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Static Public Member Functions | Static Public Attributes | Static Protected Attributes | Static Package Attributes | Static Private Attributes

jalview::bin::Cache Class Reference

Collaboration diagram for jalview::bin::Cache:
Collaboration graph

List of all members.

Static Public Member Functions

static Date getDateProperty (String property)
static boolean getDefault (String property, boolean def)
static String getDefault (String property, String def)
static Color getDefaultColour (String property, Color defcolour)
static Vector getLocalDasSources ()
static String getProperty (String key)
static boolean groovyJarsPresent ()
static void initGoogleTracker ()
static void initLogger ()
static void loadProperties (String propsFile)
static void removeProperty (String string)
static void saveProperties ()
static void setColourProperty (String property, Color colour)
static void setDateProperty (String property, Date time)
static String setProperty (String key, String obj)
static boolean vamsasJarsPresent ()

Static Public Attributes

static Properties applicationProperties = new Properties()
static final String AXISLOGLEVEL = "logs.Axis.level"
static final String CASTORLOGLEVEL = "logs.Castor.level"
static final DateFormat date_format = SimpleDateFormat.getDateTimeInstance()
static final String JALVIEWLOGLEVEL = "logs.Jalview.level"
static Logger log

Static Protected Attributes

static Class jgoogleanalyticstracker = null
static Object tracker = null
static Class trackerfocus = null

Static Package Attributes

static String propertiesFile

Static Private Attributes

static int groovyJarsArePresent = -1
static boolean propsAreReadOnly = false
static int vamsasJarsArePresent = -1

Detailed Description

Stores and retrieves Jalview Application Properties Lists and fields within list entries are separated by '|' symbols unless otherwise stated (|) clauses are alternative values for a tag.

Current properties include:

logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
logs.Jalview.Level - Cache.log stringified level.
SCREEN_WIDTH SCREEN_HEIGHT SCREEN_Y=285 SCREEN_X=371 SHOW_FULLSCREEN boolean FONT_NAME java font name for alignment text display FONT_SIZE size of displayed alignment text FONT_STYLE style of font displayed (sequence labels are always italic) GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') LAST_DIRECTORY last directory for browsing alignment USER_DEFINED_COLOURS list of user defined colour scheme files SHOW_FULL_ID show id with '/start-end' numbers appended SHOW_IDENTITY show percentage identity annotation SHOW_QUALITY show alignment quality annotation SHOW_ANNOTATIONS show alignment annotation rows SHOW_CONSERVATION show alignment conservation annotation CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row DEFAULT_COLOUR default colour scheme to apply for a new alignment DEFAULT_FILE_FORMAT file format used to save STARTUP_FILE file loaded on startup (may be a fully qualified url) SHOW_STARTUP_FILE flag to control loading of startup file VERSION the version of the jalview build BUILD_DATE date of this build LATEST_VERSION the latest jalview version advertised on the www.jalview.org PIR_MODELLER boolean indicating if PIR files are written with MODELLER descriptions (FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv suffix to file RECENT_URL list of recently retrieved URLs RECENT_FILE list of recently opened files USE_PROXY flag for whether a http proxy is to be used PROXY_SERVER the proxy PROXY_PORT NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire service QUESTIONNAIRE last questionnaire:responder id string from questionnaire service USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage statistics DAS_LOCAL_SOURCE list of local das sources SHOW_OVERVIEW boolean for overview window display ANTI_ALIAS boolean for smooth fonts RIGHT_ALIGN_IDS boolean AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus PAD_GAPS boolean ID_ITALICS boolean SHOW_JV_SUFFIX WRAP_ALIGNMENT EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering style check SORT_ALIGNMENT (No sort|Id|Pairwise Identity) SEQUENCE_LINKS list of name|URL pairs for opening a url with $SEQUENCE_ID$ GROUP_LINKS list of name|URL[|<separator>] tuples - see jalview.utils.GroupURLLink for more info DAS_REGISTRY_URL the registry to query DEFAULT_BROWSER for unix DAS_ACTIVE_SOURCE list of active sources SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop (false) VERSION_CHECK (true) check for the latest release version from www.jalview.org (or the alias given by the www.jalview.org property) SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip SHOW_UNCONSERVED (false) only render unconserved residues - conserved displayed as '.' SORT_BY_TREE (false) sort the current alignment view according to the order of a newly displayed tree DBFETCH_USEPICR (false) use PICR to recover valid DB references from sequence ID strings before attempting retrieval from any datasource SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the alignment. SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups in the alignment. SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's histogram. SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence logo. FOLLOW_SELECTIONS (true) Controls whether a new alignment view should respond to selections made in other alignments containing the same sequences. SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery warning dialog box is displayed. ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation when shading by annotation ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation www.jalview.org (http://www.jalview.org) a property enabling all HTTP requests to be redirected to a mirror of http://www.jalview.org

Deprecated settings:

DISCOVERY_START - Boolean - controls if discovery services are queried on startup (JWS1 services only) DISCOVERY_URLS - comma separated list of Discovery Service endpoints. (JWS1 services only) SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2 services in the desktop GUI ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing panel in web service preferences


Definition at line 150 of file Cache.java.

The documentation for this class was generated from the following file:

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