Merge branch 'develop' into feature/JAL-3187linkedFeatures

diff --git a/build.gradle b/build.gradle
index 0f0b8ff..f02d8ad 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -61,6 +61,9 @@ ext {
 
     case "BUILD":
     // TODO: get bamboo build artifact URL for getdown artifacts
+    getdown_channel_base = bamboo_channelbase
+    getdown_channel_name = bamboo_planKey + '/'+JAVA_VERSION
+    getdown_app_base = bamboo_channelbase + '/'+ bamboo_planKey + bamboo_getdown_channel_suffix + '/'+JAVA_VERSION
     getdown_app_dir = getdown_app_dir_alt
     buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile
     break
@@ -638,7 +641,7 @@ 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'
@@ -1180,57 +1183,61 @@ task sourceDist (type: Tar) {
   
   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  {
@@ -1238,5 +1245,5 @@ task helppages  {
   dependsOn pubhtmlhelp
   
   inputs.dir("$classes/$helpDir")
-  outputs.file("build/distribution/help/helpTOC.html")
+  outputs.dir("$helpOutputDir")
 }

diff --git a/gradle.properties b/gradle.properties
index 6605fa9..2dbdad3 100644 (file)
--- 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
@@ -135,3 +135,8 @@ getdown_install_dir = install
 getdown_rsync_dest = /Volumes/jalview/docroot/getdown
 reportRsyncCommand =
 RUNRSYNC=false
+
+bamboo_channelbase = https://builds.jalview.org/browse
+bamboo_planKey = 
+bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-channel
+ 
\ No newline at end of file

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 27a1a68..e00d390 100644 (file)
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -49,7 +49,7 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
     </em><br />
     <br /></li>
     <li>Jalview standalone executable Jar<pre>
-        &lt;Path to Java home&gt;/bin/java -jar %lt;Path to Jalview Jar&gt;/jalview-all-1.8.jar -open myalignment.fa</pre></li>
+        &lt;Path to Java home&gt;/bin/java -jar &lt;Path to Jalview Jar&gt;/jalview-all-1.8.jar -open myalignment.fa</pre></li>
   </ul>
   <p>
     If you have installed Jalview via <em>conda</em> or another package

diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html
index 8661860..27742b3 100644 (file)
--- a/help/help/html/features/jvlfiles.html
+++ b/help/help/html/features/jvlfiles.html
@@ -62,9 +62,9 @@ jalview.apparg=Clustal
 # 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/
+appbase=http://www.jalview.org/getdown/archive/2_10_5/
 </pre>
   For security, the Jalview application will only allow
-  <em>appbase</em> URLs from www.jalview.org, or your local file system.
+  <em>appbase</em> URLs from www.jalview.org.
 </body>
 </html>

diff --git a/lib/.cvsignore b/lib/.cvsignore
deleted file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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
deleted file mode 100644 (file)
index 7b5c27b..0000000
Binary files a/lib/VAqua5-patch.jar and /dev/null differ

diff --git a/lib/apache-mime4j-0.6.jar b/lib/apache-mime4j-0.6.jar
deleted file mode 100644 (file)
index 1d2282c..0000000
Binary files a/lib/apache-mime4j-0.6.jar and /dev/null differ

diff --git a/lib/axis.jar b/lib/axis.jar
deleted file mode 100755 (executable)
index 90bb798..0000000
Binary files a/lib/axis.jar and /dev/null differ

diff --git a/lib/biojava-core-4.1.0.jar b/lib/biojava-core-4.1.0.jar
deleted file mode 100644 (file)
index 5a09c1f..0000000
Binary files a/lib/biojava-core-4.1.0.jar and /dev/null differ

diff --git a/lib/biojava-ontology-4.1.0.jar b/lib/biojava-ontology-4.1.0.jar
deleted file mode 100644 (file)
index 80737d5..0000000
Binary files a/lib/biojava-ontology-4.1.0.jar and /dev/null differ

