsas.Level", Level.INFO.toString())));
}
} catch (Exception e)
{
- vamsasJarsArePresent = 0;
+ vamsasJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Vamsas Classes are not present");
}
}
- return (vamsasJarsArePresent > 0);
+ return (vamsasJarsArePresent == TRUE);
}
/**
* internal vamsas class discovery state
*/
- private static int groovyJarsArePresent = -1;
+ private static int groovyJarsArePresent = (Platform.isJS() ? FALSE
+ : UNTESTED);
/**
* Searches for vamsas client classes on class path.
*/
public static boolean groovyJarsPresent()
{
- if (groovyJarsArePresent == -1)
+ if (groovyJarsArePresent == UNTESTED)
{
try
{
{
jalview.bin.Cache.log.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
- groovyJarsArePresent = 1;
+ groovyJarsArePresent = TRUE;
Logger lgclient = Logger.getLogger("groovy");
lgclient.setLevel(Level.toLevel(Cache
.getDefault("logs.Groovy.Level", Level.INFO.toString())));
}
} catch (Error e)
{
- groovyJarsArePresent = 0;
+ groovyJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
- groovyJarsArePresent = 0;
+ groovyJarsArePresent = FALSE;
jalview.bin.Cache.log.debug("Groovy Classes are not present");
}
}
- return (groovyJarsArePresent > 0);
+ return (groovyJarsArePresent == TRUE);
}
/**
*/
protected static Object tracker = null;
- protected static Class trackerfocus = null;
+ protected static Class<?> trackerfocus = null;
- protected static Class jgoogleanalyticstracker = null;
+ protected static Class<?> jgoogleanalyticstracker = null;
/**
* Initialise the google tracker if it is not done already.
*/
public static void initGoogleTracker()
{
+
+ // TODO: SwingJS JavaScript tracker?
+
if (tracker == null)
{
if (jgoogleanalyticstracker == null)
}
/**
- * get the user's default colour if available
+ * Returns the Color value of the given property's value, or the supplied
+ * default colour if no property is found, or it cannot be parsed to a colour.
+ * Colours are normally saved as hex rgb values, though other formats may be
+ * parseable.
*
* @param property
* @param defcolour
}
/**
+ * 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
+ */
+ public static void setColourPropertyNoSave(String property, Color colour)
+ {
+ setPropertyNoSave(property, jalview.util.Format.getHexString(colour));
+ }
+
+ /**
* store a colour as a Jalview user default property
*
* @param property
/**
* Stores a formatted date in a jalview property, using a fixed locale.
+ * Updated properties are written out to the properties file.
*
* @param propertyName
* @param date
}
if (value == null || value.trim().length() < 1)
{
- Cache.applicationProperties.remove(propName);
+ getInstance().applicationProperties.remove(propName);
}
else
{
- Cache.applicationProperties.setProperty(propName, value);
+ getInstance().applicationProperties.setProperty(propName, value);
}
}
{
if (coloursFound.toString().length() > 1)
{
- setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+ // BH moved to Preferences for consistency
+ setProperty(Preferences.USER_DEFINED_COLOURS,
coloursFound.toString());
}
else
{
- applicationProperties
- .remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ // BH moved to Preferences for consistency
+ getInstance().applicationProperties
+ .remove(Preferences.USER_DEFINED_COLOURS);
}
}
}
// 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;
+ }
+
+
}
import jalview.urls.api.UrlProviderFactoryI;
import jalview.urls.api.UrlProviderI;
import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.UrlConstants;
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class Preferences extends GPreferences
{
+
+ // 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";
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 ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+ public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+ public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+ public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+ public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
+
+ public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
+
+ public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
+
+ public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
+
+ public static final String FONT_NAME = "FONT_NAME";
+
+ public static final String FONT_SIZE = "FONT_SIZE";
+
+ public static final String FONT_STYLE = "FONT_STYLE";
+
+ public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+ public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+ public static final String ID_ITALICS = "ID_ITALICS";
+
+ public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+ public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+ public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+ public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+ public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+ public static final String PAD_GAPS = "PAD_GAPS";
+
+ public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+ public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+ public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+ public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+ public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+
+ public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+ public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+ public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+ public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+ public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+ public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+ public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+ public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
+
+ public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
+
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
+ public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+ public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+ public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+ public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+ public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+ 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 USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+
