JAL-3477 merging in 3477

diff --combined gradle.properties
index 8eb78ff,1be3977..c1f3118
--- 1/gradle.properties
--- 2/gradle.properties
+++ b/gradle.properties
@@@ -2,13 -2,6 +2,13 @@@ jalviewDir = 
  
  #JAVA_VERSION = 1.8
  JAVA_VERSION = 11
 +
 +source_dir = src
 +#source_dir = utils/jalviewjs/test/src
 +
 +test_source_dir = test
 +#test_source_dir = utils/jalviewjs/test/test
 +
  JALVIEW_VERSION = DEVELOPMENT
  INSTALLATION = Source
  jalview_keystore = keys/.keystore
@@@ -25,12 -18,14 +25,12 @@@ testngGroups = Functiona
  
  j8libDir = j8lib
  j11libDir = j11lib
 -resourceDir = resources
 -helpParentDir = help
 -helpDir = help
 -helpOutputDir = build/distributions/help
 +resource_dir = resources
 +help_parent_dir = help
 +help_dir = help
  docDir = doc
 -sourceDir = src
  schemaDir = schemas
 -classesDir = classes
 +classes_dir = classes
  examplesDir = examples
  clover = false
  use_clover = false
@@@ -40,10 -35,11 +40,10 @@@ packageDir = dis
  ARCHIVEDIR =
  outputJar = jalview.jar
  
  testOutputDir = tests
  utilsDir = utils
  
 -buildPropertiesFile = .build_properties
 +build_properties_file = .build_properties
  application_codebase = *.jalview.org
  mainClass = jalview.bin.Jalview
  shadowJarMainClass = jalview.bin.Launcher
@@@ -66,7 -62,10 +66,10 @@@ getdown_build_properties = build_proper
  getdown_txt_title = Jalview
  getdown_txt_allow_offline = true
  getdown_txt_max_concurrent_downloads = 10
- getdown_txt_jalview.jvmmempc = 90
+ # now got better defaults when not set
+ #getdown_txt_jalview.jvmmempc = 90
+ # now got better defaults when not set
+ #getdown_txt_jalview.jvmmemmax = 32G
  getdown_txt_multi_jvmarg = -Dgetdownappdir=%APPDIR%
  getdown_txt_strict_comments = true
  getdown_txt_title = Jalview
@@@ -89,7 -88,7 +92,7 @@@ getdown_txt_ui.progress_text = 00000
  getdown_txt_ui.status = 20, 380, 600, 58
  getdown_txt_ui.status_text = 000066
  #getdown_txt_ui.text_shadow = FFFFFF
 -getdown_txt_ui.install_error = http://www.jalview.org/faq/getdownerror
 +getdown_txt_ui.install_error = https://www.jalview.org/faq/getdownerror
  getdown_txt_ui.mac_dock_icon = resources/images/jalview_logos.ico
  getdown_alt_java8_min_version  = 01080000
  getdown_alt_java8_max_version  = 01089999
@@@ -110,27 -109,28 +113,27 @@@ j11libDir = j11li
  j11modDir = j11mod
  j11modules = com.sun.istack.runtime,com.sun.xml.bind,com.sun.xml.fastinfoset,com.sun.xml.streambuffer,com.sun.xml.txw2,com.sun.xml.ws.policy,java.activation,java.annotation,java.base,java.compiler,java.datatransfer,java.desktop,java.logging,java.management,java.management.rmi,java.naming,java.prefs,java.rmi,java.scripting,java.security.sasl,java.sql,java.xml,java.xml.bind,java.xml.soap,java.xml.ws,javax.jws,jdk.httpserver,jdk.jsobject,jdk.unsupported,jdk.xml.dom,org.jvnet.mimepull,org.jvnet.staxex,javax.servlet.api,java.ws.rs
  
 -install4jCopyrightMessage = ...
 -install4jMacOSBundleId = org.jalview.jalview-desktop
 -install4jResourceDir = utils/install4j
 -install4jTemplate = install4j_template.install4j
 -install4jInfoPlistFileAssociations = file_associations_auto-Info_plist.xml
 -install4jInstallerFileAssociations = file_associations_auto-install4j.xml
 -install4jDMGUninstallerAppFiles = uninstall_old_jalview_files.xml
 -install4jBuildDir = build/install4j
 -install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
 -install4jFaster = false
 +install4j_home_dir = ~/buildtools/install4j8
 +install4j_copyright_message = ...
 +install4j_macOS_bundle_id = org.jalview.jalview-desktop
 +install4j_utils_dir = utils/install4j
 +install4j_template = install4j8_template.install4j
 +install4j_info_plist_file_associations = file_associations_auto-Info_plist.xml
 +install4j_installer_file_associations = file_associations_auto-install4j8.xml
 +#install4j_DMG_uninstaller_app_files = uninstall_old_jalview_files.xml
 +install4j_build_dir = build/install4j
 +install4j_media_types = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
 +install4j_faster = false
  
