From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 17 Sep 2020 17:47:10 +0000 (+0100)
Subject: Merge branch 'releases/Release_2_11_1_Branch'
X-Git-Tag: Release_2_11_2_2~1^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c6874080bf8a7ddf943200597e23a344c946a808;hp=2b6a74893883a246d40a99a2e981ef6cad4fed5a;p=jalview.git

Merge branch 'releases/Release_2_11_1_Branch'
---

diff --git a/RELEASE b/RELEASE
index 5a89907..3600be2 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_1_Branch
-jalview.version=2.11.1.0
+jalview.version=2.11.1.1
diff --git a/build.gradle b/build.gradle
index f7233f1..68d0c04 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,3 +1,6 @@
+/* Convention for properties.  Read from gradle.properties, use lower_case_underlines for property names.
+ * For properties set within build.gradle, use camelCaseNoSpace.
+ */
 import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
 import org.gradle.plugins.ide.eclipse.model.Output
@@ -13,9 +16,6 @@ buildscript {
     mavenCentral()
     mavenLocal()
   }
-  dependencies {
-    classpath 'org.openclover:clover:4.4.1'
-  }
 }
 
 
@@ -130,21 +130,25 @@ ext {
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
   resourceDir = string("${jalviewDir}/${resource_dir}")
   bareTestSourceDir = string(test_source_dir)
-  testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+  testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
-  // clover
-  cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
-  cloverDb = string("${buildDir}/clover/clover.db")
   classesDir = string("${jalviewDir}/${classes_dir}")
-  if (clover.equals("true")) {
-    use_clover = true
-    classesDir = string("${buildDir}/${cloverClassesDir}")
-  } else {
-    use_clover = false
-    classesDir = string("${jalviewDir}/${classes_dir}")
-  }
 
-  classes = classesDir
+  // clover
+  useClover = clover.equals("true")
+  cloverBuildDir = "${buildDir}/clover"
+  cloverInstrDir = file("${cloverBuildDir}/clover-instr")
+  cloverClassesDir = file("${cloverBuildDir}/clover-classes")
+  cloverReportDir = file("${buildDir}/reports/clover")
+  cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
+  cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
+  //cloverTestClassesDir = cloverClassesDir
+  cloverDb = string("${cloverBuildDir}/clover.db")
+
+  resourceClassesDir = useClover ? cloverClassesDir : classesDir
+
+  testSourceDir = useClover ? cloverTestInstrDir : testDir
+  testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
 
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   buildDist = true
@@ -173,8 +177,8 @@ ext {
     getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     jvlChannelName += "_${getdownChannelName}"
     // automatically add the test group Not-bamboo for exclusion 
-    if ("".equals(testngExcludedGroups)) { 
-      testngExcludedGroups = "Not-bamboo"
+    if ("".equals(testng_excluded_groups)) { 
+      testng_excluded_groups = "Not-bamboo"
     }
     install4jExtraScheme = "jalviewb"
     break
@@ -192,10 +196,10 @@ ext {
     getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
       buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
@@ -207,10 +211,10 @@ ext {
     getdownChannelName = string("archive/${JALVIEW_VERSION}")
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = file(getdownWebsiteDir).toURI().toString()
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
       buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
@@ -340,6 +344,7 @@ ext {
     //libDir = j8libDir
     libDir = j11libDir
     libDistDir = j8libDir
+    digestonlyDir = j8digestonlyDir
     compile_source_compatibility = 1.8
     compile_target_compatibility = 1.8
     // these are getdown.txt properties defined dependent on the JAVA_VERSION
@@ -353,6 +358,7 @@ ext {
     JAVA_INTEGER_VERSION = string("11")
     libDir = j11libDir
     libDistDir = j11libDir
+    digestonlyDir = j11digestonlyDir
     compile_source_compatibility = 11
     compile_target_compatibility = 11
     getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
@@ -409,8 +415,8 @@ ext {
 
 
 
-  buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+  helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
   helpParentDir = string("${jalviewDir}/${help_parent_dir}")
   helpSourceDir = string("${helpParentDir}/${help_dir}")
 
@@ -453,10 +459,9 @@ sourceSets {
       srcDirs += helpParentDir
     }
 
-    jar.destinationDir = file("${jalviewDir}/${packageDir}")
+    jar.destinationDir = file("${jalviewDir}/${package_dir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
-    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -464,18 +469,19 @@ sourceSets {
 
   clover {
     java {
-      srcDirs = [ cloverInstrDir ]
-      outputDir = file("${buildDir}/${cloverClassesDir}")
+      srcDirs cloverInstrDir
+      outputDir = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
-    compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
-    compileClasspath += files(sourceSets.main.java.outputDir)
-    compileClasspath += sourceSets.main.compileClasspath
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
+
+    compileClasspath = files( sourceSets.clover.java.outputDir )
+    //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
   }
@@ -483,41 +489,20 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file("${jalviewDir}/${testOutputDir}")
+      outputDir = file(testClassesDir)
     }
 
     resources {
-      srcDirs = sourceSets.main.resources.srcDirs
+      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-
-    if (use_clover) {
-      compileClasspath = sourceSets.clover.compileClasspath
-    } else {
-      compileClasspath += files(sourceSets.main.java.outputDir)
-    }
-
-    compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
+    compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
   }
-}
-
-
-// clover bits
-dependencies {
-  if (use_clover) {
-    cloverCompile 'org.openclover:clover:4.4.1'
-    testCompile 'org.openclover:clover:4.4.1'
-  }
-}
 
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
 }
 
 
@@ -656,61 +641,209 @@ eclipse {
 }
 
 
-task cloverInstr {
-  // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-  outputs.dir cloverInstrDir
+// clover bits
 
+
+task cleanClover {
   doFirst {
-    delete cloverInstrDir
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-d",
-      cloverInstrDir.getPath(),
-    ]
-    argsList.addAll(
-      inputs.files.files.collect(
-        { file -> file.absolutePath }
-      )
+    delete cloverBuildDir
+    delete cloverReportDir
+  }
+}
+
+
+task cloverInstrJava(type: JavaExec) {
+  group = "Verification"
+  description = "Create clover instrumented source java files"
+
+  dependsOn cleanClover
+
+  inputs.files(sourceSets.main.allJava)
+  outputs.dir(cloverInstrDir)
+
+  //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+  classpath = sourceSets.clover.compileClasspath
+  main = "com.atlassian.clover.CloverInstr"
+
+  def argsList = [
+    "--encoding",
+    "UTF-8",
+    "--initstring",
+    cloverDb,
+    "--destdir",
+    cloverInstrDir.getPath(),
+  ]
+  def srcFiles = sourceSets.main.allJava.files
+  argsList.addAll(
+    srcFiles.collect(
+      { file -> file.absolutePath }
     )
-    String[] args = argsList.toArray()
-    println("About to instrument "+args.length +" files")
-    com.atlassian.clover.CloverInstr.mainImpl(args)
+  )
+  args argsList.toArray()
+
+  doFirst {
+    delete cloverInstrDir
+    println("Clover: About to instrument "+srcFiles.size() +" files")
+  }
+}
+
+
+task cloverInstrTests(type: JavaExec) {
+  group = "Verification"
+  description = "Create clover instrumented source test files"
+
+  dependsOn cleanClover
+
+  inputs.files(testDir)
+  outputs.dir(cloverTestInstrDir)
+
+  classpath = sourceSets.clover.compileClasspath
+  main = "com.atlassian.clover.CloverInstr"
+
+  def argsList = [
+    "--encoding",
+    "UTF-8",
+    "--initstring",
+    cloverDb,
+    "--srcdir",
+    testDir,
+    "--destdir",
+    cloverTestInstrDir.getPath(),
+  ]
+  args argsList.toArray()
+
+  doFirst {
+    delete cloverTestInstrDir
+    println("Clover: About to instrument test files")
   }
 }
 
 
+task cloverInstr {
+  group = "Verification"
+  description = "Create clover instrumented all source files"
+
+  dependsOn cloverInstrJava
+  dependsOn cloverInstrTests
+}
+
+
 cloverClasses.dependsOn cloverInstr
 
 
-task cloverReport {
+task cloverConsoleReport(type: JavaExec) {
   group = "Verification"
-  description = "Creates the Clover report"
-  inputs.dir "${buildDir}/clover"
-  outputs.dir "${reportsDir}/clover"
+  description = "Creates clover console report"
+
   onlyIf {
     file(cloverDb).exists()
   }
-  doFirst {
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover"
-    ]
-    String[] args = argsList.toArray()
-    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-
-    // and generate ${reportsDir}/clover/clover.xml
-    args = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover/clover.xml"
-    ].toArray()
-    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+
+  inputs.dir cloverClassesDir
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.console.ConsoleReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
+  }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--unittests"
+  ]
+
+  args argsList.toArray()
+}
+
+
+task cloverHtmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover HTML report"
+
+  onlyIf {
+    file(cloverDb).exists()
+  }
+
+  def cloverHtmlDir = cloverReportDir
+  inputs.dir cloverClassesDir
+  outputs.dir cloverHtmlDir
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
+  }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outputdir",
+    cloverHtmlDir
+  ]
+
+  if (cloverreport_html_options.length() > 0) {
+    argsList += cloverreport_html_options.split(" ")
   }
+
+  args argsList.toArray()
+}
+
+
+task cloverXmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover XML report"
+
+  onlyIf {
+    file(cloverDb).exists()
+  }
+
+  def cloverXmlFile = "${cloverReportDir}/clover.xml"
+  inputs.dir cloverClassesDir
+  outputs.file cloverXmlFile
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+  if (cloverreport_mem.length() > 0) {
+    maxHeapSize = cloverreport_mem
+  }
+  if (cloverreport_jvmargs.length() > 0) {
+    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
+  }
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outfile",
+    cloverXmlFile
+  ]
+
+  if (cloverreport_xml_options.length() > 0) {
+    argsList += cloverreport_xml_options.split(" ")
+  }
+
+  args argsList.toArray()
+}
+
+
+task cloverReport {
+  group = "Verification"
+  description = "Creates clover reports"
+
+  dependsOn cloverXmlReport
+  dependsOn cloverHtmlReport
 }
 
 
@@ -722,15 +855,7 @@ compileCloverJava {
     options.compilerArgs += additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
-}
-
-
-task cleanClover {
-  doFirst {
-    delete cloverInstrDir
-    delete cloverDb
-  }
+  //classpath += configurations.cloverRuntime
 }
 // end clover bits
 
@@ -748,12 +873,6 @@ compileJava {
 
 
 compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
@@ -832,8 +951,8 @@ task cleanBuildingHTML(type: Delete) {
 
 task convertBuildingMD(type: Exec) {
   dependsOn cleanBuildingHTML
-  def buildingMD = "${jalviewDir}/${docDir}/building.md"
-  def css = "${jalviewDir}/${docDir}/github.css"
+  def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+  def css = "${jalviewDir}/${doc_dir}/github.css"
 
   def pandoc = null
   pandoc_exec.split(",").each {
@@ -875,8 +994,8 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classesDir}/${docDir}"
-  from fileTree("${jalviewDir}/${docDir}")
+  def syncDir = "${resourceClassesDir}/${doc_dir}"
+  from fileTree("${jalviewDir}/${doc_dir}")
   into syncDir
 
 }
@@ -884,7 +1003,7 @@ task syncDocs(type: Sync) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${classesDir}/${help_dir}"
+  def outputDir = "${resourceClassesDir}/${help_dir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -912,7 +1031,7 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
+  def syncDir = "${resourceClassesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
@@ -921,7 +1040,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
-  into "${classesDir}"
+  into "${resourceClassesDir}"
   preserve {
     include "**"
   }
@@ -938,18 +1057,17 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  dependsOn compileJava
-  if (use_clover) {
-    dependsOn cloverInstr
-  }
+  //dependsOn compileJava ////? DELETE
 
-  if (use_clover) {
-    print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+  if (useClover) {
+    dependsOn cloverClasses
+   } else { //?
+     dependsOn compileJava //?
   }
 
   useTestNG() {
-    includeGroups testngGroups
-    excludeGroups testngExcludedGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
@@ -958,10 +1076,25 @@ test {
 
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
+  def testLaf = project.findProperty("test_laf")
+  if (testLaf != null) {
+    println("Setting Test LaF to '${testLaf}'")
+    systemProperty "laf", testLaf
+  }
+  def testHiDPIScale = project.findProperty("test_HiDPIScale")
+  if (testHiDPIScale != null) {
+    println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+    systemProperty "sun.java2d.uiScale", testHiDPIScale
+  }
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args
 
+  doFirst {
+    if (useClover) {
+      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+    }
+  }
 }
 
 
@@ -987,22 +1120,22 @@ task buildIndices(type: JavaExec) {
 
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
-  classpath = files("${jalviewDir}/${utilsDir}")
-  destinationDir = file("${jalviewDir}/${utilsDir}")
-  source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
-
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
-  outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
+  classpath = files("${jalviewDir}/${utils_dir}")
+  destinationDir = file("${jalviewDir}/${utils_dir}")
+  source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+  outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
 }
 
 
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
 
-  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
-  classpath = files("${jalviewDir}/${utilsDir}")
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+  classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   args = [ "${classesDir}/${help_dir}", "-nointernet" ]
@@ -1023,12 +1156,12 @@ task linkCheck(type: JavaExec) {
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
-ant.importBuild "${utilsDir}/publishHelp.xml"
+ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
 task cleanPackageDir(type: Delete) {
   doFirst {
-    delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+    delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
   }
 }
 
@@ -1038,13 +1171,13 @@ jar {
   dependsOn createBuildProperties
 
   manifest {
-    attributes "Main-Class": mainClass,
+    attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
     "Application-Name": "Jalview Desktop",
     "Codebase": application_codebase
   }
 
-  destinationDir = file("${jalviewDir}/${packageDir}")
+  destinationDir = file("${jalviewDir}/${package_dir}")
   archiveName = rootProject.name+".jar"
 
   exclude "cache*/**"
@@ -1054,20 +1187,20 @@ jar {
   exclude "**/*.jar.*"
 
   inputs.dir(classesDir)
-  outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
+  outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
 }
 
 
 task copyJars(type: Copy) {
   from fileTree(dir: classesDir, include: "**/*.jar").files
-  into "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
 }
 
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
-  into "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
   preserve {
     include jar.archiveName
   }
@@ -1083,7 +1216,7 @@ task makeDist {
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
-  outputs.dir("${jalviewDir}/${packageDir}")
+  outputs.dir("${jalviewDir}/${package_dir}")
 }
 
 
@@ -1104,7 +1237,7 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
-  mainClassName = shadowJarMainClass
+  mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
@@ -1196,7 +1329,7 @@ task getdownWebsite() {
     }
 
     def codeFiles = []
-    fileTree(file(packageDir)).each{ f ->
+    fileTree(file(package_dir)).each{ f ->
       if (f.isDirectory()) {
         def files = fileTree(dir: f, include: ["*"]).getFiles()
         codeFiles += files
@@ -1214,6 +1347,16 @@ task getdownWebsite() {
       }
     }
 
+    fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f ->
+      def name = f.getName()
+      def line = "digestonly = ${getdownAppDistDir}/${name}\n"
+      getdownTextString += line
+      copy {
+        from f.getPath()
+        into getdownAppDir
+      }
+    }
+    
     // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
     /*
     if (JAVA_VERSION.equals("11")) {
@@ -1233,7 +1376,11 @@ task getdownWebsite() {
     // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
     //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
     getdownTextString += "resource = ${getdown_launcher_new}\n"
-    getdownTextString += "class = ${mainClass}\n"
+    getdownTextString += "class = ${main_class}\n"
+    /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version
+     * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
+     * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
+     */
 
     def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
@@ -1260,7 +1407,7 @@ task getdownWebsite() {
       copy {
         from getdown_txt
         from getdownLauncher
-        from "${getdownWebsiteDir}/${getdown_build_properties}"
+        from "${getdownAppDir}/${getdown_build_properties}"
         if (file(getdownLauncher).getName() != getdown_launcher) {
           rename(file(getdownLauncher).getName(), getdown_launcher)
         }
@@ -1291,7 +1438,7 @@ task getdownWebsite() {
   }
 
   if (buildDist) {
-    inputs.dir("${jalviewDir}/${packageDir}")
+    inputs.dir("${jalviewDir}/${package_dir}")
   }
   outputs.dir(getdownWebsiteDir)
   outputs.dir(getdownFilesDir)
diff --git a/doc/building.md b/doc/building.md
index ad19979..855f966 100644
--- a/doc/building.md
+++ b/doc/building.md
@@ -276,8 +276,8 @@ although without the many and compelling benefits of the `getdown` launcher.
 We have made significant customisations to the `getdown` launcher which you can find 
 in `getdown/src/getdown`.
 
-> You don't need to build this afresh as the required `gradle-core.jar` 
-and `gradle-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then 
+> You don't need to build this afresh as the required `getdown-core.jar` 
+and `getdown-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then 
 you'll need a working Maven and also a Java 8 JDK.  Ensure the Java 8 `javac` is forefront 
 in your path and do
 >
@@ -285,9 +285,9 @@ in your path and do
 >cd getdown/src/getdown
 >mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
 >```
-> and you will find the required `.jar` files in `core/target/gradle-core-XXX.jar` 
-and `launcher/target/gradle-launcher-XXX.jar`.  The `gradle-core.jar` should then be copied 
-to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `gradle-launcher.jar` only 
+> and you will find the required `.jar` files in `core/target/getdown-core-XXX.jar` 
+and `launcher/target/getdown-launcher-XXX.jar`.  The `getdown-core.jar` should then be copied 
+to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `getdown-launcher.jar` only 
 needs to be copied to `getdown/lib`.
 >
 >The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting. 
@@ -318,6 +318,7 @@ java -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview
 getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`" 
 is defined here).
 
+The command line sequence for building and relocating the getdown artifacts can be executed as a script via `getdown/src/getdown/mvn_cmd`. Please make sure this script is kept up to date should the getdown build instructions change.
 
 ### Running tests
 
diff --git a/getdown/lib/FJVL_VERSION b/getdown/lib/FJVL_VERSION
index e7a1de7..07a2dfc 100644
--- a/getdown/lib/FJVL_VERSION
+++ b/getdown/lib/FJVL_VERSION
@@ -1 +1 @@
-1.8.3-1.2.4_FJVL
+1.8.3-1.2.9_FJVL
diff --git a/getdown/lib/JVL_VERSION b/getdown/lib/JVL_VERSION
index 756f4bd..b971e64 100644
--- a/getdown/lib/JVL_VERSION
+++ b/getdown/lib/JVL_VERSION
@@ -1 +1 @@
-1.8.3-1.2.4_JVL
+1.8.3-1.2.9_JVL
diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar
index 9c0f96e..c927dae 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
index cfa96f3..31df1e6 100644
Binary files a/getdown/lib/getdown-launcher-local.jar and b/getdown/lib/getdown-launcher-local.jar differ
diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index 2f8baa7..d0e5e35 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 8dcef42..c180d5f 100644
--- a/getdown/src/getdown/ant/pom.xml
+++ b/getdown/src/getdown/ant/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.4_FJVL</version>
+    <version>1.8.3-1.2.9_FJVL</version>
   </parent>
 
   <artifactId>getdown-ant</artifactId>
diff --git a/getdown/src/getdown/core/pom.xml b/getdown/src/getdown/core/pom.xml
index 2d0e89a..dd387b1 100644
--- a/getdown/src/getdown/core/pom.xml
+++ b/getdown/src/getdown/core/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.4_FJVL</version>
+    <version>1.8.3-1.2.9_FJVL</version>
   </parent>
 
   <artifactId>getdown-core</artifactId>
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 fd53c79..313a690 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
@@ -27,6 +27,7 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.zip.GZIPInputStream;
 
+import jalview.bin.HiDPISetting;
 import jalview.bin.MemorySetting;
 //import com.install4j.api.launcher.Variables;
 
@@ -353,6 +354,11 @@ public class Application
         return _resources;
     }
 
+    public List<Resource> getDigestOnly ()
+    {
+        return _digestonly;
+    }
+
     /**
      * Returns the digest of the given {@code resource}.
      */
@@ -771,6 +777,7 @@ public class Application
         // clear our arrays as we may be reinitializing
         _codes.clear();
         _resources.clear();
+        _digestonly.clear();
         _auxgroups.clear();
         _jvmargs.clear();
         _appargs.clear();
@@ -791,6 +798,8 @@ public class Application
         parseResources(config, "presource", Resource.PRELOAD, _resources);
         parseResources(config, "nresource", Resource.NATIVE, _resources);
 
+        parseResources(config, "digestonly", Resource.NORMAL, _digestonly);
+        
         // parse our auxiliary resource groups
         for (String auxgroup : config.getList("auxgroups")) {
             ArrayList<Resource> codes = new ArrayList<>();
@@ -1071,6 +1080,13 @@ public class Application
         args.add("-Dinstaller_template_version=" + System.getProperty("installer_template_version"));
         args.add("-Dlauncher_version=" + Build.version());
 
+        // set HiDPI property if wanted
+        String scalePropertyArg = HiDPISetting.getScalePropertyArg();
+        if (scalePropertyArg != null)
+        {
+          args.add(scalePropertyArg);
+        }
+
         // set the native library path if we have native resources
         // @TODO optional getdown.txt parameter to set addCurrentLibraryPath to true or false?
         ClassPath javaLibPath = PathBuilder.buildLibsPath(this, true);
@@ -1411,6 +1427,8 @@ public class Application
             clearValidationMarkers();
             // if the new copy validates, reinitialize ourselves; otherwise report baffling hoseage
             if (_digest.validateResource(crsrc, null)) {
+                // unset _initialisedConfig so new file is initialised
+                _initialisedConfig = null;
                 init(true);
             } else {
                 log.warning(CONFIG_FILE + " failed to validate even after redownloading. " +
@@ -2066,6 +2084,7 @@ public class Application
 
     protected List<Resource> _codes = new ArrayList<>();
     protected List<Resource> _resources = new ArrayList<>();
+    protected List<Resource> _digestonly = new ArrayList<>();
 
     protected boolean _useCodeCache;
     protected int _codeCacheRetentionDays;
diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/tools/Digester.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/tools/Digester.java
index b04a653..8d96024 100644
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/tools/Digester.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/tools/Digester.java
@@ -81,6 +81,7 @@ public class Digester
         rsrcs.add(app.getConfigResource());
         rsrcs.addAll(app.getCodeResources());
         rsrcs.addAll(app.getResources());
+        rsrcs.addAll(app.getDigestOnly());
         for (Application.AuxGroup ag : app.getAuxGroups()) {
             rsrcs.addAll(ag.codes);
             rsrcs.addAll(ag.rsrcs);
diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/GetMemory.java b/getdown/src/getdown/core/src/main/java/jalview/bin/GetMemory.java
index e89bffb..b01dfb8 100644
--- a/getdown/src/getdown/core/src/main/java/jalview/bin/GetMemory.java
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/GetMemory.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin;
 
 import java.lang.management.ManagementFactory;
diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
new file mode 100644
index 0000000..497900f
--- /dev/null
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
@@ -0,0 +1,180 @@
+package jalview.bin;
+
+import java.awt.HeadlessException;
+import java.awt.Toolkit;
+
+public class HiDPISetting
+{
+  private static final int hidpiThreshold = 160;
+
+  private static final int hidpiMultiThreshold = 240;
+
+  private static final int bigScreenThreshold = 1400;
+
+  private static final String scalePropertyName = "sun.java2d.uiScale";
+
+  private static final boolean isLinux;
+
+  // private static final boolean isAMac;
+
+  // private static final boolean isWindows;
+
+  public static final String setHiDPIPropertyName = "setHiDPI";
+
+  public static final String setHiDPIScalePropertyName = "setHiDPIScale";
+
+  private static boolean setHiDPI = false;
+
+  private static int setHiDPIScale = 0;
+
+  public static int dpi = 0;
+
+  public static int mindimension = 0;
+
+  public static int width = 0;
+
+  public static int scale = 0;
+
+  private static boolean doneInit = false;
+
+  private static boolean allowScalePropertyArg = false;
+
+  static
+  {
+    String system = System.getProperty("os.name") == null ? null
+            : System.getProperty("os.name").toLowerCase();
+    if (system != null)
+    {
+      isLinux = system.indexOf("linux") > -1;
+      // isAMac = system.indexOf("mac") > -1;
+      // isWindows = system.indexOf("windows") > -1;
+    }
+    else
+    {
+      isLinux = false;
+      // isAMac = isWindows = false;
+    }
+  }
+
+  private static void init()
+  {
+    if (doneInit)
+    {
+      return;
+    }
+
+    // get and use command line property values first
+    String setHiDPIProperty = System.getProperty(setHiDPIPropertyName);
+    setHiDPI = setHiDPIProperty != null
+            && setHiDPIProperty.equalsIgnoreCase("true");
+
+    String setHiDPIScaleProperty = System
+            .getProperty(setHiDPIScalePropertyName);
+    if (setHiDPIScaleProperty != null)
+    {
+      try
+      {
+        setHiDPIScale = Integer.parseInt(setHiDPIScaleProperty);
+      } catch (NumberFormatException e)
+      {
+        System.err.println(setHiDPIScalePropertyName + " property give ("
+                + setHiDPIScaleProperty + ") but not parseable as integer");
+      }
+    }
+    if (setHiDPI && setHiDPIScale > 0)
+    {
+      setHiDPIScale(setHiDPIScale);
+      return;
+    }
+
+    // check to see if the scale property has already been set by something else
+    // (e.g. the OS)
+    String existingProperty = System.getProperty(scalePropertyName);
+    if (existingProperty != null)
+    {
+      try
+      {
+        int existingPropertyVal = Integer.parseInt(existingProperty);
+        System.out.println("Existing " + scalePropertyName + " is "
+                + existingPropertyVal);
+        if (existingPropertyVal > 1)
+        {
+          setHiDPIScale(existingPropertyVal);
+          return;
+        }
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Could not convert property " + scalePropertyName
+                + " vale '" + existingProperty + "' to number");
+      }
+    }
+
+    // Try and auto guess a good scale based on reported DPI (not trustworthy)
+    // and screen resolution (more trustworthy)
+
+    // get screen dpi
+    try
+    {
+      dpi = Toolkit.getDefaultToolkit().getScreenResolution();
+    } catch (HeadlessException e)
+    {
+      System.err.println("Cannot get screen resolution: " + e.getMessage());
+    }
+
+    // try and get screen size height and width
+    try
+    {
+      int height = Toolkit.getDefaultToolkit().getScreenSize().height;
+      int width = Toolkit.getDefaultToolkit().getScreenSize().width;
+      // using mindimension in case of portrait screens
+      mindimension = Math.min(height, width);
+    } catch (HeadlessException e)
+    {
+      System.err.println(
+              "Cannot get screen size height and width:" + e.getMessage());
+    }
+
+    // attempt at a formula for scaling based on screen dpi and mindimension.
+    // scale will be an integer >=1. This formula is based on some testing and
+    // guesswork!
+
+    // scale based on reported dpi. if dpi>hidpiThreshold then scale=2+multiples
+    // of hidpiMultiThreshold (else scale=1)
+    // (e.g. dpi of 110 scales 1. dpi of 120 scales 2. dpi of 360 scales 3)
+    int dpiScale = (dpi - hidpiThreshold > 0)
+            ? 2 + ((dpi - hidpiThreshold) / hidpiMultiThreshold)
+            : 1;
+
+    int dimensionScale = 1 + (mindimension / bigScreenThreshold);
+
+    // choose larger of dimensionScale or dpiScale (most likely dimensionScale
+    // as dpiScale often misreported)
+    int autoScale = Math.max(dpiScale, dimensionScale);
+
+    // only make an automatic change if scale is changed and other conditions
+    // (OS is linux) apply, or if setHiDPI has been specified
+    if ((autoScale > 1 && isLinux) || setHiDPI)
+    {
+      setHiDPIScale(autoScale);
+      return;
+    }
+
+    // looks like we're not doing any scaling
+    doneInit = true;
+  }
+
+  public static void setHiDPIScale(int s)
+  {
+    scale = s;
+    allowScalePropertyArg = true;
+    doneInit = true;
+  }
+
+  public static String getScalePropertyArg()
+  {
+    init();
+    // HiDPI setting. Just looking at Linux to start with. Test with Windows.
+    return allowScalePropertyArg ? "-D" + scalePropertyName + "=" + scale
+            : null;
+  }
+}
diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
index 7849ba2..159374a 100644
--- a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin;
 
 /**
diff --git a/getdown/src/getdown/launcher/pom.xml b/getdown/src/getdown/launcher/pom.xml
index ad87541..e7dbeb1 100644
--- a/getdown/src/getdown/launcher/pom.xml
+++ b/getdown/src/getdown/launcher/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.4_FJVL</version>
+    <version>1.8.3-1.2.9_FJVL</version>
   </parent>
 
   <artifactId>getdown-launcher</artifactId>
diff --git a/getdown/src/getdown/mvn_cmd b/getdown/src/getdown/mvn_cmd
index 3f9b4a2..e0d7cf1 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=1.8.3-1.2.4_JVL
+  export VERSION=1.8.3-1.2.9_JVL
 fi
 
 if [ x${VERSION%_JVL} = x$VERSION ]; then
diff --git a/getdown/src/getdown/pom.xml b/getdown/src/getdown/pom.xml
index 2ca4aa1..8c7c521 100644
--- a/getdown/src/getdown/pom.xml
+++ b/getdown/src/getdown/pom.xml
@@ -10,7 +10,7 @@
   <groupId>com.threerings.getdown</groupId>
   <artifactId>getdown</artifactId>
   <packaging>pom</packaging>
-  <version>1.8.3-1.2.4_FJVL</version>
+  <version>1.8.3-1.2.9_FJVL</version>
 
   <name>getdown</name>
   <description>An application installer and updater.</description>
diff --git a/gradle.properties b/gradle.properties
index 782a495..453572a 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,4 +1,6 @@
-org.gradle.jvmargs=-Xmx1536m -Xms512m
+# Convention for properties.  Read from gradle.properties, use lower_case_underlines for property names.
+# For properties set within build.gradle, use camelCaseNoSpace.
+#
 
 jalviewDir = .
 
@@ -23,38 +25,35 @@ proxyHost = sqid
 jalview_keyalg = SHA1withRSA
 jalview_keydig = SHA1
 
-testngGroups = Functional
-testngExcludedGroups = 
+testng_groups = Functional
+testng_excluded_groups = 
 
 j8libDir = j8lib
 j11libDir = j11lib
 resource_dir = resources
 help_parent_dir = help
 help_dir = help
-docDir = doc
-schemaDir = schemas
+doc_dir = doc
 classes_dir = classes
-examplesDir = examples
 clover = false
-use_clover = false
-cloverReportJVMHeap = 2g
-cloverReportJVMArgs = -Dfile.encoding=UTF-8
-cloverReportHTMLOptions = 
-cloverReportXMLOptions =
-cloverClassesDir = clover-classes
-cloverSourcesInstrDir = sources-instr
-packageDir = dist
+clover_classes_dir = clover-classes
+clover_sources_instr_dir = clover-instr
+clover_report_dir = clover-report
+clover_lib_dir = utils/clover/lib
+cloverreport_mem = 2g
+cloverreport_jvmargs = -Dfile.encoding=UTF-8
+cloverreport_html_options = 
+cloverreport_xml_options =
+package_dir = dist
 ARCHIVEDIR =
-outputJar = jalview.jar
 
-testOutputDir = tests
-utilsDir = utils
+test_output_dir = tests
+utils_dir = utils
 
 build_properties_file = .build_properties
 application_codebase = *.jalview.org
-mainClass = jalview.bin.Jalview
-shadowJarMainClass = jalview.bin.Launcher
-launcherClass = jalview.bin.Jalview
+main_class = jalview.bin.Jalview
+shadow_jar_main_class = jalview.bin.Launcher
 
 jalview_name = Jalview
 
@@ -107,9 +106,12 @@ getdown_alt_java11_max_version =
 jre_installs_dir = ~/buildtools/jre
 
 j8libDir = j8lib
+j8digestonlyDir = j8digestonly
 j11libDir = j11lib
 j11modDir = j11mod
 j11modules = com.sun.istack.runtime,com.sun.xml.bind,com.sun.xml.fastinfoset,com.sun.xml.streambuffer,com.sun.xml.txw2,com.sun.xml.ws.policy,java.activation,java.annotation,java.base,java.compiler,java.datatransfer,java.desktop,java.logging,java.management,java.management.rmi,java.naming,java.prefs,java.rmi,java.scripting,java.security.sasl,java.sql,java.xml,java.xml.bind,java.xml.soap,java.xml.ws,javax.jws,jdk.httpserver,jdk.jsobject,jdk.unsupported,jdk.xml.dom,org.jvnet.mimepull,org.jvnet.staxex,javax.servlet.api,java.ws.rs
+j11digestonlyDir = j11digestonly
+
 
 install4j_home_dir = ~/buildtools/install4j8
 install4j_copyright_message = ...
diff --git a/help/help/help.jhm b/help/help/help.jhm
index 99d010d..7dbb76d 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -170,4 +170,5 @@
    
    <mapID target="importvcf" url="html/features/importvcf.html" />
    <mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
+   <mapID target="logging" url="html/logging.html" />
 </map>
diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a0c7fe6..a72f5ac 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -27,7 +27,7 @@
         <tocitem text="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
 				<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
 				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-				
+        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -156,6 +156,7 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		<tocitem text="Scripting with Groovy" target="groovy">
 			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 		</tocitem>
diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 60db069..1eecfb9 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -34,6 +34,11 @@
   parameters, then include it at the beginning of the command line to
   ensure they are processed before any remaining arguments.
   <br>
+  Typical command line execution follows the following pattern:
+  <pre>
+  jalview -open &lt;Alignment File/URL&gt; [additional import arguments] [export arguments]
+  </pre>
+  
   <table width="100%" border="1" cellspacing="0" cellpadding="0">
     <tr>
       <td width="27%"><div align="center">-nodisplay</div></td>
@@ -41,7 +46,11 @@
           User Interface. (automatically disables questionnaire, version
           and usage stats checks)</div></td>
     </tr>
-
+    <tr>
+      <td><div align="center">-open FILE/URL</div></td>
+      <td><div align="left">Specify the alignment file to
+          open or process by providing additional arguments.</div></td>
+    </tr>
     <tr>
       <td><div align="center">-props FILE/URL</div></td>
       <td><div align="left">Use the given Jalview properties
@@ -225,6 +234,25 @@
           </div>
       </td>
     </tr>
+    <tr>
+      <td><div align="center">-jvmmempc=PERCENT</div></td>
+      <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+          Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+	  This defaults to 90 if total physical memory can be detected.
+	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+          </div>
+      </td>
+    </tr>
+    <tr>
+      <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
+      <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+          Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+	  gigabytes(g) or if you're lucky enough, terabytes(t).
+	  This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+          </div>
+      </td>
+    </tr>
   </table>
 </body>
 </html>
diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index e00d390..0ef78f9 100644
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -38,7 +38,7 @@
 
   <ul>
     <li>Standard installation on Linux/Unix:<pre>
-       /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</pre>
+       /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
     </li>
     <li>Standard installation on Windows:<pre>
       \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
@@ -65,10 +65,31 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
   </p>
   <p>
     <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
-    to modify parameters for Jalview's Java Virtual Machine, then take a
-    look at the instructions for how to <a href="../memory.html#jvm">setting
-      the JVM's maximum memory</a>.
+    to modify parameters for Jalview's Java Virtual Machine, or
+    configure system properties, then take a look at the instructions
+    for how to <a href="../memory.html#jvm">setting the JVM's
+      maximum memory</a>.<br /> 
+  <p>
+    <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+    are experiencing issues with the font size or layout of Jalview's
+    GUI, you can try changing Jalview's 'Look and feel' by
+    specifying a custom system property 'laf' on startup (see <a
+      href="../memory.html#jvm">setting the JVM's memory</a> for
+    instructions on how to do this for your platform). <br />For the
+    Jalview standalone executable jar, simply provide one of the
+    property settings before the -jar argument
   </p>
+  <ul>
+    <li>-Dlaf=system (default look and feel for the OS)</li>
+    <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+    <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+    <li>-Dlaf=mac (only has an effect on OSX)</li>
+    <li>-Dlaf=gtk (only has an effect on Linux)</li>
+  </ul>
+  The currently configured look and feel is logged to Jalview's console.
+  Once the look and feel has been changed, it will be stored in
+  Jalview's .jalview_properties file for future Jalview sessions.
+
   <p>&nbsp;</p>
   <p>&nbsp;</p>
 </body>
diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html
index ead4436..cc91154 100644
--- a/help/help/html/features/groovy.html
+++ b/help/help/html/features/groovy.html
@@ -39,7 +39,7 @@
     installation of Groovy. Just select <strong>Tools&#8594;Groovy
       Console...</strong> from the Jalview Desktop's drop-down menu. After a
     short pause, you should then see the <a
-      href="http://groovy-lang.org/groovyconsole.html">Groovy
+      href="https://groovy-lang.org/groovyconsole.html">Groovy
       Console</a> appear. This allows you to interactively execute Groovy
     scripts whilst Jalview is running. We've also provided a <strong>Calculations&#8594;Execute
       Groovy Script</strong> button so you can execute the currently loaded
@@ -101,7 +101,7 @@ print currentAlFrame.getTitle();</pre>
     InstallAnywhere version of Jalview, you can find additional groovy
     scripts in the examples/groovy subfolder of the installation
     directory. The examples are also available at <a
-      href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+      href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
   </p>
   <p>
     <em>Using Groovy to add new Alignment Calculations</em><br />We've
@@ -115,8 +115,8 @@ print currentAlFrame.getTitle();</pre>
     <em>Creating custom colourschemes</em><br/>
     You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
     <ul>
-    <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
-    <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
     
     </ul>
   </p>
diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html
index 27742b3..e23af30 100644
--- a/help/help/html/features/jvlfiles.html
+++ b/help/help/html/features/jvlfiles.html
@@ -46,12 +46,12 @@
   <pre>
 # Jalview Launch File
 # Please install the Jalview Desktop from 
-# http://www.jalview.org/getdown/release
+# https://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=https://www.jalview.org/examples/jpred_msa.fasta
 jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
 jalview.apparg=-colour
 jalview.apparg=Clustal
 </pre>
@@ -62,7 +62,7 @@ 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/getdown/archive/2_10_5/
+appbase=https://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.
diff --git a/help/help/html/features/search.html b/help/help/html/features/search.html
index eec68ee..837d7b3 100755
--- a/help/help/html/features/search.html
+++ b/help/help/html/features/search.html
@@ -36,7 +36,7 @@ td {
   </p>
   <p>The search box is displayed by pressing Control and F or
     selecting &quot;Find...&quot; from the &quot;Search&quot; menu.</p>
-  <img src="search.png" width="398" height="124">
+  <img src="search.png" width="400" height="152">
   <p>&quot;Find next&quot; will find the next occurrence of the
     specified and adjust the alignment window view to show it, and
     &quot;Find all&quot; highlights all matches for a pattern. The
@@ -48,18 +48,19 @@ td {
       of posix and perl style regex - see below for a summary)</li>
     <li>Gaps are ignored when matching the query to the sequences
       in the alignment.</li>
+    <li>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
     <li>The search is applied to both sequences and their IDs, and
       optionally also to the description string (<em>since Jalview
         2.10</em>)
     </li>
     <li>If a region is selected, then search will <strong>only</strong>
-      be performed on that region.
+      be performed on that region.<br />
+    <em>Tip: to quickly clear the current selection, click the
+        alignment view you wish to search, then press 'Escape'.</em>
     </li>
-    <li>To quickly clear the current selection, press the
-      &quot;Escape&quot; key.</li>
     <li>Tick the &quot;Match Case&quot; box to perform a case
       sensitive search.</li>
-    <li>To access a <a ref="#queryhistory">previously used
+    <li>To access a <a href="#queryhistory">previously used
         query</a> press the down arrow or click on the button on the right
       of the text field.
   </ul>
@@ -155,12 +156,13 @@ td {
     stored along with your Jalview user preferences. To open the search
     history, click on the button to the right of the query field, or
     press the down arrow key.</p>
-  <img src="searchhist.png" width="404" height="185" align="left" />
-  <p>The search history keeps up to 99 queries by default. To clear
+  <p><img src="searchhist.png" width="404" height="185" />
+  </p><p>The search history keeps up to 99 queries by default. To clear
     the history, or modify the size of the history, right-click the text
     box.</p>
-  <img src="searchclearhist.png" width="402" height="127" align="left" />
-  <p>
+  <p><img src="searchclearhist.png" width="402" height="127"/>
+  </p>
+<p width="100%">
     <strong>Other dialogs that provide a query history</strong>
   </p>
   <p>
diff --git a/help/help/html/features/search.png b/help/help/html/features/search.png
index 89adb1a..47c18f4 100644
Binary files a/help/help/html/features/search.png and b/help/help/html/features/search.png differ
diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html
index e726c49..4e9a75f 100755
--- a/help/help/html/features/seqfetch.html
+++ b/help/help/html/features/seqfetch.html
@@ -72,14 +72,30 @@
       &quot;OK&quot; to initiate the retrieval.</li>
   </ol>
 
-  <p>If you use the WSDBFetch sequence fetcher services (EMBL,
-    UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
-  <p>
-    Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
-    J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
-    R. <br> SOAP-based services provided by the European
-    Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
-    (2005) <br> <br>
-  </p>
+  <p>If you use the Sequence Fetcher, please remember to cite the
+    corresponding services (linked to below):</p>
+  <ul>
+    <li>Ensembl - <a
+      href="https://github.com/Ensembl/ensembl-rest/wiki#citing">The
+        Ensembl REST API</a></li>
+    <li>EMBL/EMBLCDS - Provided by the <a
+      href="https://www.ebi.ac.uk/ena/browser/api/#/ENA_Browser_Data_API/getFlatFileUsingGET">European
+        Nucleotide Archive's ENA Data API</a><br />
+    <em>Note: Versions of Jalview prior to 2.11.1.1 employed the
+        XML endpoint of the ENA browser, which was retired in August
+        2020.</em></li>
+    <li>Uniprot - Free Text Search and Retrieval via the <a
+      href="https://www.uniprot.org/help/api">Uniprot REST API</a></li>
+    <li>PDB - Free Text Search via the <a
+      href="https://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+        REST API</a> and retrieval via <a
+      href="https://www.ebi.ac.uk/Tools/dbfetch/">WSDbFetch</a><br />
+      Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+      J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+      R. <br> SOAP-based services provided by the European
+      Bioinformatics Institute.<br> Nucleic Acids Res.
+      33(1):W25-W28 (2005) <br> <br>
+    </li>
+  </ul>
 </body>
 </html>
diff --git a/help/help/html/groovy/featuresCounter.html b/help/help/html/groovy/featuresCounter.html
index 3b6705b..bd7144e 100644
--- a/help/help/html/groovy/featuresCounter.html
+++ b/help/help/html/groovy/featuresCounter.html
@@ -43,7 +43,7 @@
   </ol>
   <strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
   <em><a
-    href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
+    href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
     - rendered with <a href="http://hilite.me">hilite.me</a></em>
   <!-- HTML generated using hilite.me --><div style="background: #f8f8f8; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #408080; font-style: italic">/*</span>
 <span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
diff --git a/help/help/html/index.html b/help/help/html/index.html
index 36ed33a..a6bb1b6 100755
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -45,7 +45,7 @@
   <p>
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (<a
-      href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+      href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation</a>).
   </p>
   <p>
     If you are using the Jalview Desktop application and are looking for
@@ -54,9 +54,14 @@
     google the online version of these pages. If you don't find what you
     are looking for, or want to report a bug or make a feature request,
     then get in contact over at <a
-      href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+      href="https://www.jalview.org/community">https://www.jalview.org/community</a>
+  </p>
+  <p>
+    <strong>Logging, troubleshooting and reporting bugs</strong><br />If
+    something seems to be wrong with your Jalview installation, or you
+    think you've found a problem, take a look at <a href="logging.html">Jalview's
+      logging and bug reporting</a> documentation.
   </p>
-
   <p>
     <strong>Citing Jalview</strong><br />If you use Jalview in your
     work, please cite the Jalview 2 paper in Bioinformatics:
diff --git a/help/help/html/keys.html b/help/help/html/keys.html
index 1a5fc18..0faa1d5 100755
--- a/help/help/html/keys.html
+++ b/help/help/html/keys.html
@@ -78,32 +78,25 @@
       <td>Redo the last sequence edit undone.</td>
     </tr>
     <tr>
-      <td><strong>Up Arrow</strong></td>
-      <td>Normal</td>
-      <td>Moves selected sequence(s) up the alignment</td>
-    </tr>
-    <tr>
-      <td><strong>Down Arrow</strong></td>
-      <td>Normal</td>
-      <td>Moves selected sequence(s) down the alignment.</td>
-    </tr>
-    <tr>
-      <td><strong>Left Arrow</strong></td>
-      <td>Normal</td>
-      <td>Slides selected sequence(s) left. Press Alt key to slide
-        in cursor mode</td>
-    </tr>
-    <tr>
-      <td><strong>Right Arrow</strong></td>
-      <td>Normal</td>
-      <td>Slides selected sequence(s) right. Press Alt key to slide
-        in cursor mode</td>
+      <td><strong>Cursor Keys<br> (Arrow Keys)
+      </strong></td>
+      <td>Cursor</td>
+      <td>Move cursor around alignment.<br /> Press SHIFT to move
+        cursor from an aligned region to next gap, or to the next
+        aligned region when at a gap.
+      </td>
     </tr>
     <tr>
       <td><strong>Cursor Keys<br> (Arrow Keys)
       </strong></td>
-      <td>Cursor</td>
-      <td>Move cursor around alignment</td>
+      <td>Normal<br />
+      <em>(+Alt in Cursor)</em></td>
+      <td>Moves selected sequence(s) up, down, left, or right
+        according to the direction pressed.<br>
+      <br>
+      <em>Alt+Arrow key to move selection or sequence under cursor
+          in cursor mode.</em>
+      </td>
     </tr>
     <tr>
       <td><strong>Page Up</strong></td>
diff --git a/help/help/html/logging.html b/help/help/html/logging.html
new file mode 100644
index 0000000..0975a47
--- /dev/null
+++ b/help/help/html/logging.html
@@ -0,0 +1,212 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Java Console, Logging and Reporting Bugs</title>
+</head>
+<body>
+  <p>
+    <strong>The Java Console, Logging and Reporting Bugs<br /></strong>
+  </p>
+  <p>
+    Like most programs, Jalview contains bugs, despite our best efforts.
+    However, Jalview also produces a series of messages during its
+    operation, often referred to as 'logs'. These logs provide a record
+    of Jalview's operation. They can also be extremely useful when <a
+      href="#reportingbugs">reporting bugs</a>, since they help the
+    Jalview developers diagnose and find a workaround for specific
+    problems that you might encounter.
+  </p>
+  <p>
+    The primary place to look for logs is in the <a href="#java_console">Java
+      Console</a> which you can open from within Jalview by going to the <em>Tools</em>
+    menu and checking the box next to <em>Show Java Console</em>. This
+    option is stored in your Jalview preferences file and so is
+    remembered across Jalview sessions.
+  </p>
+  <p>The Java Console will show you information about what the
+    Jalview application is doing (often in the background) whilst it is
+    running.</p>
+  <p>However, when tracking down problems preventing Jalview from
+    starting up properly, you need to look at the startup logs - which
+    are not shown in the Jalview Console. The location of these depends
+    on how you launched Jalview:</p>
+  <p>
+    <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
+    a standard desktop version of Jalview installed from one of our
+    install4j installers, then messages about Jalview's initial launch
+    can be found in
+  <pre>JALVIEW_APP_DIR/launcher.log</pre>
+  where
+  <em>JALVIEW_APP_DIR</em> is the directory that Jalview's application
+  was installed into.
+  <br /> For Jalview 2.11.0 onwards:
+  <ul>
+    <li>In Windows this is <em>%APPDATA%\Local\Jalview</em> by
+      default
+    </li>
+    <li>In macOS this is <em>/Applications/Jalview.app/Contents/Resources/app</em>
+      by default
+    </li>
+    <li>In Linux and other Unix OSes this is <em>~/opt/jalview</em>
+      by default
+    </li>
+  </ul>
+  <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
+  used by bioconda and OSX homebrew installations) then the default run class (
+  <em>jalview.bin.Launcher</em> -- a minimised launcher that will set
+  memory and linux dpi settings before re-launching
+  <em>jalview.bin.Jalview</em>), will output logging information to
+  STDOUT and STDERR.
+  </p>
+
+  <p><strong>
+    <a name="java_console">Java Console and Log Level</a>
+  </strong></p>
+  <p>
+    The Java Console is opened by selecting <strong>Tools
+      &rarr; Show Java Console</strong>. The visibility of the console is stored
+    in your preferences, so if you quit Jalview with the console open,
+    it will be shown the next time you start Jalview. You can close the
+    console by selecting the same menu option again, or just closing the
+    console window.
+  </p>
+  <p>The Java Console's text display always shows information about
+    your system and Jalview installation details. The rest are the most
+    recent messages output during your Jalview session. Some messages
+    are only captured by the console when it is open, so to get a full
+    log for debugging a problem, enable the console and then restart
+    Jalview.</p>
+
+  <p>
+    You can temporarily control the detail of what appears as output by
+    selecting a <em>Log level</em> using the drop-down list at the
+    bottom left of the console. There are several levels to choose from:
+    The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the
+    Console is opened, the default level will be chosen (INFO).
+  </p>
+  <p>
+    <strong>Note! If you change the log level in the Java
+      Console, this change will only persist for as long as the console
+      is open. Once you close the console the log level will revert back
+      to what it had been when you opened the console (usually INFO).</strong>
+  </p>
+  <p><strong>Permanently changing Jalview's default log level</strong><br/>
+    You can change the default log level by editing the Jalview
+    preferences file, <em>.jalview_properties</em>, found in your home
+    directory (on Windows: %HOMEPATH%, or the folder above 'My
+    Documents'; on macOS: ~ or /Users/<em>username</em>; on linux/unix:
+    ~ or /home/<em>username</em>), and setting the property <em>logs.Jalview.level</em>
+    to the log level you prefer, e.g.
+  <pre>
+  logs.Jalview.level=DEBUG
+  </pre>
+  You can also set the property
+  <pre>
+  logs.Axis.level=DEBUG
+  </pre>
+  <p>to get debug information for Jalview's JPred service. The Axis log
+  level cannot be set from within the Java Console.
+  </p>
+  <p>
+    You can also set the <em>logs.jalview.level</em> property to a log level
+    not usually presented in the Java Console (though restricted to log
+    levels used by Apache Log4j -- see <a
+      href="https://logging.apache.org/log4j/2.x/manual/customloglevels.html">Log4j
+      Custom Log Levels</a> for details of the standard log levels
+    available). Jalview does not currently define any custom log levels.
+    If you do set the property with a log level that is normally not
+    visible in the Java Console this should be respected and visibly
+    selected when you open the console.
+  </p>
+  <p>
+    The <em>Clear</em> button at the bottom of the console will clear
+    all logging messages except for the initial system information which
+    is rewritten to the console.
+  </p>
+  <p>
+    The <em>Copy to clipboard</em> button at the bottom right of the
+    console will copy all of the text in the console to your system
+    clipboard, ready to paste into another application (e.g. email
+    composer or issue tracker).
+  </p>
+
+  <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
+
+  <p>
+    If you come across a problem in Jalview where something is not
+    working as described, or how you think it should, you should first
+    check the <a href="https://www.jalview.org/faq">Jalview FAQ</a> to
+    see if this is a known problem and if there is a suggested
+    workaround.
+  </p>
+  <p>
+    If there is no FAQ answer covering your problem then you can submit
+    a bug report on the <a href="https://issues.jalview.org/">Jalview
+      Issue Tracker</a>. It is good practice to search the issue tracker
+    first to see if the issue has already been reported. If an issue
+    already exists please continue to add your own comments to the issue
+    which may well help narrow down the problem, if not then you can
+    create an account and submit a new bug report:
+  </p>
+  <p>
+    Make sure that you set Project to <em>Jalview (JAL)</em>, and Issue
+    Type to <em>Bug</em> or <em>New Feature</em> or <em>Improvement</em>
+    appropriately.<br /> Give a one line summary of the issue in the <em>Summary</em>.
+    <br /> In the <em>Environment</em> text box you can describe the
+    system you are using. This is usually most easily done by opening
+    the Java Console, clicking the <em>Clear</em> button, and then
+    immediately on the <em>Copy to clipboard</em> button, and then
+    pasting the clipboard into the text box.
+  </p>
+  <p>
+    You can then give more detailed information about how to recreate
+    the problem in the <em>Description</em> text box. If you want to
+    attach any screenshots or example alignment files that demonstrate
+    the problem then you can drag them to the Create Issue dialog in
+    your browser, or use the <em>Attachment</em> browse facility to
+    locate them on your computer.
+  </p>
+
+  <p>
+    To help the Jalview team with diagnosing a particular issue, it is
+    really helpful if you can also add more detailed logs output whilst
+    re-creating the problem. To do this, open the Java Console, click
+    the <em>Clear</em> button and select TRACE in the <em>Log level</em>
+    drop down list. <br /> Whilst leaving the console open, perform the
+    task in Jalview that re-creates the problem. <br /> Then you can
+    copy the debug information in the Java Console by clicking on the <em>Copy
+      to clipboard</em> button and then paste that into the Description, or a
+    Comment of your issue.
+  </p>
+
+  <p>
+    For other queries or comments about Jalview, remember you can
+    contact the Jalview team using email via the
+    <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
+      discussion list</a>, on Twitter <a
+      href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
+    discussions, via the Jalview developer's chatroom at
+    <a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.
+  </p>
+
+</body>
+</html>
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 81190a9..7d6fb85 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -80,7 +80,7 @@
       arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. <pre>
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
       settings in Windows and macOS too: <br /> In Windows you must
       use, e.g. <pre>
       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
@@ -90,7 +90,17 @@
     <li><em><font size="3">Maximum memory limit</em><br/>
       Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit':
       <pre>jalview.jvmmemmax = 32G</pre>
-      Adjusting this default (via a JVL file, above) will allow larger amounts of memory to be allocated to Jalview in connjunction with the jalview.jvmmempc setting. 
+      Adjusting this default (via a JVL file, above) will allow larger amounts (or can limit the amount) of memory to be allocated to Jalview in conjunction with the jalview.jvmmempc setting. 
+      <br/><br/>
+    </li>
+    <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
+      If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
+      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
+      and <em>-jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
+      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
+      (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
+      <br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
+      <br/><br/>
     </li>
     <li><em><font size="3"><a name="jvm"/>Directly opening Jalview
           with a JVM</font></em> <br /> Launching Jalview directly with a JVM is
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 5b6180d..d402a12 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,6 +57,191 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
+          <em>17/09/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
+            residue in cursor mode
+          </li>
+          <li>
+            <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+            HTSJDK from 2.12 to 2.23
+          </li>
+          <li>
+            <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+            optimisations and improvements suggested by Bob Hanson and
+            improved compatibility with JalviewJS
+          </li>
+          <li>
+            <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+            alignments from Pfam and Rfam
+          </li>
+          <li>
+            <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+            import (no longer based on .gz extension)
+          </li>
+          <li>
+            <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+          </li>
+          <li>
+            <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+            ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+            EMBL flat file
+          </li>
+          <li>
+            <!-- JAL-3667 -->Improved warning messages, debug logging
+            and fixed Retry action when Jalview encounters errors when
+            saving or making backup files.
+          </li>
+          <li>
+            <!-- JAL-3676 -->Enhanced Jalview Java Console:
+            <ul>
+              <li>Jalview's logging level can be configured</li>
+              <li>Copy to Clipboard Buttion</li>
+            </ul>
+          </li>
+          <li>
+            <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+            when running on Linux (Requires Java 11+)
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+            through a system property
+          </li>
+          <li>
+            <!-- JAL-3477 -->Improved built-in documentation and command
+            line help for configuring Jalview's memory
+          </li>                   
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3691 -->Conservation and Quality tracks are shown
+            but not calculated and no protein or DNA score models are
+            available for tree/PCA calculation when launched with
+            Turkish language locale
+          </li>
+          <li>
+            <!-- JAL-3493 -->Escape does not clear highlights on the
+            alignment (Since Jalview 2.10.3)
+          </li>
+          <li>
+            <!--  JAL-3680 -->Alt+Left or Right arrow in cursor mode
+            doesn't slide selected sequences, just sequence under cursor
+          </li>
+          <li>
+            <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+            sequence under the cursor
+          </li>
+          <li>
+            <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+            multiple EMBL gene products shown for a single contig
+          </li>
+          <li>
+            <!-- JAL-3696 -->Errors encountered when processing variants
+            from VCF files yield "Error processing VCF: Format specifier
+            '%s'" on the console
+          </li>
+          <li>
+            <!-- JAL-3697 -->Count of features not shown can be wrong
+            when there are both local and complementary features mapped
+            to the position under the cursor
+          </li>
+          <li>
+            <!-- JAL-3673 -->Sequence ID for reference sequence is
+            clipped when Right align Sequence IDs enabled
+          </li>
+          <li>
+            <!-- JAL-2983 -->Slider with negative range values not
+            rendered correctly in VAqua4 (Since 2.10.4)
+          </li>
+          <li>
+            <!-- JAL-3685 -->Single quotes not displayed correctly in
+            internationalised text for some messages and log output
+          </li>
+          <li>
+            <!-- JAL-3490 -->Find doesn't report matches that span
+            hidden gapped columns
+          </li>
+          <li>
+            <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+            panels, Alignment viewport and annotation renderer.
+          </li>
+          <li>
+            <!-- JAL-3561 -->Jalview ignores file format parameter
+            specifying output format when exporting an alignment via the
+            command line
+          </li>
+          <li>
+            <!-- JAL-3667 -->Windows 10: For a minority of users, if
+            backups are not enabled, Jalview sometimes fails to
+            overwrite an existing file and raises a warning dialog. (in
+            2.11.0, and 2.11.1.0, the workaround is to try to save the
+            file again, and if that fails, delete the original file and
+            save in place.)
+          </li>
+          <li>
+            <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+            via command line
+          </li>
+          <li>
+            <!-- JAL-3741 -->References to http://www.jalview.org in
+            program and documentation
+          </li>
+        </ul> <em>Launching Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3718 -->Jalview application fails when launched the
+            first time for a version that has different jars to the
+            previous launched version.
+          </li>
+        </ul> <em>Developing Jalview</em>
+        <ul>
+          <li>
+            <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+            data, causing cloverReport gradle task to fail with an
+            OutOfMemory error.
+          </li>
+          <li>
+            <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+            monitor the release channel
+          </li>
+        </ul> <em>New Known defects</em>
+        <ul>
+          <li>
+            <!-- JAL-3748 -->CDS shown in result of submitting proteins
+            in a CDS/Protein alignment to a web service is wrong when
+            proteins share a common transcript sequence (e.g.
+            genome of RNA viruses)
+          </li>
+          <li>
+            <!-- JAL-3576 -->Co-located features exported and re-imported
+            are ordered differently when shown on alignment and in
+            tooltips. (Also affects v2.11.1.0)
+          </li>
+          <li>
+            <!-- JAL-3702 -->Drag and drop of alignment file onto
+            alignment window when in a HiDPI scaled mode in Linux only
+            works for the top left quadrant of the alignment window
+          </li>
+          <li>
+            <!-- JAL-3701 -->Stale build data in jalview standalone jar
+            builds (only affects 2.11.1.1 branch)
+          </li>
+          <li>
+            <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+            when alignment view restored from project (since Jalview 2.11.0)
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
           id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
           <em>22/04/2020</em></strong></td>
       <td align="left" valign="top">
diff --git a/help/help/html/webServices/AACon.html b/help/help/html/webServices/AACon.html
index 5cec67d..52cddb2 100644
--- a/help/help/html/webServices/AACon.html
+++ b/help/help/html/webServices/AACon.html
@@ -32,7 +32,7 @@
       Function, and Genetics</em> 43(2): 227-241. <a
       href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a>
     or available on the <a
-      href="http://valdarlab.unc.edu/publications.html">Valdar
+      href="http://valdarlab.unc.edu/publications">Valdar
       Group publications page</a>), but the SMERFs score was developed later
     and described by Manning et al. in 2008 (<a
       href="http://www.biomedcentral.com/1471-2105/9/51">BMC
diff --git a/help/help/html/webServices/msaclient.html b/help/help/html/webServices/msaclient.html
index d627c66..472bda0 100644
--- a/help/help/html/webServices/msaclient.html
+++ b/help/help/html/webServices/msaclient.html
@@ -58,7 +58,7 @@
     <ul>
       <li><a href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
       <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
-      <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</li>
+      <li><a href="https://mafft.cbrc.jp/alignment/software/index.html">Mafft</a> (version 7.310)</li>
       <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31)</li>
       <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-coffee</a> (version 11.00.8cbe486)</li>
       <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
diff --git a/help/help/html/webServices/newsreader.html b/help/help/html/webServices/newsreader.html
index c3c1d3f..2e8b69a 100644
--- a/help/help/html/webServices/newsreader.html
+++ b/help/help/html/webServices/newsreader.html
@@ -25,7 +25,7 @@
   <p>
     <strong>The Jalview Desktop RSS News Reader</strong><br /> The
     Jalview Desktop includes a built in news reader for the <a
-      href="http://www.jalview.org/feeds/desktop/rss">Jalview
+      href="https://www.jalview.org/feeds/desktop/rss">Jalview
       Desktop News Channel</a>.
   </p>
 
@@ -48,9 +48,9 @@
   <br />
   <p>
     The <em>Jalview news reader</em> was introduced in <a
-      href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+      href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
       version 2.7</a>. Its implementation is based on <a
-      href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
+      href="https://jswingreader.sourceforge.net/">JSwingReader</a>.
   </p>
   <br />
   <em>If you need to prevent the news-reader opening, then add the
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 0f0c7f1..2e18bae 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,58 +24,62 @@
 </head>
 <body>
   <p>
-    <strong>Jalview 2.11.1.0</strong>
-  </p>
-  <p>
-    Jalview 2.11.1.0 is the first minor release for the 2.11 series.
-    Along with a number of critical bug fixes and improvements it brings
-    new functionality for mapping sequence features between CDS and
-    Protein alignments. It is also the first release made under a new <em>four</em>
-    number versioning scheme, which will allow us to keep track of
-    patches and bug fixes.
+    <strong>Jalview 2.11.1.1</strong>
   </p>
+  <p>Jalview 2.11.1.1 is the first patch release for Jalview version
+    2.11.1. In addition to fixes for some critical bugs, it also
+    contains a handful of new features suggested by the Jalview
+    community.</p>
+  <ul>
+    <li>Shift+arrow keys navigate to next gap or residue in cursor
+      mode (enable with F2)</li>
+    <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+      2.23</li>
+    <li>Improved recognition of GZipped files from local disk or
+      retrieved via the web</li>
+    <li>EMBL and EMBL CDS database records retrieved from the
+      European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
+    <li>Improved <a href="logging.html">Java Console and
+        logging</a> to help track down problems
+    </li>
+    <li>Improved support for Hi-DPI (4K) screens when running on
+      Linux (Requires Java 11+)</li>
+  </ul>
+  <p>Critical bug fixes include</p>
   <ul>
-    <li><strong>Virtual Features</strong><br />In previous
-      versions of Jalview, specific nucleotide sequence features such as
-      genomic variants and exons were transferred to protein products on
-      import. Jalview 2.11.1 instead provides 'virtual features' that
-      can be enabled and overlaid on linked CDS/Protein views via their
-      <a href="features/splitView.html#virtualfeats">Sequence
-        Features dialog</a>. This allows more analyses of nucleotide and
-      peptide sequence features on alignments in a more flexible and
-      memory efficient way than in earlier versions.<br />
-    <em>Note: Virtual features work best when variants are
-        annotated with CSQ fields. Please <a
-        href="features/importvcf.html#computepepvariants">see this
-          Groovy script workaround</a> if you are working with VCF files
-        without CSQ fields.
-    </em></li>
-    <li><strong>Improved VCF data import</strong><br /> <a
-      href="features/importvcf.html#attribs">Standard attributes for
-        filtering variants</a> (e.g. position, QUAL field etc) are now
-      extracted from VCF files. This new feature was suggested by a user
-      at the Jalview booth during ISMB 2019.</li>
-    <li><strong>Extended feature attributes are exported
-        in GFF3</strong><br />Complex attributes from VCF files can be exported
-      and imported via GFF3</li>
-    <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
-      installation packages are now built with Install4j 8, which brings
-      better support for Linux and improved control of file
-      associations. New <a href="memory.html#jvm">parameters on the
-        Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
-      a Jalview launch file, to prevent it from hogging your system.</li>
+    <li>Jalview runs correctly when launched with Turkish language
+      settings</li>
+    <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+      products shown for a single contig (such as viral genomes)</li>
+    <li>Errors encountered when processing variants from VCF files
+      yield "Error processing VCF: Format specifier '%s'" on the console</li>
+    <li>Count of features not shown can be wrong when there are
+      both DNA and Protein features mapped to the position under
+      the cursor</li>
+    <li>Sequence ID for reference sequence is clipped when Right
+      align Sequence IDs enabled</li>
+    <li>Find doesn't report matches that span hidden gapped columns</li>
+    <li>Jalview ignores file format parameter specifying output
+      format when exporting an alignment via the command line</li>
   </ul>
   <p>
-    See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
-      release notes</a> for full details of bugs fixed and new known issues.
+    For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
+      Jalview 2.11.1.1 release notes</a>.
   </p>
   <p>
-    <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
-    the team are now focused on bringing JalviewJS to full production.
-    To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
-    and follow updates on our new <a
-      href="https://github.com/jalview/jalview-js/">JalviewJS
-      Releases github repository</a>.
+    <strong>Known Issues</strong>
   </p>
+  <ul>
+    <li>We've had reports from a small number of windows 10 users
+      who see a warning dialog pop up when Jalview tries to save a new
+      version of an existing file. If you are affected by this bug and
+      this latest version of Jalview doesn't fix it, please let us know!</li>
+    <li>Co-located features exported and re-imported are ordered
+      differently when shown on alignment and in tooltips. (Also affects
+      v2.11.1.0)</li>
+    <li>Drag and drop of alignment file onto alignment window when
+      in a HiDPI scaled mode in Linux only works for the top left
+      quadrant of the alignment window</li>
+  </ul>
 </body>
 </html>
diff --git a/j11digestonly/htsjdk-2.12.0.jar b/j11digestonly/htsjdk-2.12.0.jar
new file mode 100644
index 0000000..bcf201f
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diff --git a/j11digestonly/intervalstore-v1.0.jar b/j11digestonly/intervalstore-v1.0.jar
new file mode 100644
index 0000000..668b543
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diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index 9c0f96e..c927dae 100644
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diff --git a/j11lib/htsjdk-2.12.0.jar b/j11lib/htsjdk-2.12.0.jar
deleted file mode 100644
index 1df12b2..0000000
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diff --git a/j11lib/htsjdk-2.23.0.jar b/j11lib/htsjdk-2.23.0.jar
new file mode 100644
index 0000000..bcf201f
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diff --git a/j11lib/intervalstore-v1.0.jar b/j11lib/intervalstore-v1.0.jar
deleted file mode 100644
index 4f6101c..0000000
Binary files a/j11lib/intervalstore-v1.0.jar and /dev/null differ
diff --git a/j11lib/intervalstore-v1.1.jar b/j11lib/intervalstore-v1.1.jar
new file mode 100644
index 0000000..668b543
Binary files /dev/null and b/j11lib/intervalstore-v1.1.jar differ
diff --git a/j8digestonly/htsjdk-2.12.0.jar b/j8digestonly/htsjdk-2.12.0.jar
new file mode 100644
index 0000000..bcf201f
Binary files /dev/null and b/j8digestonly/htsjdk-2.12.0.jar differ
diff --git a/j8digestonly/intervalstore-v1.0.jar b/j8digestonly/intervalstore-v1.0.jar
new file mode 100644
index 0000000..668b543
Binary files /dev/null and b/j8digestonly/intervalstore-v1.0.jar differ
diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index 9c0f96e..c927dae 100644
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ
diff --git a/j8lib/htsjdk-2.12.0.jar b/j8lib/htsjdk-2.12.0.jar
deleted file mode 100644
index 1df12b2..0000000
Binary files a/j8lib/htsjdk-2.12.0.jar and /dev/null differ
diff --git a/j8lib/htsjdk-2.23.0.jar b/j8lib/htsjdk-2.23.0.jar
new file mode 100644
index 0000000..bcf201f
Binary files /dev/null and b/j8lib/htsjdk-2.23.0.jar differ
diff --git a/j8lib/intervalstore-v1.0.jar b/j8lib/intervalstore-v1.0.jar
deleted file mode 100644
index 4f6101c..0000000
Binary files a/j8lib/intervalstore-v1.0.jar and /dev/null differ
diff --git a/j8lib/intervalstore-v1.1.jar b/j8lib/intervalstore-v1.1.jar
new file mode 100644
index 0000000..668b543
Binary files /dev/null and b/j8lib/intervalstore-v1.1.jar differ
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index a4b24ed..496fad0 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -377,7 +377,7 @@ label.example = Example
 label.example_param = Example: {0}
 label.select_file_format_before_saving = You must select a file format before saving!
 label.file_format_not_specified = File format not specified
-label.couldnt_save_file = Couldn't save file: {0}
+label.couldnt_save_file = Couldn''t save file: {0}
 label.error_saving_file = Error Saving File
 label.remove_from_default_list = Remove from default list?
 label.remove_user_defined_colour = Remove user defined colour
@@ -406,11 +406,11 @@ label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be
 label.couldnt_load_file = Couldn't load file
 label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
 label.no_pdb_id_in_file = No PDB Id in File
-label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
+label.couldnt_read_pasted_text = Couldn''t read the pasted text {0}
 label.error_parsing_text = Error parsing text
 label.input_alignment_from_url = Input Alignment From URL
 label.input_alignment = Input Alignment
-label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
+label.couldnt_import_as_vamsas_session = Couldn''t import {0} as a new vamsas session.
 label.vamsas_document_import_failed = Vamsas Document Import Failed
 label.couldnt_locate = Could not locate {0}
 label.url_not_found = URL not found
@@ -855,7 +855,7 @@ label.invalid_name = Invalid name
 label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
 label.proxy_authorization_failed = Proxy Authorization Failed
 label.internal_jalview_error = Internal Jalview Error
-label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located.
+label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn''t be located.
 label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\!
 label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown
 label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
@@ -985,7 +985,7 @@ error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaW
 error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1})
 error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0}
 error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset!
-error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!"
+error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can''t locate either oldname ({0}) or presetName ({1}in the datastore!"
 error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore
 error.cannot_set_source_file_for = Cannot set source file for {0}
 error.mismatch_service_instance_preset = Probable mismatch between service instance and preset!
@@ -993,7 +993,7 @@ error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web ser
 error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets
 error.no_aacon_service_found = No AACon service found
 error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain!
-error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8.
+error.couldnt_encode_as_utf8 = Couldn''t encode {0} as UTF-8.
 error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented
 error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process
 error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
@@ -1049,18 +1049,18 @@ error.implementation_error_reset_called_for_invalid_source = Implementation Erro
 exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3})
 label.mapped = mapped
 exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns
-exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0}
+exception.couldnt_parse_concise_annotation_for_prediction = Couldn''t parse concise annotation for prediction profile.\n{0}
 exception.newfile = NewickFile\: {0}\n
 label.no_tree_read_in = No Tree read in
-exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0})
-exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})
+exception.rnaml_couldnt_access_datasource = Couldn''t access datasource ({0})
+exception.ranml_couldnt_process_data = Couldn''t process data as RNAML file ({0})
 exception.ranml_invalid_file = Invalid RNAML file ({0})
 exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
 exception.pfam_no_sequences_found = No sequences found (PFAM input)
 exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
 exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
 exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
-exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
+exception.couldnt_store_sequence_mappings = Couldn''t store sequence mappings for {0}
 exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
 exception.browser_not_found = Exception in finding browser: {0}
 exception.browser_unable_to_locate = Unable to locate browser: {0}
@@ -1071,7 +1071,6 @@ exception.unable_to_create_internet_config = Unable to create an Internet Config
 exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
 exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
 exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
 exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
 exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
 exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
@@ -1094,7 +1093,7 @@ warn.service_not_supported = Service not supported!
 warn.input_is_too_big = Input is too big!
 warn.invalid_job_param_set = Invalid job parameter set!
 warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ?   
-info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}
+info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn''t support this program.\n{0}
 info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}
 info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
 info.no_jobs_ran = No jobs ran
@@ -1346,6 +1345,7 @@ label.backupfiles_confirm_save_file = Confirm save file
 label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
 label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
 label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+label.continue_operation = Continue operation?
 label.backups = Backups
 label.backup = Backup
 label.backup_files = Backup Files
@@ -1412,3 +1412,9 @@ label.include_linked_features = Include {0} features
 label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
 label.features_not_shown = {0} feature(s) not shown
 label.no_features_to_sort_by = No features to sort by
+label.log_level = Log level
+label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
+label.copy_to_clipboard = Copy to clipboard
+label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
+label.ignore_hidden = Ignore hidden columns
+label.ignore_hidden_tooltip = Ignore any characters in hidden columns when matching
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 4e0fb1f..6364f5e 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -211,7 +211,7 @@ label.show_non_conserved = Mostrar no conservadas
 label.overview_window = Ventana resumen
 label.none = Ninguno
 label.above_identity_threshold = Por encima del umbral de identidad
-label.show_sequence_features = Mostrar las características de las secuencias
+label.show_sequence_features = Mostrar las características de secuencia
 label.nucleotide = Nucleótido
 label.to_new_alignment = A nuevo alineamiento
 label.to_this_alignment = Añadir a este alineamiento
@@ -693,7 +693,12 @@ label.annotations_for_params = Anotaciones de - {0}
 label.generating_features_for_params = Generando características de - {0}
 label.generating_annotations_for_params = Generando anotaciones de - {0}
 label.varna_params = VARNA - {0}
-label.sequence_feature_settings = Configuración de las características de la secuencia
+label.sequence_feature_settings = Configuración de las características de secuencia
+label.sequence_feature_settings_for = Configuración de las características de secuencia para {0}
+label.sequence_feature_settings_for_view = Configuración de las características de secuencia para vista "{0}"
+label.sequence_feature_settings_for_CDS_and_Protein = Configuración de las características de secuencia para CDS y Proteína 
+action.undo_changes_to_feature_settings = Deshacer todos los cambios no aplicados
+action.undo_changes_to_feature_settings_and_close_the_dialog = Deshacer cambios pendientes, cerrar diálogo
 label.pairwise_aligned_sequences = Secuencias alineadas a pares
 label.original_data_for_params = Datos originales de {0}
 label.points_for_params = Puntos de {0}
@@ -990,7 +995,6 @@ exception.unable_to_create_internet_config = Imposible crear una instancia de co
 exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
 exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0}
 exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0}
-exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
 exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
 exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB
 exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
@@ -1191,6 +1195,7 @@ warn.urls_not_contacted=URLs que no pudieron ser contactados
 label.prot_alignment_colour=Color del Alineamiento Proteico
 info.associate_wit_sequence=Asociar con secuencia
 label.protein=Proteína
+label.CDS=CDS
 warn.oneseq_msainput_selection=La selección actual sólo contiene una única secuencia. ¿Quieres enviar todas las secuencias para la alineación en su lugar?
 label.use_rnaview=Usar RNAView para estructura secondaria
 label.search_all=Introducir uno o más valores de búsqueda separados por punto y coma ";" (Nota: buscará en toda la base de datos PDB)
@@ -1341,6 +1346,7 @@ label.backupfiles_confirm_save_file = Confirmar guardar archivo
 label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos.
 label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien.
 label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien.
+label.continue_operation = ¿Continuar operación?
 label.backups = Respaldos
 label.backup = Respaldo
 label.backup_files = Archivos de respaldos
@@ -1407,3 +1413,9 @@ label.include_linked_features = Incluir caracter
 label.include_linked_tooltip = Incluir características de {0}<br>convertidas a coordenadas de secuencia local
 label.features_not_shown = {0} característica(s) no mostradas
 label.no_features_to_sort_by = No hay características para ordenar
+label.log_level = Nivel del registro
+label.log_level_tooltip = Establezca temporalmente el nivel de registro para esta consola. El nivel de registro volverá a {0} cuando se cierre esta consola de Java.
+label.copy_to_clipboard = Copiar en el portapapeles
+label.copy_to_clipboard_tooltip = Copie todo el texto de registro en esta consola al portapapeles del sistema
+label.ignore_hidden = Ignorar columnas ocultas
+label.ignore_hidden_tooltip = Ignorar caracteres en columnas ocultas
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 3cbef6d..c545c7f 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -23,17 +23,18 @@ package jalview.analysis;
 import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Range;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.VisibleContigsIterator;
 import jalview.util.Comparison;
+import jalview.util.MapList;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
 
@@ -50,7 +51,7 @@ public class Finder implements FinderI
   /*
    * sequences matched by id or description
    */
-  private Vector<SequenceI> idMatches;
+  private List<SequenceI> idMatches;
 
   /*
    * the viewport to search over
@@ -63,11 +64,24 @@ public class Finder implements FinderI
   private int sequenceIndex;
 
   /*
-   * column position in sequence to search from, base 0
-   * - absolute column number including any hidden columns
-   * (position after start of last match for a repeat search)
+   * position offset in sequence to search from, base 0
+   * (position after start of last match for a 'find next')
    */
-  private int columnIndex;
+  private int residueIndex;
+
+  /*
+   * the true sequence position of the start of the 
+   * last sequence searched (when 'ignore hidden regions' does not apply)
+   */
+  private int searchedSequenceStartPosition;
+
+  /*
+   * when 'ignore hidden regions' applies, this holds the mapping from
+   * the visible sequence positions (1, 2, ...) to true sequence positions
+   */
+  private MapList searchedSequenceMap;
+
+  private String seqToSearch;
 
   /**
    * Constructor for searching a viewport
@@ -78,33 +92,35 @@ public class Finder implements FinderI
   {
     this.viewport = av;
     this.sequenceIndex = 0;
-    this.columnIndex = -1;
+    this.residueIndex = -1;
   }
 
   @Override
   public void findAll(String theSearchString, boolean matchCase,
-          boolean searchDescription)
+          boolean searchDescription, boolean ignoreHidden)
   {
     /*
      * search from the start
      */
     sequenceIndex = 0;
-    columnIndex = -1;
+    residueIndex = -1;
 
-    doFind(theSearchString, matchCase, searchDescription, true);
+    doFind(theSearchString, matchCase, searchDescription, true,
+            ignoreHidden);
 
     /*
      * reset to start for next search
      */
     sequenceIndex = 0;
-    columnIndex = -1;
+    residueIndex = -1;
   }
 
   @Override
   public void findNext(String theSearchString, boolean matchCase,
-          boolean searchDescription)
+          boolean searchDescription, boolean ignoreHidden)
   {
-    doFind(theSearchString, matchCase, searchDescription, false);
+    doFind(theSearchString, matchCase, searchDescription, false,
+            ignoreHidden);
     
     if (searchResults.isEmpty() && idMatches.isEmpty())
     {
@@ -112,7 +128,7 @@ public class Finder implements FinderI
        * search failed - reset to start for next search
        */
       sequenceIndex = 0;
-      columnIndex = -1;
+      residueIndex = -1;
     }
   }
 
@@ -123,18 +139,19 @@ public class Finder implements FinderI
    * @param matchCase
    * @param searchDescription
    * @param findAll
+   * @param ignoreHidden
    */
   protected void doFind(String theSearchString, boolean matchCase,
-          boolean searchDescription, boolean findAll)
+          boolean searchDescription, boolean findAll, boolean ignoreHidden)
   {
+    searchResults = new SearchResults();
+    idMatches = new ArrayList<>();
+
     String searchString = matchCase ? theSearchString
             : theSearchString.toUpperCase();
     Regex searchPattern = new Regex(searchString);
     searchPattern.setIgnoreCase(!matchCase);
 
-    searchResults = new SearchResults();
-    idMatches = new Vector<>();
-
     SequenceGroup selection = viewport.getSelectionGroup();
     if (selection != null && selection.getSize() < 1)
     {
@@ -144,108 +161,202 @@ public class Finder implements FinderI
     AlignmentI alignment = viewport.getAlignment();
     int end = alignment.getHeight();
 
-    while (sequenceIndex < end)
+    getSequence(ignoreHidden);
+
+    boolean found = false;
+    while ((!found || findAll) && sequenceIndex < end)
     {
-      SequenceI seq = alignment.getSequenceAt(sequenceIndex);
-      boolean found = findNextMatch(seq, searchString, searchPattern,
-              searchDescription);
-      if (found && !findAll)
+      found = findNextMatch(searchString, searchPattern, searchDescription,
+              ignoreHidden);
+    }
+  }
+
+  /**
+   * Calculates and saves the sequence string to search. The string is restricted
+   * to the current selection region if there is one, and is saved with all gaps
+   * removed.
+   * <p>
+   * If there are hidden columns, and option {@ignoreHidden} is selected, then
+   * only visible positions of the sequence are included, and a mapping is also
+   * constructed from the returned string positions to the true sequence
+   * positions.
+   * <p>
+   * Note we have to do this each time {@code findNext} or {@code findAll} is
+   * called, in case the alignment, selection group or hidden columns have
+   * changed. In particular, if the sequence at offset {@code sequenceIndex} in
+   * the alignment is (no longer) in the selection group, search is advanced to
+   * the next sequence that is.
+   * <p>
+   * Sets sequence string to the empty string if there are no more sequences (in
+   * selection group if any) at or after {@code sequenceIndex}.
+   * <p>
+   * Returns true if a sequence could be found, false if end of alignment was
+   * reached
+   * 
+   * @param ignoreHidden
+   * @return
+   */
+  private boolean getSequence(boolean ignoreHidden)
+  {
+    AlignmentI alignment = viewport.getAlignment();
+    if (sequenceIndex >= alignment.getHeight())
+    {
+      seqToSearch = "";
+      return false;
+    }
+    SequenceI seq = alignment.getSequenceAt(sequenceIndex);
+    SequenceGroup selection = viewport.getSelectionGroup();
+    if (selection != null && !selection.contains(seq))
+    {
+      if (!nextSequence(ignoreHidden))
       {
-        return;
+        return false;
       }
-      if (!found)
+      seq = alignment.getSequenceAt(sequenceIndex);
+    }
+
+    String seqString = null;
+    if (ignoreHidden)
+    {
+      seqString = getVisibleSequence(seq);
+      this.searchedSequenceStartPosition = 1;
+    }
+    else
+    {
+      int startCol = 0;
+      int endCol = seq.getLength() - 1;
+      this.searchedSequenceStartPosition = seq.getStart();
+      if (selection != null)
       {
-        sequenceIndex++;
-        columnIndex = -1;
+        startCol = selection.getStartRes();
+        endCol = Math.min(endCol, selection.getEndRes());
+        this.searchedSequenceStartPosition = seq.findPosition(startCol);
       }
+      seqString = seq.getSequenceAsString(startCol, endCol + 1);
     }
+
+    /*
+     * remove gaps; note that even if this leaves an empty string, we 'search'
+     * the sequence anyway (for possible match on name or description)
+     */
+    String ungapped = AlignSeq.extractGaps(Comparison.GapChars, seqString);
+    this.seqToSearch = ungapped;
+
+    return true;
   }
 
   /**
-   * Answers the start-end column range of the visible region of
-   * <code>sequence</code> starting at or after the given <code>column</code>.
-   * If there are no hidden columns, this just returns the remaining width of
-   * the sequence. The range is restricted to the current <code>selection</code>
-   * if there is one. Answers null if there are no visible columns at or after
-   * <code>column</code>.
+   * Returns a string consisting of only the visible residues of {@code seq} from
+   * alignment column {@ fromColumn}, restricted to the current selection region
+   * if there is one.
+   * <p>
+   * As a side-effect, also computes the mapping from the true sequence positions
+   * to the positions (1, 2, ...) of the returned sequence. This is to allow
+   * search matches in the visible sequence to be converted to sequence positions.
+   * 
+   * @param seq
+   * @return
    */
-  protected Range getNextVisibleSequenceRegion(SequenceI sequence,
-          int column)
+  private String getVisibleSequence(SequenceI seq)
   {
-    int seqColStart = column;
-    int seqColEnd = sequence.getLength() - 1;
-
     /*
-     * restrict search to (next) visible column region, 
-     * in case there are hidden columns
+     * get start / end columns of sequence and convert to base 0
+     * (so as to match the visible column ranges)
      */
-    AlignmentI alignment = viewport.getAlignment();
-    VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
-            .getVisContigsIterator(column, alignment.getWidth(),
-                    false);
-    int[] visible = visibleRegions.hasNext() ? visibleRegions.next() : null;
-    if (visible == null)
-    {
-      columnIndex = seqColEnd + 1;
-      return null;
-    }
-    seqColStart = Math.max(seqColStart, visible[0]);
-    seqColEnd = Math.min(seqColEnd, visible[1]);
+    int seqStartCol = seq.findIndex(seq.getStart()) - 1;
+    int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1) - 1;
+    Iterator<int[]> visibleColumns = viewport.getViewAsVisibleContigs(true);
+    StringBuilder visibleSeq = new StringBuilder(seqEndCol - seqStartCol);
+    List<int[]> fromRanges = new ArrayList<>();
 
-    /*
-     * restrict search to selected region if there is one
-     */
-    SequenceGroup selection = viewport.getSelectionGroup();
-    if (selection != null)
+    while (visibleColumns.hasNext())
     {
-      int selectionStart = selection.getStartRes();
-      int selectionEnd = selection.getEndRes();
-      if (selectionStart > seqColEnd || selectionEnd < seqColStart)
+      int[] range = visibleColumns.next();
+      if (range[0] > seqEndCol)
+      {
+        // beyond the end of the sequence
+        break;
+      }
+      if (range[1] < seqStartCol)
+      {
+        // before the start of the sequence
+        continue;
+      }
+      String subseq = seq.getSequenceAsString(range[0], range[1] + 1);
+      String ungapped = AlignSeq.extractGaps(Comparison.GapChars, subseq);
+      visibleSeq.append(ungapped);
+      if (!ungapped.isEmpty())
       {
         /*
-         * sequence region doesn't overlap selection region 
+         * visible region includes at least one non-gap character,
+         * so add the range to the mapping being constructed
          */
-        columnIndex = seqColEnd + 1;
-        return null;
+        int seqResFrom = seq.findPosition(range[0]);
+        int seqResTo = seqResFrom + ungapped.length() - 1;
+        fromRanges.add(new int[] { seqResFrom, seqResTo });
       }
-      seqColStart = Math.max(seqColStart, selectionStart);
-      seqColEnd = Math.min(seqColEnd, selectionEnd);
     }
 
-    return new Range(seqColStart, seqColEnd);
+    /*
+     * construct the mapping
+     * from: visible sequence positions 1..length
+     * to:   true residue positions of the alignment sequence
+     */
+    List<int[]> toRange = Arrays
+            .asList(new int[]
+            { 1, visibleSeq.length() });
+    searchedSequenceMap = new MapList(fromRanges, toRange, 1, 1);
+
+    return visibleSeq.toString();
   }
 
   /**
-   * Finds the next match in the given sequence, starting at column at
-   * <code>columnIndex</code>. Answers true if a match is found, else false. If
-   * a match is found, <code>columnIndex</code> is advanced to the column after
-   * the start of the matched region, ready for a search from the next position.
+   * Advances the search to the next sequence in the alignment. Sequences not in
+   * the current selection group (if there is one) are skipped. The (sub-)sequence
+   * to be searched is extracted, gaps removed, and saved, or set to null if there
+   * are no more sequences to search.
+   * <p>
+   * Returns true if a sequence could be found, false if end of alignment was
+   * reached
    * 
-   * @param seq
+   * @param ignoreHidden
+   */
+  private boolean nextSequence(boolean ignoreHidden)
+  {
+    sequenceIndex++;
+    residueIndex = -1;
+
+    return getSequence(ignoreHidden);
+  }
+
+  /**
+   * Finds the next match in the given sequence, starting at offset
+   * {@code residueIndex}. Answers true if a match is found, else false.
+   * <p>
+   * If a match is found, {@code residueIndex} is advanced to the position after
+   * the start of the matched region, ready for the next search.
+   * <p>
+   * If no match is found, {@code sequenceIndex} is advanced ready to search the
+   * next sequence.
+   * 
+   * @param seqToSearch
    * @param searchString
    * @param searchPattern
    * @param matchDescription
+   * @param ignoreHidden
    * @return
    */
-  protected boolean findNextMatch(SequenceI seq, String searchString,
-          Regex searchPattern, boolean matchDescription)
+  protected boolean findNextMatch(String searchString,
+          Regex searchPattern, boolean matchDescription,
+          boolean ignoreHidden)
   {
-    SequenceGroup selection = viewport.getSelectionGroup();
-    if (selection != null && !selection.contains(seq))
-    {
-      /*
-       * this sequence is not in the selection - advance to next sequence
-       */
-      return false;
-    }
-
-    if (columnIndex < 0)
+    if (residueIndex < 0)
     {
       /*
        * at start of sequence; try find by residue number, in sequence id,
        * or (optionally) in sequence description
        */
-      if (doNonMotifSearches(seq, searchString, searchPattern,
+      if (doNonMotifSearches(searchString, searchPattern,
               matchDescription))
       {
         return true;
@@ -255,83 +366,66 @@ public class Finder implements FinderI
     /*
      * search for next match in sequence string
      */
-    int end = seq.getLength();
-    while (columnIndex < end)
+    int end = seqToSearch.length();
+    while (residueIndex < end)
     {
-      if (searchNextVisibleRegion(seq, searchPattern))
+      boolean matched = searchPattern.searchFrom(seqToSearch, residueIndex);
+      if (matched)
       {
-        return true;
+        if (recordMatch(searchPattern, ignoreHidden))
+        {
+          return true;
+        }
+      }
+      else
+      {
+        residueIndex = Integer.MAX_VALUE;
       }
-    }
-    return false;
-  }
-
-  /**
-   * Searches the sequence, starting from <code>columnIndex</code>, and adds the
-   * next match (if any) to <code>searchResults</code>. The search is restricted
-   * to the next visible column region, and to the <code>selection</code> region
-   * if there is one. Answers true if a match is added, else false.
-   * 
-   * @param seq
-   * @param searchPattern
-   * @return
-   */
-  protected boolean searchNextVisibleRegion(SequenceI seq, Regex searchPattern)
-  {
-    Range visible = getNextVisibleSequenceRegion(seq, columnIndex);
-    if (visible == null)
-    {
-      return false;
-    }
-    String seqString = seq.getSequenceAsString(visible.start, visible.end + 1);
-    String noGaps = AlignSeq.extractGaps(Comparison.GapChars, seqString);
-
-    if (searchPattern.search(noGaps))
-    {
-      int sequenceStartPosition = seq.findPosition(visible.start);
-      recordMatch(seq, searchPattern, sequenceStartPosition);
-      return true;
-    }
-    else
-    {
-      /*
-       * no match - advance columnIndex past this visible region
-       * so the next visible region (if any) is searched next
-       */
-      columnIndex = visible.end + 1;
     }
 
+    nextSequence(ignoreHidden);
     return false;
   }
 
   /**
    * Adds the match held in the <code>searchPattern</code> Regex to the
    * <code>searchResults</code>, unless it is a subregion of the last match
-   * recorded. <code>columnIndex</code> is advanced to the position after the
+   * recorded. <code>residueIndex</code> is advanced to the position after the
    * start of the matched region, ready for the next search. Answers true if a
    * match was added, else false.
+   * <p>
+   * Matches that lie entirely within hidden regions of the alignment are not
+   * added.
    * 
-   * @param seq
    * @param searchPattern
-   * @param firstResiduePosition
+   * @param ignoreHidden
    * @return
    */
-  protected boolean recordMatch(SequenceI seq, Regex searchPattern,
-          int firstResiduePosition)
+  protected boolean recordMatch(Regex searchPattern, boolean ignoreHidden)
   {
+    SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+
     /*
-     * get start/end of the match in sequence coordinates
+     * convert start/end of the match to sequence coordinates
      */
     int offset = searchPattern.matchedFrom();
-    int matchStartPosition = firstResiduePosition + offset;
+    int matchStartPosition = this.searchedSequenceStartPosition + offset;
     int matchEndPosition = matchStartPosition
             + searchPattern.charsMatched() - 1;
 
     /*
-     * update columnIndex to next column after the start of the match
+     * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    columnIndex = seq.findIndex(matchStartPosition);
+    residueIndex += offset + 1;
+
+    /*
+     * return false if the match is entirely in a hidden region
+     */
+    if (allHidden(seq, matchStartPosition, matchEndPosition))
+    {
+      return false;
+    }
 
     /*
      * check that this match is not a subset of the previous one (JAL-2302)
@@ -343,7 +437,7 @@ public class Finder implements FinderI
     if (lastMatch == null || !lastMatch.contains(seq, matchStartPosition,
             matchEndPosition))
     {
-      searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+      addMatch(seq, matchStartPosition, matchEndPosition, ignoreHidden);
       return true;
     }
 
@@ -351,6 +445,60 @@ public class Finder implements FinderI
   }
 
   /**
+   * Adds one match to the stored list. If hidden residues are being skipped, then
+   * the match may need to be split into contiguous positions of the sequence (so
+   * it does not include skipped residues).
+   * 
+   * @param seq
+   * @param matchStartPosition
+   * @param matchEndPosition
+   * @param ignoreHidden
+   */
+  private void addMatch(SequenceI seq, int matchStartPosition,
+          int matchEndPosition, boolean ignoreHidden)
+  {
+    if (!ignoreHidden)
+    {
+      /*
+       * simple case
+       */
+      searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+      return;
+    }
+
+    /*
+     *  get start-end contiguous ranges in underlying sequence
+     */
+    int[] truePositions = searchedSequenceMap
+            .locateInFrom(matchStartPosition, matchEndPosition);
+    searchResults.addResult(seq, truePositions);
+  }
+
+  /**
+   * Returns true if all residues are hidden, else false
+   * 
+   * @param seq
+   * @param fromPos
+   * @param toPos
+   * @return
+   */
+  private boolean allHidden(SequenceI seq, int fromPos, int toPos)
+  {
+    if (!viewport.hasHiddenColumns())
+    {
+      return false;
+    }
+    for (int res = fromPos; res <= toPos; res++)
+    {
+      if (isVisible(seq, res))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
    * Does searches other than for residue patterns. Currently this includes
    * <ul>
    * <li>find residue by position (if search string is a number)</li>
@@ -359,24 +507,29 @@ public class Finder implements FinderI
    * </ul>
    * Answers true if a match is found, else false.
    * 
-   * @param seq
    * @param searchString
    * @param searchPattern
    * @param includeDescription
    * @return
    */
-  protected boolean doNonMotifSearches(SequenceI seq, String searchString,
+  protected boolean doNonMotifSearches(String searchString,
           Regex searchPattern, boolean includeDescription)
   {
+    SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+
     /*
      * position sequence search to start of sequence
      */
-    columnIndex = 0;
-
-    if (searchForResidueNumber(seq, searchString))
+    residueIndex = 0;
+    try
     {
-      return true;
+      int res = Integer.parseInt(searchString);
+      return searchForResidueNumber(seq, res);
+    } catch (NumberFormatException ex)
+    {
+      // search pattern is not a number
     }
+
     if (searchSequenceName(seq, searchPattern))
     {
       return true;
@@ -402,7 +555,7 @@ public class Finder implements FinderI
     String desc = seq.getDescription();
     if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
     {
-      idMatches.addElement(seq);
+      idMatches.add(seq);
       return true;
     }
     return false;
@@ -421,45 +574,56 @@ public class Finder implements FinderI
   {
     if (searchPattern.search(seq.getName()) && !idMatches.contains(seq))
     {
-      idMatches.addElement(seq);
+      idMatches.add(seq);
       return true;
     }
     return false;
   }
 
   /**
-   * Tries to interpret the search string as a residue position, and if valid,
-   * adds the position to the search results and returns true, else answers
-   * false
+   * If the residue position is valid for the sequence, and in a visible column,
+   * adds the position to the search results and returns true, else answers false.
+   * 
+   * @param seq
+   * @param resNo
+   * @return
    */
-  protected boolean searchForResidueNumber(SequenceI seq, String searchString)
+  protected boolean searchForResidueNumber(SequenceI seq, int resNo)
   {
-    try
+    if (seq.getStart() <= resNo && seq.getEnd() >= resNo)
     {
-      int res = Integer.parseInt(searchString);
-      if (seq.getStart() <= res && seq.getEnd() >= res)
+      if (isVisible(seq, resNo))
       {
-        searchResults.addResult(seq, res, res);
+        searchResults.addResult(seq, resNo, resNo);
         return true;
       }
-    } catch (NumberFormatException ex)
-    {
     }
     return false;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.analysis.FinderI#getIdMatch()
+  /**
+   * Returns true if the residue is in a visible column, else false
+   * 
+   * @param seq
+   * @param res
+   * @return
    */
+  private boolean isVisible(SequenceI seq, int res)
+  {
+    if (!viewport.hasHiddenColumns())
+    {
+      return true;
+    }
+    int col = seq.findIndex(res); // base 1
+    return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base 0
+  }
+
   @Override
-  public Vector<SequenceI> getIdMatches()
+  public List<SequenceI> getIdMatches()
   {
     return idMatches;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.analysis.FinderI#getSearchResults()
-   */
   @Override
   public SearchResultsI getSearchResults()
   {
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 785dd14..56d25d5 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -38,6 +38,7 @@ import jalview.viewmodel.ViewportRanges;
 import java.awt.Color;
 import java.awt.Font;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -528,4 +529,16 @@ public interface AlignViewportI extends ViewStyleI
    *          - a group defined on sequences in the alignment held by the view
    */
   void addSequenceGroup(SequenceGroup sequenceGroup);
+
+  /**
+   * Returns an interator over the [start, end] column positions of the visible
+   * regions of the alignment
+   * 
+   * @param selectedRegionOnly
+   *                             if true, and the view has a selection region,
+   *                             then only the intersection of visible columns
+   *                             with the selection region is returned
+   * @return
+   */
+  Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
 }
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 8aa2858..fff3b38 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -297,4 +297,11 @@ public interface FeatureRenderer
    * @return
    */
   MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+
+  /**
+   * Sends a message to let any registered parties know that something about
+   * feature rendering has changed
+   */
+  void notifyFeaturesChanged();
+
 }
diff --git a/src/jalview/api/FeatureSettingsModelI.java b/src/jalview/api/FeatureSettingsModelI.java
index c0fc523..c8a835a 100644
--- a/src/jalview/api/FeatureSettingsModelI.java
+++ b/src/jalview/api/FeatureSettingsModelI.java
@@ -35,7 +35,8 @@ public interface FeatureSettingsModelI extends Comparator<String>
   // interface, simplifying instantiating classes
 
   /**
-   * Answers true if the specified feature type is displayed
+   * Answers true if the specified feature type is to be displayed, false if no
+   * preference
    * 
    * @param type
    * @return
@@ -43,6 +44,15 @@ public interface FeatureSettingsModelI extends Comparator<String>
   boolean isFeatureDisplayed(String type);
 
   /**
+   * Answers true if the specified feature type is to be hidden, false if no
+   * preference
+   * 
+   * @param type
+   * @return
+   */
+  boolean isFeatureHidden(String type);
+
+  /**
    * Answers true if the specified feature group is displayed
    * 
    * @param group
diff --git a/src/jalview/api/FeaturesDisplayedI.java b/src/jalview/api/FeaturesDisplayedI.java
index e69785f..9387e3f 100644
--- a/src/jalview/api/FeaturesDisplayedI.java
+++ b/src/jalview/api/FeaturesDisplayedI.java
@@ -39,6 +39,8 @@ public interface FeaturesDisplayedI
 
   void setVisible(String featureType);
 
+  void setHidden(String featureType);
+
   /**
    * Sets all the specified feature types to visible. Visibility of other
    * feature types is not changed.
diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index 71b35ef..8f6232e 100644
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -34,35 +34,48 @@ public interface FinderI
   /**
    * Performs a find for the given search string (interpreted as a regular
    * expression). Search may optionally be case-sensitive, and may optionally
-   * including match in sequence description (sequence id is always searched).
-   * If the viewport has an active selection, then the find is restricted to the
-   * selection region. Sequences matched by id or description can be retrieved
-   * by getIdMatches(), and matched residue patterns by getSearchResults().
+   * including match in sequence description (sequence id is always searched). If
+   * the viewport has an active selection, then the find is restricted to the
+   * selection region. Sequences matched by id or description can be retrieved by
+   * getIdMatches(), and matched residue patterns by getSearchResults().
+   * <p>
+   * If {@code ignoreHidden} is true, then any residues in hidden columns are
+   * ignored (skipped) when matching, so for example pattern {@code KRT} would
+   * match sequence {@code KRqmT} (where {@code qm} are in hidden columns).
+   * <p>
+   * Matches of entirely hidden patterns are not returned. Matches that span
+   * hidden regions on one or both sides may be returned.
    * 
    * @param theSearchString
    * @param caseSensitive
    * @param searchDescription
+   * @param ignoreHidden
    * @return
    */
   void findAll(String theSearchString, boolean caseSensitive,
-          boolean searchDescription);
+          boolean searchDescription, boolean ignoreHidden);
 
   /**
    * Finds the next match for the given search string (interpreted as a regular
    * expression), starting from the position after the last match found. Search
    * may optionally be case-sensitive, and may optionally including match in
-   * sequence description (sequence id is always searched). If the viewport has
-   * an active selection, then the find is restricted to the selection region.
+   * sequence description (sequence id is always searched). If the viewport has an
+   * active selection, then the find is restricted to the selection region.
    * Sequences matched by id or description can be retrieved by getIdMatches(),
    * and matched residue patterns by getSearchResults().
+   * <p>
+   * If {@code ignoreHidden} is true, any hidden residues are skipped (matches may
+   * span them). If false, they are included for matching purposes. In either
+   * cases, entirely hidden matches are not returned.
    * 
    * @param theSearchString
    * @param caseSensitive
    * @param searchDescription
+   * @param ignoreHidden
    * @return
    */
   void findNext(String theSearchString, boolean caseSensitive,
-          boolean searchDescription);
+          boolean searchDescription, boolean ignoreHidden);
 
   /**
    * Returns the (possibly empty) list of sequences matched on sequence name or
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e9081b0..365f886 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -344,7 +344,7 @@ public class AlignmentPanel extends Panel
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     // do we need to scroll the panel?
-    if (results != null && results.getSize() > 0)
+    if (results != null && results.getCount() > 0)
     {
       AlignmentI alignment = av.getAlignment();
       int seqIndex = alignment.findIndex(results);
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 2fc3441..a78e41c 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -171,11 +171,13 @@ public class Finder extends Panel implements ActionListener
     boolean doSearchDescription = searchDescription.getState();
     if (doFindAll)
     {
-      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              false);
     }
     else
     {
-      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              false);
     }
 
     searchResults = finder.getSearchResults();
@@ -209,13 +211,13 @@ public class Finder extends Panel implements ActionListener
         String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
                 : "";
         if (idMatches.size() > 0 && searchResults != null
-                && searchResults.getSize() > 0)
+                && searchResults.getCount() > 0)
         {
           message += " and ";
         }
         if (searchResults != null)
         {
-          message += searchResults.getSize() + " subsequence matches.";
+          message += searchResults.getCount() + " subsequence matches.";
         }
         ap.alignFrame.statusBar.setText(MessageManager
                 .formatMessage("label.search_results", new String[]
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 35d6aa3..600d19c 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,16 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
@@ -37,6 +27,8 @@ import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Collections;
@@ -46,12 +38,26 @@ import java.util.Locale;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
 
 import org.apache.log4j.ConsoleAppender;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 
+import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.ws.sifts.SiftsSettings;
+
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
  * list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -168,8 +174,8 @@ import org.apache.log4j.SimpleLayout;
  * when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
  * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.</li>
@@ -309,6 +315,10 @@ public class Cache
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
       // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
+      // we shouldn't need to do this
+      org.apache.log4j.Logger.getRootLogger()
+              .setLevel(org.apache.log4j.Level.INFO);
+
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
               .getDefault("logs.Jalview.level", Level.INFO.toString())));
       // laxis.addAppender(ap);
@@ -422,7 +432,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
@@ -435,8 +445,8 @@ public class Cache
 
     String jnlpVersion = System.getProperty("jalview.version");
 
-    // jnlpVersion will be null if a latest version check for the channel needs to
-    // be done
+    // 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)
@@ -446,9 +456,12 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+
         @Override
         public void run()
         {
+          String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+
           String orgtimeout = System
                   .getProperty("sun.net.client.defaultConnectTimeout");
           if (orgtimeout == null)
@@ -462,28 +475,19 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(Cache
-                    .getDefault("www.jalview.org", "http://www.jalview.org")
-                    + "/webstart/jalview.jnlp");
+            java.net.URL url = new java.net.URL(buildPropertiesUrl);
+
             BufferedReader in = new BufferedReader(
                     new InputStreamReader(url.openStream()));
-            String line = null;
-            while ((line = in.readLine()) != null)
-            {
-              if (line.indexOf("jalview.version") == -1)
-              {
-                continue;
-              }
-
-              line = line.substring(line.indexOf("value=") + 7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              remoteVersion = line;
-              break;
-            }
+
+            Properties remoteBuildProperties = new Properties();
+            remoteBuildProperties.load(in);
+            remoteVersion = remoteBuildProperties.getProperty("VERSION");
           } catch (Exception ex)
           {
-            System.out.println(
-                    "Non-fatal exception when checking version at www.jalview.org :");
+            System.out
+                    .println("Non-fatal exception when checking version at "
+                            + buildPropertiesUrl + ":");
             System.out.println(ex);
             remoteVersion = getProperty("VERSION");
           }
@@ -555,8 +559,8 @@ public class Cache
     new BuildDetails(codeVersion, null, codeInstallation);
     if (printV && reportVersion)
     {
-      System.out
-            .println("Jalview Version: " + codeVersion + codeInstallation);
+      System.out.println(
+              "Jalview Version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -1099,16 +1103,23 @@ public class Cache
   public static String getVersionDetailsForConsole()
   {
     StringBuilder sb = new StringBuilder();
-    sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+    sb.append("Jalview Version: ");
+    sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
     sb.append("\n");
-    sb.append("Jalview Installation: "
-            + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+    sb.append("Jalview Installation: ");
+    sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
     sb.append("\n");
-    sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("Build Date: ");
+    sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
     sb.append("\n");
-    sb.append("Java version: " + System.getProperty("java.version"));
+    sb.append("Java version: ");
+    sb.append(System.getProperty("java.version"));
     sb.append("\n");
-    sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
+    sb.append(System.getProperty("os.arch"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.name"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.version"));
     sb.append("\n");
     appendIfNotNull(sb, "Install4j version: ",
             System.getProperty("sys.install4jVersion"), "\n", null);
@@ -1116,9 +1127,23 @@ public class Cache
             System.getProperty("installer_template_version"), "\n", null);
     appendIfNotNull(sb, "Launcher version: ",
             System.getProperty("launcher_version"), "\n", null);
-    if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
+    LookAndFeel laf = UIManager.getLookAndFeel();
+    String lafName = laf == null ? "Not obtained" : laf.getName();
+    String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+    sb.append("LookAndFeel: ");
+    sb.append(lafName);
+    sb.append(" (");
+    sb.append(lafClass);
+    sb.append(")\n");
+    // Not displayed in release version ( determined by possible version number
+    // regex 9[9.]*9[.-_a9]* )
+    if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+            jalview.bin.Cache.getDefault("VERSION", "TEST")))
+    {
       appendIfNotNull(sb, "Getdown appdir: ",
               System.getProperty("getdownappdir"), "\n", null);
+      appendIfNotNull(sb, "Getdown appbase: ",
+              System.getProperty("getdownappbase"), "\n", null);
       appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
               "\n", "unknown");
     }
@@ -1135,4 +1160,69 @@ public class Cache
     // eg 'built from Source' or update channel
     return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
   }
+
+  public static String getStackTraceString(Throwable t)
+  {
+    StringWriter sw = new StringWriter();
+    PrintWriter pw = new PrintWriter(sw);
+    t.printStackTrace(pw);
+    return sw.toString();
+  }
+
+  /**
+   * Getdown appbase methods
+   */
+
+  private static final String releaseAppbase;
+
+  private static String getdownAppbase;
+
+  private static String getdownDistDir;
+
+  static
+  {
+    Float specversion = Float
+            .parseFloat(System.getProperty("java.specification.version"));
+    releaseAppbase = (specversion < 9)
+            ? "https://www.jalview.org/getdown/release/1.8"
+            : "https://www.jalview.org/getdown/release/11";
+  }
+
+  // look for properties (passed in by getdown) otherwise default to release
+  private static void setGetdownAppbase()
+  {
+    if (getdownAppbase != null)
+    {
+      return;
+    }
+    String appbase = System.getProperty("getdownappbase");
+    String distDir = System.getProperty("getdowndistdir");
+    if (appbase == null)
+    {
+      appbase = releaseAppbase;
+      distDir = "release";
+    }
+    if (appbase.endsWith("/"))
+    {
+      appbase = appbase.substring(0, appbase.length() - 1);
+    }
+    if (distDir == null)
+    {
+      distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+    }
+    getdownAppbase = appbase;
+    getdownDistDir = distDir;
+  }
+
+  public static String getGetdownAppbase()
+  {
+    setGetdownAppbase();
+    return getdownAppbase;
+  }
+
+  public static String getAppbaseBuildProperties()
+  {
+    String appbase = getGetdownAppbase();
+    return appbase + "/" + getdownDistDir + "/build_properties";
+  }
 }
diff --git a/src/jalview/bin/HiDPISetting.java b/src/jalview/bin/HiDPISetting.java
new file mode 100644
index 0000000..497900f
--- /dev/null
+++ b/src/jalview/bin/HiDPISetting.java
@@ -0,0 +1,180 @@
+package jalview.bin;
+
+import java.awt.HeadlessException;
+import java.awt.Toolkit;
+
+public class HiDPISetting
+{
+  private static final int hidpiThreshold = 160;
+
+  private static final int hidpiMultiThreshold = 240;
+
+  private static final int bigScreenThreshold = 1400;
+
+  private static final String scalePropertyName = "sun.java2d.uiScale";
+
+  private static final boolean isLinux;
+
+  // private static final boolean isAMac;
+
+  // private static final boolean isWindows;
+
+  public static final String setHiDPIPropertyName = "setHiDPI";
+
+  public static final String setHiDPIScalePropertyName = "setHiDPIScale";
+
+  private static boolean setHiDPI = false;
+
+  private static int setHiDPIScale = 0;
+
+  public static int dpi = 0;
+
+  public static int mindimension = 0;
+
+  public static int width = 0;
+
+  public static int scale = 0;
+
+  private static boolean doneInit = false;
+
+  private static boolean allowScalePropertyArg = false;
+
+  static
+  {
+    String system = System.getProperty("os.name") == null ? null
+            : System.getProperty("os.name").toLowerCase();
+    if (system != null)
+    {
+      isLinux = system.indexOf("linux") > -1;
+      // isAMac = system.indexOf("mac") > -1;
+      // isWindows = system.indexOf("windows") > -1;
+    }
+    else
+    {
+      isLinux = false;
+      // isAMac = isWindows = false;
+    }
+  }
+
+  private static void init()
+  {
+    if (doneInit)
+    {
+      return;
+    }
+
+    // get and use command line property values first
+    String setHiDPIProperty = System.getProperty(setHiDPIPropertyName);
+    setHiDPI = setHiDPIProperty != null
+            && setHiDPIProperty.equalsIgnoreCase("true");
+
+    String setHiDPIScaleProperty = System
+            .getProperty(setHiDPIScalePropertyName);
+    if (setHiDPIScaleProperty != null)
+    {
+      try
+      {
+        setHiDPIScale = Integer.parseInt(setHiDPIScaleProperty);
+      } catch (NumberFormatException e)
+      {
+        System.err.println(setHiDPIScalePropertyName + " property give ("
+                + setHiDPIScaleProperty + ") but not parseable as integer");
+      }
+    }
+    if (setHiDPI && setHiDPIScale > 0)
+    {
+      setHiDPIScale(setHiDPIScale);
+      return;
+    }
+
+    // check to see if the scale property has already been set by something else
+    // (e.g. the OS)
+    String existingProperty = System.getProperty(scalePropertyName);
+    if (existingProperty != null)
+    {
+      try
+      {
+        int existingPropertyVal = Integer.parseInt(existingProperty);
+        System.out.println("Existing " + scalePropertyName + " is "
+                + existingPropertyVal);
+        if (existingPropertyVal > 1)
+        {
+          setHiDPIScale(existingPropertyVal);
+          return;
+        }
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Could not convert property " + scalePropertyName
+                + " vale '" + existingProperty + "' to number");
+      }
+    }
+
+    // Try and auto guess a good scale based on reported DPI (not trustworthy)
+    // and screen resolution (more trustworthy)
+
+    // get screen dpi
+    try
+    {
+      dpi = Toolkit.getDefaultToolkit().getScreenResolution();
+    } catch (HeadlessException e)
+    {
+      System.err.println("Cannot get screen resolution: " + e.getMessage());
+    }
+
+    // try and get screen size height and width
+    try
+    {
+      int height = Toolkit.getDefaultToolkit().getScreenSize().height;
+      int width = Toolkit.getDefaultToolkit().getScreenSize().width;
+      // using mindimension in case of portrait screens
+      mindimension = Math.min(height, width);
+    } catch (HeadlessException e)
+    {
+      System.err.println(
+              "Cannot get screen size height and width:" + e.getMessage());
+    }
+
+    // attempt at a formula for scaling based on screen dpi and mindimension.
+    // scale will be an integer >=1. This formula is based on some testing and
+    // guesswork!
+
+    // scale based on reported dpi. if dpi>hidpiThreshold then scale=2+multiples
+    // of hidpiMultiThreshold (else scale=1)
+    // (e.g. dpi of 110 scales 1. dpi of 120 scales 2. dpi of 360 scales 3)
+    int dpiScale = (dpi - hidpiThreshold > 0)
+            ? 2 + ((dpi - hidpiThreshold) / hidpiMultiThreshold)
+            : 1;
+
+    int dimensionScale = 1 + (mindimension / bigScreenThreshold);
+
+    // choose larger of dimensionScale or dpiScale (most likely dimensionScale
+    // as dpiScale often misreported)
+    int autoScale = Math.max(dpiScale, dimensionScale);
+
+    // only make an automatic change if scale is changed and other conditions
+    // (OS is linux) apply, or if setHiDPI has been specified
+    if ((autoScale > 1 && isLinux) || setHiDPI)
+    {
+      setHiDPIScale(autoScale);
+      return;
+    }
+
+    // looks like we're not doing any scaling
+    doneInit = true;
+  }
+
+  public static void setHiDPIScale(int s)
+  {
+    scale = s;
+    allowScalePropertyArg = true;
+    doneInit = true;
+  }
+
+  public static String getScalePropertyArg()
+  {
+    init();
+    // HiDPI setting. Just looking at Linux to start with. Test with Windows.
+    return allowScalePropertyArg ? "-D" + scalePropertyName + "=" + scale
+            : null;
+  }
+}
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8c9d391..1e292ba 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -30,6 +30,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -61,13 +62,33 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
-import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
 