diff --git a/lib/commons-codec-1.3.jar b/lib/commons-codec-1.3.jar
deleted file mode 100644 (file)
index 957b675..0000000
Binary files a/lib/commons-codec-1.3.jar and /dev/null differ

diff --git a/lib/commons-compress-1.18.jar b/lib/commons-compress-1.18.jar
deleted file mode 100644 (file)
index e401046..0000000
Binary files a/lib/commons-compress-1.18.jar and /dev/null differ

diff --git a/lib/commons-discovery.jar b/lib/commons-discovery.jar
deleted file mode 100755 (executable)
index b885548..0000000
Binary files a/lib/commons-discovery.jar and /dev/null differ

diff --git a/lib/commons-logging-1.1.1.jar b/lib/commons-logging-1.1.1.jar
deleted file mode 100644 (file)
index 1deef14..0000000
Binary files a/lib/commons-logging-1.1.1.jar and /dev/null differ

diff --git a/lib/getdown-core.jar b/lib/getdown-core.jar
deleted file mode 100644 (file)
index 3e811b2..0000000
Binary files a/lib/getdown-core.jar and /dev/null differ

diff --git a/lib/gmbal-api-only-MODULE.jar b/lib/gmbal-api-only-MODULE.jar
deleted file mode 100644 (file)
index 06a5fcc..0000000
Binary files a/lib/gmbal-api-only-MODULE.jar and /dev/null differ

diff --git a/lib/groovy-2.5.6.jar b/lib/groovy-2.5.6.jar
deleted file mode 100644 (file)
index 3a4edfa..0000000
Binary files a/lib/groovy-2.5.6.jar and /dev/null differ

diff --git a/lib/groovy-console-2.5.6.jar b/lib/groovy-console-2.5.6.jar
deleted file mode 100644 (file)
index e18e426..0000000
Binary files a/lib/groovy-console-2.5.6.jar and /dev/null differ

diff --git a/lib/htsjdk-2.12.0.jar b/lib/htsjdk-2.12.0.jar
deleted file mode 100644 (file)
index 1df12b2..0000000
Binary files a/lib/htsjdk-2.12.0.jar and /dev/null differ

diff --git a/lib/httpclient-4.0.3.jar b/lib/httpclient-4.0.3.jar
deleted file mode 100644 (file)
index fd0d377..0000000
Binary files a/lib/httpclient-4.0.3.jar and /dev/null differ

diff --git a/lib/httpcore-4.0.1.jar b/lib/httpcore-4.0.1.jar
deleted file mode 100644 (file)
index 4aef35e..0000000
Binary files a/lib/httpcore-4.0.1.jar and /dev/null differ

diff --git a/lib/httpmime-4.0.3.jar b/lib/httpmime-4.0.3.jar
deleted file mode 100644 (file)
index 0dfd331..0000000
Binary files a/lib/httpmime-4.0.3.jar and /dev/null differ

diff --git a/lib/intervalstore-v1.0.jar b/lib/intervalstore-v1.0.jar
deleted file mode 100644 (file)
index 4f6101c..0000000
Binary files a/lib/intervalstore-v1.0.jar and /dev/null differ

diff --git a/lib/jabaws-min-client-2.2.0.jar b/lib/jabaws-min-client-2.2.0.jar
deleted file mode 100644 (file)
index 37426c3..0000000
Binary files a/lib/jabaws-min-client-2.2.0.jar and /dev/null differ

diff --git a/lib/java-json.jar b/lib/java-json.jar
deleted file mode 100755 (executable)
index 2f211e3..0000000
Binary files a/lib/java-json.jar and /dev/null differ

diff --git a/lib/jaxrpc.jar b/lib/jaxrpc.jar
deleted file mode 100755 (executable)
index ebd457b..0000000
Binary files a/lib/jaxrpc.jar and /dev/null differ

