// TODO: consider allowing this expression to be overridden by -P arg
getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
- getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+ //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
getdownLauncher = jalviewDir + '/' + getdown_launcher
getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
def getdown_alt_java_min_version
// this property is assigned below and expanded to multiple lines in the getdown task
def getdown_alt_multi_java_location
+// this property is for the Java library used in eclipse
+def eclipse_java_runtime_name
if (JAVA_VERSION.equals("1.8")) {
JAVA_INTEGER_VERSION = "8"
+ //libDir = j8libDir
libDir = j11libDir
libDistDir = j8libDir
compile_source_compatibility = 1.8
compile_target_compatibility = 1.8
getdown_alt_java_min_version = getdown_alt_java8_min_version
getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-1.8"
} else if (JAVA_VERSION.equals("11")) {
JAVA_INTEGER_VERSION = "11"
libDir = j11libDir
compile_target_compatibility = 11
getdown_alt_java_min_version = getdown_alt_java11_min_version
getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
+ eclipse_java_runtime_name = "JavaSE-11"
additional_compiler_args += [
'--module-path', ext.modules_compileClasspath.asPath,
'--add-modules', j11modules
resources {
srcDirs "$jalviewDir/$resourceDir"
- srcDirs "$jalviewDir/$libDistDir"
}
jar.destinationDir = file("$jalviewDir/$packageDir")
} else {
compileClasspath += files(sourceSets.main.java.outputDir)
}
- //compileClasspath += sourceSets.main.compileClasspath
- //compileClasspath += files( sourceSets.main.resources.srcDirs)
+
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
}
cp.entries.removeAll(removeTheseToo)
+ print ("CP="+cp.inspect())
+
cp.entries += new Output("bin/main")
cp.entries += new Library(fileReference(helpParentDir))
cp.entries += new Library(fileReference(resourceDir))
HashMap<String, Boolean> addedLibPath = new HashMap<>();
- def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
- sourceSets.main.compileClasspath.each{
- //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.main.compileClasspath.each{
+ fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+ //don't want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
return
}
}
- sourceSets.test.compileClasspath.each{
+ // changing from sourcesets.main.classpath to specific Java version lib
+ //sourceSets.test.compileClasspath.each{
+ fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
//if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
//no longer want to add outputDir as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
jdt {
// for the IDE, use java 11 compatibility
- sourceCompatibility = 11
- targetCompatibility = 11
- javaRuntimeName = "JavaSE-11"
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ javaRuntimeName = eclipse_java_runtime_name
file {
withProperties { props ->
delete cloverInstrDir
}
+// format is a string like date.format("dd MMMM yyyy")
def getDate(format) {
def date = new Date()
- //return date.format("dd MMMM yyyy")
return date.format(format)
}
-task setGitHash(type: Exec) {
- workingDir = jalviewDir
- commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = new ByteArrayOutputStream()
- project.ext.gitHash = {
- return standardOutput.toString().trim()
+task setGitVals {
+ def hashStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--short", "HEAD"
+ standardOutput = hashStdOut
+ ignoreExitValue true
}
-}
-task setGitBranch(type: Exec) {
- workingDir = jalviewDir
- commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = new ByteArrayOutputStream()
- project.ext.gitBranch = {
- return standardOutput.toString().trim()
+ def branchStdOut = new ByteArrayOutputStream()
+ exec {
+ commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
+ standardOutput = branchStdOut
+ ignoreExitValue true
}
-}
-task setGitVals {
- dependsOn setGitHash
- dependsOn setGitBranch
+ project.ext.gitHash = hashStdOut.toString().trim()
+ project.ext.gitBranch = branchStdOut.toString().trim()
+
+ outputs.upToDateWhen { false }
}
task createBuildProperties(type: WriteProperties) {
dependsOn setGitVals
inputs.dir("$jalviewDir/$sourceDir")
+ inputs.dir("$classes")
inputs.dir("$jalviewDir/$resourceDir")
outputFile "$classes/$buildPropertiesFile"
// taking time specific comment out to allow better incremental builds
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("dd MMMM yyyy")
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
property "VERSION", JALVIEW_VERSION
property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
outputs.file(outputFile)
- outputs.dir("$classes")
}
def buildingHTML = "$jalviewDir/$docDir/building.html"
jalviewDir = .
+#JAVA_VERSION = 1.8
JAVA_VERSION = 11
JALVIEW_VERSION = DEVELOPMENT
INSTALLATION = Source
testngGroups = Functional
-javac_source = 11
-javac_target = 11
-
j8libDir = j8lib
j11libDir = j11lib
resourceDir = resources
getdown_website_dir = getdown/website
getdown_resource_dir = resource
getdown_app_dir = dist
-getdown_j11lib_dir = j11lib
+#getdown_j11lib_dir = j11lib
getdown_files_dir = getdown/files
getdown_launcher = getdown/lib/getdown-launcher.jar
getdown_core = getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
nucleotide substitution matrix</a>, or by sequence percentage identity,
or sequence feature similarity.
</p>
- <img src="pcaviewer.gif">
+ <img src="pcaviewer.png">
<p>
<strong>The PCA Viewer</strong>
</p>
towards the front of the view.</p>
<p>
The 3d view can be rotated by dragging the mouse with the <strong>left
- mouse button</strong> pressed. The view can also be zoomed in and out with
+ mouse button</strong> pressed, or with the <strong>arrow
+ keys</strong> when <strong>SHIFT</strong> is pressed. The
+ view can also be zoomed in and out with
the up and down <strong>arrow keys</strong> (and the roll bar of the
mouse if present). Labels will be shown for each sequence if the
entry in the View menu is checked, and the plot background colour
<p>
Initially, the display shows the first three components of the
similarity space, but any eigenvector can be used by changing the
- selected dimension for the x, y, or z axis through each ones menu
+ selected dimension for the x, y, or z axis through each one's menu
located below the 3d display. The <strong><em>Reset</em></strong>
button will reset axis and rotation settings to their defaults.
</p>
<em>The output of points and transformed point coordinates was
added to the Jalview desktop in v2.7.</em> <em>The Reset button
and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
- for PAM250 based PCA was added in Jalview 2.8.1.</em>
+ for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em>
</p>
<p>
<strong>Reproducing PCA calculations performed with older
<tr>
<td width="60" align="center" nowrap>
<strong><a name="Jalview.2.11">2.11</a><br />
- <em>tbc/06/2019</em></strong>
+ <em>20/06/2019</em></strong>
</td>
<td align="left" valign="top">
<ul>
<li>
<!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
<li>
- <!-- JAL-3141 -->Optional automatic backups when saving
- Jalview project or alignment files</li>
- <li>
- <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
- Viewer state is saved in Jalview Project<br />The 'Change
- parameters' option has also been removed from the PCA viewer</li>
- <li>
- <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
- <li>
- <!-- JAL-2620 -->Alternative genetic code tables supported for
+ <!-- JAL-2620 -->Alternative genetic code tables for
'Translate as cDNA'</li>
<li>
- <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
- <li>
- <!-- JAL-3198 -->More efficient creation of selections and
- multiple groups when working with large alignments</li>
- <li>
- <!-- JAL-3200 -->Speedier import of annotation rows when
- parsing stockholm files</li>
- <li>
<!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
- <li>
- <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)</li>
- <li>
- <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
- <li>
- <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
- <li>
- <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)</li>
- <li>
- <!-- JAL-2527 -->Alignment Overview now by default shows
- only visible region of alignment (this can be changed in
- user preferences)</li>
- <li>
- <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</li>
- <li>
- <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when
- all sequences are hidden</li>
- <li>
- <!-- JAL-1244 -->Status bar shows bounds when dragging a selection
- region, and gap count when inserting or deleting gaps</li>
- <li>
- <!-- JAL-3132 -->Status bar updates over sequence and annotation labels</li>
- <li>
- <!-- JAL-3093 -->Show annotation tooltips and popup menus in wrapped mode</li>
- <li>
- <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
- <li>
- <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</li>
- <li>
- <!-- JAL-2814 -->Help button on Uniprot and PDB search panels</li>
- <li>
- <!-- JAL-2621 -->Cursor changes over draggable box in Overview panel</li>
- <li>
- <!-- JAL-3203 -->Overview panel default changed to not show hidden regions</li>
- <li>
- <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
- <li>
- <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