 /**
  * Main class for Jalview Application <br>
@@ -183,7 +204,7 @@ public class Jalview
    * main class for Jalview application
    * 
    * @param args
-   *               open <em>filename</em>
+   *          open <em>filename</em>
    */
   public static void main(String[] args)
   {
@@ -198,22 +219,24 @@ public class Jalview
   {
     System.setSecurityManager(null);
     System.out
-            .println("Java version: "
-                    + System.getProperty("java.version"));
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println("Java Home: " + System.getProperty("java.home"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
     String val = System.getProperty("sys.install4jVersion");
-    if (val != null) {
-    System.out.println("Install4j version: " + val);
+    if (val != null)
+    {
+      System.out.println("Install4j version: " + val);
     }
     val = System.getProperty("installer_template_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Install4j template version: " + val);
     }
     val = System.getProperty("launcher_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Launcher version: " + val);
     }
 
@@ -296,51 +319,7 @@ public class Jalview
 
     desktop = null;
 
-    try
-    {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
-    } catch (Exception ex)
-    {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
-    }
-    if (Platform.isAMac())
-    {
-
-      LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
-              .getLookAndFeel();
-      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
-              "Jalview");
-      System.setProperty("apple.laf.useScreenMenuBar", "true");
-      if (lookAndFeel != null)
-      {
-        try
-        {
-          UIManager.setLookAndFeel(lookAndFeel);
-        } catch (Throwable e)
-        {
-          System.err.println(
-                  "Failed to set QuaQua look and feel: " + e.toString());
-        }
-      }
-      if (lookAndFeel == null
-              || !(lookAndFeel.getClass().isAssignableFrom(
-                      UIManager.getLookAndFeel().getClass()))
-              || !UIManager.getLookAndFeel().getClass().toString()
-                      .toLowerCase().contains("quaqua"))
-      {
-        try
-        {
-          System.err.println(
-                  "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
-          UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
-        } catch (Throwable e)
-        {
-          System.err.println(
-                  "Failed to reset look and feel: " + e.toString());
-        }
-      }
-    }
+    setLookAndFeel();
 
     /*
      * configure 'full' SO model if preferences say to, else use the default (SO
@@ -353,6 +332,7 @@ public class Jalview
 
     if (!headless)
     {
+
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -361,11 +341,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(t.getMessage());
         // t.printStackTrace();
       }
 
@@ -401,7 +383,7 @@ public class Jalview
             // String defurl =
             // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
             // //
-            String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+            String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
             Cache.log.debug(
                     "Starting questionnaire with default url: " + defurl);
             desktop.checkForQuestionnaire(defurl);
@@ -469,7 +451,11 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      
+
+      protocol = AppletFormatAdapter.checkProtocol(file);
+      
+      if (protocol == DataSourceType.FILE)
       {
         if (!(new File(file)).exists())
         {
@@ -481,8 +467,6 @@ public class Jalview
         }
       }
 
-      protocol = AppletFormatAdapter.checkProtocol(file);
-
       try
       {
         format = new IdentifyFile().identify(file, protocol);
@@ -666,18 +650,34 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          if (af.saveAlignment(file, format))
-          {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+          FileFormatI outFormat=null;
+          try {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP) {
+            System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
           }
-          else
+          if (outFormat != null)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            if (!outFormat.isWritable())
+            {
+              System.out.println(
+                      "This version of Jalview does not support alignment export as "
+                              + outputFormat);
+            }
+            else
+            {
+              if (af.saveAlignment(file, outFormat))
+              {
+                System.out.println("Written alignment in " + format
+                        + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + format + " format!!");
+              }
+            }
           }
-
         }
 
         while (aparser.getSize() > 0)
@@ -696,13 +696,16 @@ public class Jalview
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
               jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
-                      + "/examples/exampleFile_2_7.jar");
+                      "https://www.jalview.org")
+                      + "/examples/exampleFile_2_7.jvp");
       if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+                      "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
+        file.replace("http:", "https:");
         // hardwire upgrade of the startup file
-        file.replace("_2_3.jar", "_2_7.jar");
+        file.replace("_2_3", "_2_7");
+        file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
@@ -760,6 +763,204 @@ public class Jalview
     }
   }
 
+  private static void setLookAndFeel()
+  {
+    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
+    // "mac"
+    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
+    // try Quaqua/Vaqua.
+    String lafProp = System.getProperty("laf");
+    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+    String laf = "none";
+    if (lafProp != null)
+    {
+      laf = lafProp;
+    }
+    else if (lafSetting != null)
+    {
+      laf = lafSetting;
+    }
+    boolean lafSet = false;
+    switch (laf)
+    {
+    case "crossplatform":
+      lafSet = setCrossPlatformLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "system":
+      lafSet = setSystemLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "gtk":
+      lafSet = setGtkLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "metal":
+      lafSet = setMetalLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "nimbus":
+      lafSet = setNimbusLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "quaqua":
+      lafSet = setQuaquaLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "vaqua":
+      lafSet = setVaquaLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "mac":
+      lafSet = setMacLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "none":
+      break;
+    default:
+      Cache.log.error("Requested laf=" + laf + " not implemented");
+    }
+    if (!lafSet)
+    {
+      setSystemLookAndFeel();
+      if (Platform.isLinux())
+      {
+        setMetalLookAndFeel();
+      }
+      if (Platform.isAMac())
+      {
+        setMacLookAndFeel();
+      }
+    }
+  }
+
+  private static boolean setCrossPlatformLookAndFeel()
+  {
+    return setGenericLookAndFeel(false);
+  }
+
+  private static boolean setSystemLookAndFeel()
+  {
+    return setGenericLookAndFeel(true);
+  }
+
+  private static boolean setGenericLookAndFeel(boolean system)
+  {
+    boolean set = false;
+    try
+    {
+      UIManager.setLookAndFeel(
+              system ? UIManager.getSystemLookAndFeelClassName()
+                      : UIManager.getCrossPlatformLookAndFeelClassName());
+      set = true;
+    } catch (Exception ex)
+    {
+      Cache.log.error("Unexpected Look and Feel Exception");
+      Cache.log.error(ex.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(ex));
+    }
+    return set;
+  }
+
+  private static boolean setSpecificLookAndFeel(String name,
+          String className, boolean nameStartsWith)
+  {
+    boolean set = false;
+    try
+    {
+      for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
+      {
+        if (info.getName() != null && nameStartsWith
+                ? info.getName().toLowerCase()
+                        .startsWith(name.toLowerCase())
+                : info.getName().toLowerCase().equals(name.toLowerCase()))
+        {
+          className = info.getClassName();
+          break;
+        }
+      }
+      UIManager.setLookAndFeel(className);
+      set = true;
+    } catch (Exception ex)
+    {
+      Cache.log.error("Unexpected Look and Feel Exception");
+      Cache.log.error(ex.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(ex));
+    }
+    return set;
+  }
+
+  private static boolean setGtkLookAndFeel()
+  {
+    return setSpecificLookAndFeel("gtk",
+            "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
+  }
+
+  private static boolean setMetalLookAndFeel()
+  {
+    return setSpecificLookAndFeel("metal",
+            "javax.swing.plaf.metal.MetalLookAndFeel", false);
+  }
+
+  private static boolean setNimbusLookAndFeel()
+  {
+    return setSpecificLookAndFeel("nimbus",
+            "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
+  }
+
+  private static boolean setQuaquaLookAndFeel()
+  {
+    return setSpecificLookAndFeel("quaqua",
+            ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
+                    .getName(),
+            false);
+  }
+
+  private static boolean setVaquaLookAndFeel()
+  {
+    return setSpecificLookAndFeel("vaqua",
+            "org.violetlib.aqua.AquaLookAndFeel", false);
+  }
+
+  private static boolean setMacLookAndFeel()
+  {
+    boolean set = false;
+    System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+            "Jalview");
+    System.setProperty("apple.laf.useScreenMenuBar", "true");
+    set = setQuaquaLookAndFeel();
+    if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
+            .toLowerCase().contains("quaqua"))
+    {
+      set = setVaquaLookAndFeel();
+    }
+    return set;
+  }
+
   private static void showUsage()
   {
     System.out.println(
@@ -798,7 +999,9 @@ public class Jalview
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
-                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                    + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+                    + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+                    + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
   private static void startUsageStats(final Desktop desktop)
@@ -836,10 +1039,10 @@ public class Jalview
    * Locate the given string as a file and pass it to the groovy interpreter.
    * 
    * @param groovyscript
-   *                         the script to execute
+   *          the script to execute
    * @param jalviewContext
-   *                         the Jalview Desktop object passed in to the groovy
-   *                         binding as the 'Jalview' object.
+   *          the Jalview Desktop object passed in to the groovy binding as the
+   *          'Jalview' object.
    */
   private void executeGroovyScript(String groovyscript, AlignFrame af)
   {
@@ -968,8 +1171,8 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode when
-   * it just ends the JVM
+   * Quit method delegates to Desktop.quit - unless running in headless mode
+   * when it just ends the JVM
    */
   public void quit()
   {
diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java
index fb1c5cd..fecacbe 100644
--- a/src/jalview/bin/Launcher.java
+++ b/src/jalview/bin/Launcher.java
@@ -49,8 +49,8 @@ public class Launcher
 
   /**
    * main method for jalview.bin.Launcher. This restarts the same JRE's JVM with
-   * the same arguments but with memory adjusted based on extracted -jvmmempc and
-   * -jvmmemmax application arguments. If on a Mac then extra dock:icon and
+   * the same arguments but with memory adjusted based on extracted -jvmmempc
+   * and -jvmmemmax application arguments. If on a Mac then extra dock:icon and
    * dock:name arguments are also set.
    * 
    * @param args
@@ -130,7 +130,7 @@ public class Launcher
     if (!memSet)
     {
       long maxMemLong = MemorySetting.getMemorySetting(jvmmemmax, jvmmempc);
-      
+
       if (maxMemLong > 0)
       {
         memSetting = "-Xmx" + Long.toString(maxMemLong);
@@ -153,6 +153,14 @@ public class Launcher
       }
     }
 
+    String scalePropertyArg = HiDPISetting.getScalePropertyArg();
+    if (scalePropertyArg != null)
+    {
+      System.out.println("Running " + startClass + " with scale setting "
+              + scalePropertyArg);
+      command.add(scalePropertyArg);
+    }
+
     command.add(startClass);
     command.addAll(arguments);
 
@@ -160,7 +168,8 @@ public class Launcher
 
     // System.out.println("COMMAND: " + String.join(" ", builder.command()));
     System.out.println("Running " + startClass + " with "
-            + (memSetting == null ? "no memory setting" : memSetting));
+            + (memSetting == null ? "no memory setting"
+                    : ("memory setting " + memSetting)));
 
     if (Boolean.parseBoolean(System.getProperty("launcherstop")))
     {
@@ -176,7 +185,8 @@ public class Launcher
       if (e.getMessage().toLowerCase().contains("memory"))
       {
         System.out.println("Caught a memory exception: " + e.getMessage());
-        // Probably the "Cannot allocate memory" error, try without the memory setting
+        // Probably the "Cannot allocate memory" error, try without the memory
+        // setting
         ArrayList<String> commandNoMem = new ArrayList<>();
         for (int i = 0; i < command.size(); i++)
         {
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 31736e5..7c3bba7 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -33,6 +33,7 @@ import java.util.List;
  */
 public class SearchResults implements SearchResultsI
 {
+  private int count;
 
   private List<SearchResultMatchI> matches = new ArrayList<>();
 
@@ -168,18 +169,41 @@ public class SearchResults implements SearchResultsI
     if (!matches.contains(m))
     {
       matches.add(m);
+      count++;
     }
     return m;
   }
 
   @Override
+  public void addResult(SequenceI seq, int[] positions)
+  {
+    /*
+     * we only increment the match count by 1 - or not at all,
+     * if the matches are all duplicates of existing
+     */
+    int beforeCount = count;
+    for (int i = 0; i < positions.length - 1; i += 2)
+    {
+      addResult(seq, positions[i], positions[i + 1]);
+    }
+    if (count > beforeCount)
+    {
+      count = beforeCount + 1;
+    }
+  }
+
+  @Override
   public boolean involvesSequence(SequenceI sequence)
   {
+    final int start = sequence.getStart();
+    final int end = sequence.getEnd();
+
     SequenceI ds = sequence.getDatasetSequence();
-    for (SearchResultMatchI _m : matches)
+    for (SearchResultMatchI m : matches)
     {
-      SequenceI matched = _m.getSequence();
-      if (matched != null && (matched == sequence || matched == ds))
+      SequenceI matched = m.getSequence();
+      if (matched != null && (matched == sequence || matched == ds)
+              && (m.getEnd() >= start) && (m.getStart() <= end))
       {
         return true;
       }
@@ -282,9 +306,9 @@ public class SearchResults implements SearchResultsI
   }
 
   @Override
-  public int getSize()
+  public int getCount()
   {
-    return matches.size();
+    return count;
   }
 
   @Override
diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index 3c3ad4e..c89f363 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -41,6 +41,17 @@ public interface SearchResultsI
   SearchResultMatchI addResult(SequenceI seq, int start, int end);
 
   /**
+   * Adds one ore more [start, end] ranges to the results (unless already added
+   * to avoid duplicates). This method only increments the match count by 1.
+   * This is for the case where a match spans ignored hidden residues - it is
+   * formally two or more contiguous matches, but only counted as one match.
+   * 
+   * @param seq
+   * @param positions
+   */
+  void addResult(SequenceI seq, int[] positions);
+
+  /**
    * adds all match results in the argument to this set
    * 
    * @param toAdd
@@ -74,11 +85,13 @@ public interface SearchResultsI
   int[] getResults(SequenceI sequence, int start, int end);
 
   /**
-   * Returns the number of matches found
+   * Returns the number of matches found. Note that if a match straddles ignored
+   * hidden residues, it is counted as one match, although formally recorded as
+   * two (or more) contiguous matched sequence regions
    * 
    * @return
    */
-  int getSize();
+  int getCount();
 
   /**
    * Returns true if no search result matches are held.
diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index 54c0d59..7651016 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -30,7 +28,9 @@ import java.util.Set;
 
 import intervalstore.api.IntervalStoreI;
 import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.BinarySearcher.Compare;
 import intervalstore.impl.IntervalStore;
+import jalview.datamodel.SequenceFeature;
 
 /**
  * A data store for a set of sequence features that supports efficient lookup of
@@ -277,7 +277,7 @@ public class FeatureStore
      * binary search the sorted list to find the insertion point
      */
     int insertPosition = BinarySearcher.findFirst(contactFeatureStarts,
-            f -> f.getBegin() >= feature.getBegin());
+            true, Compare.GE, feature.getBegin());
     contactFeatureStarts.add(insertPosition, feature);
 
 
@@ -286,7 +286,7 @@ public class FeatureStore
      * binary search the sorted list to find the insertion point
      */
     insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
-            f -> f.getEnd() >= feature.getEnd());
+            false, Compare.GE, feature.getEnd());
     contactFeatureEnds.add(insertPosition, feature);
 
     return true;
@@ -314,8 +314,8 @@ public class FeatureStore
      */
     // int pos = binarySearch(features,
     // SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
-    int pos = BinarySearcher.findFirst(features,
-            val -> val.getBegin() >= feature.getBegin());
+    int pos = BinarySearcher.findFirst(features, true, Compare.GE,
+            feature.getBegin());
     int len = features.size();
     while (pos < len)
     {
@@ -396,7 +396,7 @@ public class FeatureStore
      * whose end point is not before the target range
      */
     int index = BinarySearcher.findFirst(contactFeatureEnds,
-            f -> f.getEnd() >= from);
+            false, Compare.GE, (int) from);
 
     while (index < contactFeatureEnds.size())
     {
@@ -449,7 +449,7 @@ public class FeatureStore
           List<SequenceFeature> result)
   {
     int index = BinarySearcher.findFirst(contactFeatureStarts,
-            f -> f.getBegin() >= from);
+            true, Compare.GE, (int) from);
 
     while (index < contactFeatureStarts.size())
     {
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index db2f0e1..8ac4991 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,11 +20,8 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.io.gff.SequenceOntologyI;
-
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -33,6 +30,9 @@ import java.util.Set;
 import java.util.TreeMap;
 
 import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
 
 /**
  * A class that stores sequence features in a way that supports efficient
@@ -44,7 +44,6 @@ import intervalstore.api.IntervalI;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-
   /*
    * map from feature type to structured store of features for that type
    * null types are permitted (but not a good idea!)
@@ -414,7 +413,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   public static void sortFeatures(List<? extends IntervalI> features,
           final boolean forwardStrand)
   {
-    IntervalI.sortIntervals(features, forwardStrand);
+    Collections.sort(features,
+            forwardStrand
+                    ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 9c7ce63..461226b 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -629,10 +629,10 @@ public class EnsemblGene extends EnsemblSeqProxy
       SequenceOntologyI so = SequenceOntologyFactory.getInstance();
 
       @Override
-      public boolean isFeatureDisplayed(String type)
+      public boolean isFeatureHidden(String type)
       {
-        return (so.isA(type, SequenceOntologyI.EXON)
-                || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+        return (!so.isA(type, SequenceOntologyI.EXON)
+                && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
       }
 
       @Override
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 1ceabd1..b2224ab 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -22,11 +22,13 @@ package jalview.ext.jmol;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -37,6 +39,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -1190,7 +1193,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;
diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index 232561c..54b2989 100644
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -296,7 +296,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
   private void jbInit() throws Exception
   {
 
-    txt_search = new JvCacheableInputBox<>(getCacheKey());
+    txt_search = new JvCacheableInputBox<>(getCacheKey(), 45);
     populateCmbSearchTargetOptions();
     Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800
             : getTempUserPrefs().get("FTSPanel.width");
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b7d8b3a..4be7d0e 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,54 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -91,6 +139,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -100,53 +149,6 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
 /**
  * DOCUMENT ME!
  * 
@@ -536,7 +538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
           break;
 
@@ -547,9 +550,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
-
           break;
 
         case KeyEvent.VK_LEFT:
@@ -560,7 +563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -572,7 +575,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1168,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
-              { fileName, format }));
+              { file, format }));
 
     }
     else
@@ -1197,39 +1200,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
+        Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
         BackupFiles backupfiles = new BackupFiles(file);
 
         try
         {
-          PrintWriter out = new PrintWriter(
-                  new FileWriter(backupfiles.getTempFilePath()));
+          String tempFilePath = backupfiles.getTempFilePath();
+          Cache.log.trace(
+                  "ALIGNFRAME setting PrintWriter to " + tempFilePath);
+          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+          Cache.log.trace(
+                  "ALIGNFRAME about to write to temp file " + tempFilePath);
 
           out.print(output);
+          Cache.log.trace("ALIGNFRAME about to close file");
           out.close();
+          Cache.log.trace("ALIGNFRAME closed file");
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+                  { file, format.getName() }));
+        } catch (IOException e)
+        {
+          success = false;
+          Cache.log.error(
+                  "ALIGNFRAME Something happened writing the temp file");
+          Cache.log.error(e.getMessage());
+          Cache.log.debug(Cache.getStackTraceString(e));
+
         } catch (Exception ex)
         {
           success = false;
-          ex.printStackTrace();
+          Cache.log.error(
+                  "ALIGNFRAME Something unexpected happened writing the temp file");
+          Cache.log.error(ex.getMessage());
+          Cache.log.debug(Cache.getStackTraceString(ex));
         }
 
         backupfiles.setWriteSuccess(success);
+        Cache.log.debug("ALIGNFRAME writing temp file was "
+                + (success ? "" : "NOT ") + "successful");
         // do the backup file roll and rename the temp file to actual file
+        Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
         success = backupfiles.rollBackupsAndRenameTempFile();
+        Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                + (success ? "" : "un") + "successfully");
 
       }
     }
 
     if (!success)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { fileName }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { file }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
     }
 
     return success;
@@ -1719,10 +1749,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode 
    * 
    * @param up
-   *          DOCUMENT ME!
+   *          or down (if !up)
    */
   public void moveSelectedSequences(boolean up)
   {
@@ -1730,8 +1760,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      return;
+      if (viewport.cursorMode) 
+      {
+        sg = new SequenceGroup();
+        sg.addSequence(viewport.getAlignment()
+                .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
+      } else {
+        return;
+      }
+    }
+    
+    if (sg.getSize() < 1)
+    {
+        return;
     }
+    
+    // TODO: JAL-3733 - add an event to the undo buffer for this !
+    
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);
@@ -1740,19 +1785,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   synchronized void slideSequences(boolean right, int size)
   {
     List<SequenceI> sg = new ArrayList<>();
-    if (viewport.cursorMode)
-    {
-      sg.add(viewport.getAlignment()
-              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
-    }
-    else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport
-                    .getAlignment().getHeight())
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
+            .getSize() != viewport.getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup()
               .getSequences(viewport.getHiddenRepSequences());
     }
 
+    if (sg.size() == 0 && viewport.cursorMode)
+    {
+      sg.add(viewport.getAlignment()
+              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
+    }
+
     if (sg.size() < 1)
     {
       return;
@@ -2450,7 +2495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
+    viewport.setSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -2687,15 +2732,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens a Finder dialog
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder();
+    new Finder(alignPanel);
   }
 
   /**
@@ -2736,8 +2780,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.getViewName() == null)
     {
-      viewport.setViewName(MessageManager
-              .getString("label.view_name_original"));
+      viewport.setViewName(
+              MessageManager.getString("label.view_name_original"));
     }
 
     /*
@@ -3366,8 +3410,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
-            viewport,
-            viewport.getAlignment(), viewport.getHiddenRepSequences());
+            viewport, viewport.getAlignment(),
+            viewport.getHiddenRepSequences());
     changeColour(cs);
   }
 
@@ -5694,6 +5738,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   private Rectangle lastFeatureSettingsBounds = null;
+
   @Override
   public void setFeatureSettingsGeometry(Rectangle bounds)
   {
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 05e446e..8e12ff5 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -59,7 +59,6 @@ import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JInternalFrame;
@@ -446,31 +445,6 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * returns the visible column regions of the alignment
-   * 
-   * @param selectedRegionOnly
-   *          true to just return the contigs intersecting with the selected
-   *          area
-   * @return
-   */
-  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
-  {
-    int start = 0;
-    int end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes() + 1;
-    }
-    else
-    {
-      end = alignment.getWidth();
-    }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
-  }
-
-  /**
    * get hash of undo and redo list for the alignment
    * 
    * @return long[] { historyList.hashCode, redoList.hashCode };
@@ -1018,8 +992,8 @@ public class AlignViewport extends AlignmentViewport
     
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
-    List<String> origRenderOrder = new ArrayList(),
-            origGroups = new ArrayList();
+    List<String> origRenderOrder = new ArrayList<>();
+    List<String> origGroups = new ArrayList<>();
     // preserve original render order - allows differentiation between user configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
@@ -1030,7 +1004,7 @@ public class AlignViewport extends AlignmentViewport
     if (!mergeOnly)
     {
       // only clear displayed features if we are mergeing
-      displayed.clear();
+      // displayed.clear();
     }
     // TODO this clears displayed.featuresRegistered - do we care?
     //
@@ -1062,6 +1036,10 @@ public class AlignViewport extends AlignmentViewport
         {
           displayed.setVisible(type);
         }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }
 
@@ -1090,6 +1068,8 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
   }
 
   public String getViewName()
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 60ad75d..7ed178b 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -53,8 +53,6 @@ import net.miginfocom.swing.MigLayout;
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
-  private static final int ONETHOUSAND = 1000;
-
   private ColourSchemeI oldcs;
 
   private JButton defColours;
@@ -147,7 +145,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 "error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
-      thresholdValue.setText("" + acg.getAnnotationThreshold());
+      thresholdValue
+              .setText(String.valueOf(acg.getAnnotationThreshold()));
     }
 
     jbInit();
@@ -338,7 +337,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         updateView();
       }
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
       ap.paintAlignment(false, false);
@@ -378,6 +377,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -386,33 +386,26 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       thresholdIsMin.setEnabled(false);
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
-            && getCurrentAnnotation().threshold == null)
+            && currentAnnotation.threshold == null)
     {
-      getCurrentAnnotation().setThreshold(new GraphLine(
-              (getCurrentAnnotation().graphMax
-                      - getCurrentAnnotation().graphMin) / 2f,
+      currentAnnotation.setThreshold(new GraphLine(
+              (currentAnnotation.graphMax - currentAnnotation.graphMin)
+                      / 2f,
               "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
-              - getCurrentAnnotation().graphMin * ONETHOUSAND;
-
-      slider.setMinimum(
-              (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
-      slider.setMaximum(
-              (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
-      slider.setMajorTickSpacing((int) (range / 10f));
+      setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
       slider.setEnabled(true);
+
+      setThresholdValueText();
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 
     ap.alignmentChanged();
   }
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 5adecad..d941107 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,6 +21,7 @@
 
 package jalview.gui;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.HiddenColumns;
 import jalview.io.cache.JvCacheableInputBox;
 import jalview.schemes.AnnotationColourGradient;
@@ -254,7 +255,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
   {
     if (slider.isEnabled())
     {
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       updateView();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
@@ -284,6 +285,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     percentThreshold.setEnabled(true);
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -294,26 +296,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
-      if (getCurrentAnnotation().threshold == null)
+      if (currentAnnotation.threshold == null)
       {
-        getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
-                (getCurrentAnnotation().graphMax
-                        - getCurrentAnnotation().graphMin) / 2f,
+        currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+                (currentAnnotation.graphMax
+                        - currentAnnotation.graphMin) / 2f,
                 "Threshold", Color.black));
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
 
-      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
-      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * 1000));
+      setSliderModel(currentAnnotation.graphMin,
+              currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
 
       setThresholdValueText();
 
-      slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
       adjusting = false;
@@ -321,10 +319,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       // build filter params
       filterParams.setThresholdType(
               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().isQuantitative())
+      if (currentAnnotation.isQuantitative())
       {
         filterParams
-                .setThresholdValue(getCurrentAnnotation().threshold.value);
+                .setThresholdValue(currentAnnotation.threshold.value);
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
@@ -380,7 +378,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     // adding them to the selection
     av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
-            getCurrentAnnotation().annotations, filterParams);
+            currentAnnotation.annotations, filterParams);
 
     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
     if (hideCols)
@@ -720,7 +718,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 
     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
-            FILTER_BY_ANN_CACHE_KEY);
+            FILTER_BY_ANN_CACHE_KEY, 23);
 
     public SearchPanel(AnnotationColumnChooser aColChooser)
     {
@@ -730,7 +728,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       this.setBorder(new TitledBorder(
               MessageManager.getString("label.search_filter")));
 
-      searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
       searchBox.setToolTipText(
               MessageManager.getString("info.enter_search_text_here"));
       searchBox.getEditor().getEditorComponent()
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 16db94c..10fc3cf 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -629,6 +629,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     mouseDragLastX = -1;
     mouseDragLastY = -1;
     mouseDragging = false;
+    if (dragMode == DragMode.Resize)
+    {
+      ap.adjustAnnotationHeight();
+    }
     dragMode = DragMode.Undefined;
     ap.getScalePanel().mouseReleased(evt);
 
@@ -668,16 +672,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on starting or continuing a mouse drag. There are two possible
+   * actions:
+   * <ul>
+   * <li>drag up or down on a graphed annotation increases or decreases the
+   * height of the graph</li>
+   * <li>dragging left or right selects the columns dragged across</li>
+   * </ul>
+   * A drag on a graph annotation is treated as column selection if it starts
+   * with more horizontal than vertical movement, and as resize if it starts
+   * with more vertical than horizontal movement. Once started, the drag does
+   * not change mode.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseDragged(MouseEvent evt)
   {
     /*
-     * todo: if dragMode is Undefined:
+     * if dragMode is Undefined:
      * - set to Select if dx > dy
      * - set to Resize if dy > dx
      * - do nothing if dx == dy
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index f13cb10..6f72e10 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -35,6 +35,8 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.math.BigDecimal;
+import java.math.MathContext;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -44,7 +46,6 @@ import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
-import javax.swing.JSlider;
 import javax.swing.JTextField;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -52,6 +53,10 @@ import javax.swing.event.ChangeListener;
 @SuppressWarnings("serial")
 public abstract class AnnotationRowFilter extends JPanel
 {
+  private static final String TWO_DP = "%.2f";
+
+  private final static MathContext FOUR_SIG_FIG = new MathContext(4);
+
   protected AlignViewport av;
 
   protected AlignmentPanel ap;
@@ -64,7 +69,7 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected JCheckBox percentThreshold = new JCheckBox();
 
-  protected JSlider slider = new JSlider();
+  protected Slider slider;
 
   protected JTextField thresholdValue = new JTextField(20);
 
@@ -103,6 +108,8 @@ public abstract class AnnotationRowFilter extends JPanel
   {
     this.av = viewport;
     this.ap = alignPanel;
+    this.slider = new Slider(0f, 100f, 50f);
+
     thresholdValue.addFocusListener(new FocusAdapter()
     {
       @Override
@@ -140,16 +147,62 @@ public abstract class AnnotationRowFilter extends JPanel
     adjusting = true;
     if (percentThreshold.isSelected())
     {
-      thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
-              * 100f / (slider.getMaximum() - slider.getMinimum()));
+      thresholdValue
+              .setText(String.format(TWO_DP, getSliderPercentageValue()));
     }
     else
     {
-      thresholdValue.setText((slider.getValue() / 1000f) + "");
+      /*
+       * round to 4 significant digits without trailing zeroes
+       */
+      float f = getSliderValue();
+      BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
+              .stripTrailingZeros();
+      thresholdValue.setText(formatted.toPlainString());
     }
     adjusting = oldadj;
   }
 
+  /**
+   * Answers the value of the slider position (descaled to 'true' value)
+   * 
+   * @return
+   */
+  protected float getSliderValue()
+  {
+    return slider.getSliderValue();
+  }
+
+  /**
+   * Sets the slider value (scaled from the true value to the slider range)
+   * 
+   * @param value
+   */
+  protected void setSliderValue(float value)
+  {
+    slider.setSliderValue(value);
+  }
+  /**
+   * Answers the value of the slider position as a percentage between minimum and
+   * maximum of its range
+   * 
+   * @return
+   */
+  protected float getSliderPercentageValue()
+  {
+    return slider.getSliderPercentageValue();
+  }
+
+  /**
+   * Sets the slider position for a given percentage value of its min-max range
+   * 
+   * @param pct
+   */
+  protected void setSliderPercentageValue(float pct)
+  {
+    slider.setSliderPercentageValue(pct);
+  }
+
   protected void addSliderMouseListeners()
   {
 
@@ -290,6 +343,10 @@ public abstract class AnnotationRowFilter extends JPanel
     updateView();
   }
 
+  /**
+   * Updates the slider position, and the display, for an update in the slider's
+   * text input field
+   */
   protected void thresholdValue_actionPerformed()
   {
     try
@@ -297,12 +354,11 @@ public abstract class AnnotationRowFilter extends JPanel
       float f = Float.parseFloat(thresholdValue.getText());
       if (percentThreshold.isSelected())
       {
-        slider.setValue(slider.getMinimum() + ((int) ((f / 100f)
-                * (slider.getMaximum() - slider.getMinimum()))));
+        setSliderPercentageValue(f);
       }
       else
       {
-        slider.setValue((int) (f * 1000));
+        setSliderValue(f);
       }
       updateView();
     } catch (NumberFormatException ex)
@@ -528,4 +584,23 @@ public abstract class AnnotationRowFilter extends JPanel
       valueChanged(true);
     }
   }
+
+  /**
+   * Sets the min-max range and current value of the slider, with rescaling from
+   * true values to slider range as required
+   * 
+   * @param min
+   * @param max
+   * @param value
+   */
+  protected void setSliderModel(float min, float max, float value)
+  {
+    slider.setSliderModel(min, max, value);
+
+    /*
+     * tick mark every 10th position
+     */
+    slider.setMajorTickSpacing(
+            (slider.getMaximum() - slider.getMinimum()) / 10);
+  }
 }
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 724cec1..3432911 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -208,11 +208,6 @@ public class AppJmolBinding extends JalviewJmolBinding
     AlignmentPanel ap = (alignment == null)
             ? appJmolWindow.getAlignmentPanel()
             : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
-    }
-
-    return null;
+    return ap.av.getAlignPanel().getFeatureRenderer();
   }
 }
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 65c8b5a..c43c699 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -256,7 +256,7 @@ public class BlogReader extends JPanel
     chan.setURL(
             jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
                     jalview.bin.Cache.getDefault("www.jalview.org",
-                            "http://www.jalview.org")
+                            "https://www.jalview.org")
                             + "/feeds/desktop/rss"));
     loadLastM();
     _channelModel.addChannel(chan);
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index a7349b8..47bad81 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -575,7 +575,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       /*
        * ensure that any newly discovered features (e.g. RESNUM)
-       * are added to any open feature settings dialog
+       * are notified to the FeatureRenderer (and added to any 
+       * open feature settings dialog)
        */
       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
       if (fr != null)
diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4c019a6..6cd8106 100644
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -20,15 +20,20 @@
  */
 package jalview.gui;
 
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
+import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.GraphicsEnvironment;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
@@ -38,12 +43,19 @@ import java.io.PipedOutputStream;
 import java.io.PrintStream;
 
 import javax.swing.JButton;
+import javax.swing.JComboBox;
 import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 
+import org.apache.log4j.Level;
 import org.apache.log4j.SimpleLayout;
 
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
 /**
  * Simple Jalview Java Console. Version 1 - allows viewing of console output
  * after desktop is created. Acquired with thanks from RJHM's site
@@ -88,6 +100,10 @@ public class Console extends WindowAdapter
 
   private int MIN_HEIGHT = 250;
 
+  private JComboBox<Level> logLevelCombo = new JComboBox<Level>();
+
+  protected Level startingLogLevel = Level.INFO;
+
   public Console()
   {
     // create all components and add them
@@ -115,17 +131,107 @@ public class Console extends WindowAdapter
     // textArea = cpt.getTextArea();
     textArea = new JTextArea();
     textArea.setEditable(false);
-    JButton button = new JButton(MessageManager.getString("action.clear"));
+    JButton clearButton = new JButton(
+            MessageManager.getString("action.clear"));
+    JButton copyToClipboardButton = new JButton(
+            MessageManager.getString("label.copy_to_clipboard"));
+    copyToClipboardButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copyConsoleTextToClipboard();
+      }
+    });
+    copyToClipboardButton.addMouseListener(new MouseAdapter()
+    {
+      private Color bg = textArea.getBackground();
+
+      private Color fg = textArea.getForeground();
+
+      public void mousePressed(MouseEvent e)
+      {
+        textArea.setBackground(textArea.getSelectionColor());
+        textArea.setForeground(textArea.getSelectedTextColor());
+      }
+
+      public void mouseReleased(MouseEvent e)
+      {
+        textArea.setBackground(bg);
+        textArea.setForeground(fg);
+      }
+
+    });
+    copyToClipboardButton.setToolTipText(
+            MessageManager.getString("label.copy_to_clipboard_tooltip"));
+
+    JLabel logLevelLabel = new JLabel(
+            MessageManager.getString("label.log_level") + ":");
+
+    // logLevelCombo.addItem(Level.ALL);
+    logLevelCombo.addItem(Level.TRACE);
+    logLevelCombo.addItem(Level.DEBUG);
+    logLevelCombo.addItem(Level.INFO);
+    logLevelCombo.addItem(Level.WARN);
+    // logLevelCombo.addItem(Level.ERROR);
+    // logLevelCombo.addItem(Level.FATAL);
+    // logLevelCombo.addItem(Level.OFF);
+    // set startingLogLevel
+    startingLogLevel = Cache.log == null ? Level.INFO
+            : Cache.log.getLevel();
+    setChosenLogLevelCombo();
+    logLevelCombo.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        if (Cache.log != null)
+        {
+          Cache.log.setLevel((Level) logLevelCombo.getSelectedItem());
+        }
+      }
+
+    });
 
     // frame = cpt;
     frame.getContentPane().setLayout(new BorderLayout());
     frame.getContentPane().add(new JScrollPane(textArea),
             BorderLayout.CENTER);
-    frame.getContentPane().add(button, BorderLayout.SOUTH);
+    JPanel southPanel = new JPanel();
+    southPanel.setLayout(new GridBagLayout());
+
+    JPanel logLevelPanel = new JPanel();
+    logLevelPanel.setAlignmentX(JPanel.LEFT_ALIGNMENT);
+    logLevelPanel.add(logLevelLabel);
+    logLevelPanel.add(logLevelCombo);
+    String logLevelTooltip = MessageManager.formatMessage(
+            "label.log_level_tooltip", startingLogLevel.toString());
+    logLevelLabel.setToolTipText(logLevelTooltip);
+    logLevelCombo.setToolTipText(logLevelTooltip);
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.gridx = 0;
+    gbc.gridy = 0;
+    gbc.gridwidth = 1;
+    gbc.gridheight = 1;
+    gbc.weightx = 0.1;
+    southPanel.add(logLevelPanel, gbc);
+
+    gbc.gridx++;
+    gbc.weightx = 0.8;
+    gbc.fill = GridBagConstraints.HORIZONTAL;
+    southPanel.add(clearButton, gbc);
+
+    gbc.gridx++;
+    gbc.weightx = 0.1;
+    gbc.fill = GridBagConstraints.NONE;
+    southPanel.add(copyToClipboardButton, gbc);
+
+    southPanel.setVisible(true);
+    frame.getContentPane().add(southPanel, BorderLayout.SOUTH);
     frame.setVisible(visible);
     updateConsole = visible;
     frame.addWindowListener(this);
-    button.addActionListener(this);
+    clearButton.addActionListener(this);
+
     if (redirect)
     {
       redirectStreams();
@@ -151,6 +257,53 @@ public class Console extends WindowAdapter
     textAppender.start();
   }
 