diff --git a/lib/jaxws-rt-java9.jar b/lib/jaxws-rt-java9.jar
deleted file mode 100644 (file)
index f380d18..0000000
Binary files a/lib/jaxws-rt-java9.jar and /dev/null differ

diff --git a/lib/jersey-client-1.19.jar b/lib/jersey-client-1.19.jar
deleted file mode 100644 (file)
index c9e0f56..0000000
Binary files a/lib/jersey-client-1.19.jar and /dev/null differ

diff --git a/lib/jersey-core-1.19.jar b/lib/jersey-core-1.19.jar
deleted file mode 100644 (file)
index 92feb63..0000000
Binary files a/lib/jersey-core-1.19.jar and /dev/null differ

diff --git a/lib/jersey-json-1.19.jar b/lib/jersey-json-1.19.jar
deleted file mode 100644 (file)
index b609411..0000000
Binary files a/lib/jersey-json-1.19.jar and /dev/null differ

diff --git a/lib/jetty-http-9.2.10.v20150310.jar b/lib/jetty-http-9.2.10.v20150310.jar
deleted file mode 100644 (file)
index 15aff51..0000000
Binary files a/lib/jetty-http-9.2.10.v20150310.jar and /dev/null differ

diff --git a/lib/jetty-io-9.2.10.v20150310.jar b/lib/jetty-io-9.2.10.v20150310.jar
deleted file mode 100644 (file)
index 56cee2c..0000000
Binary files a/lib/jetty-io-9.2.10.v20150310.jar and /dev/null differ

diff --git a/lib/jetty-server-9.2.10.v20150310.jar b/lib/jetty-server-9.2.10.v20150310.jar
deleted file mode 100644 (file)
index 815cb08..0000000
Binary files a/lib/jetty-server-9.2.10.v20150310.jar and /dev/null differ

diff --git a/lib/jetty-util-9.2.10.v20150310.jar b/lib/jetty-util-9.2.10.v20150310.jar
deleted file mode 100644 (file)
index fe27758..0000000
Binary files a/lib/jetty-util-9.2.10.v20150310.jar and /dev/null differ

diff --git a/lib/jfreesvg-2.1.jar b/lib/jfreesvg-2.1.jar
deleted file mode 100644 (file)
index 91d453c..0000000
Binary files a/lib/jfreesvg-2.1.jar and /dev/null differ

diff --git a/lib/jhall.jar b/lib/jhall.jar
deleted file mode 100755 (executable)
index ff08af0..0000000
Binary files a/lib/jhall.jar and /dev/null differ

diff --git a/lib/json_simple-1.1.jar b/lib/json_simple-1.1.jar
deleted file mode 100644 (file)
index f395f41..0000000
Binary files a/lib/json_simple-1.1.jar and /dev/null differ

diff --git a/lib/jsoup-1.8.1.jar b/lib/jsoup-1.8.1.jar
deleted file mode 100644 (file)
index ae717d4..0000000
Binary files a/lib/jsoup-1.8.1.jar and /dev/null differ

diff --git a/lib/jswingreader-0.3.jar b/lib/jswingreader-0.3.jar
deleted file mode 100644 (file)
index c632130..0000000
Binary files a/lib/jswingreader-0.3.jar and /dev/null differ

diff --git a/lib/libquaqua-8.0.jnilib.jar b/lib/libquaqua-8.0.jnilib.jar
deleted file mode 100644 (file)
index 79383b0..0000000
Binary files a/lib/libquaqua-8.0.jnilib.jar and /dev/null differ

diff --git a/lib/libquaqua64-8.0.jnilib.jar b/lib/libquaqua64-8.0.jnilib.jar
deleted file mode 100644 (file)
index efb46a4..0000000
Binary files a/lib/libquaqua64-8.0.jnilib.jar and /dev/null differ

diff --git a/lib/log4j-to-slf4j-2.0-rc2.jar b/lib/log4j-to-slf4j-2.0-rc2.jar
deleted file mode 100644 (file)
index 4bbf54a..0000000
Binary files a/lib/log4j-to-slf4j-2.0-rc2.jar and /dev/null differ