- <li>
- <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent
- to a hidden column marker</li>
- <li>
- <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
- <li>
- <!-- JAL-2965 -->PCA depth cueing with graduated colours</li>
- </ul>
+ <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+ <ul>
+ <li>
+ <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
+ shaded according to any associated attributes (e.g. variant
+ attributes from VCF file, or key-value pairs imported from
+ column 9 of GFF file)
+ </li>
+ <li>
+ <!-- JAL-2897 -->Show synonymous codon variants on peptide
+ sequences
+ </li>
+ <li>
+ <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
+ details
+ </li>
+ <li>
+ <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+ </li>
+ <li>
+ <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
+ dialog
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3141 -->Backup files created when saving Jalview project
+ or alignment files
+ </li>
+ <li><strong>Principal Components Analysis Viewer</strong>
+ <ul>
+ <li>
+ <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
+ and Viewer state saved in Jalview Project
+ </li>
+ <li>'Change parameters' option removed from viewer's
+ drop-down menus</li>
+ <li>
+ <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
+ incrementally
+ </li>
+ <li>
+ <!-- JAL-2965 -->PCA plot is depth cued
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3127 -->New 'Colour by Sequence ID' option
+ </li>
+ <li><strong>Speed and Efficiency</strong>
+ <ul>
+ <li>
+ <!-- JAL-3198 -->More efficient creation of selections and
+ multiple groups when working with large alignments
+ </li>
+ <li>
+ <!-- JAL-3200 -->Speedier import of annotation rows when parsing
+ Stockholm files
+ </li>
+ </ul>
+ <li><strong>User Interface</strong>
+ <ul>
+ <li>
+ <!-- JAL-2933 -->Finder panel remembers last position in each
+ view
+ </li>
+ <li>
+ <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
+ what is shown)<br />Only visible region of alignment is shown by
+ default (can be changed in user preferences)
+ </li>
+ <li>
+ <!-- JAL-3169 -->File Chooser stays open after responding Cancel
+ to the Overwrite Dialog
+ </li>
+ <li>
+ <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
+ sequences are hidden
+ </li>
+ <li>
+ <!-- JAL-1244 -->Status bar shows bounds when dragging a
+ selection region, and gap count when inserting or deleting gaps
+ </li>
+ <li>
+ <!-- JAL-3132 -->Status bar updates over sequence and annotation
+ labels
+ </li>
+ <li>
+ <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
+ when in wrapped mode
+ </li>
+ <li>
+ <!-- JAL-3073 -->Can select columns by dragging left/right in
+ annotations
+ </li>
+ <li>
+ <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
+ </li>
+ <li>
+ <!-- JAL-2621 -->Cursor changes over draggable box in Overview
+ panel
+ </li>
+ <li>
+ <!-- JAL-3181 -->Consistent ordering of links in sequence id
+ popup menu
+ </li>
+ </ul></li>
+ <li><strong>Java 11 Support</strong>
+ <ul>
+ <li>
+ <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
+ and getdown release channels
+ </li>
+ <li>
+ <!-- -->OSX GUI integrations for App menu's 'About' entry and
+ trapping CMD-Q
+ </li>
+ </ul></li>
+ </ul>
<em>Deprecations</em>
<ul>
<li>
<!-- JAL-3035 -->DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
</li>
+ <li>
+ <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients</li>
+ <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
+ <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
</ul>
- <em>Release Processes</em>
+ <em>Development and Release Processes</em>
<ul>
- <li>
- Atlassian Bamboo continuous integration server for
+ <li>
+ <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
+ Installers built with Install4j (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+ </li>
+ <li>
+ <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (<a href="https://github.com/threerings/getdown">Three
+ Rings' GetDown</a>)
+ </li>
+ <li>
+ <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
+ </li>
+ <li>
+ <!-- JAL-3225 -->Eclipse project configuration managed with
+ gradle-eclipse
+ </li>
+ <li>
+ Atlassian Bamboo continuous integration for
unattended Test Suite execution</li>
<li>
<!-- JAL-2864 -->Memory test suite to detect leaks in common
operations</li>
<li>
- <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections</li>
- <li>
- <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients</li>
+ <!-- JAL-3140 -->IntervalStoreJ (NCList