+  private void setChosenLogLevelCombo()
+  {
+    setChosenLogLevelCombo(startingLogLevel);
+  }
+
+  private void setChosenLogLevelCombo(Level setLogLevel)
+  {
+    logLevelCombo.setSelectedItem(setLogLevel);
+    if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
+    {
+      // setLogLevel not (yet) in list
+      if (setLogLevel != null && setLogLevel instanceof Level)
+      {
+        // add new item to list (might be set via .jalview_properties)
+        boolean added = false;
+        for (int i = 0; i < logLevelCombo.getItemCount(); i++)
+        {
+          Level l = (Level) logLevelCombo.getItemAt(i);
+          if (l.isGreaterOrEqual(setLogLevel))
+          {
+            logLevelCombo.insertItemAt(setLogLevel, i);
+            added = true;
+            break;
+          }
+        }
+        if (!added) // lower priority than others or some confusion -- add to
+                    // end of list
+        {
+          logLevelCombo.addItem(setLogLevel);
+        }
+        logLevelCombo.setSelectedItem(setLogLevel);
+      }
+      else
+      {
+        logLevelCombo.setSelectedItem(Level.INFO);
+      }
+    }
+  }
+
+  private void copyConsoleTextToClipboard()
+  {
+    String consoleText = textArea.getText();
+    StringSelection consoleTextSelection = new StringSelection(consoleText);
+    Clipboard cb = Toolkit.getDefaultToolkit().getSystemClipboard();
+    cb.setContents(consoleTextSelection, null);
+  }
+
   PipedOutputStream pout = null, perr = null;
 
   public void redirectStreams()
@@ -644,12 +797,19 @@ public class Console extends WindowAdapter
     frame.setVisible(selected);
     if (selected == true)
     {
+      setChosenLogLevelCombo();
       redirectStreams();
       updateConsole = true;
       frame.toFront();
     }
     else
     {
+      // reset log level to what it was before
+      if (Cache.log != null)
+      {
+        Cache.log.setLevel(startingLogLevel);
+      }
+
       unredirectStreams();
       updateConsole = false;
     }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index b3bff0d..279d89f 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -272,11 +272,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
        */
       if (viewport != null && viewport.getAlignment() != null)
       {
-        if (proxyColourScheme != null)
-        {
-          viewport.applyFeaturesStyle(proxyColourScheme);
-        }
         ((AlignViewport) viewport).addAlignment(al, title);
+        viewport.applyFeaturesStyle(proxyColourScheme);
       }
       else
       {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7564dda..0441e5e 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -927,7 +927,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (java.lang.ClassCastException cex)
     {
       Cache.log.warn(
-              "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
               cex);
     }
   }
@@ -1135,7 +1135,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     panel.add(history);
     history.setPreferredSize(new Dimension(400, 20));
     history.setEditable(true);
-    history.addItem("http://www.");
+    history.addItem("https://www.");
 
     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
 
@@ -1351,7 +1351,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                       "..Checking..")
               + " is available for download from "
               + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
+                      "https://www.jalview.org")
               + " !!");
       if (red)
       {
@@ -1362,7 +1362,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             "AUTHORFNAMES",
             "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
-            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
             + "<br><br>If  you use Jalview, please cite:"
             + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
             + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index b87e4bf..aeac959 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -162,7 +162,7 @@ public class FeatureSettings extends JPanel
 
   JPanel groupPanel;
 
-  JSlider transparency = new JSlider();
+  JSlider transparency= new JSlider();
 
   private JCheckBox showComplementOnTop;
 
diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 5b77dfc..512cf06 100644
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -49,6 +49,8 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.math.BigDecimal;
+import java.math.MathContext;
 import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
@@ -63,7 +65,6 @@ import javax.swing.JComboBox;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
-import javax.swing.JSlider;
 import javax.swing.JTextField;
 import javax.swing.border.EmptyBorder;
 import javax.swing.border.LineBorder;
@@ -79,6 +80,8 @@ import javax.swing.event.ChangeListener;
  */
 public class FeatureTypeSettings extends JalviewDialog
 {
+  private final static MathContext FOUR_SIG_FIG = new MathContext(4);
+
   private final static String LABEL_18N = MessageManager
           .getString("label.label");
 
@@ -142,11 +145,6 @@ public class FeatureTypeSettings extends JalviewDialog
   private float max;
 
   /*
-   * scale factor for conversion between absolute min-max and slider
-   */
-  private float scaleFactor;
-
-  /*
    * radio button group, to select what to colour by:
    * simple colour, by category (text), or graduated
    */
@@ -169,7 +167,7 @@ public class FeatureTypeSettings extends JalviewDialog
 
   private JComboBox<Object> threshold = new JComboBox<>();
 
-  private JSlider slider = new JSlider();
+  private Slider slider;
 
   private JTextField thresholdValue = new JTextField(20);
 
@@ -348,12 +346,11 @@ public class FeatureTypeSettings extends JalviewDialog
        * update min-max scaling if there is a range to work with,
        * else disable the widgets (this shouldn't happen if only 
        * valid options are offered in the combo box)
+       * offset slider to have only non-negative values if necessary (JAL-2983)
        */
-      scaleFactor = (max == min) ? 1f : 100f / (max - min);
-      float range = (max - min) * scaleFactor;
-      slider.setMinimum((int) (min * scaleFactor));
-      slider.setMaximum((int) (max * scaleFactor));
-      slider.setMajorTickSpacing((int) (range / 10f));
+      slider.setSliderModel(min, max, min);
+      slider.setMajorTickSpacing(
+              (int) ((slider.getMaximum() - slider.getMinimum()) / 10f));
 
       threshline = new GraphLine((max - min) / 2f, "Threshold",
               Color.black);
@@ -365,8 +362,8 @@ public class FeatureTypeSettings extends JalviewDialog
                 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
                         : BELOW_THRESHOLD_OPTION);
         slider.setEnabled(true);
-        slider.setValue((int) (fc.getThreshold() * scaleFactor));
-        thresholdValue.setText(String.valueOf(fc.getThreshold()));
+        slider.setSliderValue(fc.getThreshold());
+        setThresholdValueText(fc.getThreshold());
         thresholdValue.setEnabled(true);
         thresholdIsMin.setEnabled(true);
       }
@@ -641,6 +638,7 @@ public class FeatureTypeSettings extends JalviewDialog
         thresholdValue_actionPerformed();
       }
     });
+    slider = new Slider(0f, 100f, 50f);
     slider.setPaintLabels(false);
     slider.setPaintTicks(true);
     slider.setBackground(Color.white);
@@ -657,8 +655,7 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (!adjusting)
         {
-          thresholdValue
-                  .setText(String.valueOf(slider.getValue() / scaleFactor));
+          setThresholdValueText(slider.getSliderValue());
           thresholdValue.setBackground(Color.white); // to reset red for invalid
           sliderValueChanged();
         }
@@ -1033,8 +1030,8 @@ public class FeatureTypeSettings extends JalviewDialog
       float f = Float.parseFloat(thresholdValue.getText());
       f = Float.max(f,  this.min);
       f = Float.min(f, this.max);
-      thresholdValue.setText(String.valueOf(f));
-      slider.setValue((int) (f * scaleFactor));
+      setThresholdValueText(f);
+      slider.setSliderValue(f);
       threshline.value = f;
       thresholdValue.setBackground(Color.white); // ok
       adjusting = false;
@@ -1047,13 +1044,25 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
+   * Sets the text field for threshold value, rounded to four significant figures
+   * 
+   * @param f
+   */
+  void setThresholdValueText(float f)
+  {
+    BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
+            .stripTrailingZeros();
+    thresholdValue.setText(formatted.toPlainString());
+  }
+
+  /**
    * Action on change of threshold slider value. This may be done interactively
    * (by moving the slider), or programmatically (to update the slider after
    * manual input of a threshold value).
    */
   protected void sliderValueChanged()
   {
-    threshline.value = getRoundedSliderValue();
+    threshline.value = slider.getSliderValue();
 
     /*
      * repaint alignment, but not Overview or structure,
@@ -1062,21 +1071,6 @@ public class FeatureTypeSettings extends JalviewDialog
     colourChanged(false);
   }
 
-  /**
-   * Converts the slider value to its absolute value by dividing by the
-   * scaleFactor. Rounding errors are squashed by forcing min/max of slider
-   * range to the actual min/max of feature score range
-   * 
-   * @return
-   */
-  private float getRoundedSliderValue()
-  {
-    int value = slider.getValue();
-    float f = value == slider.getMaximum() ? max
-            : (value == slider.getMinimum() ? min : value / scaleFactor);
-    return f;
-  }
-
   void addActionListener(ActionListener listener)
   {
     if (featureSettings != null)
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index a4d7ad0..537c323 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -28,9 +28,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GFinder;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Dimension;
+import java.awt.Graphics;
 import java.awt.event.ActionEvent;
 import java.awt.event.KeyEvent;
 import java.util.ArrayList;
@@ -65,7 +65,7 @@ public class Finder extends GFinder
 
   private static final int MIN_HEIGHT = 120;
 
-  private static final int MY_HEIGHT = 120;
+  private static final int MY_HEIGHT = 150;
 
   private static final int MY_WIDTH = 400;
 
@@ -82,33 +82,17 @@ public class Finder extends GFinder
 
   private SearchResultsI searchResults;
 
-  /*
-   * true if we only search a given alignment view
-   */
-  private boolean focusfixed;
-
-  /**
-   * Creates a new Finder object with no associated viewport or panel. Each Find
-   * or Find Next action will act on whichever viewport has focus at the time.
-   */
-  public Finder()
-  {
-    this(null, null);
-  }
-
   /**
-   * Constructor given an associated viewport and alignment panel. Constructs
-   * and displays an internal frame where the user can enter a search string.
+   * Constructor given an associated alignment panel. Constructs and displays an
+   * internal frame where the user can enter a search string.
    * 
-   * @param viewport
    * @param alignPanel
    */
-  public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
+  public Finder(AlignmentPanel alignPanel)
   {
-    av = viewport;
+    av = alignPanel.getAlignViewport();
     ap = alignPanel;
     finders = new HashMap<>();
-    focusfixed = viewport != null;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -122,6 +106,7 @@ public class Finder extends GFinder
               }
             });
     addEscapeHandler();
+
     Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
             MY_WIDTH, MY_HEIGHT);
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
@@ -172,13 +157,14 @@ public class Finder extends GFinder
   /**
    * if !focusfixed and not in a desktop environment, checks that av and ap are
    * valid. Otherwise, gets the topmost alignment window and sets av and ap
-   * accordingly
+   * accordingly. Also sets the 'ignore hidden' checkbox disabled if the viewport
+   * has no hidden columns.
    * 
    * @return false if no alignment window was found
    */
   boolean getFocusedViewport()
   {
-    if (focusfixed || Desktop.desktop == null)
+    if (Desktop.desktop == null)
     {
       if (ap != null && av != null)
       {
@@ -198,6 +184,7 @@ public class Finder extends GFinder
       {
         av = ((AlignFrame) alignFrame).viewport;
         ap = ((AlignFrame) alignFrame).alignPanel;
+        ignoreHidden.setEnabled(av.hasHiddenColumns());
         return true;
       }
     }
@@ -274,13 +261,16 @@ public class Finder extends GFinder
 
     boolean isCaseSensitive = caseSensitive.isSelected();
     boolean doSearchDescription = searchDescription.isSelected();
+    boolean skipHidden = ignoreHidden.isSelected();
     if (doFindAll)
     {
-      finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+      finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
     }
     else
     {
-      finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              skipHidden);
     }
 
     searchResults = finder.getSearchResults();
@@ -314,11 +304,11 @@ public class Finder extends GFinder
                 : "";
         if (searchResults != null)
         {
-          if (idMatch.size() > 0 && searchResults.getSize() > 0)
+          if (idMatch.size() > 0 && searchResults.getCount() > 0)
           {
             message += " and ";
           }
-          message += searchResults.getSize()
+          message += searchResults.getCount()
                   + " subsequence matches found.";
         }
         JvOptionPane.showInternalMessageDialog(this, message, null,
@@ -388,4 +378,15 @@ public class Finder extends GFinder
       ap.alignFrame.requestFocus();
     }
   }
+
+  @Override
+  protected void paintComponent(Graphics g)
+  {
+    /*
+     * enable 'hidden regions' option only if
+     * 'top' viewport has hidden columns
+     */
+    getFocusedViewport();
+    super.paintComponent(g);
+  }
 }
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index a925227..541c253 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -320,6 +320,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
       {
         g.setFont(getHiddenFont(sequence, alignViewport));
+        fm = g.getFontMetrics();
       }
 
       // Selected sequence colours
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 5342c90..92b612a 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -53,7 +53,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
-import javax.swing.JSlider;
 import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.border.TitledBorder;
@@ -93,7 +92,7 @@ public class OptsAndParamsPage
 
     JLabel optlabel = new JLabel();
 
-    JComboBox val = new JComboBox();
+    JComboBox<String> val = new JComboBox<>();
 
     public OptionBox(OptionI opt)
     {
@@ -127,7 +126,7 @@ public class OptsAndParamsPage
         }
       }
       add(enabled, BorderLayout.NORTH);
-      for (Object str : opt.getPossibleValues())
+      for (String str : opt.getPossibleValues())
       {
         val.addItem(str);
       }
@@ -277,7 +276,7 @@ public class OptsAndParamsPage
 
     boolean choice = false;
 
-    JComboBox choicebox;
+    JComboBox<String> choicebox;
 
     JPanel controlPanel = new JPanel();
 
@@ -289,7 +288,7 @@ public class OptsAndParamsPage
 
     boolean integ = false;
 
-    Object lastVal;
+    String lastVal;
 
     ParameterI parameter;
 
@@ -299,7 +298,7 @@ public class OptsAndParamsPage
 
     JButton showDesc = new JButton();
 
-    JSlider slider = null;
+    Slider slider = null;
 
     JTextArea string = new JTextArea();
 
@@ -363,7 +362,7 @@ public class OptsAndParamsPage
       validate();
     }
 
-    private void makeExpanderParam(ParameterI parm)
+    private void makeExpanderParam(final ParameterI parm)
     {
       setPreferredSize(new Dimension(PARAM_WIDTH, PARAM_CLOSEDHEIGHT));
       setBorder(new TitledBorder(parm.getName()));
@@ -451,6 +450,9 @@ public class OptsAndParamsPage
       validate();
     }
 
+    /**
+     * Action on input in text field
+     */
     @Override
     public void actionPerformed(ActionEvent e)
     {
@@ -467,24 +469,20 @@ public class OptsAndParamsPage
 
     private void checkIfModified()
     {
-      Object cstate = updateSliderFromValueField();
-      boolean notmod = false;
-      if (cstate.getClass() == lastVal.getClass())
-      {
-        if (cstate instanceof int[])
-        {
-          notmod = (((int[]) cstate)[0] == ((int[]) lastVal)[0]);
-        }
-        else if (cstate instanceof float[])
-        {
-          notmod = (((float[]) cstate)[0] == ((float[]) lastVal)[0]);
-        }
-        else if (cstate instanceof String[])
-        {
-          notmod = (((String[]) cstate)[0].equals(((String[]) lastVal)[0]));
-        }
-      }
-      pmdialogbox.argSetModified(this, !notmod);
+      Object cstate = getCurrentValue();
+      boolean modified = !cstate.equals(lastVal);
+      pmdialogbox.argSetModified(this, modified);
+    }
+
+    /**
+     * Answers the current value of the parameter, as text
+     * 
+     * @return
+     */
+    private String getCurrentValue()
+    {
+      return choice ? (String) choicebox.getSelectedItem()
+              : valueField.getText();
     }
 
     @Override
@@ -566,16 +564,20 @@ public class OptsAndParamsPage
 
     }
 
+    /**
+     * Action on change of slider value
+     */
     @Override
     public void stateChanged(ChangeEvent e)
     {
       if (!adjusting)
       {
-        valueField.setText("" + ((integ) ? ("" + slider.getValue())
-                : ("" + slider.getValue() / 1000f)));
+        float value = slider.getSliderValue();
+        valueField.setText(
+                integ ? Integer.toString((int) value)
+                        : Float.toString(value));
         checkIfModified();
       }
-
     }
 
     public void updateControls(ParameterI parm)
@@ -586,14 +588,12 @@ public class OptsAndParamsPage
       {
         if (choice)
         {
-          choicebox = new JComboBox();
+          choicebox = new JComboBox<>();
           choicebox.addActionListener(this);
           controlPanel.add(choicebox, BorderLayout.CENTER);
         }
         else
         {
-          slider = new JSlider();
-          slider.addChangeListener(this);
           valueField = new JTextField();
           valueField.addActionListener(this);
           valueField.addKeyListener(new KeyListener()
@@ -622,9 +622,13 @@ public class OptsAndParamsPage
             }
           });
           valueField.setPreferredSize(new Dimension(60, 25));
+          valueField.setText(parm.getValue());
+          slider = makeSlider(parm.getValidValue());
+          updateSliderFromValueField();
+          slider.addChangeListener(this);
+
           controlPanel.add(slider, BorderLayout.WEST);
           controlPanel.add(valueField, BorderLayout.EAST);
-
         }
       }
 
@@ -634,8 +638,8 @@ public class OptsAndParamsPage
         {
           if (init)
           {
-            List vals = parm.getPossibleValues();
-            for (Object val : vals)
+            List<String> vals = parm.getPossibleValues();
+            for (String val : vals)
             {
               choicebox.addItem(val);
             }
@@ -651,96 +655,105 @@ public class OptsAndParamsPage
           valueField.setText(parm.getValue());
         }
       }
-      lastVal = updateSliderFromValueField();
+      lastVal = getCurrentValue();
       adjusting = false;
     }
 
-    public Object updateSliderFromValueField()
+    private Slider makeSlider(ValueConstrainI validValue)
+    {
+      if (validValue != null)
+      {
+        final Number minValue = validValue.getMin();
+        final Number maxValue = validValue.getMax();
+        if (minValue != null && maxValue != null)
+        {
+          return new Slider(minValue.floatValue(), maxValue.floatValue(),
+                  minValue.floatValue());
+        }
+      }
+
+      /*
+       * otherwise, a nominal slider which will not be visible
+       */
+      return new Slider(0, 100, 50);
+    }
+
+    public void updateSliderFromValueField()
     {
-      int iVal;
-      float fVal;
       if (validator != null)
       {
+        final Number minValue = validator.getMin();
+        final Number maxValue = validator.getMax();
         if (integ)
         {
-          iVal = 0;
+          int iVal = 0;
           try
           {
             valueField.setText(valueField.getText().trim());
             iVal = Integer.valueOf(valueField.getText());
-            if (validator.getMin() != null
-                    && validator.getMin().intValue() > iVal)
+            if (minValue != null
+                    && minValue.intValue() > iVal)
             {
-              iVal = validator.getMin().intValue();
+              iVal = minValue.intValue();
               // TODO: provide visual indication that hard limit was reached for
               // this parameter
             }
-            if (validator.getMax() != null
-                    && validator.getMax().intValue() < iVal)
+            if (maxValue != null && maxValue.intValue() < iVal)
             {
-              iVal = validator.getMax().intValue();
-              // TODO: provide visual indication that hard limit was reached for
-              // this parameter
+              iVal = maxValue.intValue();
             }
-          } catch (Exception e)
+          } catch (NumberFormatException e)
           {
+            System.err.println(e.toString());
           }
-          ;
-          // update value field to reflect any bound checking we performed.
-          valueField.setText("" + iVal);
-          if (validator.getMin() != null && validator.getMax() != null)
+          if (minValue != null || maxValue != null)
           {
-            slider.getModel().setRangeProperties(iVal, 1,
-                    validator.getMin().intValue(),
-                    validator.getMax().intValue() + 1, true);
+            valueField.setText(String.valueOf(iVal));
+            slider.setSliderValue(iVal);
           }
           else
           {
             slider.setVisible(false);
           }
-          return new int[] { iVal };
         }
         else
         {
-          fVal = 0f;
+          float fVal = 0f;
           try
           {
             valueField.setText(valueField.getText().trim());
             fVal = Float.valueOf(valueField.getText());
-            if (validator.getMin() != null
-                    && validator.getMin().floatValue() > fVal)
+            if (minValue != null
+                    && minValue.floatValue() > fVal)
             {
-              fVal = validator.getMin().floatValue();
+              fVal = minValue.floatValue();
               // TODO: provide visual indication that hard limit was reached for
               // this parameter
               // update value field to reflect any bound checking we performed.
               valueField.setText("" + fVal);
             }
-            if (validator.getMax() != null
-                    && validator.getMax().floatValue() < fVal)
+            if (maxValue != null
+                    && maxValue.floatValue() < fVal)
             {
-              fVal = validator.getMax().floatValue();
+              fVal = maxValue.floatValue();
               // TODO: provide visual indication that hard limit was reached for
               // this parameter
               // update value field to reflect any bound checking we performed.
               valueField.setText("" + fVal);
             }
-          } catch (Exception e)
+          } catch (NumberFormatException e)
           {
+            System.err.println(e.toString());
           }
-          ;
-          if (validator.getMin() != null && validator.getMax() != null)
+          if (minValue != null && maxValue != null)
           {
-            slider.getModel().setRangeProperties((int) (fVal * 1000f), 1,
-                    (int) (validator.getMin().floatValue() * 1000f),
-                    1 + (int) (validator.getMax().floatValue() * 1000f),
-                    true);
+            slider.setSliderModel(minValue.floatValue(),
+                    maxValue.floatValue(), fVal);
           }
           else
           {
             slider.setVisible(false);
           }
-          return new float[] { fVal };
         }
       }
       else
@@ -748,14 +761,8 @@ public class OptsAndParamsPage
         if (!choice)
         {
           slider.setVisible(false);
-          return new String[] { valueField.getText().trim() };
-        }
-        else
-        {
-          return new String[] { (String) choicebox.getSelectedItem() };
         }
       }
-
     }
   }
 
@@ -801,9 +808,9 @@ public class OptsAndParamsPage
 
   URL linkImageURL = getClass().getResource("/images/link.gif");
 
-  Map<String, OptionBox> optSet = new java.util.LinkedHashMap<String, OptionBox>();
+  Map<String, OptionBox> optSet = new java.util.LinkedHashMap<>();
 
-  Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<String, ParamBox>();
+  Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<>();
 
   public Map<String, OptionBox> getOptSet()
   {
@@ -904,7 +911,7 @@ public class OptsAndParamsPage
    */
   public List<ArgumentI> getCurrentSettings()
   {
-    List<ArgumentI> argSet = new ArrayList<ArgumentI>();
+    List<ArgumentI> argSet = new ArrayList<>();
     for (OptionBox opts : getOptSet().values())
     {
       OptionI opt = opts.getOptionIfEnabled();
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 4f660a2..3512e42 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -141,6 +141,12 @@ public class PCAPanel extends GPCAPanel
   protected void close_actionPerformed()
   {
     setPcaModel(null);
+    if (this.rc != null)
+    {
+      this.rc.sequencePoints = null;
+      this.rc.setAxisEndPoints(null);
+      this.rc = null;
+    }
   }
 
   @Override
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 1f61bae..f51bfbf 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -289,8 +289,8 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
-                    + "/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+                    + "/examples/exampleFile_2_7.jvp"));
 
     /*
      * Set Colours tab defaults
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index cd974a4..bb85948 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -460,47 +460,80 @@ public class SeqPanel extends JPanel
 
   void moveCursor(int dx, int dy)
   {
-    seqCanvas.cursorX += dx;
-    seqCanvas.cursorY += dy;
-
+    moveCursor(dx, dy,false);
+  }
+  void moveCursor(int dx, int dy, boolean nextWord)
+  {
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+    if (nextWord)
     {
-      int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
-
-      if (!hidden.isVisible(seqCanvas.cursorX))
-      {
-        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
-        int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
-        if (region != null) // just in case
+      int maxHeight=av.getAlignment().getHeight();
+      SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+      // look for next gap or residue
+      boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+      int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+      do
+      {
+        lastP = p;
+        lastR = r;
+        if (dy != 0)
         {
-          if (dx == 1)
+          r += dy;
+          if (r < 0)
           {
-            // moving right
-            seqCanvas.cursorX = region[1] + 1;
+            r = 0;
           }
-          else if (dx == -1)
+          if (r >= maxHeight)
           {
-            // moving left
-            seqCanvas.cursorX = region[0] - 1;
+            r = maxHeight - 1;
           }
+          seqAtRow = av.getAlignment().getSequenceAt(r);
         }
-        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
-      }
+        p = nextVisible(hidden, maxWidth, p, dx);
+      } while ((dx != 0 ? p != lastP : r != lastR)
+              && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
+      seqCanvas.cursorX=p;
+      seqCanvas.cursorY=r;
+    } else {
+      int maxWidth = av.getAlignment().getWidth();
+      seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+      seqCanvas.cursorY += dy;
+    }
+    scrollToVisible(false);
+  }
+
+  private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+  {
+    int newCursorX=original+dx;
+    if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+    {
+      int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+      int[] region = hidden.getRegionWithEdgeAtRes(visx);
 
-      if (seqCanvas.cursorX >= maxWidth
-              || !hidden.isVisible(seqCanvas.cursorX))
+      if (region != null) // just in case
       {
-        seqCanvas.cursorX = original;
+        if (dx == 1)
+        {
+          // moving right
+          newCursorX = region[1] + 1;
+        }
+        else if (dx == -1)
+        {
+          // moving left
+          newCursorX = region[0] - 1;
+        }
       }
     }
-
-    scrollToVisible(false);
+    newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+    if (newCursorX >= maxWidth
+            || !hidden.isVisible(newCursorX))
+    {
+      newCursorX = original;
+    }
+    return newCursorX;
   }
-
   /**
    * Scroll to make the cursor visible in the viewport.
    * 
@@ -893,11 +926,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {
@@ -1065,7 +1099,7 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeatures(tooltipText,
+            unshownFeatures += seqARep.appendFeatures(tooltipText,
                     pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
@@ -1200,7 +1234,7 @@ public class SeqPanel extends JPanel
   {
     char sequenceChar = sequence.getCharAt(column);
     int pos = sequence.findPosition(column);
-    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+    setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
 
     return pos;
   }
@@ -1216,7 +1250,7 @@ public class SeqPanel extends JPanel
    * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
    * </pre>
    * 
-   * @param sequence
+   * @param seqName
    * @param seqIndex
    *          sequence position in the alignment (1..)
    * @param sequenceChar
@@ -1224,7 +1258,7 @@ public class SeqPanel extends JPanel
    * @param residuePos
    *          the sequence residue position (if not over a gap)
    */
-  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+  protected void setStatusMessage(String seqName, int seqIndex,
           char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
@@ -1234,7 +1268,7 @@ public class SeqPanel extends JPanel
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
-            .append(sequence.getName());
+            .append(seqName);
 
     String residue = null;
 
@@ -1279,7 +1313,8 @@ public class SeqPanel extends JPanel
     {
       return;
     }
-    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+    SequenceI ds = alignedSeq.getDatasetSequence();
     for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
@@ -1291,8 +1326,8 @@ public class SeqPanel extends JPanel
       if (seq == ds)
       {
         int start = m.getStart();
-        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
-                start);
+        setStatusMessage(alignedSeq.getName(), sequenceIndex,
+                seq.getCharAt(start - 1), start);
         return;
       }
     }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 1c4e6a6..7451646 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1023,10 +1023,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           }
         }
 
-        if (preferredFeatureColours != null)
-        {
-          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
-        }
+        af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);
diff --git a/src/jalview/gui/Slider.java b/src/jalview/gui/Slider.java
new file mode 100644
index 0000000..714e770
--- /dev/null
+++ b/src/jalview/gui/Slider.java
@@ -0,0 +1,119 @@
+package jalview.gui;
+
+import javax.swing.JSlider;
+
+/**
+ * A modified {@code javax.swing.JSlider} that
+ * <ul>
+ * <li>supports float valued numbers (by scaling up integer values)</li>
+ * <li>rescales 'true' value range to avoid negative values, as these are not
+ * rendered correctly by some look and feel libraries</li>
+ * </ul>
+ * 
+ * @author gmcarstairs
+ */
+@SuppressWarnings("serial")
+public class Slider extends JSlider
+{
+  /*
+   * the number of nominal positions the slider represents
+   * (higher number = more fine-grained positioning)
+   */
+  private static final int SCALE_TICKS = 1000;
+
+  /*
+   * 'true' value corresponding to zero on the slider
+   */
+  private float trueMin;
+
+  /*
+   * 'true' value corresponding to slider maximum
+   */
+  private float trueMax;
+
+  /*
+   * scaleFactor applied to true value range to give a
+   * slider range of 0 - 100
+   */
+  private float sliderScaleFactor;
+
+  /**
+   * Constructor that rescales min - max to 0 - 100 for the slider
+   * 
+   * @param min
+   * @param max
+   * @param value
+   */
+  public Slider(float min, float max, float value)
+  {
+    super();
+    setSliderModel(min, max, value);
+  }
+
+  /**
+   * Sets the min-max range and current value of the slider, with rescaling from
+   * true values to slider range as required
+   * 
+   * @param min
+   * @param max
+   * @param value
+   */
+  public void setSliderModel(float min, float max, float value)
+  {
+    trueMin = min;
+    trueMax = max;
+    setMinimum(0);
+    sliderScaleFactor = SCALE_TICKS / (max - min);
+    int sliderMax = (int) ((max - min) * sliderScaleFactor);
+    setMaximum(sliderMax);
+    setSliderValue(value);
+  }
+
+  /**
+   * Answers the value of the slider position (descaled to 'true' value)
+   * 
+   * @return
+   */
+  public float getSliderValue()
+  {
+    /*
+     * convert slider max to 'true max' in case of rounding errors
+     */
+    int value = getValue();
+    return value == getMaximum() ? trueMax
+            : value / sliderScaleFactor + trueMin;
+  }
+
+  /**
+   * Sets the slider value (scaled from the true value to the slider range)
+   * 
+   * @param value
+   */
+  public void setSliderValue(float value)
+  {
+    setValue(Math.round((value - trueMin) * sliderScaleFactor));
+  }
+
+  /**
+   * Answers the value of the slider position as a percentage between minimum and
+   * maximum of its range
+   * 
+   * @return
+   */
+  public float getSliderPercentageValue()
+  {
+    return (getValue() - getMinimum()) * 100f
+            / (getMaximum() - getMinimum());
+  }
+
+  /**
+   * Sets the slider position for a given percentage value of its min-max range
+   * 
+   * @param pct
+   */
+  public void setSliderPercentageValue(float pct)
+  {
+    float pc = pct / 100f * getMaximum();
+    setValue((int) pc);
+  }
+}
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 574cf04..f7c93db 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -814,7 +814,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
         if (c != null && c instanceof AlignFrame)
         {
           AlignFrame af = (AlignFrame) c;
-          new Finder(af.viewport, af.alignPanel);
+          new Finder(af.alignPanel);
         }
       }
     };
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index ca4f84e..6c9c892 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -159,6 +159,7 @@ public class TreePanel extends GTreePanel
         {
           getViewport().removePropertyChangeListener(listener);
         }
+        releaseReferences();
       }
     });
 
@@ -168,6 +169,17 @@ public class TreePanel extends GTreePanel
   }
 
   /**
+   * Ensure any potentially large object references are nulled
+   */
+  public void releaseReferences()
+  {
+    this.tree = null;
+    this.treeCanvas.tree = null;
+    this.treeCanvas.nodeHash = null;
+    this.treeCanvas.nameHash = null;
+  }
+
+  /**
    * @return
    */
   protected PropertyChangeListener addAlignmentListener()
diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 0150579..2acd6cc 100644
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -20,19 +20,24 @@
  */
 package jalview.io;
 
-import jalview.bin.Cache;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.util.MessageManager;
-
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.TreeMap;
 
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /*
  * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
  * User configurable options are:
@@ -95,6 +100,10 @@ public class BackupFiles
   private static final SimpleDateFormat sdf = new SimpleDateFormat(
           "yyyy-MM-dd HH:mm:ss");
 
+  private static final String newTempFileSuffix = "_newfile";
+
+  private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+
   public BackupFiles(String filename)
   {
     this(new File(filename));
@@ -106,7 +115,8 @@ public class BackupFiles
   {
     classInit();
     this.file = file;
-    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
     this.suffix = bfpe.suffix;
     this.noMax = bfpe.keepAll;
     this.max = bfpe.rollMax;
@@ -121,30 +131,48 @@ public class BackupFiles
       {
         String tempfilename = file.getName();
         File tempdir = file.getParentFile();
-        temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
-                tempdir);
+        Cache.log.trace(
+                "BACKUPFILES [file!=null] attempting to create temp file for "
+                        + tempfilename + " in dir " + tempdir);
+        temp = File.createTempFile(tempfilename,
+                TEMP_FILE_EXT + newTempFileSuffix, tempdir);
+        Cache.log.debug(
+                "BACKUPFILES using temp file " + temp.getAbsolutePath());
       }
       else
       {
+        Cache.log.trace(
+                "BACKUPFILES [file==null] attempting to create default temp file "
+                        + DEFAULT_TEMP_FILE + " with extension "
+                        + TEMP_FILE_EXT);
         temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
       }
     } catch (IOException e)
     {
-      System.out.println(
-              "Could not create temp file to save into (IOException)");
+      Cache.log
+              .error("Could not create temp file to save to (IOException)");
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(e));
     } catch (Exception e)
     {
-      System.out.println("Exception ctreating temp file for saving");
+      Cache.log.error("Exception ctreating temp file for saving");
+      Cache.log.debug(Cache.getStackTraceString(e));
     }
     this.setTempFile(temp);
   }
 
   public static void classInit()
   {
-    setEnabled(Cache.getDefault(ENABLED, true));
+    Cache.initLogger();
+    Cache.log.trace("BACKUPFILES classInit");
+    boolean e = Cache.getDefault(ENABLED, true);
+    setEnabled(e);
+    Cache.log.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
             .getSavedBackupEntry();
+    Cache.log.trace("BACKUPFILES preset scheme " + bfpe.toString());
     setConfirmDelete(bfpe.confirmDelete);
+    Cache.log.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
   }
 
   public static void setEnabled(boolean flag)
@@ -188,9 +216,10 @@ public class BackupFiles
       path = this.getTempFile().getCanonicalPath();
     } catch (IOException e)
     {
-      System.out.println(
+      Cache.log.error(
               "IOException when getting Canonical Path of temp file '"
                       + this.getTempFile().getName() + "'");
+      Cache.log.debug(Cache.getStackTraceString(e));
     }
     return path;
   }
@@ -209,7 +238,7 @@ public class BackupFiles
 
   public boolean renameTempFile()
   {
-    return tempFile.renameTo(file);
+    return moveFileToFile(tempFile, file);
   }
 
   // roll the backupfiles
@@ -226,24 +255,35 @@ public class BackupFiles
             || suffix.length() == 0)
     {
       // nothing to do
+      Cache.log.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+              + "filename: " + (file != null ? file.getName() : "null")
+              + ", " + "file exists: " + file.exists() + ", " + "enabled: "
+              + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
+              + "'");
       return true;
     }
 
+    Cache.log.trace("BACKUPFILES rollBackupFiles starting");
+
     String dir = "";
     File dirFile;
     try
     {
       dirFile = file.getParentFile();
       dir = dirFile.getCanonicalPath();
+      Cache.log.trace("BACKUPFILES dir: " + dir);
     } catch (Exception e)
     {
-      System.out.println(
+      Cache.log.error(
               "Could not get canonical path for file '" + file + "'");
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(e));
       return false;
     }
     String filename = file.getName();
     String basename = filename;
 
+    Cache.log.trace("BACKUPFILES filename is " + filename);
     boolean ret = true;
     // Create/move backups up one
 
@@ -255,9 +295,13 @@ public class BackupFiles
     File[] backupFiles = dirFile.listFiles(bff);
     int nextIndexNum = 0;
 
+    Cache.log
+            .trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
     if (backupFiles.length == 0)
     {
       // No other backup files. Just need to move existing file to backupfile_1
+      Cache.log.trace(
+              "BACKUPFILES no existing backup files, setting index to 1");
       nextIndexNum = 1;
     }
     else
@@ -270,7 +314,7 @@ public class BackupFiles
       if (reverseOrder)
       {
         // backup style numbering
-
+        Cache.log.trace("BACKUPFILES rolling files in reverse order");
 
         int tempMax = noMax ? -1 : max;
         // noMax == true means no limits
@@ -287,7 +331,7 @@ public class BackupFiles
             tempMax = i;
           }
         }
-        
+
         File previousFile = null;
         File fileToBeDeleted = null;
         for (int n = tempMax; n > 0; n--)
@@ -302,6 +346,7 @@ public class BackupFiles
             // no "oldest" file to delete
             previousFile = backupfile_n;
             fileToBeDeleted = null;
+            Cache.log.trace("BACKUPFILES No oldest file to delete");
             continue;
           }
 
@@ -312,19 +357,23 @@ public class BackupFiles
             File replacementFile = backupfile_n;
             long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
             long replacementFileLMT = replacementFile.lastModified();
+            Cache.log.trace("BACKUPFILES fileToBeDeleted is "
+                    + fileToBeDeleted.getAbsolutePath());
+            Cache.log.trace("BACKUPFILES replacementFile is "
+                    + backupfile_n.getAbsolutePath());
 
             try
             {
               File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
                       dirFile);
-              
+
               if (fileToBeDeletedLMT > replacementFileLMT)
               {
                 String fileToBeDeletedLMTString = sdf
                         .format(fileToBeDeletedLMT);
                 String replacementFileLMTString = sdf
                         .format(replacementFileLMT);
-                System.out.println("WARNING! I am set to delete backupfile "
+                Cache.log.warn("WARNING! I am set to delete backupfile "
                         + fileToBeDeleted.getName()
                         + " has modification time "
                         + fileToBeDeletedLMTString
@@ -335,6 +384,11 @@ public class BackupFiles
 
                 boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
                         replacementFile, true);
+                Cache.log.trace("BACKUPFILES "
+                        + (delete ? "confirmed" : "not") + " deleting file "
+                        + fileToBeDeleted.getAbsolutePath()
+                        + " which is newer than "
+                        + replacementFile.getAbsolutePath());
 
                 if (delete)
                 {
@@ -343,21 +397,27 @@ public class BackupFiles
                 }
                 else
                 {
-                  fileToBeDeleted.renameTo(oldestTempFile);
+                  Cache.log.debug("BACKUPFILES moving "
+                          + fileToBeDeleted.getAbsolutePath() + " to "
+                          + oldestTempFile.getAbsolutePath());
+                  moveFileToFile(fileToBeDeleted, oldestTempFile);
                 }
               }
               else
               {
-                fileToBeDeleted.renameTo(oldestTempFile);
+                Cache.log.debug("BACKUPFILES going to move "
+                        + fileToBeDeleted.getAbsolutePath() + " to "
+                        + oldestTempFile.getAbsolutePath());
+                moveFileToFile(fileToBeDeleted, oldestTempFile);
                 addDeleteFile(oldestTempFile);
               }
 
             } catch (Exception e)
             {
-              System.out.println(
+              Cache.log.error(
                       "Error occurred, probably making new temp file for '"
                               + fileToBeDeleted.getName() + "'");
-              e.printStackTrace();
+              Cache.log.error(Cache.getStackTraceString(e));
             }
 
             // reset
@@ -372,7 +432,9 @@ public class BackupFiles
           {
             if (previousFile != null)
             {
-              ret = ret && backupfile_n.renameTo(previousFile);
+              // using boolean '&' instead of '&&' as don't want moveFileToFile
+              // attempt to be conditional (short-circuit)
+              ret = ret & moveFileToFile(backupfile_n, previousFile);
             }
           }
 