diff --git a/lib/mail-MODULE.jar b/lib/mail-MODULE.jar
deleted file mode 100644 (file)
index 367ca9e..0000000
Binary files a/lib/mail-MODULE.jar and /dev/null differ

diff --git a/lib/miglayout-4.0-swing.jar b/lib/miglayout-4.0-swing.jar
deleted file mode 100644 (file)
index 7b6a22c..0000000
Binary files a/lib/miglayout-4.0-swing.jar and /dev/null differ

diff --git a/lib/quaqua-filechooser-only-8.0.jar b/lib/quaqua-filechooser-only-8.0.jar
deleted file mode 100644 (file)
index 182e0da..0000000
Binary files a/lib/quaqua-filechooser-only-8.0.jar and /dev/null differ

diff --git a/lib/regex.jar b/lib/regex.jar
deleted file mode 100755 (executable)
index 3e29d22..0000000
Binary files a/lib/regex.jar and /dev/null differ

diff --git a/lib/saaj-impl.jar b/lib/saaj-impl.jar
deleted file mode 100644 (file)
index 7eda25c..0000000
Binary files a/lib/saaj-impl.jar and /dev/null differ

diff --git a/lib/slf4j-api-1.7.7.jar b/lib/slf4j-api-1.7.7.jar
deleted file mode 100644 (file)
index b28e220..0000000
Binary files a/lib/slf4j-api-1.7.7.jar and /dev/null differ

diff --git a/lib/slf4j-log4j12-1.7.7.jar b/lib/slf4j-log4j12-1.7.7.jar
deleted file mode 100644 (file)
index 12c804e..0000000
Binary files a/lib/slf4j-log4j12-1.7.7.jar and /dev/null differ

diff --git a/lib/vamsas-client.jar b/lib/vamsas-client.jar
deleted file mode 100644 (file)
index 2634954..0000000
Binary files a/lib/vamsas-client.jar and /dev/null differ

diff --git a/lib/xercesImpl.jar b/lib/xercesImpl.jar
deleted file mode 100644 (file)
index 0aaa990..0000000
Binary files a/lib/xercesImpl.jar and /dev/null differ

diff --git a/src/jalview/fts/core/DecimalFormatTableCellRenderer.java b/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
index 8a8e7ab..2453742 100644 (file)
--- a/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
+++ b/src/jalview/fts/core/DecimalFormatTableCellRenderer.java
@@ -61,16 +61,15 @@ public class DecimalFormatTableCellRenderer extends DefaultTableCellRenderer
     super.setHorizontalAlignment(JLabel.RIGHT);
   }
 
+  /**
+   * Adapts the default method to ensure that double values are formatted for
+   * display
+   */
   @Override
   public Component getTableCellRendererComponent(JTable table, Object value,
           boolean isSelected, boolean hasFocus, int row, int column)
   {
-    if (value == null)
-    {
-      return null;
-    }
-
-    value = formatter.format(value);
+    value = value == null ? "" : formatter.format(value);
 
     return super.getTableCellRendererComponent(table, value, isSelected,
             hasFocus, row, column);

diff --git a/utils/publishHelp.xml b/utils/publishHelp.xml
index 17ef9e2..c626a21 100644 (file)
--- a/utils/publishHelp.xml
+++ b/utils/publishHelp.xml
@@ -1,7 +1,7 @@
 <project name="Publish Help Webpages for Jalview" default="pubhtmlhelp">
 
 <target name="pubhtmlhelp">
-  <property name="appletHelpDir" value="../build/distribution/help"/>
+  <property name="appletHelpDir" value="../build/distributions/help"/>
         <!-- finally, publish the help files -->
         <javac srcdir="." destdir="." includes="help2Website.java"/>
         <java fork="true" dir="${helpBuildDir}" classpath="." classname="help2Website"/>