+ implementation that alows updates) used for Sequence Feature collections</li>
</ul>
</td>
<td align="left" valign="top">
<!-- JAL-2750 -->Tree and PCA calculation fails for selected
region if columns were selected by dragging right-to-left
and the mouse moved to the left of the first column</li>
+ <li>
+ <!-- JAL-3218 -->Couldn't hide selected columns adjacent
+ to a hidden column marker via scale popup menu</li>
<li>
<!-- JAL-2846 -->Error message for trying to load in invalid
URLs doesn't tell users the invalid URL</li>
<li>
<!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
<li>
+ <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
+ <li>
<!-- JAL-914 -->Help page can be opened twice</li>
</ul>
<em>Editing</em>
}
+ /**
+ * update singleton Strings with these build details
+ *
+ * @param version
+ * @param buildDate
+ * @param installation
+ */
public BuildDetails(String version, String buildDate, String installation)
{
BuildDetails.version = version;
BuildDetails.installation = installation;
}
+ @Override
public String getBuildDate()
{
return buildDate;
BuildDetails.buildDate = buildDate;
}
+ @Override
public String getVersion()
{
return version;
BuildDetails.version = version;
}
+ @Override
public String getInstallation()
{
return installation;
applicationProperties.remove("YEAR");
}
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
- {
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
- }
-
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
- String codeInstallation = getProperty("INSTALLATION");
- if (codeVersion == null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- codeInstallation = "";
- }
- else
- {
- codeInstallation = " (" + codeInstallation + ")";
- }
- new BuildDetails(codeVersion, null, codeInstallation);
+ loadBuildProperties(false);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
-
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
// StructureImportSettings
// .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
- // jnlpVersion will be null if we're using InstallAnywhere
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // jnlpVersion will be null if a latest version check for the channel needs to
+ // be done
// Dont do this check if running in headless mode
+
if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
false);
}
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printV = codeInstallation == null;
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ try
+ {
+ String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/.build_properties"));
+
+ java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
+ String codeVersion = getProperty("VERSION");
+ codeInstallation = getProperty("INSTALLATION");
+
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ setProperty("VERSION", codeVersion);
+ new BuildDetails(codeVersion, null, codeInstallation);
+ if (printV && reportVersion)
+ {
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
}
}
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ return "Jalview Version: "
+ + jalview.bin.Cache.getDefault("VERSION", "TEST")
+ + "\n" + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION",
+ "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "\n" + "Java version: "
+ + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version")
+ + (jalview.bin.Cache.getDefault("VERSION", "TEST")
+ .equals("DEVELOPMENT")
+ ? "\nJava path:"
+ + System.getProperty(
+ "java.home")
+ + File.separator + "bin"
+ + File.separator + "java"
+ : "");
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
}
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ // report Jalview version
+ Cache.loadBuildProperties(true);
String appdirString = System.getProperty("getdownappdir");
if (appdirString != null && appdirString.length() > 0)
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
+ Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToList((JSONArray) obj.get("alleles"));
String clinSig = JSONUtils
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
+ if (phase != null)
+ {
+ sf.setPhase(phase.toString());
+ }
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader(
- "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version")
- + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
- ? "\nJava path:"
- + System.getProperty(
- "java.home")
- + File.separator + "bin"
- + File.separator + "java"
- : "")
- );
+ jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
showConsole(showjconsole);
message.append("<h1><strong>Version: "
+ jalview.bin.Cache.getProperty("VERSION")