@@ -382,19 +444,37 @@ public class BackupFiles
         // index to use for the latest backup
         nextIndexNum = 1;
       }
-      else
+      else // not reverse numbering
       {
         // version style numbering (with earliest file deletion if max files
         // reached)
 
         bfTreeMap.values().toArray(backupFiles);
+        StringBuilder bfsb = new StringBuilder();
+        for (int i = 0; i < backupFiles.length; i++)
+        {
+          if (bfsb.length() > 0)
+          {
+            bfsb.append(", ");
+          }
+          bfsb.append(backupFiles[i].getName());
+        }
+        Cache.log.trace("BACKUPFILES backupFiles: " + bfsb.toString());
 
         // noMax == true means keep all backup files
         if ((!noMax) && bfTreeMap.size() >= max)
         {
+          Cache.log.trace("BACKUPFILES noMax: " + noMax + ", " + "max: "
+                  + max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
           // need to delete some files to keep number of backups to designated
-          // max
-          int numToDelete = bfTreeMap.size() - max + 1;
+          // max.
+          // Note that if the suffix is not numbered then do not delete any
+          // backup files later or we'll delete the new backup file (there can
+          // be only one).
+          int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
+                  ? bfTreeMap.size() - max + 1
+                  : 0;
+          Cache.log.trace("BACKUPFILES numToDelete: " + numToDelete);
           // the "replacement" file is the latest backup file being kept (it's
           // not replacing though)
           File replacementFile = numToDelete < backupFiles.length
@@ -407,6 +487,9 @@ public class BackupFiles
             File fileToBeDeleted = backupFiles[i];
             boolean delete = true;
 
+            Cache.log.trace(
+                    "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+
             boolean newer = false;
             if (replacementFile != null)
             {
@@ -421,14 +504,13 @@ public class BackupFiles
                 String replacementFileLMTString = sdf
                         .format(replacementFileLMT);
 
-                System.out
-                        .println("WARNING! I am set to delete backupfile '"
-                                + fileToBeDeleted.getName()
-                                + "' has modification time "
+                Cache.log.warn("WARNING! I am set to delete backupfile '"
+                        + fileToBeDeleted.getName()
+                        + "' has modification time "
                         + fileToBeDeletedLMTString
-                                + " which is newer than the oldest backupfile being kept '"
+                        + " which is newer than the oldest backupfile being kept '"
                         + replacementFile.getName()
-                                + "' with modification time "
+                        + "' with modification time "
                         + replacementFileLMTString);
 
                 delete = confirmNewerDeleteFile(fileToBeDeleted,
@@ -437,17 +519,23 @@ public class BackupFiles
                 {
                   // User has confirmed delete -- no need to add it to the list
                   fileToBeDeleted.delete();
+                  Cache.log.debug("BACKUPFILES deleting fileToBeDeleted: "
+                          + fileToBeDeleted);
                   delete = false;
                 }
                 else
                 {
                   // keeping file, nothing to do!
+                  Cache.log.debug("BACKUPFILES keeping fileToBeDeleted: "
+                          + fileToBeDeleted);
                 }
               }
             }
             if (delete)
             {
               addDeleteFile(fileToBeDeleted);
+              Cache.log.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+                      + fileToBeDeleted);
             }
 
           }
@@ -462,10 +550,17 @@ public class BackupFiles
     String latestBackupFilename = dir + File.separatorChar
             + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
                     suffix, digits);
-    ret |= file.renameTo(new File(latestBackupFilename));
-
+    Cache.log.trace("BACKUPFILES Moving old file [" + file
+            + "] to latestBackupFilename [" + latestBackupFilename + "]");
+    // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+    // be conditional (short-circuit)
+    ret = ret & moveFileToFile(file, new File(latestBackupFilename));
+    Cache.log.debug(
+            "BACKUPFILES moving " + file + " to " + latestBackupFilename
+                    + " was " + (ret ? "" : "NOT ") + "successful");
     if (tidyUp)
     {
+      Cache.log.debug("BACKUPFILES tidying up files");
       tidyUpFiles();
     }
 
@@ -521,7 +616,7 @@ public class BackupFiles
         saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
       } catch (Exception e)
       {
-        System.out.println(
+        Cache.log.error(
                 "Error when confirming to keep backup file newer than other backup files.");
         e.printStackTrace();
       }
@@ -529,19 +624,27 @@ public class BackupFiles
               "label.newerdelete_replacement_line", new String[]
               { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
                   rfSize }));
+      // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
+      // replaced by apparently older file \n''{1}''\t(modified {3}, size
+      // {5}).""
       messageSB.append("\n\n");
       messageSB.append(MessageManager.formatMessage(
               "label.confirm_deletion_or_rename", new String[]
               { ftbd.getName(), saveFile.getName() }));
+      // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
       String[] options = new String[] {
           MessageManager.getString("label.delete"),
           MessageManager.getString("label.rename") };
 
-      confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
-              messageSB.toString(),
-              MessageManager.getString("label.backupfiles_confirm_delete"),
-              JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
-              null, options, options[0]);
+      confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+              : JvOptionPane.showOptionDialog(Desktop.desktop,
+                      messageSB.toString(),
+                      MessageManager.getString(
+                              "label.backupfiles_confirm_delete"),
+                      // "Confirm delete"
+                      JvOptionPane.YES_NO_OPTION,
+                      JvOptionPane.WARNING_MESSAGE, null, options,
+                      options[0]);
     }
     else
     {
@@ -549,22 +652,29 @@ public class BackupFiles
               .formatMessage("label.newerdelete_line", new String[]
               { ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
                   rfSize }));
+      // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
+      // is newer than the oldest remaining backup file \n''{1}''\t(modified
+      // {3}, size {5})."
       messageSB.append("\n\n");
       messageSB.append(MessageManager
               .formatMessage("label.confirm_deletion", new String[]
               { ftbd.getName() }));
+      // "Confirm deletion of ''{0}''?"
       String[] options = new String[] {
           MessageManager.getString("label.delete"),
           MessageManager.getString("label.keep") };
 
-      confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
-              messageSB.toString(),
-              MessageManager.getString("label.backupfiles_confirm_delete"),
-              JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
-              null, options, options[0]);
+      confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+              : JvOptionPane.showOptionDialog(Desktop.desktop,
+                      messageSB.toString(),
+                      MessageManager.getString(
+                              "label.backupfiles_confirm_delete"),
+                      // "Confirm delete"
+                      JvOptionPane.YES_NO_OPTION,
+                      JvOptionPane.WARNING_MESSAGE, null, options,
+                      options[0]);
     }
 
-
     // return should be TRUE if file is to be deleted
     return (confirmButton == JvOptionPane.YES_OPTION);
   }
@@ -580,6 +690,8 @@ public class BackupFiles
         messageSB = new StringBuilder();
         messageSB.append(MessageManager
                 .getString("label.backupfiles_confirm_delete_old_files"));
+        // "Delete the following older backup files? (see the Backups tab in
+        // Preferences for more options)"
         for (int i = 0; i < deleteFiles.size(); i++)
         {
           File df = deleteFiles.get(i);
@@ -590,13 +702,17 @@ public class BackupFiles
                   new String[]
                   { sdf.format(df.lastModified()),
                       Long.toString(df.length()) }));
+          // "(modified {0}, size {1})"
         }
 
-        int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
-                messageSB.toString(),
-                MessageManager
-                        .getString("label.backupfiles_confirm_delete"),
-                JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+        int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+                : JvOptionPane.showConfirmDialog(Desktop.desktop,
+                        messageSB.toString(),
+                        MessageManager.getString(
+                                "label.backupfiles_confirm_delete"),
+                        // "Confirm delete"
+                        JvOptionPane.YES_NO_OPTION,
+                        JvOptionPane.WARNING_MESSAGE);
 
         doDelete = (confirmButton == JvOptionPane.YES_OPTION);
       }
@@ -610,8 +726,10 @@ public class BackupFiles
         for (int i = 0; i < deleteFiles.size(); i++)
         {
           File fileToDelete = deleteFiles.get(i);
+          Cache.log.trace("BACKUPFILES about to delete fileToDelete:"
+                  + fileToDelete);
           fileToDelete.delete();
-          System.out.println("DELETING '" + fileToDelete.getName() + "'");
+          Cache.log.warn("deleted '" + fileToDelete.getName() + "'");
         }
       }
 
@@ -621,8 +739,7 @@ public class BackupFiles
   }
 
   private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
-          File[] backupFiles,
-          String basename)
+          File[] backupFiles, String basename)
   {
     // sort the backup files (based on integer found in the suffix) using a
     // precomputed Hashmap for speed
@@ -647,7 +764,7 @@ public class BackupFiles
     boolean rename = false;
     if (write)
     {
-      roll = this.rollBackupFiles(false);
+      roll = this.rollBackupFiles(false); // tidyUpFiles at the end
       rename = this.renameTempFile();
     }
 
@@ -661,7 +778,9 @@ public class BackupFiles
     if (!okay)
     {
       StringBuilder messageSB = new StringBuilder();
-      messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+      messageSB.append(MessageManager.getString(
+              "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+      // "Something possibly went wrong with the backups of this file."
       if (rename)
       {
         if (messageSB.length() > 0)
@@ -670,6 +789,7 @@ public class BackupFiles
         }
         messageSB.append(MessageManager.getString(
                 "label.backupfiles_confirm_save_new_saved_file_ok"));
+        // "The new saved file seems okay."
       }
       else
       {
@@ -679,13 +799,22 @@ public class BackupFiles
         }
         messageSB.append(MessageManager.getString(
                 "label.backupfiles_confirm_save_new_saved_file_not_ok"));
+        // "The new saved file might not be okay."
       }
-
-      int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
-              messageSB.toString(),
-              MessageManager
-                      .getString("label.backupfiles_confirm_save_file"),
-              JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
+      if (messageSB.length() > 0)
+      {
+        messageSB.append("\n");
+      }
+      messageSB
+              .append(MessageManager.getString("label.continue_operation"));
+
+      int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
+              : JvOptionPane.showConfirmDialog(Desktop.desktop,
+                      messageSB.toString(),
+                      MessageManager.getString(
+                              "label.backupfiles_confirm_save_file"),
+                      // "Confirm save file"
+                      JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
       okay = confirmButton == JvOptionPane.OK_OPTION;
     }
     if (okay)
@@ -709,7 +838,7 @@ public class BackupFiles
       dirFile = file.getParentFile();
     } catch (Exception e)
     {
-      System.out.println(
+      Cache.log.error(
               "Could not get canonical path for file '" + file + "'");
       return new TreeMap<>();
     }
@@ -751,13 +880,49 @@ public class BackupFiles
     int pos = deleteFiles.indexOf(fileToBeDeleted);
     if (pos > -1)
     {
+      Cache.log.debug("BACKUPFILES not adding file "
+              + fileToBeDeleted.getAbsolutePath()
+              + " to the delete list (already at index" + pos + ")");
       return true;
     }
     else
     {
+      Cache.log.debug("BACKUPFILES adding file "
+              + fileToBeDeleted.getAbsolutePath() + " to the delete list");
       deleteFiles.add(fileToBeDeleted);
     }
     return ret;
   }
 
+  public static boolean moveFileToFile(File oldFile, File newFile)
+  {
+    Cache.initLogger();
+    boolean ret = false;
+    Path oldPath = Paths.get(oldFile.getAbsolutePath());
+    Path newPath = Paths.get(newFile.getAbsolutePath());
+    try
+    {
+      // delete destination file - not usually necessary but Just In Case...
+      Cache.log.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+      newFile.delete();
+      Cache.log.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
+              + " to " + newFile.getAbsolutePath());
+      Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
+      ret = true;
+      Cache.log.trace("BACKUPFILES move seems to have succeeded");
+    } catch (IOException e)
+    {
+      Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
+              + newPath.toString() + "'");
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(e));
+      ret = false;
+    } catch (Exception e)
+    {
+      Cache.log.error(e.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(e));
+      ret = false;
+    }
+    return ret;
+  }
 }
diff --git a/src/jalview/io/BackupFilesPresetEntry.java b/src/jalview/io/BackupFilesPresetEntry.java
index 69130d0..ff8a5e6 100644
--- a/src/jalview/io/BackupFilesPresetEntry.java
+++ b/src/jalview/io/BackupFilesPresetEntry.java
@@ -20,13 +20,13 @@
  */
 package jalview.io;
 
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-
 import java.util.HashMap;
 import java.util.Map;
 import java.util.StringTokenizer;
 
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
 public class BackupFilesPresetEntry
 {
 
diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
new file mode 100644
index 0000000..bfae4ed
--- /dev/null
+++ b/src/jalview/io/EmblFlatFile.java
@@ -0,0 +1,900 @@
+package jalview.io;
+
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
+/**
+ * A class that provides selective parsing of the EMBL flatfile format.
+ * <p>
+ * The initial implementation is limited to extracting fields used by Jalview
+ * after fetching an EMBL or EMBLCDS entry:
+ * 
+ * <pre>
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * </pre>
+ * 
+ * For a complete parser, it may be best to adopt that provided in
+ * https://github.com/enasequence/sequencetools/tree/master/src/main/java/uk/ac/ebi/embl/flatfile
+ * (but note this has a dependency on the Apache Commons library)
+ * 
+ * @author gmcarstairs
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
+ * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
+ */
+public class EmblFlatFile extends AlignFile // FileParse
+{
+  private static final String QUOTE = "\"";
+
+  private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
+
+  /**
+   * A data bean class to hold values parsed from one CDS Feature (FT)
+   */
+  class CdsData
+  {
+    String translation; // from CDS feature /translation
+
+    String cdsLocation; // CDS /location raw value
+
+    int codonStart = 1; // from CDS /codon_start
+
+    String proteinName; // from CDS /product; used for protein description
+
+    String proteinId; // from CDS /protein_id
+
+    List<DBRefEntry> xrefs = new ArrayList<>(); // from CDS /db_xref qualifiers
+
+    Map<String, String> cdsProps = new Hashtable<>(); // CDS other qualifiers
+  }
+
+  private static final String WHITESPACE = "\\s+";
+
+  private String sourceDb;
+
+  /*
+   * values parsed from the EMBL flatfile record
+   */
+  private String accession; // from ID (first token)
+
+  private String version; // from ID (second token)
+
+  private String description; // from (first) DE line
+
+  private int length = 128; // from ID (7th token), with usable default
+
+  private List<DBRefEntry> dbrefs; // from DR
+
+  private String sequenceString; // from SQ lines
+
+  /*
+   * parsed CDS data fields, keyed by protein_id
+   */
+  private Map<String, CdsData> cds;
+
+  /**
+   * Constructor
+   * 
+   * @param fp
+   * @param sourceId
+   * @throws IOException
+   */
+  public EmblFlatFile(FileParse fp, String sourceId) throws IOException
+  {
+    super(false, fp); // don't parse immediately
+    this.sourceDb = sourceId;
+    dbrefs = new ArrayList<>();
+
+    /*
+     * using TreeMap gives CDS sequences in alphabetical, so readable, order
+     */
+    cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+  }
+
+  /**
+   * Parses the flatfile, and if successful, saves as an annotated sequence
+   * which may be retrieved by calling {@code getSequence()}
+   * 
+   * @throws IOException
+   */
+  @Override
+  public void parse() throws IOException
+  {
+    String line = nextLine();
+    while (line != null)
+    {
+      if (line.startsWith("ID"))
+      {
+        line = parseID(line);
+      }
+      else if (line.startsWith("DE"))
+      {
+        line = parseDE(line);
+      }
+      else if (line.startsWith("DR"))
+      {
+        line = parseDR(line);
+      }
+      else if (line.startsWith("SQ"))
+      {
+        line = parseSQ();
+      }
+      else if (line.startsWith("FT"))
+      {
+        line = parseFT(line);
+      }
+      else
+      {
+        line = nextLine();
+      }
+    }
+    buildSequence();
+  }
+
+  /**
+   * Extracts and saves the primary accession and version (SV value) from an ID
+   * line, or null if not found. Returns the next line after the one processed.
+   * 
+   * @param line
+   * @throws IOException
+   */
+  String parseID(String line) throws IOException
+  {
+    String[] tokens = line.substring(2).split(";");
+
+    /*
+     * first is primary accession
+     */
+    String token = tokens[0].trim();
+    if (!token.isEmpty())
+    {
+      this.accession = token;
+    }
+
+    /*
+     * second token is 'SV versionNo'
+     */
+    if (tokens.length > 1)
+    {
+      token = tokens[1].trim();
+      if (token.startsWith("SV"))
+      {
+        String[] bits = token.trim().split(WHITESPACE);
+        this.version = bits[bits.length - 1];
+      }
+    }
+
+    /*
+     * seventh token is 'length BP'
+     */
+    if (tokens.length > 6)
+    {
+      token = tokens[6].trim();
+      String[] bits = token.trim().split(WHITESPACE);
+      try
+      {
+        this.length = Integer.valueOf(bits[0]);
+      } catch (NumberFormatException e)
+      {
+        Cache.log.error("bad length read in flatfile, line: " + line);
+      }
+    }
+
+    return nextLine();
+  }
+
+  /**
+   * Reads sequence description from the first DE line found. Any trailing
+   * period is discarded. If there are multiple DE lines, only the first (short
+   * description) is read, the rest are ignored.
+   * 
+   * @param line
+   * @return
+   * @throws IOException
+   */
+  String parseDE(String line) throws IOException
+  {
+    String desc = line.substring(2).trim();
+    if (desc.endsWith("."))
+    {
+      desc = desc.substring(0, desc.length() - 1);
+    }
+    this.description = desc;
+
+    /*
+     * pass over any additional DE lines
+     */
+    while ((line = nextLine()) != null)
+    {
+      if (!line.startsWith("DE"))
+      {
+        break;
+      }
+    }
+
+    return line;
+  }
+
+  /**
+   * Processes one DR line and saves as a DBRefEntry cross-reference. Returns
+   * the line following the line processed.
+   * 
+   * @param line
+   * @throws IOException
+   */
+  String parseDR(String line) throws IOException
+  {
+    String[] tokens = line.substring(2).split(";");
+    if (tokens.length > 1)
+    {
+      /*
+       * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+       */
+      String db = tokens[0].trim();
+      db = DBRefUtils.getCanonicalName(db);
+      String acc = tokens[1].trim();
+      if (acc.endsWith("."))
+      {
+        acc = acc.substring(0, acc.length() - 1);
+      }
+      String version = "0";
+      if (tokens.length > 2)
+      {
+        String secondaryId = tokens[2].trim();
+        if (!secondaryId.isEmpty())
+        {
+          // todo: is this right? secondary id is not a version number
+          // version = secondaryId;
+        }
+      }
+      this.dbrefs.add(new DBRefEntry(db, version, acc));
+    }
+
+    return nextLine();
+  }
+
+  /**
+   * Reads and saves the sequence, read from the lines following the SQ line.
+   * Whitespace and position counters are discarded. Returns the next line
+   * following the sequence data (the next line that doesn't start with
+   * whitespace).
+   * 
+   * @throws IOException
+   */
+  String parseSQ() throws IOException
+  {
+    StringBuilder sb = new StringBuilder(this.length);
+    String line = nextLine();
+    while (line != null && line.startsWith(" "))
+    {
+      line = line.trim();
+      String[] blocks = line.split(WHITESPACE);
+
+      /*
+       * omit the last block (position counter) on each line
+       */
+      for (int i = 0; i < blocks.length - 1; i++)
+      {
+        sb.append(blocks[i]);
+      }
+      line = nextLine();
+    }
+    this.sequenceString = sb.toString();
+
+    return line;
+  }
+
+  /**
+   * Processes an FT line. If it declares a feature type of interest (currently,
+   * only CDS is processed), processes all of the associated lines (feature
+   * qualifiers), and returns the next line after that, otherwise simply returns
+   * the next line.
+   * 
+   * @param line
+   * @return
+   * @throws IOException
+   */
+  String parseFT(String line) throws IOException
+  {
+    String[] tokens = line.split(WHITESPACE);
+    if (tokens.length < 3 || !"CDS".equals(tokens[1]))
+    {
+      return nextLine();
+    }
+
+    /*
+     * parse location - which may be over more than one line e.g. EAW51554
+     */
+    CdsData data = new CdsData();
+    StringBuilder sb = new StringBuilder().append(tokens[2]);
+    line = parseFeatureQualifier(sb, "CDS");
+    data.cdsLocation = sb.toString();
+
+    while (line != null)
+    {
+      if (!line.startsWith("FT    ")) // 4 spaces
+      {
+        // e.g. start of next feature "FT source..."
+        break;
+      }
+
+      /*
+       * extract qualifier, e.g. FT    /protein_id="CAA37824.1"
+       * - the value may extend over more than one line
+       * - if the value has enclosing quotes, these are removed
+       * - escaped double quotes ("") are reduced to a single character
+       */
+      int slashPos = line.indexOf('/');
+      if (slashPos == -1)
+      {
+        Cache.log.error("Unexpected EMBL line ignored: " + line);
+        line = nextLine();
+        continue;
+      }
+      int eqPos = line.indexOf('=', slashPos + 1);
+      if (eqPos == -1)
+      {
+        // can happen, e.g. /ribosomal_slippage
+        // Cache.log.error("Unexpected EMBL line ignored: " + line);
+        line = nextLine();
+        continue;
+      }
+      String qualifier = line.substring(slashPos + 1, eqPos);
+      String value = line.substring(eqPos + 1);
+      value = removeQuotes(value);
+      sb = new StringBuilder().append(value);
+      line = parseFeatureQualifier(sb, qualifier);
+      String featureValue = sb.toString();
+
+      if ("protein_id".equals(qualifier))
+      {
+        data.proteinId = featureValue;
+      }
+      else if ("codon_start".equals(qualifier))
+      {
+        try
+        {
+          data.codonStart = Integer.parseInt(featureValue.trim());
+        } catch (NumberFormatException e)
+        {
+          Cache.log.error("Invalid codon_start in XML for " + this.accession
+                  + ": " + e.getMessage());
+        }
+      }
+      else if ("db_xref".equals(qualifier))
+      {
+        String[] parts = featureValue.split(":");
+        if (parts.length == 2)
+        {
+          String db = parts[0].trim();
+          db = DBRefUtils.getCanonicalName(db);
+          DBRefEntry dbref = new DBRefEntry(db, "0", parts[1].trim());
+          data.xrefs.add(dbref);
+        }
+      }
+      else if ("product".equals(qualifier))
+      {
+        data.proteinName = featureValue;
+      }
+      else if ("translation".equals(qualifier))
+      {
+        data.translation = featureValue;
+      }
+      else if (!"".equals(featureValue))
+      {
+        // throw anything else into the additional properties hash
+        data.cdsProps.put(qualifier, featureValue);
+      }
+    }
+
+    if (data.proteinId != null)
+    {
+      this.cds.put(data.proteinId, data);
+    }
+    else
+    {
+      Cache.log.error("Ignoring CDS feature with no protein_id for "
+              + sourceDb + ":" + accession);
+    }
+
+    return line;
+  }
+
+  /**
+   * Removes leading or trailing double quotes (") unless doubled, and changes
+   * any 'escaped' (doubled) double quotes to single characters. As per the
+   * Feature Table specification for Qualifiers, Free Text.
+   * 
+   * @param value
+   * @return
+   */
+  static String removeQuotes(String value)
+  {
+    if (value == null)
+    {
+      return null;
+    }
+    if (value.startsWith(QUOTE) && !value.startsWith(DOUBLED_QUOTE))
+    {
+      value = value.substring(1);
+    }
+    if (value.endsWith(QUOTE) && !value.endsWith(DOUBLED_QUOTE))
+    {
+      value = value.substring(0, value.length() - 1);
+    }
+    value = value.replace(DOUBLED_QUOTE, QUOTE);
+    return value;
+  }
+
+  /**
+   * Reads the value of a feature (FT) qualifier from one or more lines of the
+   * file, and returns the next line after that. Values are appended to the
+   * string buffer, which should be already primed with the value read from the
+   * first line for the qualifier (with any leading double quote removed).
+   * Enclosing double quotes are removed, and escaped (repeated) double quotes
+   * reduced to one only. For example for
+   * 
+   * <pre>
+   * FT      /note="gene_id=hCG28070.3 
+   * FT      ""foobar"" isoform=CRA_b"
+   * the returned value is
+   * gene_id=hCG28070.3 "foobar" isoform=CRA_b
+   * </pre>
+   * 
+   * Note the side-effect of this method, to advance data reading to the next
+   * line after the feature qualifier.
+   * 
+   * @param sb
+   *          a string buffer primed with the first line of the value
+   * @param qualifierName
+   * @return
+   * @throws IOException
+   */
+  String parseFeatureQualifier(StringBuilder sb, String qualifierName)
+          throws IOException
+  {
+    String line;
+    while ((line = nextLine()) != null)
+    {
+      if (!line.startsWith("FT    "))
+      {
+        break; // reached next feature or other input line
+      }
+      String[] tokens = line.split(WHITESPACE);
+      if (tokens.length < 2)
+      {
+        Cache.log.error("Ignoring bad EMBL line for " + this.accession
+                + ": " + line);
+        break;
+      }
+      if (tokens[1].startsWith("/"))
+      {
+        break; // next feature qualifier
+      }
+
+      /*
+       * heuristic rule: most multi-line value (e.g. /product) are text,
+       * so add a space for word boundary at a new line; not for translation
+       */
+      if (!"translation".equals(qualifierName)
+              && !"CDS".equals(qualifierName))
+      {
+        sb.append(" ");
+      }
+
+      /*
+       * remove trailing " and unescape doubled ""
+       */
+      String data = removeQuotes(tokens[1]);
+      sb.append(data);
+    }
+
+    return line;
+  }
+
+  /**
+   * Constructs and saves the sequence from parsed components
+   */
+  void buildSequence()
+  {
+    if (this.accession == null || this.sequenceString == null)
+    {
+      Cache.log.error("Failed to parse data from EMBL");
+      return;
+    }
+
+    String name = this.accession;
+    if (this.sourceDb != null)
+    {
+      name = this.sourceDb + "|" + name;
+    }
+    SequenceI seq = new Sequence(name, this.sequenceString);
+    seq.setDescription(this.description);
+
+    /*
+     * add a DBRef to itself
+     */
+    DBRefEntry selfRef = new DBRefEntry(sourceDb, version, accession);
+    int[] startEnd = new int[] { 1, seq.getLength() };
+    selfRef.setMap(new Mapping(null, startEnd, startEnd, 1, 1));
+    seq.addDBRef(selfRef);
+
+    for (DBRefEntry dbref : this.dbrefs)
+    {
+      seq.addDBRef(dbref);
+    }
+
+    processCDSFeatures(seq);
+
+    seq.deriveSequence();
+
+    addSequence(seq);
+  }
+
+  /**
+   * Process the CDS features, including generation of cross-references and
+   * mappings to the protein products (translation)
+   * 
+   * @param seq
+   */
+  protected void processCDSFeatures(SequenceI seq)
+  {
+    /*
+     * record protein products found to avoid duplication i.e. >1 CDS with 
+     * the same /protein_id [though not sure I can find an example of this]
+     */
+    Map<String, SequenceI> proteins = new HashMap<>();
+    for (CdsData data : cds.values())
+    {
+      processCDSFeature(seq, data, proteins);
+    }
+  }
+
+  /**
+   * Processes data for one parsed CDS feature to
+   * <ul>
+   * <li>create a protein product sequence for the translation</li>
+   * <li>create a cross-reference to protein with mapping from dna</li>
+   * <li>add a CDS feature to the sequence for each CDS start-end range</li>
+   * <li>add any CDS dbrefs to the sequence and to the protein product</li>
+   * </ul>
+   * 
+   * @param SequenceI
+   *          dna
+   * @param proteins
+   *          map of protein products so far derived from CDS data
+   */
+  void processCDSFeature(SequenceI dna, CdsData data,
+          Map<String, SequenceI> proteins)
+  {
+    /*
+     * parse location into a list of [start, end, start, end] positions
+     */
+    int[] exons = getCdsRanges(this.accession, data.cdsLocation);
+
+    MapList maplist = buildMappingToProtein(dna, exons, data);
+
+    int exonNumber = 0;
+
+    for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
+    {
+      int exonStart = exons[xint];
+      int exonEnd = exons[xint + 1];
+      int begin = Math.min(exonStart, exonEnd);
+      int end = Math.max(exonStart, exonEnd);
+      exonNumber++;
+      String desc = String.format("Exon %d for protein EMBLCDS:%s",
+              exonNumber, data.proteinId);
+
+      SequenceFeature sf = new SequenceFeature("CDS", desc, begin, end,
+              this.sourceDb);
+      for (Entry<String, String> val : data.cdsProps.entrySet())
+      {
+        sf.setValue(val.getKey(), val.getValue());
+      }
+
+      sf.setEnaLocation(data.cdsLocation);
+      boolean forwardStrand = exonStart <= exonEnd;
+      sf.setStrand(forwardStrand ? "+" : "-");
+      sf.setPhase(String.valueOf(data.codonStart - 1));
+      sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+      sf.setValue(FeatureProperties.EXONPRODUCT, data.proteinName);
+
+      dna.addSequenceFeature(sf);
+    }
+
+    boolean hasUniprotDbref = false;
+    for (DBRefEntry xref : data.xrefs)
+    {
+      dna.addDBRef(xref);
+      if (xref.getSource().equals(DBRefSource.UNIPROT))
+      {
+        /*
+         * construct (or find) the sequence for (data.protein_id, data.translation)
+         */
+        SequenceI protein = buildProteinProduct(dna, xref, data, proteins);
+        Mapping map = new Mapping(protein, maplist);
+        map.setMappedFromId(data.proteinId);
+        xref.setMap(map);
+
+        /*
+         * add DBRefs with mappings from dna to protein and the inverse
+         */
+        DBRefEntry db1 = new DBRefEntry(sourceDb, version, accession);
+        db1.setMap(new Mapping(dna, maplist.getInverse()));
+        protein.addDBRef(db1);
+
+        hasUniprotDbref = true;
+      }
+    }
+
+    /*
+     * if we have a product (translation) but no explicit Uniprot dbref
+     * (example: EMBL M19487 protein_id AAB02592.1)
+     * then construct mappings to an assumed EMBLCDSPROTEIN accession
+     */
+    if (!hasUniprotDbref)
+    {
+      SequenceI protein = proteins.get(data.proteinId);
+      if (protein == null)
+      {
+        protein = new Sequence(data.proteinId, data.translation);
+        protein.setDescription(data.proteinName);
+        proteins.put(data.proteinId, protein);
+      }
+      // assuming CDSPROTEIN sequence version = dna version (?!)
+      DBRefEntry db1 = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+              this.version, data.proteinId);
+      protein.addDBRef(db1);
+
+      DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+              DBRefSource.EMBLCDSProduct, this.version, data.proteinId);
+      Mapping map = new Mapping(protein, maplist);
+      map.setMappedFromId(data.proteinId);
+      dnaToEmblProteinRef.setMap(map);
+      dna.addDBRef(dnaToEmblProteinRef);
+    }
+
+    /*
+     * comment brought forward from EmblXmlSource, lines 447-451:
+     * TODO: if retrieved from EMBLCDS, add a DBRef back to the parent EMBL
+     * sequence with the exon  map; if given a dataset reference, search
+     * dataset for parent EMBL sequence if it exists and set its map;
+     * make a new feature annotating the coding contig
+     */
+  }
+
+  /**
+   * Computes a mapping from CDS positions in DNA sequence to protein product
+   * positions, with allowance for stop codon or incomplete start codon
+   * 
+   * @param dna
+   * @param exons
+   * @param data
+   * @return
+   */
+  MapList buildMappingToProtein(final SequenceI dna, final int[] exons,
+          final CdsData data)
+  {
+    MapList dnaToProteinMapping = null;
+    int peptideLength = data.translation.length();
+
+    int[] proteinRange = new int[] { 1, peptideLength };
+    if (exons != null && exons.length > 0)
+    {
+      /*
+       * We were able to parse 'location'; do a final 
+       * product length truncation check
+       */
+      int[] cdsRanges = adjustForProteinLength(peptideLength, exons);
+      dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+    }
+    else
+    {
+      /*
+       * workaround until we handle all 'location' formats fully
+       * e.g. X53828.1:60..1058 or <123..>289
+       */
+      Cache.log.error(String.format(
+              "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
+                      + " - Making up the CDNA region of (%s:%s)... may be incorrect",
+              data.cdsLocation, sourceDb, this.accession));
+
+      int completeCodonsLength = 1 - data.codonStart + dna.getLength();
+      int mappedDnaEnd = dna.getEnd();
+      if (peptideLength * 3 == completeCodonsLength)
+      {
+        // this might occur for CDS sequences where no features are marked
+        Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+        mappedDnaEnd = dna.getEnd();
+      }
+      else if ((peptideLength + 1) * 3 == completeCodonsLength)
+      {
+        Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+        mappedDnaEnd = dna.getEnd() - 3;
+      }
+
+      if (mappedDnaEnd != -1)
+      {
+        int[] cdsRanges = new int[] {
+            dna.getStart() + (data.codonStart - 1), mappedDnaEnd };
+        dnaToProteinMapping = new MapList(cdsRanges, proteinRange, 3, 1);
+      }
+    }
+
+    return dnaToProteinMapping;
+  }
+
+  /**
+   * Constructs a sequence for the protein product for the CDS data (if there is
+   * one), and dbrefs with mappings from CDS to protein and the reverse
+   * 
+   * @param dna
+   * @param xref
+   * @param data
+   * @param proteins
+   * @return
+   */
+  SequenceI buildProteinProduct(SequenceI dna, DBRefEntry xref,
+          CdsData data, Map<String, SequenceI> proteins)
+  {
+    /*
+     * check we have some data to work with
+     */
+    if (data.proteinId == null || data.translation == null)
+    {
+      return null;
+    }
+
+    /*
+     * Construct the protein sequence (if not already seen)
+     */
+    String proteinSeqName = xref.getSource() + "|" + xref.getAccessionId();
+    SequenceI protein = proteins.get(proteinSeqName);
+    if (protein == null)
+    {
+      protein = new Sequence(proteinSeqName, data.translation, 1,
+              data.translation.length());
+      protein.setDescription(data.proteinName != null ? data.proteinName
+              : "Protein Product from " + sourceDb);
+      proteins.put(proteinSeqName, protein);
+    }
+
+    return protein;
+  }
+
+  /**
+   * Returns the CDS location as a single array of [start, end, start, end...]
+   * positions. If on the reverse strand, these will be in descending order.
+   * 
+   * @param accession
+   * @param location
+   * @return
+   */
+  protected int[] getCdsRanges(String accession, String location)
+  {
+    if (location == null)
+    {
+      return new int[] {};
+    }
+
+    try
+    {
+      List<int[]> ranges = DnaUtils.parseLocation(location);
+      return MappingUtils.listToArray(ranges);
+    } catch (ParseException e)
+    {
+      Cache.log.warn(
+              String.format("Not parsing inexact CDS location %s in ENA %s",
+                      location, accession));
+      return new int[] {};
+    }
+  }
+
+  /**
+   * Output (print) is not implemented for EMBL flat file format
+   */
+  @Override
+  public String print(SequenceI[] seqs, boolean jvsuffix)
+  {
+    return null;
+  }
+
+  /**
+   * Truncates (if necessary) the exon intervals to match 3 times the length of
+   * the protein; also accepts 3 bases longer (for stop codon not included in
+   * protein)
+   * 
+   * @param proteinLength
+   * @param exon
+   *          an array of [start, end, start, end...] intervals
+   * @return the same array (if unchanged) or a truncated copy
+   */
+  static int[] adjustForProteinLength(int proteinLength, int[] exon)
+  {
+    if (proteinLength <= 0 || exon == null)
+    {
+      return exon;
+    }
+    int expectedCdsLength = proteinLength * 3;
+    int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+    /*
+     * if exon length matches protein, or is shorter, or longer by the 
+     * length of a stop codon (3 bases), then leave it unchanged
+     */
+    if (expectedCdsLength >= exonLength
+            || expectedCdsLength == exonLength - 3)
+    {
+      return exon;
+    }
+
+    int origxon[];
+    int sxpos = -1;
+    int endxon = 0;
+    origxon = new int[exon.length];
+    System.arraycopy(exon, 0, origxon, 0, exon.length);
+    int cdspos = 0;
+    for (int x = 0; x < exon.length; x += 2)
+    {
+      cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+      if (expectedCdsLength <= cdspos)
+      {
+        // advanced beyond last codon.
+        sxpos = x;
+        if (expectedCdsLength != cdspos)
+        {
+          // System.err
+          // .println("Truncating final exon interval on region by "
+          // + (cdspos - cdslength));
+        }
+
+        /*
+         * shrink the final exon - reduce end position if forward
+         * strand, increase it if reverse
+         */
+        if (exon[x + 1] >= exon[x])
+        {
+          endxon = exon[x + 1] - cdspos + expectedCdsLength;
+        }
+        else
+        {
+          endxon = exon[x + 1] + cdspos - expectedCdsLength;
+        }
+        break;
+      }
+    }
+
+    if (sxpos != -1)
+    {
+      // and trim the exon interval set if necessary
+      int[] nxon = new int[sxpos + 2];
+      System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+      nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+                                // set
+      exon = nxon;
+    }
+    return exon;
+  }
+}
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 92473ec..7e62f6b 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -28,6 +28,7 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TreeMap;
@@ -346,7 +347,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     String line;
     while ((line = nextLine()) != null)
     {
-      if (line.toUpperCase().startsWith(ENDFILTERS))
+      // TODO: use .trim().equalsIgnoreCase here instead ? 
+      if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
       {
         return;
       }
diff --git a/src/jalview/io/FileFormats.java b/src/jalview/io/FileFormats.java
index aadcdb9..de83e9b 100644
--- a/src/jalview/io/FileFormats.java
+++ b/src/jalview/io/FileFormats.java
@@ -24,6 +24,7 @@ import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 
@@ -102,7 +103,7 @@ public class FileFormats
   protected void registerFileFormat(FileFormatI format,
           boolean isIdentifiable)
   {
-    String name = format.getName().toUpperCase();
+    String name = format.getName().toUpperCase(Locale.ROOT);
     if (formats.containsKey(name))
     {
       System.err.println("Overwriting file format: " + format.getName());
@@ -121,7 +122,7 @@ public class FileFormats
    */
   public void deregisterFileFormat(String name)
   {
-    FileFormatI ff = formats.remove(name.toUpperCase());
+    FileFormatI ff = formats.remove(name.toUpperCase(Locale.ROOT));
     identifiable.remove(ff);
   }
 
@@ -174,7 +175,7 @@ public class FileFormats
    */
   public FileFormatI forName(String format)
   {
-    return format == null ? null : formats.get(format.toUpperCase());
+    return format == null ? null : formats.get(format.toUpperCase(Locale.ROOT));
   }
 
