- * </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>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>
+ * 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>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>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
+ * LABEL_AND_SEQUENCE</li>
+ * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
+ * sequence annotations</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>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * collecting usage statistics</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>STORED_LINKS list of name|url pairs which user has entered but are not
+ * currently used
+ * <li>DEFAULT_LINK name of single url to be used when user double clicks a
+ * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
+ * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
+ * jalview.utils.GroupURLLink for more info</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>VERSION_CHECK (true) check for the latest release version from
+ * www.jalview.org (or the alias given by the www.jalview.org property)</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>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
+ * sequence ID strings before attempting retrieval from any datasource</li>
+ * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
+ * alignment.</li>
+ * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
+ * in the alignment.</li>
+ * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
+ * histogram.</li>
+ * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
+ * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
+ * respond to selections made in other alignments containing the same sequences.
+ * </li>
+ * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
+ * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
+ * warning dialog box is displayed.</li>
+ * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
+ * when shading by annotation</li>
+ * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
+ * when shading by annotation</li>
+ * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
+ * alignment figure to accommodate even the longest sequence ID or annotation
+ * label.</li>
+ * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
+ * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
+ * will override this).</li>
+ * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record</li>
+ * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
+ * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
+ * display</li>
+ * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display</li>
+ * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display</li>
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
+ * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls