From: sduce Date: Fri, 25 Sep 2020 10:02:42 +0000 (+0100) Subject: Updated manual after testing Jalview develop X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=5077e6a3c7d0f92d4b0f2d297704ae18917cd00e Updated manual after testing Jalview develop --- diff --git a/.metadata/.lock b/.metadata/.lock new file mode 100644 index 0000000..e69de29 diff --git a/.metadata/.log b/.metadata/.log new file mode 100644 index 0000000..49b666d --- /dev/null +++ b/.metadata/.log @@ -0,0 +1,88 @@ +!SESSION 2019-09-07 11:16:02.896 ----------------------------------------------- +eclipse.buildId=4.12.0.I20190605-1800 +java.version=12.0.2 +java.vendor=Oracle Corporation +BootLoader constants: OS=macosx, ARCH=x86_64, WS=cocoa, NL=en_GB +Framework arguments: -product org.eclipse.epp.package.java.product -keyring /Users/sduce/.eclipse_keyring +Command-line arguments: -os macosx -ws cocoa -arch x86_64 -product org.eclipse.epp.package.java.product -keyring /Users/sduce/.eclipse_keyring + +!ENTRY org.eclipse.mylyn.bugzilla.core 4 0 2019-09-07 11:16:03.544 +!MESSAGE FrameworkEvent ERROR +!STACK 0 +org.osgi.framework.BundleException: Could not resolve module: org.eclipse.mylyn.bugzilla.core [267] + Unresolved requirement: Require-Bundle: org.eclipse.mylyn.commons.xmlrpc; bundle-version="[3.8.0,4.0.0)" + -> Bundle-SymbolicName: org.eclipse.mylyn.commons.xmlrpc; bundle-version="3.24.2.v20180904-2231"; singleton:="true" + org.eclipse.mylyn.commons.xmlrpc [284] + Unresolved requirement: Require-Bundle: org.apache.xmlrpc; bundle-version="[3.0.0,4.0.0)" + -> Bundle-SymbolicName: org.apache.xmlrpc; bundle-version="3.0.0.v20100427-1100" + org.apache.xmlrpc [56] + Unresolved requirement: Import-Package: javax.xml.bind + Unresolved requirement: Require-Bundle: org.apache.xmlrpc + -> Bundle-SymbolicName: org.apache.xmlrpc; bundle-version="3.0.0.v20100427-1100" + + at org.eclipse.osgi.container.Module.start(Module.java:457) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$1.run(ModuleContainer.java:1820) + at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$2$1.execute(EquinoxContainerAdaptor.java:150) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1813) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1769) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1735) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1661) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1) + at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234) + at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345) + +!ENTRY org.eclipse.mylyn.bugzilla.ui 4 0 2019-09-07 11:16:03.545 +!MESSAGE FrameworkEvent ERROR +!STACK 0 +org.osgi.framework.BundleException: Could not resolve module: org.eclipse.mylyn.bugzilla.ui [269] + Unresolved requirement: Require-Bundle: org.eclipse.mylyn.bugzilla.core; bundle-version="[3.8.0,4.0.0)" + -> Bundle-SymbolicName: org.eclipse.mylyn.bugzilla.core; bundle-version="3.24.2.v20180905-0003"; singleton:="true" + org.eclipse.mylyn.bugzilla.core [267] + Unresolved requirement: Require-Bundle: org.eclipse.mylyn.commons.xmlrpc; bundle-version="[3.8.0,4.0.0)" + -> Bundle-SymbolicName: org.eclipse.mylyn.commons.xmlrpc; bundle-version="3.24.2.v20180904-2231"; singleton:="true" + org.eclipse.mylyn.commons.xmlrpc [284] + Unresolved requirement: Require-Bundle: org.apache.xmlrpc; bundle-version="[3.0.0,4.0.0)" + -> Bundle-SymbolicName: org.apache.xmlrpc; bundle-version="3.0.0.v20100427-1100" + org.apache.xmlrpc [56] + Unresolved requirement: Import-Package: javax.xml.bind + Unresolved requirement: Require-Bundle: org.apache.xmlrpc + -> Bundle-SymbolicName: org.apache.xmlrpc; bundle-version="3.0.0.v20100427-1100" + + at org.eclipse.osgi.container.Module.start(Module.java:457) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$1.run(ModuleContainer.java:1820) + at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$2$1.execute(EquinoxContainerAdaptor.java:150) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1813) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1769) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1735) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1661) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1) + at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234) + at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345) + +!ENTRY org.eclipse.mylyn.commons.xmlrpc 4 0 2019-09-07 11:16:03.546 +!MESSAGE FrameworkEvent ERROR +!STACK 0 +org.osgi.framework.BundleException: Could not resolve module: org.eclipse.mylyn.commons.xmlrpc [284] + Unresolved requirement: Require-Bundle: org.apache.xmlrpc; bundle-version="[3.0.0,4.0.0)" + -> Bundle-SymbolicName: org.apache.xmlrpc; bundle-version="3.0.0.v20100427-1100" + org.apache.xmlrpc [56] + Unresolved requirement: Import-Package: javax.xml.bind + + at org.eclipse.osgi.container.Module.start(Module.java:457) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$1.run(ModuleContainer.java:1820) + at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$2$1.execute(EquinoxContainerAdaptor.java:150) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1813) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1769) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1735) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1661) + at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1) + at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234) + at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345) + +!ENTRY