+
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static UrlProviderI sequenceUrlLinks;
+ public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
- public static UrlLinkTableModel dataModel;
+ public final static UrlLinkTableModel dataModel;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static List<String> groupURLLinks;
+ public static final List<String> groupURLLinks; // not implemented
+
static
{
// get links selected to be in the menu (SEQUENCE_LINKS)
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<>();
+ groupURLLinks = new ArrayList<>(); // not implemented
}
JInternalFrame frame;
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
}
- int width = 500, height = 450;
+ int width = 700, height = 510; // BH 2019.07.12 added 60 to height and 40 to
+ // width (for Visual check boxes and Links
+ // "Double Click" header)
+ // BH 2019.09.24 added 20 to width
+ // (structure panel was too small anyway, and I added a default dimension
+ // for Jmol
if (Platform.isAMacAndNotJS())
{
width = 570;
- height = 480;
+ height = 540; // BH 2019.07.12 added 30
}
Desktop.addInternalFrame(frame,
/*
* Set Visual tab defaults
*/
- seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
- rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
- annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
- openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true));
+ rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false));
+ fullScreen.setSelected(Cache.getDefault(SHOW_FULLSCREEN, false));
+ annotations.setSelected(Cache.getDefault(SHOW_ANNOTATIONS, true));
+
+ conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true));
+ quality.setSelected(Cache.getDefault(SHOW_QUALITY, true));
+ identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true));
+ openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
showUnconserved
- .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
showGroupConsensus
- .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ .setSelected(Cache.getDefault(SHOW_GROUP_CONSENSUS, false));
showGroupConservation.setSelected(
- Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ Cache.getDefault(SHOW_GROUP_CONSERVATION, false));
showConsensHistogram.setSelected(
- Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ Cache.getDefault(SHOW_CONSENSUS_HISTOGRAM, true));
showConsensLogo
- .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ .setSelected(Cache.getDefault(SHOW_CONSENSUS_LOGO, false));
showNpTooltip
- .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ .setSelected(Cache.getDefault(SHOW_NPFEATS_TOOLTIP, true));
showDbRefTooltip
- .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ .setSelected(Cache.getDefault(SHOW_DBREFS_TOOLTIP, true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontStyleCB.addItem("bold");
fontStyleCB.addItem("italic");
- fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+ fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
fontStyleCB.setSelectedItem(
- Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+ Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
+ smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
scaleProteinToCdna
.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+ idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+ wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
- gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
+ gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+ sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort"));
sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
sortAnnBy
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
minColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MIN, Color.orange));
maxColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MAX, Color.red));
/*
* Set overview panel defaults
addTempFactor.setEnabled(structSelected);
structViewer.setSelectedItem(
Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+ Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
+ DEFAULT_STRUCTURE_DIMENSIONS);
+ String s = d.width + "," + d.height;
+ structureDimensions.setText(s);
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
}
});
- if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ if (Cache.getDefault(MAP_WITH_SIFTS, false))
{
siftsMapping.setSelected(true);
}
}
SiftsSettings
- .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+ .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
/*
* Set Connections tab defaults
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
// note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null);
versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
/*
setupOutputCombo(epsRendering, "EPS_RENDERING");
setupOutputCombo(htmlRendering, "HTML_RENDERING");
setupOutputCombo(svgRendering, "SVG_RENDERING");
- autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+ 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
* Set Editing tab defaults
*/
autoCalculateConsCheck
- .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
- sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+ .setSelected(Cache.getDefault(AUTO_CALC_CONSENSUS, true));
+ padGaps.setSelected(Cache.getDefault(PAD_GAPS, false));
+ sortByTree.setSelected(Cache.getDefault(SORT_BY_TREE, false));
annotations_actionPerformed(null); // update the display of the annotation
// settings
/*
* Set Backups tab defaults
*/
- loadLastSavedBackupsOptions();
+ if (!Platform.isJS())
+ {
+ loadLastSavedBackupsOptions();
+ }
+
}
/**
/*
* Save Visual settings
*/
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+ Cache.setPropertyNoSave(SHOW_JVSUFFIX,
Boolean.toString(seqLimit.isSelected()));
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+ Cache.setPropertyNoSave(RIGHT_ALIGN_IDS,
Boolean.toString(rightAlign.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+ Cache.setPropertyNoSave(SHOW_FULLSCREEN,
Boolean.toString(fullScreen.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+ Cache.setPropertyNoSave(SHOW_OVERVIEW,
