From: Jim Procter Date: Thu, 4 Jul 2019 15:34:48 +0000 (+0100) Subject: Merge branch 'develop' into releases/Release_2_11_Branch X-Git-Tag: Release_2_11_0~1 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4b1c279987cdfe6ebdb894059cbc29d24d804e9d;hp=948c990b3de3f97bcc6d08cfa565b1350a9f7513 Merge branch 'develop' into releases/Release_2_11_Branch --- diff --git a/build.gradle b/build.gradle index 2332643..0bb89f9 100644 --- a/build.gradle +++ b/build.gradle @@ -56,6 +56,7 @@ ext { reportRsyncCmd = false buildDist = true buildProperties = buildPropertiesFile + getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher switch (CHANNEL) { case "BUILD": @@ -103,6 +104,7 @@ ext { buildDist = false } reportRsyncCommand = true + getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local break case "DEVELOP": @@ -136,6 +138,7 @@ ext { getdown_app_base = file(getdownWebsiteDir).toURI().toString() getdown_app_dir = getdown_app_dir_alt buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local break default: // something wrong specified @@ -150,7 +153,6 @@ ext { //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir - getdownLauncher = jalviewDir + '/' + getdown_launcher getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/' getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir /* compile without modules -- using classpath libraries @@ -636,7 +638,7 @@ task copyHelp(type: Copy) { exclude '**/*.gif' exclude '**/*.jpg' exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION]) + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) } from(inputDir) { include '**/*.gif' @@ -962,6 +964,9 @@ task getdownWebsite() { copy { from getdownLauncher + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } into project.ext.getdownWebsiteDir } @@ -970,6 +975,9 @@ task getdownWebsite() { from getdown_txt from getdownLauncher from getdownWebsiteDir+"/"+getdown_build_properties + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } into getdownInstallDir } @@ -984,6 +992,9 @@ task getdownWebsite() { from launch_jvl from getdownLauncher from getdownWebsiteDir+"/"+getdown_build_properties + if (file(getdownLauncher).getName() != getdown_launcher) { + rename(file(getdownLauncher).getName(), getdown_launcher) + } into getdownFilesDir } @@ -1004,7 +1015,9 @@ task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" dependsOn getdownWebsite - classpath = files(jalviewDir + '/' + getdown_core, jalviewDir+'/'+getdown_launcher) + doFirst { + classpath = files(getdownWebsiteDir + '/' + getdown_launcher) + } main = "com.threerings.getdown.tools.Digester" args project.ext.getdownWebsiteDir inputs.dir(project.ext.getdownWebsiteDir) @@ -1157,61 +1170,71 @@ clean { task sourceDist (type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") - archiveFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz" + def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz" + // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] + try { + archiveFileName = outputFileName + } catch (Exception e) { + archiveName = outputFileName + } compression Compression.GZIP - from jalviewDir into project.name - - - exclude (".*") - exclude ("**/.*") - exclude ("*.class") - exclude ("**/*.class") - include (eclipse_extra_jdt_prefs_file) - include ("AUTHORS") - include ("CITATION") - include ("FEATURETODO") - include ("JAVA-11-README") - include ("FEATURETODO") - include ("LICENSE") - include ("README") - include ("RELEASE") - include ("THIRDPARTYLIBS") - include ("build.gradle") - include ("gradle.properties") - include ("$sourceDir/*.java") - include ("$sourceDir/**/*.java") - include ("$sourceDir/**/*.cdr") - include ("$j8libDir/**/*.jar") - include ("$j11libDir/**/*.jar") - include ("$resourceDir/**/*") - include ("$helpDir/**/*") - include ("$schemaDir/**/*") - include ("$utilsDir/**/*") - include ("$docDir/**/*") - include ("$examplesDir/**/*") - include ("getdown/**/*") - //include ("jalview-jalopy.xml") - //include ("JalviewApplet.jpx") - //include ("JalviewX.jpx") - //include ("nbbuild.xml") - //include ("nbproject/genfiles.properties") - //include ("nbproject/project.properties") - //include ("nbproject/project.xml") - + + def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*" + ,".*" + ,"benchmarking/*" + ,"**/.