+ "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
+ message.append("<strong>Built: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
+ + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
+ + "</strong>");
}
else
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals("Checking"))
{
- message.append("<br>...Checking latest version...</br>");
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
}
else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals(jalview.bin.Cache.getProperty("VERSION")))
{ "snRNA", "transcript" },
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
+ { "lnc_RNA", "transcript" },
{ "rRNA", "transcript" },
{ "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
return false;
}
return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
- & e.getModifiersEx()) != 0; // getModifiers()) != 0;
+ & jalview.util.ShortcutKeyMaskExWrapper
+ .getModifiersEx(e)) != 0; // getModifiers()) != 0;
}
return e.isControlDown();
}
package jalview.util;
-import java.awt.Toolkit;
-import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
public class ShortcutKeyMaskExWrapper
{
- private static boolean init = false;
+ private static final Float specversion;
- private static final Float specversion = Float
- .parseFloat(System.getProperty("java.specification.version"));
+ private static final float modern;
- private static final float modern = 11;
+ public static final int SHIFT_DOWN_MASK;
- public static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
+ public static final int ALT_DOWN_MASK;
- public static int ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ private static final ShortcutKeyMaskExWrapperI wrapper;
- public ShortcutKeyMaskExWrapper()
+ static
{
- }
+ specversion = Float
+ .parseFloat(System.getProperty("java.specification.version"));
+ modern = 11;
- private static void init()
- {
- if (init)
- {
- return;
- }
- if (specversion < modern)
+ if (specversion >= modern)
{
- SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
- ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+ wrapper = new ShortcutKeyMaskExWrapper11();
}
else
{
- SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
- ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+ wrapper = new ShortcutKeyMaskExWrapper8();
}
-
- init = true;
+ SHIFT_DOWN_MASK = wrapper.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = wrapper.ALT_DOWN_MASK;
}
public static int getMenuShortcutKeyMaskEx()
{
- init();
- if (specversion < modern)
- {
- return Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
- }
- else
- {
- return Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx();
- }
+ return wrapper.getMenuShortcutKeyMaskEx();
+ }
+
+ public static int getModifiersEx(MouseEvent e)
+ {
+ return wrapper.getModifiersEx(e);
}
}
--- /dev/null
+package jalview.util;
+
+import java.awt.GraphicsEnvironment;
+import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+
+public class ShortcutKeyMaskExWrapper11 implements ShortcutKeyMaskExWrapperI
+{
+ public final static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
+ public final static int ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+
+ @Override
+ public int getMenuShortcutKeyMaskEx()
+ {
+ try
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ return Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx();
+ }
+ } catch (java.lang.Throwable t)
+ {
+ }
+ return 0;
+ }
+
+ @Override
+ public int getModifiersEx(MouseEvent e)
+ {
+ return e.getModifiersEx();
+ }
+
+}
--- /dev/null
+package jalview.util;
+
+import java.awt.GraphicsEnvironment;
+import java.awt.Toolkit;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+
+public class ShortcutKeyMaskExWrapper8 implements ShortcutKeyMaskExWrapperI
+{
+ public final static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
+ public final static int ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+
+ @Override
+ public int getMenuShortcutKeyMaskEx()
+ {
+ try
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ return Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
+ }
+ } catch (java.lang.Throwable t)
+ {
+ }
+ return 0;
+ }
+
+ @Override
+ public int getModifiersEx(MouseEvent e)
+ {
+ return e.getModifiers();
+ }
+
+}
--- /dev/null
+package jalview.util;
+
+import java.awt.event.MouseEvent;
+
+public interface ShortcutKeyMaskExWrapperI
+{
+ public static int SHIFT_DOWN_MASK = 0;
+
+ public static int ALT_DOWN_MASK = 0;
+
+ public int getMenuShortcutKeyMaskEx();
+
+ public int getModifiersEx(MouseEvent e);
+}
git://source.jalview.org / jalview.git / commitdiff
