- * Stores and retrieves Jalview Application Properties
- * <br><br>Current properties include:
- * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
- * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
- * <br>logs.Jalview.Level - Cache.log stringified level.
- * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
- * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
- * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
- * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
- * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
- * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE
-
+ * 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. <br>
+ * <br>
+ * Current properties include:
+ * <ul>
+ * <br>
+ * logs.Axis.Level - one of the stringified Levels for log4j controlling the
+ * logging level for axis (used for web services) <br>
+ * </li>
+ * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
+ * the logging level for castor (used for serialization) <br>
+ * </li>
+ * <li>logs.Jalview.Level - Cache.log stringified level. <br>
+ * </li>
+ * <li>DISCOVERY_START - Boolean - controls if discovery services are queried
+ * on startup </li>
+ * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
+ * </li>
+ * <li>SCREEN_WIDTH </li>
+ * <li>SCREEN_HEIGHT </li>
+ * <li>SCREEN_Y=285 </li>
+ * <li>SCREEN_X=371 </li>
+ * <li>SHOW_FULLSCREEN boolean </li>
+ * <li>FONT_NAME java font name for alignment text display </li>
+ * <li>FONT_SIZE size of displayed alignment text </li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always italic)
+ * </li>
+ * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') </li>
+ * <li>LAST_DIRECTORY last directory for browsing alignment </li>
+ * <li>USER_DEFINED_COLOURS list of user defined colour scheme files </li>
+ * <li>SHOW_FULL_ID show id with '/start-end' numbers appended </li>
+ * <li>SHOW_IDENTITY show percentage identity annotation </li>
+ * <li>SHOW_QUALITY show alignment quality annotation </li>
+ * <li>SHOW_ANNOTATIONS show alignment annotation rows </li>
+ * <li>SHOW_CONSERVATION show alignment conservation annotation </li>
+ * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
+ * annotation row </li>
+ * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment </li>
+ * <li>DEFAULT_FILE_FORMAT file format used to save </li>
+ * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url) </li>
+ * <li>SHOW_STARTUP_FILE flag to control loading of startup file </li>
+ * <li>VERSION the version of the jalview build </li>
+ * <li>BUILD_DATE date of this build </li>
+ * <li>LATEST_VERSION the latest jalview version advertised on the
+ * www.jalview.org </li>
+ * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
+ * descriptions </li>
+ * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
+ * suffix to file </li>
+ * <li>RECENT_URL list of recently retrieved URLs </li>
+ * <li>RECENT_FILE list of recently opened files </li>
+ * <li>USE_PROXY flag for whether a http proxy is to be used </li>
+ * <li>PROXY_SERVER the proxy </li>
+ * <li>PROXY_PORT </li>
+ * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
+ * service </li>
+ * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
+ * service </li>
+ * <li>DAS_LOCAL_SOURCE list of local das sources </li>
+ * <li>SHOW_OVERVIEW boolean for overview window display </li>
+ * <li>ANTI_ALIAS boolean for smooth fonts </li>
+ * <li>RIGHT_ALIGN_IDS boolean </li>
+ * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
+ * </li>
+ * <li>PAD_GAPS boolean </li>
+ * <li>ID_ITALICS boolean </li>
+ * <li>SHOW_JV_SUFFIX </li>
+ * <li>WRAP_ALIGNMENT </li>
+ * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
+ * style check </li>
+ * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity) </li>
+ * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
+ * $SEQUENCE_ID$ </li>
+ * <li>DAS_REGISTRY_URL the registry to query </li>
+ * <li>DEFAULT_BROWSER for unix </li>
+ * <li>DAS_ACTIVE_SOURCE list of active sources </li>
+ * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
+ * (false) </li>
+ * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip</li>
+ * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip</li>
+ * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved displayed as '.'</li>
+ * <li>SORT_BY_TREE (false) sort the current alignment view according to the order of a newly displayed tree</li>
+ *
+ * <li> </li>
+ *
+ * </ul>
+ *