*" + ,"*.class" + ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales" + ,"*locales/**", + ,"utils/InstallAnywhere"] + def PROCESS_FILES=[ "AUTHORS", + "CITATION", + "FEATURETODO", + "JAVA-11-README", + "FEATURETODO", + "LICENSE", + "**/README", + "RELEASE", + "THIRDPARTYLIBS","TESTNG", + "build.gradle", + "gradle.properties", + "**/*.java", + "**/*.html", + "**/*.xml", + "**/*.gradle", + "**/*.groovy", + "**/*.properties", + "**/*.perl", + "**/*.sh"] + + from(jalviewDir) { + exclude (EXCLUDE_FILES) + include (PROCESS_FILES) + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + } + from(jalviewDir) { + exclude (EXCLUDE_FILES) + exclude (PROCESS_FILES) exclude ("appletlib") exclude ("**/*locales") exclude ("*locales/**") exclude ("utils/InstallAnywhere") - exclude (libDir) - exclude (getdown_files_dir) + + exclude (getdown_files_dir) exclude (getdown_website_dir) // exluding these as not using jars as modules yet exclude ("$j11modDir/**/*.jar") - +} +// from (jalviewDir) { +// // explicit includes for stuff that seemed to not get included +// include(fileTree("test/**/*.")) +// exclude(EXCLUDE_FILES) +// exclude(PROCESS_FILES) +// } } task helppages { @@ -1219,5 +1242,5 @@ task helppages { dependsOn pubhtmlhelp inputs.dir("$classes/$helpDir") - outputs.file("build/distribution/help/helpTOC.html") + outputs.dir("$helpOutputDir") } diff --git a/doc/building.md b/doc/building.md index cc3d7f2..5f5fa6d 100644 --- a/doc/building.md +++ b/doc/building.md @@ -24,7 +24,7 @@ java -jar getdown-launcher.jar . jalview The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows. * Java 11 compliant JDK -* gradle 5.1 or above +* gradle 5.2 or above * git > The versions and installation methods here are just suggestions (which we have tested diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar index 7849bc7..bbe1476 100644 Binary files a/getdown/lib/getdown-core.jar and b/getdown/lib/getdown-core.jar differ diff --git a/getdown/lib/getdown-launcher-local.jar b/getdown/lib/getdown-launcher-local.jar new file mode 100644 index 0000000..4a36222 Binary files /dev/null and b/getdown/lib/getdown-launcher-local.jar differ diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar index 7f99732..85ede0c 100644 Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ diff --git a/getdown/src/getdown/ant/pom.xml b/getdown/src/getdown/ant/pom.xml index a2f95e3..6d6f8e9 100644 --- a/getdown/src/getdown/ant/pom.xml +++ b/getdown/src/getdown/ant/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.1.4_JVL + 1.8.3-1.1.8_FJVL getdown-ant diff --git a/getdown/src/getdown/core/pom.xml b/getdown/src/getdown/core/pom.xml index 4cd0507..51d3d5f 100644 --- a/getdown/src/getdown/core/pom.xml +++ b/getdown/src/getdown/core/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.1.4_JVL + 1.8.3-1.1.8_FJVL getdown-core @@ -37,6 +37,7 @@ jalview.org,*.jalview.org 8 15 + false @@ -87,6 +88,7 @@ + diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java index 2dddd6f..7c2a427 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java @@ -286,7 +286,6 @@ public class Application _envc = envc; _config = getLocalPath(envc.appDir, CONFIG_FILE); _backupConfig = getLocalPath(envc.appDir, BACKUP_CONFIG_DIR+File.separator+CONFIG_FILE); - log.warning("Backup config file now", "_backupConfig", _backupConfig, "exists", _backupConfig.exists(), "isReadable", _backupConfig.canRead()); } /** @@ -820,14 +819,16 @@ public class Application ARG: for (int i = 0; i < _jvmargs.size(); i++) { if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) { _jvmargs.remove(i); + break ARG; } } addAll(maxMemHeapArg, _jvmargs); + log.info("Max memory set", "maxMemHeapArg", maxMemHeapArg[0]); } } else if (jvmmempc != -1) { - System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')"); + log.warning("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')"); } // get the set of optimum JVM arguments @@ -1129,7 +1130,7 @@ public class Application if (j > -1) { ext = filename.substring(j+1); } - if (LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) { + if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) { // this file extension should have been dealt with in Getdown class } else { _appargs.add(0, "-open"); diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Build.java.tmpl b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Build.java.tmpl index 86ea47b..1023ede 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Build.java.tmpl +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Build.java.tmpl @@ -62,4 +62,15 @@ public class Build { return 30; } } + + /* + *