   /**
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3afbaad..20db946 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -391,12 +391,9 @@ public class FileLoader implements Runnable
                   .getFeatureColourScheme();
           if (viewport != null)
           {
-            if (proxyColourScheme != null)
-            {
-              viewport.applyFeaturesStyle(proxyColourScheme);
-            }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            viewport.applyFeaturesStyle(proxyColourScheme);
           }
           else
           {
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 7117d0f..3013c0b 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -24,21 +24,25 @@ import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
+import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.io.StringReader;
+import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.net.URLConnection;
 import java.util.zip.GZIPInputStream;
 
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -56,6 +60,7 @@ public class FileParse
 
   public File inFile = null;
 
+
   /**
    * a viewport associated with the current file operation. May be null. May
    * move to different object.
@@ -182,29 +187,91 @@ public class FileParse
     }
     if (!error)
     {
-      if (fileStr.toLowerCase().endsWith(".gz"))
+      try
       {
-        try
-        {
-          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
-          dataName = fileStr;
-          return error;
-        } catch (Exception x)
-        {
-          warningMessage = "Failed  to resolve as a GZ stream ("
-                  + x.getMessage() + ")";
-          // x.printStackTrace();
-        }
-        ;
+        dataIn = checkForGzipStream(new FileInputStream(fileStr));
+        dataName = fileStr;
+      } catch (Exception x)
+      {
+        warningMessage = "Failed to resolve " + fileStr
+                + " as a data source. (" + x.getMessage() + ")";
+        // x.printStackTrace();
+        error = true;
       }
-
-      dataIn = new BufferedReader(new FileReader(fileStr));
-      dataName = fileStr;
+      ;
     }
     return error;
   }
 
-  private BufferedReader tryAsGzipSource(InputStream inputStream)
+  /**
+   * Recognise the 2-byte magic header indicating a gzipped stream
+   * 
+   * see
+   * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
+   * 
+   * @param input
+   *          - input stream that supports mark and contains at least two bytes
+   * 
+   * @return false if mark not supported or no magic header found
+   *
+   * @throws IOException
+   */
+  public static boolean isGzipStream(InputStream input) throws IOException
+  {
+    if (!input.markSupported())
+    {
+      Cache.log.error(
+              "FileParse.izGzipStream: input stream must support mark/reset");
+      return false;
+    }
+    input.mark(4);
+
+    // get first 2 bytes or return false
+    byte[] bytes = new byte[2];
+    int read = input.read(bytes);
+    input.reset();
+    if (read != bytes.length)
+    {
+      return false;
+    }
+
+    int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+    return (GZIPInputStream.GZIP_MAGIC == header);
+  }
+
+  /**
+   * Returns a Reader for the given input after wrapping it in a buffered input
+   * stream, and then checking if it needs to be wrapped by a GZipInputStream
+   * 
+   * @param input
+   * @return
+   */
+  private BufferedReader checkForGzipStream(InputStream input) throws Exception {
+
+    // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped
+    // could use a PushBackInputStream rather than a BufferedInputStream
+        
+    if (!input.markSupported()) {
+       input = new BufferedInputStream(input,16);
+    }
+    if (isGzipStream(input)) {
+      return getGzipReader(input);
+    }
+    // return a buffered reader for the stream.
+    InputStreamReader isReader= new InputStreamReader(input);
+    BufferedReader toReadFrom=new BufferedReader(isReader);
+    return toReadFrom;
+  }
+  /**
+   * Returns a {@code BufferedReader} which wraps the input stream with a
+   * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
+   * occurs or the compression method used is unsupported.
+   * 
+   * @param inputStream
+   * @return
+   * @throws Exception
+   */
+  private BufferedReader getGzipReader(InputStream inputStream)
           throws Exception
   {
     BufferedReader inData = new BufferedReader(
@@ -215,44 +282,74 @@ public class FileParse
     return inData;
   }
 
-  private boolean checkURLSource(String fileStr)
+  /**
+   * Tries to read from the given URL. If successful, saves a reader to the
+   * response in field {@code dataIn}, otherwise (on exception, or HTTP response
+   * status not 200), throws an exception.
+   * <p>
+   * If the response status includes
+   * 
+   * <pre>
+   * Content-Type : application/x-gzip
+   * </pre>
+   * 
+   * then tries to read as gzipped content.
+   * 
+   * @param urlStr
+   * @throws IOException
+   * @throws MalformedURLException
+   */
+  private void checkURLSource(String urlStr)
           throws IOException, MalformedURLException
   {
     errormessage = "URL NOT FOUND";
-    URL url = new URL(fileStr);
-    //
-    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
-    // Kenny Sabir
-    Exception e = null;
-    if (fileStr.toLowerCase().endsWith(".gz"))
+    URL url = new URL(urlStr);
+    URLConnection _conn = url.openConnection();
+    if (_conn instanceof HttpURLConnection)
     {
-      try
+      HttpURLConnection conn = (HttpURLConnection) _conn;
+      int rc = conn.getResponseCode();
+      if (rc != HttpURLConnection.HTTP_OK)
       {
-        InputStream inputStream = url.openStream();
-        dataIn = tryAsGzipSource(inputStream);
-        dataName = fileStr;
-        return false;
+        throw new IOException(
+                "Response status from " + urlStr + " was " + rc);
+      }
+    } else {
+      try {
+      dataIn = checkForGzipStream(_conn.getInputStream());
+      dataName=urlStr;
+      } catch (IOException ex)
+      {
+        throw new IOException("Failed to handle non-HTTP URI stream",ex);
       } catch (Exception ex)
       {
-        e = ex;
+        throw new IOException("Failed to determine type of input stream for given URI",ex);
       }
+      return;
     }
-
-    try
-    {
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q)
+    String encoding = _conn.getContentEncoding();
+    String contentType = _conn.getContentType();
+    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+            || "gzip".equals(encoding);
+    Exception e = null;
+    InputStream inputStream = _conn.getInputStream();
+    if (isgzipped)
     {
-      if (e != null)
+      try
+      {
+        dataIn = getGzipReader(inputStream);
+        dataName = urlStr;
+      } catch (Exception e1)
       {
         throw new IOException(MessageManager
                 .getString("exception.failed_to_resolve_gzip_stream"), e);
       }
-      throw q;
+      return;
     }
-    // record URL as name of datasource.
-    dataName = fileStr;
-    return false;
+
+    dataIn = new BufferedReader(new InputStreamReader(inputStream));
+    dataName = urlStr;
+    return;
   }
 
   /**
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6d3c18a..4d8794f 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.io.IOException;
+import java.util.Locale;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -161,7 +162,7 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+    return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
             true);
   }
 
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ff959b0..ed1c29f 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import java.io.IOException;
+import java.util.Locale;
 
 /**
  * DOCUMENT ME!
@@ -143,7 +144,7 @@ public class IdentifyFile
             break;
           }
         }
-        data = data.toUpperCase();
+        data = data.toUpperCase(Locale.ROOT);
 
         if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
         {
@@ -284,7 +285,7 @@ public class IdentifyFile
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
                              // RNAML, XML
         {
-          String upper = data.toUpperCase();
+          String upper = data.toUpperCase(Locale.ROOT);
           if (upper.substring(lessThan).startsWith("<HTML"))
           {
             reply = FileFormat.Html;
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 6732e82..8f93b48 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -33,6 +33,7 @@ import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.Hashtable;
+import java.util.Locale;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -408,7 +409,7 @@ public class JPredFile extends AlignFile
     // check that no stray annotations have been added at the end.
     {
       SequenceI sq = seqs.elementAt(j - 1);
-      if (sq.getName().toUpperCase().startsWith("JPRED"))
+      if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
       {
         annotSeqs.addElement(sq);
         seqs.removeElementAt(--j);
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index fda22dc..0e3cca7 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -71,7 +71,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private static String version = new BuildDetails().getVersion();
 
-  private String webstartUrl = "http://www.jalview.org/services/launchApp";
+  private String webstartUrl = "https://www.jalview.org/services/launchApp";
 
   private String application = "Jalview";
 
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 6828202..27fc869 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -88,7 +90,7 @@ public class JnetAnnotationMaker
 
     while (i < preds.length)
     {
-      String id = preds[i].getName().toUpperCase();
+      String id = preds[i].getName().toUpperCase(Locale.ROOT);
 
       if (id.startsWith("LUPAS") || id.startsWith("JNET")
               || id.startsWith("JPRED"))
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index df2bed2..db29848 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -29,6 +29,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
 /**
@@ -184,7 +185,7 @@ public class MSFfile extends AlignFile
   public int checkSum(String seq)
   {
     int check = 0;
-    String sequence = seq.toUpperCase();
+    String sequence = seq.toUpperCase(Locale.ROOT);
 
     for (int i = 0; i < sequence.length(); i++)
     {
diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index 0f2b0ac..ee82418 100644
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -36,10 +36,9 @@ public class PDBFeatureSettings extends FeatureSettingsAdapter
   private static final String FEATURE_RES_NUM = PDBChain.RESNUM_FEATURE;
 
   @Override
-  public boolean isFeatureDisplayed(String type)
+  public boolean isFeatureHidden(String type)
   {
-    return type.equalsIgnoreCase(FEATURE_INSERTION)
-            || type.equalsIgnoreCase(FEATURE_RES_NUM);
+    return type.equalsIgnoreCase(FEATURE_RES_NUM);
   }
 
   @Override
diff --git a/src/jalview/io/ScoreMatrixFile.java b/src/jalview/io/ScoreMatrixFile.java
index 0b70dce..ee7503d 100644
--- a/src/jalview/io/ScoreMatrixFile.java
+++ b/src/jalview/io/ScoreMatrixFile.java
@@ -20,13 +20,13 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+import java.util.StringTokenizer;
+
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.SequenceI;
 
-import java.io.IOException;
-import java.util.StringTokenizer;
-
 /**
  * A class that can parse a file containing a substitution matrix and register
  * it for use in Jalview
@@ -131,7 +131,8 @@ public class ScoreMatrixFile extends AlignFile
       {
         continue;
       }
-      if (data.toUpperCase().startsWith(SCOREMATRIX))
+      // equivalent to data.startsWithIgnoreCase(SCOREMATRIX)
+      if (data.regionMatches(true, 0, SCOREMATRIX, 0, SCOREMATRIX.length()))
       {
         /*
          * Parse name from ScoreMatrix <name>
diff --git a/src/jalview/io/cache/JvCacheableInputBox.java b/src/jalview/io/cache/JvCacheableInputBox.java
index beef3e7..71e7c62 100644
--- a/src/jalview/io/cache/JvCacheableInputBox.java
+++ b/src/jalview/io/cache/JvCacheableInputBox.java
@@ -25,8 +25,8 @@ import jalview.util.MessageManager;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -64,12 +64,19 @@ public class JvCacheableInputBox<E> extends JComboBox<String>
     return enterWasPressed;
   }
 
-  public JvCacheableInputBox(String newCacheKey)
+  /**
+   * Constructor given the key to cached values, and the (approximate) length in
+   * characters of the input field
+   * 
+   * @param newCacheKey
+   * @param length
+   */
+  public JvCacheableInputBox(String newCacheKey, int length)
   {
     super();
     this.cacheKey = newCacheKey;
     setEditable(true);
-    addKeyListener(new KeyListener()
+    addKeyListener(new KeyAdapter()
     {
 
       @Override
@@ -82,23 +89,16 @@ public class JvCacheableInputBox<E> extends JComboBox<String>
         }
         // let event bubble up
       }
-
-      @Override
-      public void keyReleased(KeyEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void keyPressed(KeyEvent e)
+    });
+    if (length > 0)
+    {
+      StringBuilder sb = new StringBuilder();
+      for (int i = 0; i < length; i++)
       {
-        // TODO Auto-generated method stub
-
+        sb.append("X");
       }
-    });
-    setPrototypeDisplayValue(
-            "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+      setPrototypeDisplayValue(sb.toString());
+    }
     appCache = AppCache.getInstance();
     initCachePopupMenu();
     initCache(newCacheKey);
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 1635682..91575bf 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -34,6 +34,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 
 public class ParsePackedSet
 {
@@ -234,7 +235,7 @@ public class ParsePackedSet
       String type = args[i++];
       final String file = args[i++];
       final JvDataType jtype = DataProvider.JvDataType
-              .valueOf(type.toUpperCase());
+              .valueOf(type.toUpperCase(Locale.ROOT));
       if (jtype != null)
       {
         final FileParse fp;
@@ -253,7 +254,7 @@ public class ParsePackedSet
       else
       {
         System.out.println("Couldn't parse source type token '"
-                + type.toUpperCase() + "'");
+                + type.toUpperCase(Locale.ROOT) + "'");
       }
     }
     if (i < args.length)
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index a44ee26..d6a530b 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -48,6 +48,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -569,7 +570,7 @@ public class VCFLoader
   {
     for (Pattern p : filters)
     {
-      if (p.matcher(id.toUpperCase()).matches())
+      if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
       {
         return true;
       }
@@ -663,7 +664,7 @@ public class VCFLoader
     {
       try
       {
-      patterns.add(Pattern.compile(token.toUpperCase()));
+      patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
       } catch (PatternSyntaxException e)
       {
         System.err.println("Invalid pattern ignored: " + token);
@@ -912,7 +913,7 @@ public class VCFLoader
          * RuntimeException throwable by htsjdk
          */
         String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
-                map.chromosome, vcfStart, vcfEnd);
+                map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
         Cache.log.error(msg);
       }
     }
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index b433570..1600b75 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -28,11 +28,11 @@ import jalview.io.cache.JvCacheableInputBox;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
-import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.GridLayout;
-import java.awt.Insets;
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 
 import javax.swing.JButton;
@@ -47,19 +47,26 @@ import javax.swing.text.JTextComponent;
 
 public class GFinder extends JPanel
 {
-  private static final java.awt.Font VERDANA_12 = new java.awt.Font("Verdana", 0,
-          12);
+  private static final java.awt.Font VERDANA_12 = new Font("Verdana",
+          Font.PLAIN, 12);
 
   private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
 
-  protected JButton createFeatures = new JButton();
+  /*
+   * if more checkboxes are wanted, increase this value
+   * and add to centrePanel in jbInit()  
+   */
+  private static final int PANEL_ROWS = 4;
+
+  protected JButton createFeatures;
 
-  protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
-          getCacheKey());
+  protected JvCacheableInputBox<String> searchBox;
 
-  protected JCheckBox caseSensitive = new JCheckBox();
+  protected JCheckBox caseSensitive;
 
-  protected JCheckBox searchDescription = new JCheckBox();
+  protected JCheckBox searchDescription;
+
+  protected JCheckBox ignoreHidden;
 
   public GFinder()
   {
@@ -72,20 +79,98 @@ public class GFinder extends JPanel
     }
   }
 
+  /**
+   * Constructs the widgets and adds them to the layout
+   */
   private void jbInit() throws Exception
   {
-    BorderLayout mainBorderLayout = new BorderLayout();
-    this.setLayout(mainBorderLayout);
-    mainBorderLayout.setHgap(5);
-    mainBorderLayout.setVgap(5);
+    /*
+     * border layout
+     * West: 4 rows
+     *   first row 'Find'
+     *   remaining rows empty
+     * Center: 4 rows
+     *   first row search box
+     *   second row 'match case' checkbox
+     *   third row 'include description' checkbox
+     *   fourth row 'ignore hidden' checkbox
+     * East: four rows
+     *   first row 'find next' button
+     *   second row 'find all' button
+     *   third row 'new feature' button
+     *   fourth row empty
+     */
+    this.setLayout(new BorderLayout());
+    JPanel eastPanel = new JPanel();
+    eastPanel.setLayout(new GridLayout(PANEL_ROWS, 1));
+    this.add(eastPanel, BorderLayout.EAST);
+    JPanel centrePanel = new JPanel();
+    centrePanel.setLayout(new GridLayout(PANEL_ROWS, 1));
+    this.add(centrePanel, BorderLayout.CENTER);
+    JPanel westPanel = new JPanel();
+    westPanel.setLayout(new GridLayout(PANEL_ROWS, 1));
+    this.add(westPanel, BorderLayout.WEST);
 
-    JLabel jLabelFind = new JLabel(MessageManager.getString("label.find"));
-    jLabelFind.setFont(VERDANA_12);
+    /*
+     * 'Find' prompt goes top left
+     */
+    JLabel findLabel = new JLabel(
+            " " + MessageManager.getString("label.find") + " ");
+    findLabel.setFont(VERDANA_12);
+    westPanel.add(findLabel);
 
+    /*
+     * search box
+     */
+    searchBox = new JvCacheableInputBox<>(FINDER_CACHE_KEY, 25);
+    searchBox.setFont(VERDANA_12);
+    ((JTextComponent) searchBox.getEditor().getEditorComponent())
+            .addCaretListener(new CaretListener()
+            {
+              @Override
+              public void caretUpdate(CaretEvent e)
+              {
+                textfield_caretUpdate();
+              }
+            });
+    searchBox.getEditor().getEditorComponent()
+            .addKeyListener(new KeyAdapter()
+            {
+              @Override
+              public void keyPressed(KeyEvent e)
+              {
+                textfield_keyPressed(e);
+              }
+            });
+    centrePanel.add(searchBox);
+
+    /*
+     * search options checkboxes
+     */
+    caseSensitive = new JCheckBox();
+    caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
+    caseSensitive.setText(MessageManager.getString("label.match_case"));
+
+    searchDescription = new JCheckBox();
+    searchDescription
+            .setText(MessageManager.getString("label.include_description"));
+
+    ignoreHidden = new JCheckBox();
+    ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
+    ignoreHidden.setToolTipText(
+            MessageManager.getString("label.ignore_hidden_tooltip"));
+    
+    centrePanel.add(caseSensitive);
+    centrePanel.add(searchDescription);
+    centrePanel.add(ignoreHidden);
+
+    /*
+     * action buttons
+     */
     JButton findAll = new JButton(
             MessageManager.getString("action.find_all"));
     findAll.setFont(VERDANA_12);
-    findAll.addActionListener(new java.awt.event.ActionListener()
+    findAll.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -93,11 +178,10 @@ public class GFinder extends JPanel
         findAll_actionPerformed();
       }
     });
-
     JButton findNext = new JButton(
             MessageManager.getString("action.find_next"));
     findNext.setFont(VERDANA_12);
-    findNext.addActionListener(new java.awt.event.ActionListener()
+    findNext.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -105,19 +189,11 @@ public class GFinder extends JPanel
         findNext_actionPerformed();
       }
     });
-
-    JPanel actionsPanel = new JPanel();
-    GridLayout gridLayout1 = new GridLayout();
-    actionsPanel.setLayout(gridLayout1);
-    gridLayout1.setHgap(0);
-    gridLayout1.setRows(3);
-    gridLayout1.setVgap(2);
-
+    createFeatures = new JButton();
     createFeatures.setEnabled(false);
     createFeatures.setFont(VERDANA_12);
-    createFeatures.setMargin(new Insets(0, 0, 0, 0));
     createFeatures.setText(MessageManager.getString("label.new_feature"));
-    createFeatures.addActionListener(new java.awt.event.ActionListener()
+    createFeatures.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -125,60 +201,9 @@ public class GFinder extends JPanel
         createFeatures_actionPerformed();
       }
     });
-    searchBox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
-    ((JTextComponent) searchBox.getEditor().getEditorComponent())
-            .addCaretListener(new CaretListener()
-            {
-              @Override
-              public void caretUpdate(CaretEvent e)
-              {
-                textfield_caretUpdate();
-              }
-            });
-    searchBox.getEditor().getEditorComponent()
-            .addKeyListener(new java.awt.event.KeyAdapter()
-            {
-              @Override
-              public void keyPressed(KeyEvent e)
-              {
-                textfield_keyPressed(e);
-              }
-            });
-
-    caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
-    caseSensitive.setText(MessageManager.getString("label.match_case"));
-
-    searchDescription
-            .setText(MessageManager.getString("label.include_description"));
-
-    actionsPanel.add(findNext, null);
-    actionsPanel.add(findAll, null);
-    actionsPanel.add(createFeatures, null);
-    this.add(jLabelFind, java.awt.BorderLayout.WEST);
-    this.add(actionsPanel, java.awt.BorderLayout.EAST);
-
-    JPanel jPanel2 = new JPanel();
-    jPanel2.setPreferredSize(new Dimension(10, 1));
-    JPanel jPanel3 = new JPanel();
-    jPanel3.setPreferredSize(new Dimension(10, 1));
-    JPanel jPanel4 = new JPanel();
-    jPanel4.setLayout(new BorderLayout());
-    this.add(jPanel2, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel3, java.awt.BorderLayout.NORTH);
-    this.add(jPanel4, java.awt.BorderLayout.CENTER);
-    jPanel4.add(searchBox, java.awt.BorderLayout.NORTH);
-
-    JPanel optionsPanel = new JPanel();
-
-    GridLayout optionsGridLayout = new GridLayout();
-    optionsGridLayout.setHgap(0);
-    optionsGridLayout.setRows(2);
-    optionsGridLayout.setVgap(2);
-    optionsPanel.setLayout(optionsGridLayout);
-    optionsPanel.add(caseSensitive, null);
-    optionsPanel.add(searchDescription, null);
-
-    jPanel4.add(optionsPanel, java.awt.BorderLayout.WEST);
+    eastPanel.add(findNext);
+    eastPanel.add(findAll);
+    eastPanel.add(createFeatures);
   }
 
   protected void textfield_keyPressed(KeyEvent e)
@@ -236,15 +261,4 @@ public class GFinder extends JPanel
     }
   }
 
-  /**
-   * Returns unique key used for storing Finder cache items in the cache data
-   * structure
-   * 
-   * @return
-   */
-  public String getCacheKey()
-  {
-    return FINDER_CACHE_KEY;
-  }
-
 }
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index adca17e..671bf6b 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -150,6 +150,7 @@ public class AnnotationRenderer
    */
   public void dispose()
   {
+    hiddenColumns = null;
     hconsensus = null;
     complementConsensus = null;
     hStrucConsensus = null;
diff --git a/src/jalview/schemes/FeatureSettingsAdapter.java b/src/jalview/schemes/FeatureSettingsAdapter.java
index b15e4cf..6e8554f 100644
--- a/src/jalview/schemes/FeatureSettingsAdapter.java
+++ b/src/jalview/schemes/FeatureSettingsAdapter.java
@@ -36,6 +36,12 @@ public class FeatureSettingsAdapter implements FeatureSettingsModelI
   }
 
   @Override
+  public boolean isFeatureHidden(String type)
+  {
+    return false;
+  }
+
+  @Override
   public boolean isGroupDisplayed(String group)
   {
     return true;
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index b552c21..915293e 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -1020,4 +1020,23 @@ public final class MappingUtils
       }
     }
   }
+
+  /**
+   * Converts a list of [start, end] ranges to a single array of [start, end,
+   * start, end ...]
+   * 
+   * @param ranges
+   * @return
+   */
+  public static int[] listToArray(List<int[]> ranges)
+  {
+    int[] result = new int[ranges.size() * 2];
+    int i = 0;
+    for (int[] range : ranges)
+    {
+      result[i++] = range[0];
+      result[i++] = range[1];
+    }
+    return result;
+  }
 }
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index e8558fa..a5bee7c 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -29,11 +29,23 @@ import java.awt.event.MouseEvent;
  */
 public class Platform
 {
-  private static Boolean isAMac = null, isWindows = null;
+  private static Boolean isAMac = null, isWindows = null, isLinux = null;
 
   private static Boolean isHeadless = null;
 
   /**
+   * added to check LaF for Linux
+   * 
+   * @return
+   */
+  public static boolean isLinux()
+  {
+    return (isLinux == null
+            ? (isLinux = (System.getProperty("os.name").indexOf("Linux") >= 0))
+            : isLinux);
+  }
+
+  /**
    * sorry folks - Macs really are different
    * 
    * @return true if we do things in a special way.
@@ -131,7 +143,8 @@ public class Platform
       {
         return false;
       }
-      return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
+      return (jalview.util.ShortcutKeyMaskExWrapper
+              .getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
               & jalview.util.ShortcutKeyMaskExWrapper
                       .getModifiersEx(e)) != 0; // getModifiers()) != 0;
     }
@@ -139,8 +152,8 @@ public class Platform
   }
 
   /**
-   * A (case sensitive) file path comparator that ignores the difference between /
-   * and \
+   * A (case sensitive) file path comparator that ignores the difference between
+   * / and \
    * 
    * @param path1
    * @param path2
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 8dcd1b3..c9a3a80 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -959,6 +959,7 @@ public abstract class AlignmentViewport
     ranges = null;
     currentTree = null;
     selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -3044,4 +3045,22 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
+
+  @Override
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int start = 0;
+    int end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      end = alignment.getWidth();
+    }
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
+  }
 }
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 426ec1f..b348766 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -102,11 +102,11 @@ public abstract class FeatureRendererModel
 
   Map<String, Float> featureOrder = null;
 
-  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
-          this);
-
   protected AlignViewportI av;
 
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
   @Override
   public AlignViewportI getViewport()
   {
@@ -299,13 +299,19 @@ public abstract class FeatureRendererModel
       {
         firing = Boolean.TRUE;
         findAllFeatures(true); // add all new features as visible
-        changeSupport.firePropertyChange("changeSupport", null, null);
+        notifyFeaturesChanged();
         firing = Boolean.FALSE;
       }
     }
   }
 
   @Override
+  public void notifyFeaturesChanged()
+  {
+    changeSupport.firePropertyChange("changeSupport", null, null);
+  }
+
+  @Override
   public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
     /*
diff --git a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
index f44a2d1..d7da519 100644
--- a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
+++ b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
@@ -29,9 +29,9 @@ import java.util.Set;
 
 public class FeaturesDisplayed implements FeaturesDisplayedI
 {
-  private Set<String> featuresDisplayed = new HashSet<String>();
+  private Set<String> featuresDisplayed = new HashSet<>();
 
-  private Set<String> featuresRegistered = new HashSet<String>();
+  private Set<String> featuresRegistered = new HashSet<>();
 
   public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2)
   {
@@ -93,6 +93,13 @@ public class FeaturesDisplayed implements FeaturesDisplayedI
   }
 
   @Override
+  public void setHidden(String featureType)
+  {
+    featuresDisplayed.remove(featureType);
+    featuresRegistered.add(featureType);
+  }
+
+  @Override
   public boolean isRegistered(String type)
   {
     return featuresRegistered.contains(type);
diff --git a/src/jalview/ws/dbsources/EmblCdsSource.java b/src/jalview/ws/dbsources/EmblCdsSource.java
index a73af61..d02910c 100644
--- a/src/jalview/ws/dbsources/EmblCdsSource.java
+++ b/src/jalview/ws/dbsources/EmblCdsSource.java
@@ -23,9 +23,7 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import com.stevesoft.pat.Regex;
-
-public class EmblCdsSource extends EmblXmlSource
+public class EmblCdsSource extends EmblFlatfileSource // was EmblXmlSource
 {
 
   public EmblCdsSource()
@@ -34,31 +32,12 @@ public class EmblCdsSource extends EmblXmlSource
   }
 
   @Override
-  public String getAccessionSeparator()
-  {
-    return null;
-  }
-
-  @Override
-  public Regex getAccessionValidator()
-  {
-    return new Regex("^[A-Z]+[0-9]+");
-  }
-
-  @Override
   public String getDbSource()
   {
     return DBRefSource.EMBLCDS;
   }
 
   @Override
-  public String getDbVersion()
-  {
-    return "0"; // TODO : this is dynamically set for a returned record - not
-    // tied to proxy
-  }
-
-  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     if (queries.indexOf(".") > -1)
@@ -68,15 +47,6 @@ public class EmblCdsSource extends EmblXmlSource
     return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
   }
 
-  @Override
-  public boolean isValidReference(String accession)
-  {
-    // most embl CDS refs look like ..
-    // TODO: improve EMBLCDS regex
-    return (accession == null || accession.length() < 2) ? false
-            : getAccessionValidator().search(accession);
-  }
-
   /**
    * cDNA for LDHA_CHICK swissprot sequence
    */
@@ -92,10 +62,4 @@ public class EmblCdsSource extends EmblXmlSource
     return "EMBL (CDS)";
   }
 
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
-
 }
diff --git a/src/jalview/ws/dbsources/EmblFlatfileSource.java b/src/jalview/ws/dbsources/EmblFlatfileSource.java
new file mode 100644
index 0000000..6536958
--- /dev/null
+++ b/src/jalview/ws/dbsources/EmblFlatfileSource.java
@@ -0,0 +1,121 @@
+package jalview.ws.dbsources;
+
+import java.io.File;
+import java.io.IOException;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.EmblFlatFile;
+import jalview.io.FileParse;
+import jalview.ws.ebi.EBIFetchClient;
+
+/**
+ * A class that does partial parsing of an EMBL flatfile.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
+{
+  private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
+
+  @Override
+  public String getDbVersion()
+  {
+    return "0";
+  }
+
+  @Override
+  public String getAccessionSeparator()
+  {
+    return null;
+  }
+
+  @Override
+  public Regex getAccessionValidator()
+  {
+    return ACCESSION_REGEX;
+  }
+
+  @Override
+  public boolean isValidReference(String accession)
+  {
+    if (accession == null || accession.length() < 2)
+    {
+      return false;
+    }
+    return getAccessionValidator().search(accession);
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null;
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
+  protected AlignmentI getEmblSequenceRecords(String dbName, String query)
+          throws Exception
+  {
+    startQuery();
+    EBIFetchClient dbFetch = new EBIFetchClient();
+    File reply;
+    try
+    {
+      reply = dbFetch.fetchDataAsFile(
+              dbName.toLowerCase() + ":" + query.trim(), null, "gz");
+    } catch (Exception e)
+    {
+      stopQuery();
+      throw new Exception(
+              String.format("EBI EMBL retrieval failed for %s:%s",
+                      dbName.toLowerCase(), query.trim()),
+              e);
+    }
+    return getEmblSequenceRecords(dbName, query, reply);
+  }
+
+  private AlignmentI getEmblSequenceRecords(String dbName, String query,
+          File reply) throws IOException
+  {
+    AlignmentI al = null;
+
+    if (reply != null && reply.exists())
+    {
+      file = reply.getAbsolutePath();
+      FileParse fp = new FileParse(file, DataSourceType.FILE);
+      EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
+      emblParser.parse();
+      SequenceI[] seqs = emblParser.getSeqsAsArray();
+      if (seqs.length > 0)
+      {
+        al = new Alignment(seqs);
+      }
+
+      if (al == null)
+      {
+        Cache.log.error(
+                "No record found for '" + dbName + ":" + query + "'");
+      }
+    }
+
+    stopQuery();
+    return al;
+  }
+
+  @Override
+  public boolean isDnaCoding()
+  {
+    return true;
+  }
+}
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 6bbe2e1..df43bc3 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -23,13 +23,11 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * @author JimP
  * 
  */
-public class EmblSource extends EmblXmlSource
+public class EmblSource extends EmblFlatfileSource // was EmblXmlSource
 {
 
   public EmblSource()
@@ -40,29 +38,6 @@ public class EmblSource extends EmblXmlSource
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  @Override
-  public String getAccessionSeparator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  @Override
-  public Regex getAccessionValidator()
-  {
-    return new Regex("^[A-Z]+[0-9]+");
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   @Override
@@ -74,18 +49,6 @@ public class EmblSource extends EmblXmlSource
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  @Override
-  public String getDbVersion()
-  {
-    // TODO Auto-generated method stub
-    return "0";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   @Override
@@ -94,21 +57,6 @@ public class EmblSource extends EmblXmlSource
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  @Override
-  public boolean isValidReference(String accession)
-  {
-    // most embl refs look like ..
-
-    return (accession == null || accession.length() < 2) ? false
-            : getAccessionValidator().search(accession);
-
-  }
-
   /**
    * return LHD_CHICK coding gene
    */
@@ -123,10 +71,4 @@ public class EmblSource extends EmblXmlSource
   {
     return "EMBL"; // getDbSource();
   }
-
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
 }
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index a420d9f..97d7c9f 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -20,6 +20,27 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
 import jalview.analysis.SequenceIdMatcher;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -35,33 +56,23 @@ import jalview.util.DBRefUtils;
 import jalview.util.DnaUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.xml.binding.embl.EntryType;
 import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.embl.XrefType;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
+/**
+ * Provides XML binding and parsing of EMBL or EMBLCDS records retrieved from
+ * (e.g.) {@code https://www.ebi.ac.uk/ena/data/view/x53828&display=xml}.
+ * 
+ * @deprecated endpoint withdrawn August 2020 (JAL-3692), use EmblFlatfileSource
+ */
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
+  private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
+
   /*
    * JAL-1856 Embl returns this text for query not found
    */
@@ -96,9 +107,10 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     } catch (Exception e)
     {
       stopQuery();
-      throw new Exception(MessageManager.formatMessage(
-              "exception.ebiembl_retrieval_failed_on", new String[]
-              { emprefx.toLowerCase(), query.trim() }), e);
+      throw new Exception(
+              String.format("EBI EMBL XML retrieval failed for %s:%s",
+                      emprefx.toLowerCase(), query.trim()),
+              e);
     }
     return getEmblSequenceRecords(emprefx, query, reply);
   }
@@ -180,8 +192,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(is);
       javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
-              .unmarshal(streamReader);
+      JAXBElement<ROOT> rootElement = um.unmarshal(streamReader,
+              ROOT.class);
+      ROOT root = rootElement.getValue();
 
       /*
        * document root contains either "entry" or "entrySet"
@@ -561,6 +574,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
               proteinSeq = new Sequence(proteinSeqName,
                       product.getSequenceAsString());
               matcher.add(proteinSeq);
+              proteinSeq.setDescription(product.getDescription());
               peptides.add(proteinSeq);
             }
             dnaToProteinMapping.setTo(proteinSeq);
@@ -614,8 +628,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
               && dnaToProteinMapping.getTo() != null)
       {
         DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
-                DBRefSource.EMBLCDSProduct, sequenceVersion,
-                proteinId);
+                DBRefSource.EMBLCDSProduct, sequenceVersion, proteinId);
         dnaToEmblProteinRef.setMap(dnaToProteinMapping);
         dnaToProteinMapping.setMappedFromId(proteinId);
         dna.addDBRef(dnaToEmblProteinRef);
@@ -644,7 +657,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     {
       return new int[] {};
     }
-  
+
     try
     {
       List<int[]> ranges = DnaUtils.parseLocation(location);
@@ -708,6 +721,40 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     return sf;
   }
 
+  @Override
+  public String getAccessionSeparator()
+  {
+    return null;
+  }
+
+  @Override
+  public Regex getAccessionValidator()
+  {
+    return ACCESSION_REGEX;
+  }
+
+  @Override
+  public String getDbVersion()
+  {
+    return "0";
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
+  @Override
+  public boolean isValidReference(String accession)
+  {
+    if (accession == null || accession.length() < 2)
+    {
+      return false;
+    }
+    return getAccessionValidator().search(accession);
+  }
+
   /**
    * Truncates (if necessary) the exon intervals to match 3 times the length of
    * the protein; also accepts 3 bases longer (for stop codon not included in
@@ -726,7 +773,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     }
     int expectedCdsLength = proteinLength * 3;
     int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-  
+
     /*
      * if exon length matches protein, or is shorter, or longer by the 
      * length of a stop codon (3 bases), then leave it unchanged
@@ -736,7 +783,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     {
       return exon;
     }
-  
+
     int origxon[];
     int sxpos = -1;
     int endxon = 0;
@@ -756,7 +803,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
           // .println("Truncating final exon interval on region by "
           // + (cdspos - cdslength));
         }
-  
+
         /*
          * shrink the final exon - reduce end position if forward
          * strand, increase it if reverse
@@ -772,7 +819,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
         break;
       }
     }
-  
+
     if (sxpos != -1)
     {
       // and trim the exon interval set if necessary
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 8877c34..47e66ac 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -35,6 +35,11 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
+  /*
+   * append to URLs to retrieve as a gzipped file
+   */
+  protected static final String GZIPPED = "/gzipped";
+
   static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
 
   private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 0600427..d71892b 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -34,7 +34,7 @@ public class PfamFull extends Pfam
   @Override
   public String getURLSuffix()
   {
-    return "/alignment/full";
+    return "/alignment/full" + GZIPPED;
   }
 
   /*
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index dff8a17..f64d07f 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -36,7 +36,7 @@ public class PfamSeed extends Pfam
   @Override
   public String getURLSuffix()
   {
-    return "/alignment/seed";
+    return "/alignment/seed" + GZIPPED;
   }
 
   /*
diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 1d9d99a..c9ee7fc 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -36,6 +36,11 @@ abstract public class Rfam extends Xfam
 
   private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
 
+  /*
+   * append to URLs to retrieve as a gzipped file
+   */
+  protected static final String GZIPPED = "?gzip=1&download=1";
+
   @Override
   protected String getURLPrefix()
   {
diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index d815336..396511c 100644
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -36,7 +36,7 @@ public class RfamFull extends Rfam
   @Override
   public String getURLSuffix()
   {
-    return "/alignment/full";
+    return "/alignment/full" + GZIPPED;
   }
 
   /*
diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index a74e829..eaa574b 100644
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -36,8 +36,7 @@ public class RfamSeed extends Rfam
   @Override
   public String getURLSuffix()
   {
-    // to download gzipped file add '?gzip=1'
-    return "/alignment/stockholm";
+    return "/alignment/stockholm" + GZIPPED;
   }
 
   /*
diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index b83f558..f0cb14b 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -36,7 +36,6 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  */
 public abstract class Xfam extends DbSourceProxyImpl
 {
-
   public Xfam()
   {
     super();
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 07a9df4..8ab5fbb 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -27,6 +27,7 @@ import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
@@ -91,7 +92,7 @@ public class EBIFetchClient
    *          the query formatted as db:query1;query2;query3
    * @param format
    *          the format wanted
-   * @param extension
+   * @param ext
    *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
@@ -201,7 +202,8 @@ public class EBIFetchClient
   {
     // long time = System.currentTimeMillis();
     String url = buildUrl(ids, database, format);
-
+    InputStream is = null;
+    BufferedReader br = null;
     try
     {
       URL rcall = new URL(url);
@@ -213,7 +215,7 @@ public class EBIFetchClient
         System.err.println("Warning: response code " + responseCode
                 + " for " + url);
       }
-      InputStream is = new BufferedInputStream(conn.getInputStream());
+      is = new BufferedInputStream(conn.getInputStream());
       if (outFile != null)
       {
         FileOutputStream fio = new FileOutputStream(outFile);
@@ -228,7 +230,7 @@ public class EBIFetchClient
       }
       else
       {
-        BufferedReader br = new BufferedReader(new InputStreamReader(is));
+        br = new BufferedReader(new InputStreamReader(is));
         String rtn;
         List<String> arl = new ArrayList<String>();
         while ((rtn = br.readLine()) != null)
@@ -257,6 +259,24 @@ public class EBIFetchClient
     {
       // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
       // time) + " ms");
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+        }
+      }
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+        }
+      }
     }
     return null;
   }
@@ -275,8 +295,8 @@ public class EBIFetchClient
     if (database.equalsIgnoreCase(DBRefSource.EMBL)
             || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
     {
-      url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
-              + (format != null ? "&" + format : "");
+      url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+              + ids.toLowerCase() + "?download=true&gzip=true";
     }
     else
     {
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index b5f9653..9790f79 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -20,28 +20,6 @@
  */
 package jalview.ws.sifts;
 
