From: Ben Soares <bsoares@dundee.ac.uk>
Date: Wed, 19 Feb 2020 16:40:09 +0000 (+0000)
Subject: Merge branch 'develop' into improvement/JAL-3449_add_install4j_installer_getdown_vers... 
X-Git-Tag: Develop-2_11_2_0-d20201215~80^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56f4324f197ac20954ce304d103ff26f1dda58e2;hp=699fe86b373eb59aa5e082ccfe313994204c8e34;p=jalview.git

Merge branch 'develop' into improvement/JAL-3449_add_install4j_installer_getdown_versions_to_jalview_console.2
---

diff --git a/build.gradle b/build.gradle
index 9dae53a..36b75fd 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1387,33 +1387,47 @@ task sourceDist(type: Tar) {
   
   into project.name
 
-  def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
-  ,".*"
-  ,"benchmarking/*"
-  ,"**/.*"
-  ,"*.class"
-  ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
-  ,"*locales/**",
-  ,"utils/InstallAnywhere"] 
-  def PROCESS_FILES=[   "AUTHORS",
-  "CITATION",
-  "FEATURETODO",
-  "JAVA-11-README",
-  "FEATURETODO",
-  "LICENSE",
-  "**/README",
-  "RELEASE",
-  "THIRDPARTYLIBS","TESTNG",
-  "build.gradle",
-  "gradle.properties",
-  "**/*.java",
-  "**/*.html",
-  "**/*.xml",
-  "**/*.gradle",
-  "**/*.groovy",
-  "**/*.properties",
-  "**/*.perl",
-  "**/*.sh"]
+  def EXCLUDE_FILES=[
+    "build/*",
+    "bin/*",
+    "test-output/",
+    "test-reports",
+    "tests",
+    "clover*/*",
+    ".*",
+    "benchmarking/*",
+    "**/.*",
+    "*.class",
+    "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
+    "*locales/**",
+    "utils/InstallAnywhere",
+    "**/*.log",
+  ] 
+  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",
+  ]
+  def INCLUDE_FILES=[
+    ".settings/org.eclipse.jdt.core.jalview.prefs",
+  ]
 
   from(jalviewDir) {
     exclude (EXCLUDE_FILES)
@@ -1439,14 +1453,17 @@ task sourceDist(type: Tar) {
     exclude (getdown_website_dir)
 
     // exluding these as not using jars as modules yet
-    exclude ("${j11modDir}/**/*.jar")
-  }
-  //  from (jalviewDir) {
-  //    // explicit includes for stuff that seemed to not get included
-  //    include(fileTree("test/**/*."))
-  //    exclude(EXCLUDE_FILES)
-  //    exclude(PROCESS_FILES)
-  //  }
+    exclude ("$j11modDir/**/*.jar")
+  }
+  from(jalviewDir) {
+    include(INCLUDE_FILES)
+  }
+//  from (jalviewDir) {
+//    // explicit includes for stuff that seemed to not get included
+//    include(fileTree("test/**/*."))
+//    exclude(EXCLUDE_FILES)
+//    exclude(PROCESS_FILES)
+//  }
 }
 
 
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index bb4b386..d7f3ee1 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -58,17 +58,21 @@ li:before {
     <tr>
       <td width="60" align="center" nowrap><strong><a
           name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
-          <em>16/2/2020</em></strong></td>
+          <em>25/2/2020</em></strong></td>
       <td align="left" valign="top">
         <ul>
           <li>
-            <!-- JAL-3376 -->Record &quot;fixed column&quot; values POS, ID, QUAL, FILTER from VCF as Feature Attributes
+            <!-- JAL-3376 -->Record &quot;fixed column&quot; values POS,
+            ID, QUAL, FILTER from VCF as Feature Attributes
           </li>
           <li>
-            <!-- JAL-3375 -->More robust VCF numeric data field validation
-            while parsing (e.g. AF* attributes)
+            <!-- JAL-3375 -->More robust VCF numeric data field
+            validation while parsing (e.g. AF* attributes)
+          </li>
+          <li>
+            <!-- JAL-3538 -->Font anti-aliasing in alignment views
+            enabled by default
           </li>
-          
           <li>
           <!-- JAL -->
           </li>
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 61b0d1b..91af323 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -208,7 +208,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 9754e0d..0d7d1b4 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -253,7 +253,7 @@ public class Preferences extends GPreferences
     fontStyleCB.setSelectedItem(
             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
     scaleProteinToCdna
             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
@@ -401,7 +401,7 @@ public class Preferences extends GPreferences
     doReset.addActionListener(onReset);
 
     // filter to display only custom urls
-    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
     {
       @Override
       public boolean include(