Whether to allow the local "file://" scheme for appbase + */ + public static boolean allowLocatorFileProtocol() { + try { + return Boolean.valueOf("@allow_file_protocol@"); + } catch (Exception e) { + return false; + } + } } diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/Config.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/Config.java index 6ad2b4f..8767ae0 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/Config.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/Config.java @@ -471,7 +471,7 @@ public class Config private final Map _data; - public static final List allowedReplaceKeys = Arrays.asList("appbase","apparg","jvmarg"); // these are the ones we might use + public static final List allowedReplaceKeys = Arrays.asList("appbase","apparg","jvmarg","jvmmempc"); // these are the ones we might use public static final List allowedMergeKeys = Arrays.asList("apparg","jvmarg"); // these are the ones we might use //private final List allowedMergeKeys = Arrays.asList("apparg","jvmarg","resource","code","java_location"); // (not exhaustive list here) } diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/HostWhitelist.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/HostWhitelist.java index f2f7ef3..ff0661b 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/HostWhitelist.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/HostWhitelist.java @@ -59,5 +59,5 @@ public final class HostWhitelist throw new MalformedURLException( "The host for the specified URL (" + url + ") is not in the host whitelist: " + hosts); } - private static boolean ALLOW_LOCATOR_FILE_PROTOCOL = true; + private static final boolean ALLOW_LOCATOR_FILE_PROTOCOL = Build.allowLocatorFileProtocol(); } diff --git a/getdown/src/getdown/launcher/pom.xml b/getdown/src/getdown/launcher/pom.xml index 4c6b982..bf0b736 100644 --- a/getdown/src/getdown/launcher/pom.xml +++ b/getdown/src/getdown/launcher/pom.xml @@ -4,7 +4,7 @@ com.threerings.getdown getdown - 1.8.3-1.1.4_JVL + 1.8.3-1.1.8_FJVL getdown-launcher diff --git a/getdown/src/getdown/mvn_cmd b/getdown/src/getdown/mvn_cmd index fd7c716..0cd54eb 100755 --- a/getdown/src/getdown/mvn_cmd +++ b/getdown/src/getdown/mvn_cmd @@ -3,7 +3,7 @@ if [ x$JVLVERSION != x ]; then export VERSION=$JVLVERSION else - export VERSION=1.8.3-1.1.4_JVL + export VERSION=1.8.3-1.1.8_JVL fi if [ x${VERSION%_JVL} = x$VERSION ]; then @@ -11,14 +11,21 @@ if [ x${VERSION%_JVL} = x$VERSION ]; then fi echo "Setting VERSION to '$VERSION'" - perl -p -i -e 's|()[^<]*JVL[^<]*()|${1}$ENV{VERSION}${2}|;' pom.xml */pom.xml +mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dallow_file_protocol=false -Dconnect_timeout=8 -Dread_timeout=15 +RET=$? +if [ x$RET = x0 ]; then + cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher.jar && echo "Copied getdown-launcher-$VERSION.jar to getdown/lib" + cp core/target/getdown-core-$VERSION.jar ../../../getdown/lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to getdown/lib" + cp core/target/getdown-core-$VERSION.jar ../../../j8lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j8lib" + cp core/target/getdown-core-$VERSION.jar ../../../j11lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j11lib" +fi -mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dconnect_timeout=8 -Dread_timeout=15 +VERSION=${VERSION/JVL/FJVL} +echo "Setting VERSION to '$VERSION'" +perl -p -i -e 's|()[^<]*JVL[^<]*()|${1}$ENV{VERSION}${2}|;' pom.xml */pom.xml +mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dallow_file_protocol=true -Dconnect_timeout=4 -Dread_timeout=4 RET=$? if [ x$RET = x0 ]; then - cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher.jar && echo "Copied getdown-launcher.jar to getdown/lib" - cp core/target/getdown-core-$VERSION.jar ../../../getdown/lib/getdown-core.jar && echo "Copied getdown-core.jar to getdown/lib" - cp core/target/getdown-core-$VERSION.jar ../../../j8lib/getdown-core.jar && echo "Copied getdown-core.jar to j8lib" - cp core/target/getdown-core-$VERSION.jar ../../../j11lib/getdown-core.jar && echo "Copied getdown-core.jar to j11lib" + cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher-local.jar && echo "Copied getdown-launcher-$VERSION.jar to getdown/lib/getdown-launcher-local.jar" fi diff --git a/getdown/src/getdown/pom.xml b/getdown/src/getdown/pom.xml index 24efba8..a73b59e 100644 --- a/getdown/src/getdown/pom.xml +++ b/getdown/src/getdown/pom.xml @@ -10,7 +10,7 @@ com.threerings.getdown getdown pom - 1.8.3-1.1.4_JVL + 1.8.3-1.1.8_FJVL getdown An application installer and updater. diff --git a/gradle.properties b/gradle.properties index 4fcb636..53189f0 100644 --- a/gradle.properties +++ b/gradle.properties @@ -21,7 +21,7 @@ j11libDir = j11lib resourceDir = resources helpParentDir = help helpDir = help -helpOutputDir = build/distribution/help +helpOutputDir = build/distributions/help docDir = doc sourceDir = src schemaDir = schemas @@ -52,7 +52,9 @@ getdown_website_dir = getdown/website getdown_resource_dir = resource #getdown_j11lib_dir = j11lib getdown_files_dir = getdown/files -getdown_launcher = getdown/lib/getdown-launcher.jar +getdown_lib_dir = getdown/lib +getdown_launcher = getdown-launcher.jar +getdown_launcher_local = getdown-launcher-local.jar getdown_launcher_new = getdown-launcher-new.jar getdown_core = getdown/lib/getdown-core.jar getdown_launch_jvl = channel_launch.jvl diff --git a/help/help/help.jhm b/help/help/help.jhm index 0802bf1..47f7d53 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -61,6 +61,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 179fb06..7e358d6 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -154,13 +154,14 @@ - - + + + diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index ebdfcf3..60db069 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -27,6 +27,12 @@ See running Jalview from the command line for more information. +
+
Jalview processes arguments on the command line sequentially. If + you would like to pass a 'JVL' file containing + memory settings or any other launch + parameters, then include it at the beginning of the command line to + ensure they are processed before any remaining arguments.
diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index 92d9323..27a1a68 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -26,38 +26,48 @@