org.eclipse.egit.core 1 0 2019-09-07 11:16:53.714 +!MESSAGE Using Apache MINA sshd as ssh client. + +!ENTRY org.eclipse.mylyn.tasks.core 4 0 2019-09-07 11:16:54.318 +!MESSAGE Unexpected error while loading repository template extensions +!SUBENTRY 1 org.eclipse.mylyn.tasks.core 4 0 2019-09-07 11:16:54.318 +!MESSAGE Could not load repository template extension contributed by 'org.eclipse.mylyn.bugzilla.ide' with connectorKind 'bugzilla' diff --git a/.metadata/.mylyn/.taskListIndex/segments_1 b/.metadata/.mylyn/.taskListIndex/segments_1 new file mode 100644 index 0000000..911bf4b Binary files /dev/null and b/.metadata/.mylyn/.taskListIndex/segments_1 differ diff --git a/.metadata/.mylyn/.taskListIndex/write.lock b/.metadata/.mylyn/.taskListIndex/write.lock new file mode 100644 index 0000000..e69de29 diff --git a/.metadata/.mylyn/repositories.xml.zip b/.metadata/.mylyn/repositories.xml.zip new file mode 100644 index 0000000..5c71138 Binary files /dev/null and b/.metadata/.mylyn/repositories.xml.zip differ diff --git a/.metadata/.mylyn/tasks.xml.zip b/.metadata/.mylyn/tasks.xml.zip new file mode 100644 index 0000000..3e587e7 Binary files /dev/null and b/.metadata/.mylyn/tasks.xml.zip differ diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version new file mode 100644 index 0000000..25cb955 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index new file mode 100644 index 0000000..ed9b514 Binary files /dev/null and b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.index differ diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version new file mode 100644 index 0000000..6b2aaa7 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree b/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree new file mode 100644 index 0000000..8a1fc9e Binary files /dev/null and b/.metadata/.plugins/org.eclipse.core.resources/.root/1.tree differ diff --git a/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources new file mode 100644 index 0000000..cc5442b Binary files /dev/null and b/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources differ diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000..dffc6b5 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +version=1 diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs new file mode 100644 index 0000000..bceb0cd --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs @@ -0,0 +1,10 @@ +content_assist_proposals_background=255,255,255 +content_assist_proposals_foreground=0,0,0 +eclipse.preferences.version=1 +org.eclipse.jdt.ui.formatterprofiles.version=16 +org.eclipse.jdt.ui.text.code_templates_migrated=true +org.eclipse.jdt.ui.text.custom_code_templates= +spelling_locale=en_GB +spelling_locale_initialized=true +useAnnotationsPrefPage=true +useQuickDiffPrefPage=true diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.m2e.discovery.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.m2e.discovery.prefs new file mode 100644 index 0000000..67b1d96 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.m2e.discovery.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +org.eclipse.m2e.discovery.pref.projects= diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs new file mode 100644 index 0000000..43e97e4 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +mylyn.attention.migrated=true diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs new file mode 100644 index 0000000..8d462a6 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +org.eclipse.mylyn.monitor.activity.tracking.enabled.checked=true diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.tasks.ui.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.tasks.ui.prefs new file mode 100644 index 0000000..2b60c21 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.tasks.ui.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +migrated.task.repositories.secure.store=true +org.eclipse.mylyn.tasks.ui.filters.nonmatching=true +org.eclipse.mylyn.tasks.ui.filters.nonmatching.encouraged=true +org.eclipse.mylyn.tasks.ui.welcome.message=true diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs new file mode 100644 index 0000000..497aa66 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs @@ -0,0 +1,5 @@ +PROBLEMS_FILTERS_MIGRATE=true +eclipse.preferences.version=1 +platformState=1567851146886 +quickStart=false +tipsAndTricks=true diff --git a/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs new file mode 100644 index 0000000..aa3dc02 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs @@ -0,0 +1,3 @@ +//org.eclipse.ui.commands/state/org.eclipse.ui.navigator.resources.nested.changeProjectPresentation/org.eclipse.ui.commands.radioState=false +PLUGINS_NOT_ACTIVATED_ON_STARTUP=;org.eclipse.m2e.discovery; +eclipse.preferences.version=1 diff --git a/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi b/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi new file mode 100644 index 0000000..04f7053 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi @@ -0,0 +1,2518 @@ + + + + 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a/.metadata/.plugins/org.eclipse.jdt.core/assumedExternalFilesCache b/.metadata/.plugins/org.eclipse.jdt.core/assumedExternalFilesCache new file mode 100644 index 0000000..593f470 Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/assumedExternalFilesCache differ diff --git a/.metadata/.plugins/org.eclipse.jdt.core/externalFilesCache b/.metadata/.plugins/org.eclipse.jdt.core/externalFilesCache new file mode 100644 index 0000000..593f470 Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/externalFilesCache differ diff --git a/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache b/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache new file mode 100644 index 0000000..593f470 Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/nonChainingJarsCache differ diff --git a/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat b/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat new file mode 100644 index 0000000..0edae4b Binary files /dev/null and b/.metadata/.plugins/org.eclipse.jdt.core/variablesAndContainers.dat differ diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml b/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml new file mode 100644 index 0000000..a4ee3cb --- /dev/null +++ b/.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml @@ -0,0 +1,2 @@ + + diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml b/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml new file mode 100644 index 0000000..9e390f5 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml @@ -0,0 +1,2 @@ + + diff --git a/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml b/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml new file mode 100644 index 0000000..f4a13e9 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml @@ -0,0 +1,10 @@ + +
+
+ + + + + +
+
diff --git a/.metadata/.plugins/org.eclipse.m2e.logback.configuration/0.log b/.metadata/.plugins/org.eclipse.m2e.logback.configuration/0.log new file mode 100644 index 0000000..032c0c8 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.m2e.logback.configuration/0.log @@ -0,0 +1 @@ +2019-09-07 11:16:57,433 [Worker-0: Loading available Gradle versions] INFO o.e.b.c.i.u.g.PublishedGradleVersions - Gradle version information cache is up-to-date. Trying to read. diff --git a/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.12.0.20190529-1916.xml b/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.12.0.20190529-1916.xml new file mode 100644 index 0000000..e33758c --- /dev/null +++ b/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.12.0.20190529-1916.xml @@ -0,0 +1,43 @@ + + + + %date [%thread] %-5level %logger{35} - %msg%n + + + OFF + + + + + ${org.eclipse.m2e.log.dir}/0.log + + ${org.eclipse.m2e.log.dir}/%i.log + 1 + 10 + + + 100MB + + + %date [%thread] %-5level %logger{35} - %msg%n + + + + + + WARN + + + + + + + + + + + + + + + diff --git a/.metadata/.plugins/org.eclipse.oomph.setup/workspace.setup b/.metadata/.plugins/org.eclipse.oomph.setup/workspace.setup new file mode 100644 index 0000000..1f73e14 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.oomph.setup/workspace.setup @@ -0,0 +1,6 @@ + + diff --git a/.metadata/.plugins/org.eclipse.tips.ide/dialog_settings.xml b/.metadata/.plugins/org.eclipse.tips.ide/dialog_settings.xml new file mode 100644 index 0000000..5ca0b77 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.tips.ide/dialog_settings.xml @@ -0,0 +1,3 @@ + +
+
diff --git a/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml new file mode 100644 index 0000000..ae6c9b8 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.ui.ide/dialog_settings.xml @@ -0,0 +1,14 @@ + +
+
+ + + + + + + + + +
+
diff --git a/.metadata/.plugins/org.eclipse.ui.intro/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.intro/dialog_settings.xml new file mode 100644 index 0000000..4868369 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.ui.intro/dialog_settings.xml @@ -0,0 +1,4 @@ + +
+ +
diff --git a/.metadata/.plugins/org.eclipse.ui.intro/introstate b/.metadata/.plugins/org.eclipse.ui.intro/introstate new file mode 100644 index 0000000..236d56c --- /dev/null +++ b/.metadata/.plugins/org.eclipse.ui.intro/introstate @@ -0,0 +1,2 @@ + + \ No newline at end of file diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml new file mode 100644 index 0000000..c7ed1df --- /dev/null +++ b/.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml @@ -0,0 +1,15 @@ + +
+
+ + + + + + + + + + +
+
diff --git a/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml b/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml new file mode 100644 index 0000000..2316c49 --- /dev/null +++ b/.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.metadata/version.ini b/.metadata/version.ini new file mode 100644 index 0000000..1c97b94 --- /dev/null +++ b/.metadata/version.ini @@ -0,0 +1,3 @@ +#Sat Sep 07 11:16:52 BST 2019 +org.eclipse.core.runtime=2 +org.eclipse.platform=4.12.0.v20190605-1800