Boolean.toString(openoverv.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave(SHOW_ANNOTATIONS,
Boolean.toString(annotations.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_CONSERVATION,
Boolean.toString(conservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave(SHOW_QUALITY,
Boolean.toString(quality.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave(SHOW_IDENTITY,
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL",
+ Cache.setPropertyNoSave(GAP_SYMBOL,
gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME",
+ Cache.setPropertyNoSave(FONT_NAME,
fontNameCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE",
+ Cache.setPropertyNoSave(FONT_STYLE,
fontStyleCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE",
+ Cache.setPropertyNoSave(FONT_SIZE,
fontSizeCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("ID_ITALICS",
+ Cache.setPropertyNoSave(ID_ITALICS,
Boolean.toString(idItalics.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Cache.setPropertyNoSave(SHOW_UNCONSERVED,
Boolean.toString(showUnconserved.isSelected()));
- Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Cache.setPropertyNoSave(SHOW_OCCUPANCY,
Boolean.toString(showOccupancy.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS,
Boolean.toString(showGroupConsensus.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION,
Boolean.toString(showGroupConservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM,
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
Boolean.toString(showConsensLogo.isSelected()));
- Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Cache.setPropertyNoSave(ANTI_ALIAS,
Boolean.toString(smoothFont.isSelected()));
- Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
Boolean.toString(scaleProteinToCdna.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP,
Boolean.toString(showNpTooltip.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP,
Boolean.toString(showDbRefTooltip.isSelected()));
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+ Cache.setPropertyNoSave(WRAP_ALIGNMENT,
Boolean.toString(wrap.isSelected()));
- Cache.applicationProperties.setProperty("STARTUP_FILE",
- startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText());
+ Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+ Cache.setPropertyNoSave(SORT_ALIGNMENT,
sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
- annSortOrder.name());
+ Cache.setPropertyNoSave(SORT_ANNOTATIONS, annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
protColour.getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
nucColour.getSelectedItem().toString());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MIN,
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MAX,
maxColour.getBackground());
/*
* Save Overview settings
*/
- Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
- Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
- Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourPropertyNoSave(HIDDEN_COLOUR,
+ hiddenColour.getBackground());
+ Cache.setPropertyNoSave(USE_LEGACY_GAP,
Boolean.toString(useLegacyGap.isSelected()));
- Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
Boolean.toString(showHiddenAtStart.isSelected()));
/*
* Save Structure settings
*/
- Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
Boolean.toString(addTempFactor.isSelected()));
- Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Cache.setPropertyNoSave(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Cache.setPropertyNoSave(USE_RNAVIEW,
Boolean.toString(useRnaView.isSelected()));
- Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Cache.setPropertyNoSave(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+ Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
structViewer.getSelectedItem().toString());
+ Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS,
+ structureDimensions.getText()); // BH 2019.07.12
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
- Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Cache.setPropertyNoSave(MAP_WITH_SIFTS,
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("EPS_RENDERING",
+ Cache.setPropertyNoSave("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
- Cache.applicationProperties.setProperty("HTML_RENDERING",
+ Cache.setPropertyNoSave("HTML_RENDERING",
((OptionsParam) htmlRendering.getSelectedItem()).getCode());
- Cache.applicationProperties.setProperty("SVG_RENDERING",
+ Cache.setPropertyNoSave("SVG_RENDERING",
((OptionsParam) svgRendering.getSelectedItem()).getCode());
- /*
- * Save Connections settings
+ if (!Platform.isJS())
+ /**
+ * @j2sNative
*/
- Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
-
- jalview.util.BrowserLauncher.resetBrowser();
+ {
+ // Java only
+ // Save Connections settings
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+ BrowserLauncher.resetBrowser();
+ }
// save user-defined and selected links
String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
if (menuLinks.isEmpty())
{
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ Cache.removePropertyNoSave("SEQUENCE_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
- menuLinks.toString());
+ Cache.setPropertyNoSave("SEQUENCE_LINKS", menuLinks.toString());
}
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
if (nonMenuLinks.isEmpty())
{
- Cache.applicationProperties.remove("STORED_LINKS");
+ Cache.removePropertyNoSave("STORED_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("STORED_LINKS",
- nonMenuLinks.toString());
+ Cache.setPropertyNoSave("STORED_LINKS", nonMenuLinks.toString());
}
- Cache.applicationProperties.setProperty("DEFAULT_URL",
+ Cache.setPropertyNoSave("DEFAULT_URL",
sequenceUrlLinks.getPrimaryUrlId());
- Cache.applicationProperties.setProperty("USE_PROXY",
+ Cache.setPropertyNoSave("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
}
if (!questionnaire.isSelected())
{
- Cache.setProperty("NOQUESTIONNAIRES", "true");
+ Cache.setProperty(NOQUESTIONNAIRES, "true");
}
else
{
// special - made easy to edit a property file to disable questionnaires
// by just adding the given line
- Cache.removeProperty("NOQUESTIONNAIRES");