Running Jalview from the command line

-

Jalview is most easily run from the command line if you have - built it from source, or via the 'Jalview' executable created from - the InstallAnywhere Jalview installation. Both of these mechanisms - allow true command line execution of Jalview - allowing you to - provide additional options.

-

The Java Webstart version of Jalview can be executed from the - command line using something like : - 

javaws http://www.jalview.org/webstart/jalview.jnlp -open
- yourFileName
-
- But, this is not guaranteed to work on all versions of webstart on all - operating systems, and doesn't let you execute Jalview with any - additional parameters.

- Running Jalview from the InstallAnywhere - installation + Jalview can be run from the command line, and provides a range of arguments. These arguments + can also be passed via .JVL files, which are opened + automatically by the Jalview application when double-clicked in a + file browser on Windows and OSX.

+ The way that you launch Jalview from the command line depends on the + platform you are on, and how it has been installed. + +
    +
  • Standard installation on Linux/Unix:
    +       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
    +
    • +
  • Standard installation on Windows:
    +      \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa
    +
    • +
  • OSX Application:
    +open /Applications/Jalview.app --args -open ~/myalignment.fa
    (put + all the Jalview arguments after the --args parameter) +
    +
    • +
  • Jalview standalone executable Jar
    +        <Path to Java home>/bin/java -jar %lt;Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa
    • +

- If you install with InstallAnywhere you can use several more - commands. However, if you call the application with the link - provided by InstallAnywhere any output from the application will be - sent to output.txt, not standard out.
The Jalview - application also requires a number of additional libraries on the - class path. The command line below adds all the jar files in the - Jalview installation's 'lib' directory to the classpath, as well as - the Jalview application jar file: + If you have installed Jalview via conda or another package + manager then you most likely have a 'jalview' command available in + your terminal shell's default path. Alternately, if you have built + Jalview from source, then take a look at the doc/building.md file + included in the source distribution.