  OSX_KEYSTORE =
  OSX_KEYPASS =
  JSIGN_SH = echo
  
 -eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
 -
  pandoc_exec = /usr/local/bin/pandoc,/usr/bin/pandoc
  dev = false
  
  CHANNEL=LOCAL
 -getdown_channel_base = http://www.jalview.org/getdown
 +getdown_channel_base = https://www.jalview.org/getdown
  getdown_channel_name = SCRATCH-DEFAULT
  getdown_app_dir_release = release
  getdown_app_dir_alt = alt
@@@ -142,72 -142,4 +145,72 @@@ RUNRSYNC=fals
  bamboo_channelbase = https://builds.jalview.org/browse
  bamboo_planKey = 
  bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-channel
 - 
 +
 +eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
 +eclipse_project_name = jalview
 +eclipse_bin_dir = bin
 +eclipse_debug = false
 +
 +# for developing in Eclipse as IDE, set this to automatically copy current swingjs/net.sf.j2s.core.jar to your dropins dir
 +jalviewjs_eclipseIDE_auto_copy_j2s_plugin = false
 +# Override this in a local.properties file
 +jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09
 +
 +jalviewjs_eclipse_dropins_dir = utils/jalviewjs/eclipse/dropins
 +jalviewjs_swingjs_zip = swingjs/SwingJS-site.zip
 +jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core.jar
 +jalviewjs_libjs_dir = utils/jalviewjs/libjs
 +jalviewjs_site_resource_dir = utils/jalviewjs/site-resources
 +jalviewjs_classlists_dir = utils/jalviewjs/classlists
 +jalviewjs_classlist_jalview = utils/jalviewjs/_j2sclasslist.txt
 +jalviewjs_j2s_settings = .j2s
 +#jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace
 +# these 3 files/dirs found in build/jalviewjs
 +jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins
 +jalviewjs_eclipse_workspace_location_file = eclipse_workspace_location
 +jalviewjs_site_dir = site
 +# these dirs are subdirs of the site dir
 +jalviewjs_swingjs_subdir = swingjs
 +jalviewjs_j2s_subdir = swingjs/j2s
 +jalviewjs_js_subdir = swingjs/js
 +#jalviewjs_eclipseBuildArg = build
 +jalviewjs_eclipse_build_arg = cleanBuild
 +jalviewjs_server_port = 9001
 +jalviewjs_server_wait = 30
 +jalviewjs_server_resource = /jalview_bin_Jalview.html
 +jalviewjs_core_name = _jalview
 +jalviewjs_name = JalviewJS
 +jalviewjs_core_key = core
 +#jalviewjs_core_key = preloadCore
 +
 +j2s.compiler.status = enable
 +#j2s.site.directory = null ## site defined from buildDir+'/jalviewjs/'+jalviewjs_site_dir
 +#j2s.log.methods.declared = j2s_methods_declared.log
 +#j2s.log.methods.called = j2s_methods_called.log
 +#a semicolon-separated list of package-level file paths to be excluded
 +j2s.excluded.paths = test;testng;util
 +#j2s.include.tests = true
 +#j2s.testing = null
 +#j2s.compiler.nonqualified.packages = null
 +#j2s.compiler.nonqualified.classes = null
 +#j2s.compiler.mode = debug
 +#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made 
 +j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
 +j2s.template.html = utils/jalviewjs/template.html
 +j2s_coretemplate_html = utils/jalviewjs/coretemplate.html
 +#output file name for logging methods declared - delete the file to regenerate a listing 
 +#j2s.prop.j2s.log.methods.declared=swingjs/methodsDeclared_csv
 +#output file name for logging methods called - delete the file to regenerate a listing
 +#j2s.prop.j2s.log.methods_called=swingjs/methodsCalled_csv
 +#if set, every instance of methods called will be logged
 +#otherwise, only the first call to a method will be logged 
 +#output will be comma-separated: called method,caller class 
 +#j2s.prop.j2s.log.all.calls=true
 +
 +jalviewjs_j2s_transpile_stdout = j2s-transpile.out
 +#jalviewjs_j2s_stderr = j2s-transpile.err # all going into out
 +jalviewjs_j2s_to_console = true
 +jalviewjs_j2s_closure_stdout = j2s-closure.out
 +
 +
 +testp=gradle.properties