+ Cache.removeProperty(NOQUESTIONNAIRES);
}
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+ Cache.setPropertyNoSave("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+ Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
Boolean.toString(clustaljv.isSelected()));
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+ Cache.setPropertyNoSave("FASTA_JVSUFFIX",
Boolean.toString(fastajv.isSelected()));
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+ Cache.setPropertyNoSave("MSF_JVSUFFIX",
Boolean.toString(msfjv.isSelected()));
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+ Cache.setPropertyNoSave("PFAM_JVSUFFIX",
Boolean.toString(pfamjv.isSelected()));
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+ Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
Boolean.toString(pileupjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+ Cache.setPropertyNoSave("PIR_JVSUFFIX",
Boolean.toString(pirjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_MODELLER",
+ Cache.setPropertyNoSave("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
- Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
- Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
- userIdWidth.getText());
+ Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText());
/*
* Save Editing settings
*/
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS,
Boolean.toString(autoCalculateConsCheck.isSelected()));
- Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Cache.setPropertyNoSave(SORT_BY_TREE,
Boolean.toString(sortByTree.isSelected()));
- Cache.applicationProperties.setProperty("PAD_GAPS",
+ Cache.setPropertyNoSave(PAD_GAPS,
Boolean.toString(padGaps.isSelected()));
if (!Platform.isJS())
wsPrefs.updateAndRefreshWsMenuConfig(false);
}
- /*
- * Save Backups settings
- */
- Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
- Boolean.toString(enableBackupFiles.isSelected()));
+ /*
+ * Save Backups settings
+ */
+ Cache.setPropertyNoSave(BackupFiles.ENABLED,
+ Boolean.toString(enableBackupFiles.isSelected()));
int preset = getComboIntStringKey(backupfilesPresetsCombo);
- Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+ Cache.setPropertyNoSave(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());
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
+ customBFPE.toString());
}
BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
.get(preset);
- Cache.applicationProperties.setProperty(
- BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.SAVEDCONFIG,
+ savedBFPE.toString());
Cache.saveProperties();
- Desktop.instance.doConfigureStructurePrefs();
+ Desktop.getInstance().doConfigureStructurePrefs();
try
{
frame.setClosed(true);
}
}
+ public static void setAppletDefaults()
+ {
+
+ // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+ // showConservation true or false Default is true.
+ // showQuality true or false Default is true.
+ // showConsensus true or false Default is true.
+ // showFeatureSettings true or false Shows the feature settings window when
+ // startin
+ // showTreeBootstraps true or false (default is true) show or hide branch
+ // bootstraps
+ // showTreeDistances true or false (default is true) show or hide branch
+ // lengths
+ // showUnlinkedTreeNodes true or false (default is false) indicate if
+ // unassociated nodes should be highlighted in the tree view
+ // showUnconserved true of false (default is false) When true, only gaps and
+ // symbols different to the consensus sequence ions of the alignment
+ // showGroupConsensus true of false (default is false) When true, shows
+ // consensus annotation row for any groups on the alignment. (since 2.7)
+ // showGroupConservation true of false (default is false) When true, shows
+ // amino-acid property conservation annotation row for any groups on the
+ // showConsensusHistogram true of false (default is true) When true, shows
+ // the percentage occurence of the consensus symbol for each column as a
+ // showSequenceLogo true of false (default is false) When true, shows a
+ // sequence logo above the consensus sequence (overlaid above the Consensus
+
+ Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
+ Cache.setPropertyNoSave(SHOW_QUALITY, "false");
+ Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
+ Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
+
+ // TODO -- just a start here
+ }
+
/**
* Do any necessary validation before saving settings. Return focus to the
* first tab which fails validation.
}
/**
- * DOCUMENT ME!
+ * Opens a file browser, and if a file is chosen, sets its path as the text of
+ * the 'startup file' text field
*/
@Override
public void startupFileTextfield_mouseClicked()
FileFormatI format = chooser.getSelectedFormat();
if (format != null)
{
- Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
- format.getName());
+ /*
+ * saving properties to file is deferred to the 'OK' action
+ */
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", format.getName());
}
startupFileTextfield
.setText(chooser.getSelectedFile().getAbsolutePath());
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.new_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.edit_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
super.showunconserved_actionPerformed(e);
}
+ /**
+ * not implemented -- returns empty list
+ *
+ * @return
+ */
public static List<String> getGroupURLLinks()
{
return groupURLLinks;
} catch (NumberFormatException x)
{
userIdWidth.setText("");
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
* Returns true if chimera path is to a valid executable, else show an error
* dialog.
*/
- private boolean validateChimeraPath()
+ protected boolean validateChimeraPath()
{
if (chimeraPath.getText().trim().length() > 0)
{
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
JvOptionPane.ERROR_MESSAGE);
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
}
}
- private class UrlListSelectionHandler implements ListSelectionListener
+ protected class UrlListSelectionHandler implements ListSelectionListener
{
@Override
{
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);
}
}
}
git://source.jalview.org / jalview.git / commitdiff