- 
java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]

Use '-help' to get more information on the command line arguments that - Jalview accepts. + href="clarguments.html">command line arguments that Jalview + accepts. +

+

+ Passing JVM Arguments to Jalview
If you need + to modify parameters for Jalview's Java Virtual Machine, then take a + look at the instructions for how to setting + the JVM's maximum memory.

 

 

diff --git a/help/help/html/features/featureschemes.html b/help/help/html/features/featureschemes.html index 688e492..63dd0e5 100644 --- a/help/help/html/features/featureschemes.html +++ b/help/help/html/features/featureschemes.html @@ -80,7 +80,7 @@
  • Numeric - specify a threshold above, equal to or below which a feature will be selected or ignored.
  • String - select or ignore features based on - presence, absence, equivalence, or containment of a string.
    • + presence, absence, equivalence, or containment of a string (not case sensitive).

    The filters and colour schemes active for a particular feature type @@ -109,21 +109,21 @@

    + feature Score (or other attribute) + feature Score (or other attribute) - +
    Graduated colour thresholded (less than) by - feature Score
    Graduated colour thresholded (greater than) by - feature Score
    Colour by Feature Label (may also be thresholded)Colour by Feature Label
    The - current threshold and attribute is given in the icon's tooltip. + current threshold and attribute is shown in the icon's tooltip.
    diff --git a/help/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html index d94e2a6..555e2ba 100755 --- a/help/help/html/features/featuresettings.html +++ b/help/help/html/features/featuresettings.html @@ -29,7 +29,7 @@

    Select View→Feature Settings... in an alignment window to open the feature settings dialog box, which allows - precise control the visibility and appearance of sequence features for + precise control of the visibility and appearance of sequence features for an alignment view.

    @@ -39,7 +39,7 @@

    The top section of the dialog box lists all the sequence feature groups, along with a tickbox for each that controls whether its features are displayed. When many groups are present, their names may - be truncated, but the full name be shown in a tooltip when the mouse + be truncated, but the full name is shown in a tooltip when the mouse hovers over their checkbox.

    Feature colour schemes and filters

    diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html index bbc9f78..e013472 100755 --- a/help/help/html/features/importvcf.html +++ b/help/help/html/features/importvcf.html @@ -57,7 +57,7 @@ ##reference header that define what species and assembly name the VCF was generated against.

  • Look at ensembl.org to identify the species' short name, - and the assembly's unique.
    • + and the assembly's unique id.
  • Add mappings to the VCF_SPECIES and VCF_ASSEMBLY properties in your .jalview_properties file. For example:
     VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html
new file mode 100644
index 0000000..8661860
--- /dev/null
+++ b/help/help/html/features/jvlfiles.html
@@ -0,0 +1,70 @@
+
+
+JVL - Jalview Launch Files
+
+  
    
+    Jalview Launch Files - JVL
+  
    
+  
    Files with a '.jvl' (or .JVL) extension can be opened by the
+    Jalview desktop application, and allow you to:
    
+  
+  
    
+    Some example JVL files are given below - copy and paste them into a
+    text editor and save them as a file with the extension '.jvl'. To
+    test, open your saved .jvl file via the OSX File Chooser or Windows
+    file explorer, or pass it to Jalview via the command line
+  
    
+  
    
+    Passing command line arguments
+  
    +# Jalview Launch File
+# Please install the Jalview Desktop from 
+# http://www.jalview.org/getdown/release
+# and then try to open this file again
+jalview.apparg=-open
+jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=-annotations
+jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=-colour
+jalview.apparg=Clustal
+
    
+  
    
+    Launching a different version of Jalview
+  
    +# Jalview Launch File
+# Please install the Jalview Desktop from 
+# http://www.jalview.org/getdown/release
+# and then try to open this file again
+appbase=http://www.jalview.org/old/v2_10_5/
+
    
+  For security, the Jalview application will only allow
+  appbase URLs from www.jalview.org, or your local file system.
+
+
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index e583398..4baebf2 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -28,20 +28,18 @@
       Memory Usage Settings for Jalview
     
   
+  
    When launched as an Application, Jalview will automatically
+    configure the amount of memory allocated to the program to be 90% of
+    physical memory. You may wish to change this behaviour -
+    particularly if you are working on a machine that runs other memory
+    intensive processes.
   
    
-    When launched as an Application, Jalview automatically tries to
-    maximise the amount of memory allocated to it, but sometimes it may
-    run out of memory. This is because of the way that Java runs on a
-    computer - what is actually run is a program called a virtual
-    machine (the JVM) which executes the java instructions. The JVM has
-    limits on the memory that can be allocated to the java program - and
-    you might need to increase them if you are working with particularly
-    large datasets.
     If Jalview has not explicitly told you that
-    it has run out of memory, then a common sign is that a function that
-    normally works seems to have no effect when working with a larger
-    set of sequences (this might include open dialog boxes for saving
-    PNG files, or when interpreting the result of a web service
-    calculation).
+    Signs that Jalview is Running out of Memory
     If
+    Jalview has not explicitly told you that it has run out of memory,
+    then a common sign is that a function that normally works seems to
+    have no effect when working with a larger set of sequences (this
+    might include open dialog boxes for saving PNG files, or when
+    interpreting the result of a web service calculation).
   
    
   
    
     Jalview Memory Usage Monitor: If you are concerned about
@@ -54,8 +52,82 @@
     window's background.
   
    
   
    
-    Increasing the memory available to Jalview
    
-    Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory. 
-      
     
    
+    Increasing the memory available to Jalview
     The
+    amount of memory allocated is defined wheb Jalview is launched
+    because of the way that Java runs on a computer - what is actually
+    run is a program called a Java virtual machine (a JVM) which
+    executes the java program instructions. The JVM has limits on the
+    memory that can be allocated to the java program - and it is often
+    necessary to adjust them if you are working with particularly large
+    datasets, or need to make room for other processes on the machine.
    
+    
    Jalview 2.11 includes a launcher that automatically
+    configures the proportion of memory allocated to Jalview's JVM, and
+    its behaviour can be altered in a number of different ways:
+  
    
+
+  
 
 
diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html
index 3a057a8..e26707f 100755
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -547,7 +547,7 @@
     
  • Calculate Tree or PCA ... 
     Opens the 
     calculations dialog for
         for calculating trees or
-         principle component analysis 
+         principal component analysis 
          plots on the alignment or the currently selected
         region. 
       
    • 
diff --git a/help/help/html/menus/alwcalculate.html b/help/help/html/menus/alwcalculate.html
index 8862955..3804538 100755
--- a/help/help/html/menus/alwcalculate.html
+++ b/help/help/html/menus/alwcalculate.html
@@ -56,7 +56,7 @@
     
  • Calculate Tree or PCA ... 
     Opens the 
     calculations dialog for
         for calculating trees or
-         principle component analysis 
+         principal component analysis 
          plots on the alignment or the currently selected
         region. 
       
    
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 996d060..0a20650 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -75,7 +75,7 @@ li:before {
           
    • 
 					
  • 
 						File type associations for
-						formats supported by jalview (including .jvp project files)
+						formats supported by Jalview (including .jvp project files)
 					
    • 
 					
  • 
 						Jalview launch files (.jvl) to pass command line
@@ -100,7 +100,6 @@ li:before {
             IntervalStoreJ (NCList
             implementation that allows updates) used for Sequence Feature collections
    • 
           
  • 
-							
  • 
                 Sequence
                 features can be filtered and shaded according to any
                 associated attributes (e.g. variant attributes from VCF
@@ -176,7 +175,7 @@ li:before {
 							
    • 
 							
  • 
 								Alignment Overview now WYSIWIS (What you see is
-								what is shown)
    Only visible region of alignment is shown by
+								what is shown)
    Only visible regions of alignment are shown by
 								default (can be changed in user preferences)
 							
    • 
 							
  • 
@@ -232,59 +231,55 @@ li:before {
 				
         Deprecations
         
      
-          
    • 
-            DAS sequence retrieval and annotation
+          
    • DAS sequence retrieval and annotation
             capabilities removed from the Jalview Desktop
           
      • 
-          
    • 
-            Castor library for XML marshalling and
+          
    • Castor library for XML marshalling and
             unmarshalling has been replaced by JAXB for Jalview projects
             and XML based data retrieval clients
      • 
           
    • Disable VAMSAS menu in preparation for removal
      •  
           
    • Jalview Desktop no longer distributed via Java Web Start
      • 
         
     Documentation
 				
      
-					
    • 
-						Added remarks about transparent rendering effects
+					
    • Added remarks about transparent rendering effects
 						not supported in EPS figure export
 					
      • 
 					
    • Typos in documentation for Preferences dialog
      • 
 				
     Development and Release Processes
         
      
         	
    • 
-						Build system migrated from Ant to Gradle
+        	Build system migrated from Ant to Gradle
 					
      • 
-					
    • Enhanced checks for missing and duplicated keys in Message bundles
      • 
+			
    • 
+			Enhanced checks for missing and duplicated keys in Message bundles
      • 
           
    • 
-            Eclipse project configuration managed with
+          Eclipse project configuration managed with
             gradle-eclipse
           
      • 
           
    • 
-             Atlassian
+          Atlassian
             Bamboo continuous integration for unattended Test Suite
             execution
           
      • 
           
    • 
-            Memory test suite to detect leaks in common
+          Memory test suite to detect leaks in common
             operations
           
      • 
           
    • 
-            More unit test coverage, and minor
-            issues resolved.
+          More unit test coverage, and minor
+            issues resolved
           
      • 
           
    • 
-            Developer documentation migrated to
+          Developer documentation migrated to
             markdown (with HTML rendering)
           
      • 
           
    • 
-            HelpLinksChecker runs on Windows
+          HelpLinksChecker runs on Windows
           
      • 
           
    • 
-            New URLs for publishing development
+          New URLs for publishing development
             versions of Jalview
           
      • 
-          
    • 
-          
    • 
         
    
       
 			
@@ -327,8 +322,8 @@ li:before {
 						Settings and Jalview Preferences panels
 					
    • 
 					
  • 
-						Jalview hangs when closing windows or the
-						overview updates with large alignments
+						Jalview hangs when closing windows, or redrawing the
+						overview with large alignments
 					
    • 
 					
  • 
 						Tree and PCA calculation fails for selected
@@ -358,7 +353,7 @@ li:before {
           
    • 
 					
  • 
 						'Graduated colour' option not offered for
-						manually created features (where if feature score is Float.NaN)
+						manually created features (where feature score is Float.NaN)
 					
    • 
 					
  • 
 						Blank extra columns drawn or printed
@@ -474,23 +469,22 @@ li:before {
 						Structure colours not updated when associated tree
 						repartitions the alignment view (Regression in 2.10.5)
 					
    • 
-				
-				Datamodel
-				
      
-					
    • 
-						Sequence.findIndex returns wrong value when
-						sequence's End is greater than its length
-					
      • 
-          
    • Bugs fixed for Java 11 Support (not
-              yet on general release)
-            
        
-              
      • 
-                Menus work properly in split-screen
-              
        • 
-            
      • 
+				
     Datamodel
+        
      
+          
    • 
+            Sequence.findIndex returns wrong value when
+            sequence's End is greater than its length
+          
      • 
+        
     Bugs fixed for Java 11 Support (not yet on
+          general release)
+        
      
+          
    • 
+            Menus work properly in split-screen
+          
      • 
         
     New Known Defects
-				
      
-				
    • Select columns containing feature by double clicking ignores bounds of an existing selected region
+        
        
+				
      • 
+				Select columns containing feature by double clicking ignores bounds of an existing selected region
 				
        • 
 					
      • 
 						Codon consensus logo incorrectly scaled in gapped
@@ -519,7 +513,8 @@ li:before {
 						not shown as thresholded features in 2.11. To workaround please
 						create a Score filter instead.
 					
        • 
-					
      • Cancel on Feature Settings dialog doesn't reset group visibility
        •  
+					
      • 
+					Cancel on Feature Settings dialog doesn't reset group visibility
        •  
 					
      • 
 					F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
 					
        • 
@@ -527,15 +522,14 @@ li:before {
             Closing tree windows with CMD/CTRL-W for
             alignments with multiple views can close views unexpectedly
           
-          
      • Java 11 Specific defects
+          
      
+          Java 11 Specific defects
             
        
               
      • 
                 Jalview Properties file is not sorted
                 alphabetically when saved
               
        • 
-            
      
-          
      • 
-        
    
+          
 			
 		
     
@@ -555,7 +549,7 @@ li:before {
               Hidden sequence markers and representative
               sequence bolding included when exporting alignment as EPS,
               SVG, PNG or HTML. Display is configured via the
-                Format menu, or for command-line use via a jalview
+                Format menu, or for command-line use via a Jalview
                 properties file.
  • @@ -629,7 +623,7 @@ li:before {
  • .jvp should be used as default extension - (not .jar) when saving a jalview project file. + (not .jar) when saving a Jalview project file.
  • Mac Users: closing a window correctly diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index eb318f0..4b406be 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -64,7 +64,7 @@ also been improved.
  • Backup files. Jalview will automatically create backups when overwriting existing files, and - unlike with - earlier versions, should Jalview crash during a save, the original + earlier versions - should Jalview crash during a save, the original file will be unaffected. The Backups tab in Jalview's preferences dialog allows the number and format of diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar index 7849bc7..bbe1476 100644 Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar index 7849bc7..bbe1476 100644 Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ diff --git a/lib/.cvsignore b/lib/.cvsignore deleted file mode 100644 index 5feaa93..0000000 --- a/lib/.cvsignore +++ /dev/null @@ -1,35 +0,0 @@ -NOBACK -XmlSchema-SNAPSHOT.jar -annogen-0.1.0.jar -axiom-api-1.0-RC2.jar -axiom-dom-1.0-RC2.jar -axiom-impl-1.0-RC2.jar -axis-wsdl4j-1.2.jar -axis.jar.bak -axis.jar.commons -axis2-adb-1.0-RC2.jar -axis2-kernel-1.0-RC2.jar -backport-util-concurrent-2.0_01_pd.jar -backport-util-concurrent-2.1.jar -castor.zip -commons-codec-1.2.jar -commons-codec-1.3.jar -commons-fileupload-1.0.jar -commons-httpclient-3.0.jar -commons-logging-1.0.4.jar -geronimo-spec-activation-1.0.2-rc4.jar -geronimo-spec-javamail-1.3.1-rc5.jar -geronimo-spec-jms-1.1-rc4.jar -jaxen-1.1-beta-7.jar -jhall.jar.bak -log4j-1.2.13.jar -maven-itest-plugin-1.0.jar -phylip-client-axis-1.3.jar -policy-1.0.1-RC.jar -policy-1.0.jar -servletapi-2.3.jar -stax-api-1.0.jar -wstx-asl-2.8.2.jar -wstx-asl-2.9.2.jar -xercesImpl.jar.bak -xml-apis.jar.bak diff --git a/lib/JGoogleAnalytics_0.3.jar b/lib/JGoogleAnalytics_0.3.jar deleted file mode 100644 index 0dbc98c..0000000 Binary files a/lib/JGoogleAnalytics_0.3.jar and /dev/null differ diff --git a/lib/Jmol-14.6.4_2016.10.26-no_netscape.jar b/lib/Jmol-14.6.4_2016.10.26-no_netscape.jar deleted file mode 100644 index f214bb4..0000000 Binary files a/lib/Jmol-14.6.4_2016.10.26-no_netscape.jar and /dev/null differ diff --git a/lib/VARNAv3-93.jar b/lib/VARNAv3-93.jar deleted file mode 100644 index 9d41f6b..0000000 Binary files a/lib/VARNAv3-93.jar and /dev/null differ diff --git a/lib/VAqua5-patch.jar b/lib/VAqua5-patch.jar 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index 0aaa990..0000000 Binary files a/lib/xercesImpl.jar and /dev/null differ diff --git a/utils/publishHelp.xml b/utils/publishHelp.xml index 17ef9e2..c626a21 100644 --- a/utils/publishHelp.xml +++ b/utils/publishHelp.xml @@ -1,7 +1,7 @@ - +