-import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.DBRefEntryI;
-import jalview.api.SiftsClientI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.Format;
-import jalview.xml.binding.sifts.Entry;
-import jalview.xml.binding.sifts.Entry.Entity;
-import jalview.xml.binding.sifts.Entry.Entity.Segment;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -73,6 +51,28 @@ import javax.xml.stream.XMLStreamReader;
 
 import MCview.Atom;
 import MCview.PDBChain;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.DBRefEntryI;
+import jalview.api.SiftsClientI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.Format;
+import jalview.xml.binding.sifts.Entry;
+import jalview.xml.binding.sifts.Entry.Entity;
+import jalview.xml.binding.sifts.Entry.Entity.Segment;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
 
 public class SiftsClient implements SiftsClientI
 {
@@ -123,6 +123,7 @@ public class SiftsClient implements SiftsClientI
   private enum CoordinateSys
   {
     UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+
     private String name;
 
     private CoordinateSys(String name)
@@ -140,6 +141,7 @@ public class SiftsClient implements SiftsClientI
   {
     NAME_SEC_STRUCTURE("nameSecondaryStructure"),
     CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
+
     private String code;
 
     private ResidueDetailType(String code)
@@ -225,7 +227,7 @@ public class SiftsClient implements SiftsClientI
               SiftsSettings.getCacheThresholdInDays()))
       {
         File oldSiftsFile = new File(siftsFileName + "_old");
-        siftsFile.renameTo(oldSiftsFile);
+        BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
         try
         {
           siftsFile = downloadSiftsFile(pdbId.toLowerCase());
@@ -234,7 +236,7 @@ public class SiftsClient implements SiftsClientI
         } catch (IOException e)
         {
           e.printStackTrace();
-          oldSiftsFile.renameTo(siftsFile);
+          BackupFiles.moveFileToFile(oldSiftsFile, siftsFile);
           return new File(siftsFileName);
         }
       }
@@ -461,7 +463,7 @@ public class SiftsClient implements SiftsClientI
           SequenceI seq, java.io.PrintStream os) throws SiftsException
   {
     List<Integer> omitNonObserved = new ArrayList<>();
-    int nonObservedShiftIndex = 0,pdbeNonObserved=0;
+    int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
     // System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
@@ -492,7 +494,7 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
     List<Segment> segments = entity.getSegment();
     SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
-            omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
+            omitNonObserved, nonObservedShiftIndex, pdbeNonObserved);
     processSegments(segments, shp);
     try
     {
@@ -514,18 +516,20 @@ public class SiftsClient implements SiftsClientI
     {
       throw new SiftsException("SIFTS mapping failed");
     }
-    // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
+    // also construct a mapping object between the seq-coord sys and the PDB
+    // seq's coord sys
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
     Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
-    List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
-    int[]_cfrom=null,_cto=null;
+    List<int[]> from = new ArrayList<>(), to = new ArrayList<>();
+    int[] _cfrom = null, _cto = null;
     String matchedSeq = originalSeq;
-    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
+    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb
+                                // sequence that starts <-1
     {
-      for (int seqps:keys)
+      for (int seqps : keys)
       {
         int pdbpos = mapping.get(seqps)[PDBE_POS];
         if (pdbpos == UNASSIGNED)
@@ -533,19 +537,23 @@ public class SiftsClient implements SiftsClientI
           // not correct - pdbpos might be -1, but leave it for now
           continue;
         }
-        if (_cfrom==null || seqps!=_cfrom[1]+1)
+        if (_cfrom == null || seqps != _cfrom[1] + 1)
         {
-          _cfrom = new int[] { seqps,seqps};
+          _cfrom = new int[] { seqps, seqps };
           from.add(_cfrom);
           _cto = null; // discontinuity
-        } else {
-          _cfrom[1]= seqps;
         }
-        if (_cto==null || pdbpos!=1+_cto[1])
+        else
+        {
+          _cfrom[1] = seqps;
+        }
+        if (_cto == null || pdbpos != 1 + _cto[1])
         {
-          _cto = new int[] { pdbpos,pdbpos};
+          _cto = new int[] { pdbpos, pdbpos };
           to.add(_cto);
-        } else {
+        }
+        else
+        {
           _cto[1] = pdbpos;
         }
       }
@@ -567,8 +575,7 @@ public class SiftsClient implements SiftsClientI
       ;
 
       seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
-              1,
-              1);
+              1, 1);
       pdbStart = mapping.get(seqStart)[PDB_RES_POS];
       pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
       int orignalSeqStart = seq.getStart();
@@ -699,12 +706,12 @@ public class SiftsClient implements SiftsClientI
         }
         // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
         // true
-                                                                         // numbering
-                                                                         // is
-                                                                         // not
-                                                                         // up
-                                                                         // to
-                                                                         // seq.getEnd()
+        // numbering
+        // is
+        // not
+        // up
+        // to
+        // seq.getEnd()
         {
 
           int resNum = (pdbRefDb == null)
@@ -1044,6 +1051,7 @@ public class SiftsClient implements SiftsClientI
     {
       return pdbeNonObserved;
     }
+
     public SequenceI getSeq()
     {
       return seq;
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 5f64b28..95e6c0d 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -71,8 +71,13 @@ public class FinderTest
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.FALSE.toString());
 
-    String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
-            + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
+    //@formatter:off
+    String seqData = 
+        "seq1/8-18 ABCD--EF-GHIJI\n" + 
+        "seq2      A--BCDefHI\n" + 
+        "seq3      --bcdEFH\n" + 
+        "seq4      aa---aMMMMMaaa\n";
+    //@formatter:on
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
     av = af.getViewport();
@@ -95,20 +100,20 @@ public class FinderTest
      * find next match only
      */
     Finder f = new Finder(av);
-    f.findNext("E.H", false, false); // 'E, any character, H'
+    f.findNext("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 1);
+    assertEquals(sr.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 7);
 
     f = new Finder(av);
-    f.findAll("E.H", false, false); // 'E, any character, H'
+    f.findAll("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 2);
+    assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
@@ -129,9 +134,9 @@ public class FinderTest
     /*
      * find first match should return seq1 residue 9
      */
-    f.findNext("9", false, false);
+    f.findNext("9", false, false, false);
     SearchResultsI sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 1);
+    assertEquals(sr.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
     assertEquals(matches.get(0).getStart(), 9);
@@ -139,11 +144,14 @@ public class FinderTest
 
     /*
      * find all matches should return seq1 and seq4 (others are too short)
+     * (and not matches in sequence ids)
      */
     f = new Finder(av);
-    f.findAll("9", false, false);
+    String name = al.getSequenceAt(0).getName();
+    al.getSequenceAt(0).setName("Q9XA0");
+    f.findAll("9", false, false, false);
     sr = f.getSearchResults();
-    assertEquals(sr.getSize(), 2);
+    assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
     assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
@@ -151,12 +159,13 @@ public class FinderTest
     assertEquals(matches.get(0).getEnd(), 9);
     assertEquals(matches.get(1).getStart(), 9);
     assertEquals(matches.get(1).getEnd(), 9);
+    al.getSequenceAt(0).setName(name);
 
     /*
      * parsing of search string as integer is strict
      */
     f = new Finder(av);
-    f.findNext(" 9", false, false);
+    f.findNext(" 9", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -167,41 +176,41 @@ public class FinderTest
   public void testFindNext()
   {
     /*
-     * start at second sequence; colIndex of -1
+     * start at second sequence; residueIndex of -1
      * means sequence id / description is searched
      */
     Finder f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", -1);
-    f.findNext("e", false, false); // matches id
+    PA.setValue(f, "residueIndex", -1);
+    f.findNext("e", false, false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
 
-    // colIndex is now 0 - for use in next find next
+    // residueIndex is now 0 - for use in next find next
     // searching A--BCDefHI
-    assertEquals(PA.getValue(f, "columnIndex"), 0);
+    assertEquals(PA.getValue(f, "residueIndex"), 0);
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", 0);
-    f.findNext("e", false, false); // matches in sequence
+    PA.setValue(f, "residueIndex", 0);
+    f.findNext("e", false, false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
-    assertEquals(f.getSearchResults().getSize(), 1);
+    assertEquals(f.getSearchResults().getCount(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 5);
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     // still in the second sequence
     assertEquals(PA.getValue(f, "sequenceIndex"), 1);
-    // next column position to search from is 7
-    assertEquals(PA.getValue(f, "columnIndex"), 7);
+    // next residue offset to search from is 5
+    assertEquals(PA.getValue(f, "residueIndex"), 5);
 
     // find next from end of sequence - finds next sequence id
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", 7);
-    f.findNext("e", false, false);
+    PA.setValue(f, "residueIndex", 7);
+    f.findNext("e", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
@@ -223,7 +232,7 @@ public class FinderTest
      * find first match only
      */
     Finder f = new Finder(av2);
-    f.findNext("rAF", false, true);
+    f.findNext("rAF", false, true, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -232,7 +241,7 @@ public class FinderTest
      * find all matches
      */
     f = new Finder(av2);
-    f.findAll("rAF", false, true);
+    f.findAll("rAF", false, true, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -242,7 +251,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av2);
-    f.findAll("RAF", true, true);
+    f.findAll("RAF", true, true, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -258,12 +267,12 @@ public class FinderTest
     /*
      * sequence matches should have no duplicates
      */
-    f.findAll("EFH", false, true);
+    f.findAll("EFH", false, true, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
 
-    assertEquals(f.getSearchResults().getSize(), 2);
+    assertEquals(f.getSearchResults().getCount(), 2);
     SearchResultMatchI match = f.getSearchResults().getResults().get(0);
     assertSame(match.getSequence(), al2.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -286,7 +295,7 @@ public class FinderTest
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.findAll("SEQ1", false, false);
+    f.findAll("SEQ1", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
@@ -296,7 +305,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av);
-    f.findAll("SEQ1", true, false);
+    f.findAll("SEQ1", true, false, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -307,11 +316,11 @@ public class FinderTest
     AlignViewportI av2 = new AlignViewport(al2);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
     f = new Finder(av2);
-    f.findAll("ABZ", false, false);
+    f.findAll("ABZ", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al2.getSequenceAt(4));
     assertEquals(match.getStart(), 4);
@@ -328,13 +337,17 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findNext()
   {
+    // "seq1/8-18 ABCD--EF-GHIJI\n" +
+    // "seq2 A--BCDefHI\n" +
+    // "seq3 --bcdEFH\n" +
+    // "seq4 aa---aMMMMMaaa\n";
     /*
      * efh should be matched in seq2 only
      */
     FinderI f = new Finder(av);
-    f.findNext("EfH", false, false);
+    f.findNext("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -344,39 +357,39 @@ public class FinderTest
      * I should be found in seq1 (twice) and seq2 (once)
      */
     f = new Finder(av);
-    f.findNext("I", false, false); // find next: seq1/16
+    f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.findNext("I", false, false); // find next: seq1/18
+    f.findNext("I", false, false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.findNext("I", false, false); // find next: seq2/8
+    f.findNext("I", false, false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.findNext("I", false, false);
+    f.findNext("I", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find should reset to start of alignment after a failed search
      */
-    f.findNext("I", false, false); // find next: seq1/16
+    f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -388,12 +401,12 @@ public class FinderTest
    * result
    */
   @Test(groups = "Functional")
-  public void testFind_maximalResultOnly()
+  public void testFindAll_maximalResultOnly()
   {
     Finder f = new Finder(av);
-    f.findAll("M+", false, false);
+    f.findAll("M+", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 4); // dataset sequence positions
@@ -404,12 +417,12 @@ public class FinderTest
    * Test finding all matches of a sequence pattern in an alignment
    */
   @Test(groups = "Functional")
-  public void testFind_findAll()
+  public void testFindAll()
   {
     Finder f = new Finder(av);
-    f.findAll("EfH", false, false);
+    f.findAll("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 5);
@@ -422,9 +435,9 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.findAll("I", false, false);
+    f.findAll("I", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 3);
+    assertEquals(searchResults.getCount(), 3);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -443,16 +456,16 @@ public class FinderTest
    * Test finding all matches, case-sensitive
    */
   @Test(groups = "Functional")
-  public void testFind_findAllCaseSensitive()
+  public void testFindAll_caseSensitive()
   {
     Finder f = new Finder(av);
 
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.findAll("BC", true, false);
+    f.findAll("BC", true, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 9);
@@ -466,15 +479,15 @@ public class FinderTest
      * bc should match seq3/1-2
      */
     f = new Finder(av);
-    f.findAll("bc", true, false);
+    f.findAll("bc", true, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.findAll("bC", true, false);
+    f.findAll("bC", true, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -482,7 +495,7 @@ public class FinderTest
    * Test finding next match of a sequence pattern in a selection group
    */
   @Test(groups = "Functional")
-  public void testFind_inSelection()
+  public void testFindNext_inSelection()
   {
     /*
      * select sequences 2 and 3, columns 4-6 which contains
@@ -497,10 +510,10 @@ public class FinderTest
     av.setSelectionGroup(sg);
 
     FinderI f = new Finder(av);
-    f.findNext("b", false, false);
+    f.findNext("b", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 2);
@@ -509,23 +522,23 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.findNext("b", false, false);
+    f.findNext("b", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
     assertTrue(f.getIdMatches().isEmpty());
 
     f = new Finder(av);
-    f.findNext("d", false, false);
+    f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.findNext("d", false, false);
+    f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 3);
@@ -536,7 +549,7 @@ public class FinderTest
    * Test finding all matches of a search pattern in a selection group
    */
   @Test(groups = "Functional")
-  public void testFind_findAllInSelection()
+  public void testFindAll_inSelection()
   {
     /*
      * select sequences 2 and 3, columns 4-6 which contains
@@ -554,12 +567,12 @@ public class FinderTest
      * search for 'e' should match two sequence ids and one residue
      */
     Finder f = new Finder(av);
-    f.findAll("e", false, false);
+    f.findAll("e", false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 4);
@@ -569,7 +582,7 @@ public class FinderTest
      * search for 'Q' should match two sequence ids only
      */
     f = new Finder(av);
-    f.findAll("Q", false, false);
+    f.findAll("Q", false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -600,10 +613,10 @@ public class FinderTest
      * search for 'I' should match two sequence positions
      */
     Finder f = new Finder(av);
-    f.findAll("I", false, false);
+    f.findAll("I", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(0));
     assertEquals(match.getStart(), 16);
@@ -615,7 +628,8 @@ public class FinderTest
   }
 
   /**
-   * Test that find does not report hidden positions
+   * Test that find does not report hidden positions, but does report matches that
+   * span hidden gaps
    */
   @Test(groups = "Functional")
   public void testFind_withHiddenColumns()
@@ -629,43 +643,92 @@ public class FinderTest
      */
 
     /*
-     * hide 2-4 (CD- -BC bcd ---)
+     * hide column 3 only, search for aaa
+     * should find two matches: aa-[-]-aa and trailing aaa
      */
     HiddenColumns hc = new HiddenColumns();
-    hc.hideColumns(2, 4);
+    hc.hideColumns(3, 3);
     al.setHiddenColumns(hc);
+    Finder f = new Finder(av);
+    f.findAll("aaa", false, false, false);
+    SearchResultsI searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 2);
+    SearchResultMatchI match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 9);
+    assertEquals(match.getEnd(), 11);
+
+    /*
+     * hide 2-4 (CD- -BC bcd ---)
+     */
+    hc.hideColumns(2, 4);
 
     /*
      * find all search for D should ignore hidden positions in seq1 and seq3,
      * find the visible D in seq2
      */
-    Finder f = new Finder(av);
-    f.findAll("D", false, false);
-    SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
-    SearchResultMatchI match = searchResults.getResults().get(0);
+    f = new Finder(av);
+    f.findAll("D", false, false, false);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 1);
+    match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
 
     /*
+     * search for AD should fail although these are now
+     * consecutive in the visible columns
+     */
+    f = new Finder(av);
+    f.findAll("AD", false, false, false);
+    searchResults = f.getSearchResults();
+    assertTrue(searchResults.isEmpty());
+
+    /*
+     * find all 'aaa' should find both start and end of seq4
+     * (first run includes hidden gaps)
+     */
+    f = new Finder(av);
+    f.findAll("aaa", false, false, false);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 9);
+    assertEquals(match.getEnd(), 11);
+
+    /*
      * hide columns 2-5:
-     * find all 'aaa' should find end of seq4 only
+     * find all 'aaa' should match twice in seq4
+     * (first match partly hidden, second all visible)
      */
     hc.hideColumns(2, 5);
     f = new Finder(av);
-    f.findAll("aaa", false, false);
+    f.findAll("aaa", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 9);
     assertEquals(match.getEnd(), 11);
 
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.findAll("BE", false, false);
+    f.findAll("BE", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -675,9 +738,9 @@ public class FinderTest
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
     f = new Finder(av);
-    f.findNext("H", false, false);
+    f.findNext("H", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(2));
     assertEquals(match.getStart(), 6);
@@ -718,9 +781,9 @@ public class FinderTest
      * should match seq2/1, seq2/7, not seq3/6
      */
     Finder f = new Finder(av);
-    f.findAll("[AH]", false, false);
+    f.findAll("[AH]", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 2);
+    assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 1);
@@ -730,4 +793,123 @@ public class FinderTest
     assertEquals(match.getStart(), 7);
     assertEquals(match.getEnd(), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_ignoreHiddenColumns()
+  {
+    /*
+     * 0    5   9
+     * ABCD--EF-GHI
+     * A--BCDefHI
+     * --bcdEFH
+     * aa---aMMMMMaaa
+     */
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(2, 4);
+    hc.hideColumns(7, 7);
+    al.setHiddenColumns(hc);
+
+    /*
+     * now have
+     * 015689
+     * AB-E-GHI
+     * A-DeHI
+     * --EF
+     * aaaMMMMaaa
+     */
+    Finder f = new Finder(av);
+    f.findAll("abe", false, false, true); // true = ignore hidden
+    SearchResultsI searchResults = f.getSearchResults();
+
+    /*
+     * match of seq1 ABE made up of AB and E
+     * note only one match is counted
+     */
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
+    SearchResultMatchI match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 8); // A
+    assertEquals(match.getEnd(), 9); // B
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+
+    f = new Finder(av);
+    f.findNext("a.E", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 8); // A
+    assertEquals(match.getEnd(), 9); // B
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+
+    f.findNext("a.E", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 1); // a
+    assertEquals(match.getEnd(), 1);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 4); // D
+    assertEquals(match.getEnd(), 5); // e
+
+    /*
+     * find all matching across two hidden column regions
+     * note one 'match' is returned as three contiguous matches
+     */
+    f.findAll("BEG", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 3);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 9); // B
+    assertEquals(match.getEnd(), 9);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+    match = searchResults.getResults().get(2);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 14); // G
+    assertEquals(match.getEnd(), 14);
+
+    /*
+     * now select columns 0-9 and search for A.*H
+     * this should match in the second sequence (split as 3 matches)
+     * but not the first (as H is outside the selection)
+     */
+    SequenceGroup selection = new SequenceGroup();
+    selection.setStartRes(0);
+    selection.setEndRes(9);
+    al.getSequences().forEach(seq -> selection.addSequence(seq, false));
+    av.setSelectionGroup(selection);
+    f.findAll("A.*H", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getCount(), 1);
+    assertEquals(searchResults.getResults().size(), 3);
+    // match made of contiguous matches A, DE, H
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 1); // A
+    assertEquals(match.getEnd(), 1);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 4); // D
+    assertEquals(match.getEnd(), 5); // E
+    match = searchResults.getResults().get(2);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 7); // H (there is no G)
+    assertEquals(match.getEnd(), 7);
+  }
 }
diff --git a/test/jalview/bin/CacheTest.java b/test/jalview/bin/CacheTest.java
index e762dd5..9edfd3b 100644
--- a/test/jalview/bin/CacheTest.java
+++ b/test/jalview/bin/CacheTest.java
@@ -20,9 +20,10 @@
  */
 package jalview.bin;
 
+import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertTrue;
 import static org.testng.AssertJUnit.assertEquals;
-
-import jalview.gui.JvOptionPane;
+import static org.testng.AssertJUnit.assertNotNull;
 
 import java.text.SimpleDateFormat;
 import java.util.Date;
@@ -32,6 +33,8 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class CacheTest
 {
 
@@ -70,9 +73,28 @@ public class CacheTest
     assertEquals(formattedDate, formattedDate2);
 
     // currently using Locale.UK to format dates:
-    assertEquals(
-            formattedDate2,
-            SimpleDateFormat.getDateTimeInstance(SimpleDateFormat.MEDIUM,
-                    SimpleDateFormat.MEDIUM, Locale.UK).format(now));
+    assertEquals(formattedDate2,
+            SimpleDateFormat
+                    .getDateTimeInstance(SimpleDateFormat.MEDIUM,
+                            SimpleDateFormat.MEDIUM, Locale.UK)
+                    .format(now));
+  }
+
+  @Test(groups = "Functional")
+  public void testVersionChecker()
+  {
+    Cache.loadProperties("test/jalview/bin/testProps.jvprops");
+    try
+    {
+      // 10s sleep to allow VersionChecker thread to run
+      Thread.sleep(10000);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    String latestVersion = Cache.getProperty("LATEST_VERSION");
+    assertNotNull(latestVersion);
+    assertNotEquals(latestVersion, "test");
+    assertTrue(latestVersion.startsWith("2."));
   }
 }
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 59fc79d..a5067be 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -20,10 +20,17 @@
  */
 package jalview.bin;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.IdentifyFile;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -279,7 +286,7 @@ public class CommandLineOperations
     dataProvider = "headlessModeOutputOperationsData")
   public void testHeadlessModeOutputOperations(String harg, String type,
           String fileName, boolean withAWT, int expectedMinFileSize,
-          int timeout)
+          int timeout, String fileFormatType)
   {
     String cmd = harg + type + " " + fileName;
     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
@@ -291,6 +298,25 @@ public class CommandLineOperations
     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);
+    if (fileFormatType!=null && fileFormatType.length()>0)
+    {
+      FileFormatI format = FileFormats.getInstance()
+              .forName(fileFormatType);
+      if (format!=null)
+      {
+        try
+        {
+          FileFormatI exportedType = new IdentifyFile()
+                  .identify(file.getAbsolutePath(), DataSourceType.FILE);
+          assertEquals(exportedType, format,
+                  "Exported file type was wrong");
+        } catch (FileFormatException e)
+        {
+          Assert.fail("Couldn't identify file " + file
+                  + " as an alignment format", e);
+        }
+      }
+    }
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
@@ -343,51 +369,51 @@ public class CommandLineOperations
     String workingDir = "test/jalview/bin/";
     return new Object[][] { { "nodisplay -open examples/uniref50.fa",
         " -eps", workingDir + "test_uniref50_out.eps", true,
-        MINFILESIZE_BIG, TEST_TIMEOUT },
+        MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "nodisplay -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -svg",
             workingDir + "test_uniref50_out.svg", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -png",
             workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -html",
             workingDir + "test_uniref50_out.html", true,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            MINFILESIZE_BIG, TEST_TIMEOUT, null },
         { "headless -open examples/uniref50.fa", " -fasta",
             workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Fasta.toString() },
         { "headless -open examples/uniref50.fa", " -clustal",
             workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Clustal.toString() },
         { "headless -open examples/uniref50.fa", " -msf",
             workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.MSF.toString() },
         { "headless -open examples/uniref50.fa", " -pileup",
             workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Pileup.toString() },
         { "headless -open examples/uniref50.fa", " -pir",
             workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.PIR.toString() },
         { "headless -open examples/uniref50.fa", " -pfam",
             workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.Pfam.toString() },
         { "headless -open examples/uniref50.fa", " -blc",
             workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT },
+            TEST_TIMEOUT, FileFormat.BLC.toString() },
         { "headless -open examples/uniref50.fa", " -jalview",
             workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT }, };
+            TEST_TIMEOUT, FileFormat.Jalview.toString() }, };
   }
 }
diff --git a/test/jalview/bin/testProps.jvprops b/test/jalview/bin/testProps.jvprops
new file mode 100644
index 0000000..a1ab82a
--- /dev/null
+++ b/test/jalview/bin/testProps.jvprops
@@ -0,0 +1,2 @@
+VERSION_CHECK=true
+LATEST_VERSION=test
diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 7990d21..fde4da1 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -225,7 +225,7 @@ public class AlignViewControllerTest
      *  test Match/Find works first
      */
     FinderI f = new Finder(af.getViewport());
-    f.findAll("M+", true, false);
+    f.findAll("M+", true, false, false);
     assertEquals(
             "Finder found different set of results to manually created SearchResults",
             sr, f.getSearchResults());
diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 349b5d1..838b259 100644
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -25,14 +25,14 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
 import java.util.BitSet;
 
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class SearchResultsTest
 {
 
@@ -297,10 +297,74 @@ public class SearchResultsTest
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
     SearchResultsI sr = new SearchResults();
     sr.addResult(seq1, 3, 5);
-    assertEquals(1, sr.getSize());
+    assertEquals(1, sr.getCount());
     sr.addResult(seq1, 3, 5);
-    assertEquals(1, sr.getSize());
+    assertEquals(1, sr.getCount());
     sr.addResult(seq1, 3, 6);
-    assertEquals(2, sr.getSize());
+    assertEquals(2, sr.getCount());
+  }
+
+  /**
+   * Test for method that checks if search results matches a sequence region
+   */
+  @Test(groups = { "Functional" })
+  public void testInvolvesSequence()
+  {
+    SequenceI dataset = new Sequence("genome", "ATGGCCCTTTAAGCAACATTT");
+    // first 'exon':
+    SequenceI cds1 = new Sequence("cds1/1-12", "ATGGCCCTTTAA");
+    cds1.setDatasetSequence(dataset);
+    // overlapping second 'exon':
+    SequenceI cds2 = new Sequence("cds2/7-18", "CTTTAAGCAACA");
+    cds2.setDatasetSequence(dataset);
+    // unrelated sequence
+    SequenceI cds3 = new Sequence("cds3", "ATGGCCCTTTAAGCAACA");
+
+    SearchResults sr = new SearchResults();
+    assertFalse(sr.involvesSequence(cds1));
+
+    /*
+     * cds1 and cds2 share the same dataset sequence, but
+     * only cds1 overlaps match 4:6 (fixes bug JAL-3613)
+     */
+    sr.addResult(dataset, 4, 6);
+    assertTrue(sr.involvesSequence(cds1));
+    assertFalse(sr.involvesSequence(cds2));
+    assertFalse(sr.involvesSequence(cds3));
+
+    /*
+     * search results overlap cds2 only
+     */
+    sr = new SearchResults();
+    sr.addResult(dataset, 18, 18);
+    assertFalse(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * add a search result overlapping cds1
+     */
+    sr.addResult(dataset, 1, 1);
+    assertTrue(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * single search result overlapping both
+     */
+    sr = new SearchResults();
+    sr.addResult(dataset, 10, 12);
+    assertTrue(sr.involvesSequence(cds1));
+    assertTrue(sr.involvesSequence(cds2));
+
+    /*
+     * search results matching aligned sequence
+     */
+    sr = new SearchResults();
+    sr.addResult(cds1, 10, 12);
+    assertTrue(sr.involvesSequence(cds1));
+    assertFalse(sr.involvesSequence(cds2));
+    sr.addResult(cds2, 1, 3); // no start-end overlap
+    assertFalse(sr.involvesSequence(cds2));
+    sr.addResult(cds2, 7, 9); // start-end overlap
+    assertTrue(sr.involvesSequence(cds2));
   }
 }
diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 4198a37..56512cd 100644
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -5,8 +5,6 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
-import jalview.datamodel.SequenceFeature;
-
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -15,6 +13,7 @@ import java.util.Set;
 
 import org.testng.annotations.Test;
 
+import jalview.datamodel.SequenceFeature;
 import junit.extensions.PA;
 
 public class SequenceFeaturesTest
@@ -1052,7 +1051,8 @@ public class SequenceFeaturesTest
   public void testSortFeatures()
   {
     List<SequenceFeature> sfs = new ArrayList<>();
-    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 80,
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30,
+            60,
             Float.NaN, null);
     sfs.add(sf1);
     SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
@@ -1061,18 +1061,34 @@ public class SequenceFeaturesTest
     SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
             Float.NaN, null);
     sfs.add(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30,
+            80,
+            Float.NaN, null);
+    sfs.add(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30,
+            90,
+            Float.NaN, null);
+    sfs.add(sf5);
 
-    // sort by end position descending
+    /*
+     * sort by end position descending, order unchanged if matched
+     */
     SequenceFeatures.sortFeatures(sfs, false);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf3);
-    assertSame(sfs.get(2), sf2);
+    assertSame(sfs.get(0), sf5); // end 90
+    assertSame(sfs.get(1), sf4); // end 80
+    assertSame(sfs.get(2), sf1); // end 60, start 50
+    assertSame(sfs.get(3), sf3); // end 60, start 30
+    assertSame(sfs.get(4), sf2); // end 50
 
-    // sort by start position ascending
+    /*
+     * resort {5, 4, 1, 3, 2} by start position ascending, end descending
+     */
     SequenceFeatures.sortFeatures(sfs, true);
-    assertSame(sfs.get(0), sf1);
-    assertSame(sfs.get(1), sf2);
-    assertSame(sfs.get(2), sf3);
+    assertSame(sfs.get(0), sf5); // start 30, end 90
+    assertSame(sfs.get(1), sf4); // start 30, end 80
+    assertSame(sfs.get(2), sf1); // start 30, end 60
+    assertSame(sfs.get(3), sf2); // start 40
+    assertSame(sfs.get(4), sf3); // start 50
   }
 
   @Test(groups = "Functional")
diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 8b1e840..ef12ed4 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -271,18 +271,24 @@ public class EnsemblGeneTest
 
   /**
    * Check behaviour of feature colour scheme for EnsemblGene sequences.
-   * Currently coded to display exon and sequence_variant (or sub-types) only,
-   * with sequence_variant in red above exon coloured by label.
+   * Currently coded to hide all except exon and sequence_variant (or sub-types)
+   * only, with sequence_variant in red above exon coloured by label.
    */
   @Test(groups = "Functional")
   public void testGetFeatureColourScheme()
   {
     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
-    assertTrue(fc.isFeatureDisplayed("exon"));
-    assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
-    assertTrue(fc.isFeatureDisplayed("sequence_variant"));
-    assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
-    assertFalse(fc.isFeatureDisplayed("transcript"));
+    assertFalse(fc.isFeatureDisplayed("exon"));
+    assertFalse(fc.isFeatureHidden("exon"));
+    assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureDisplayed("sequence_variant"));
+    assertFalse(fc.isFeatureHidden("sequence_variant"));
+    assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
+    assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
+    assertTrue(fc.isFeatureHidden("transcript"));
+    assertTrue(fc.isFeatureHidden("CDS"));
+
     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
             .getColour());
     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
diff --git a/test/jalview/gui/FreeUpMemoryTest.java b/test/jalview/gui/FreeUpMemoryTest.java
index 24697c0..3a5a9e4 100644
--- a/test/jalview/gui/FreeUpMemoryTest.java
+++ b/test/jalview/gui/FreeUpMemoryTest.java
@@ -1,17 +1,8 @@
 package jalview.gui;
 
-import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-
 import java.awt.event.MouseEvent;
 import java.io.File;
 import java.io.IOException;
@@ -20,20 +11,96 @@ import java.io.PrintStream;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
 import junit.extensions.PA;
 
+/**
+ * Provides a simple test that memory is released when all windows are closed.
+ * <ul>
+ * <li>generates a reasonably large alignment and loads it</li>
+ * <li>performs various operations on the alignment</li>
+ * <li>closes all windows</li>
+ * <li>requests garbage collection</li>
+ * <li>asserts that the remaining memory footprint (heap usage) is 'not large'
+ * </li>
+ * </ul>
+ * If the test fails, this means that reference(s) to large object(s) have
+ * failed to be garbage collected. In this case:
+ * <ul>
+ * <li>set a breakpoint just before the test assertion in
+ * {@code checkUsedMemory}</li>
+ * <li>if the test fails intermittently, make this breakpoint conditional on
+ * {@code usedMemory > expectedMax}</li>
+ * <li>run the test to this point (and check that it is about to fail i.e.
+ * {@code usedMemory > expectedMax})</li>
+ * <li>use <a href="https://visualvm.github.io/">visualvm</a> to obtain a heap
+ * dump from the suspended process (and kill the test or let it fail)</li>
+ * <li>inspect the heap dump using visualvm for large objects and their
+ * referers</li>
+ * <li>Tips:</li>
+ * <ul>
+ * <li>Perform GC from the Monitor view in visualvm before requesting the heap
+ * dump - test failure might be simply a delay to GC</li>
+ * <li>View 'Objects' and filter classes to {@code jalview}. Sort columns by
+ * Count, or Size, and look for anything suspicious. For example, if the object
+ * count for {@code Sequence} is non-zero (it shouldn't be), pick any instance,
+ * and follow the chain of {@code references} to find which class(es) still hold
+ * references to sequence objects</li>
+ * <li>If this chain is impracticably long, re-run the test with a smaller
+ * alignment (set width=100, height=10 in {@code generateAlignment()}), to
+ * capture a heap which is qualitatively the same, but much smaller, so easier
+ * to analyse; note this requires an unconditional breakpoint</li>
+ * </ul>
+ * </ul>
+ * <p>
+ * <h2>Fixing memory leaks</h2>
+ * <p>
+ * Experience shows that often a reference is retained (directly or indirectly)
+ * by a Swing (or related) component (for example a {@code MouseListener} or
+ * {@code ActionListener}). There are two possible approaches to fixing:
+ * <ul>
+ * <li>Purist: ensure that all listeners and similar objects are removed when no
+ * longer needed. May be difficult, to achieve and to maintain as code
+ * changes.</li>
+ * <li>Pragmatic: null references to potentially large objects from Jalview
+ * application classes when no longer needed, typically when a panel is closed.
+ * This ensures that even if the JVM keeps a reference to a panel or viewport,
+ * it does not retain a large heap footprint. This is the approach taken in, for
+ * example, {@code AlignmentPanel.closePanel()} and
+ * {@code AnnotationPanel.dispose()}.</li>
+ * <li>Adjust code if necessary; for example an {@code ActionListener} should
+ * act on {@code av.getAlignment()} and not directly on {@code alignment}, as
+ * the latter pattern could leave persistent references to the alignment</li>
+ * </ul>
+ * Add code to 'null unused large object references' until the test passes. For
+ * a final sanity check, capture the heap dump for a passing test, and satisfy
+ * yourself that only 'small' or 'harmless' {@code jalview} object instances
+ * (such as enums or singletons) are left in the heap.
+ */
 public class FreeUpMemoryTest
 {
   private static final int ONE_MB = 1000 * 1000;
 
+  /*
+   * maximum retained heap usage (in MB) for a passing test
+   */
+  private static int MAX_RESIDUAL_HEAP = 45;
+
   /**
    * Configure (read-only) Jalview property settings for test
    */
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Jalview.main(new String[] { "-nonews", "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(
+            new String[]
+            { "-nonews", "-props", "test/jalview/testProps.jvprops" });
     String True = Boolean.TRUE.toString();
     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", True);
     Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
@@ -42,98 +109,79 @@ public class FreeUpMemoryTest
     Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
   }
 
-  /**
-   * A simple test that memory is released when all windows are closed.
-   * <ul>
-   * <li>generates a reasonably large alignment and loads it</li>
-   * <li>performs various operations on the alignment</li>
-   * <li>closes all windows</li>
-   * <li>requests garbage collection</li>
-   * <li>asserts that the remaining memory footprint (heap usage) is 'not large'
-   * </li>
-   * </ul>
-   * If the test fails, this suggests that a reference to some large object
-   * (perhaps the alignment data, or some annotation / Tree / PCA data) has
-   * failed to be garbage collected. If this is the case, the heap will need to
-   * be inspected manually (suggest using jvisualvm) in order to track down
-   * where large objects are still referenced. The code (for example
-   * AlignmentViewport.dispose()) should then be updated to ensure references to
-   * large objects are set to null when they are no longer required.
-   * 
-   * @throws IOException
-   */
   @Test(groups = "Memory")
   public void testFreeMemoryOnClose() throws IOException
   {
     File f = generateAlignment();
     f.deleteOnExit();
 
-    long expectedMin = 35L;
-    long usedMemoryAtStart=getUsedMemory();
-    if (usedMemoryAtStart>expectedMin)
-    {
-      System.err.println("used memory before test is "+usedMemoryAtStart+" > "+expectedMin+"MB .. adjusting minimum.");
-      expectedMin = usedMemoryAtStart;
-    }
     doStuffInJalview(f);
 
     Desktop.instance.closeAll_actionPerformed(null);
 
-    checkUsedMemory(expectedMin);
+    checkUsedMemory(MAX_RESIDUAL_HEAP);
   }
 
-  private static long getUsedMemory()
+  /**
+   * Returns the current total used memory (available memory - free memory),
+   * rounded down to the nearest MB
+   * 
+   * @return
+   */
+  private static int getUsedMemory()
   {
-    long availableMemory = Runtime.getRuntime().totalMemory() / ONE_MB;
-    long freeMemory = Runtime.getRuntime().freeMemory() / ONE_MB;
+    long availableMemory = Runtime.getRuntime().totalMemory();
+    long freeMemory = Runtime.getRuntime().freeMemory();
     long usedMemory = availableMemory - freeMemory;
-    return usedMemory;
+
+    return (int) (usedMemory / ONE_MB);
   }
+
   /**
    * Requests garbage collection and then checks whether remaining memory in use
    * is less than the expected value (in Megabytes)
    * 
    * @param expectedMax
    */
-  protected void checkUsedMemory(long expectedMax)
+  protected void checkUsedMemory(int expectedMax)
   {
     /*
-     * request garbage collection and wait for it to run;
+     * request garbage collection and wait for it to run (up to 3 times);
      * NB there is no guarantee when, or whether, it will do so
-     * wait time depends on JRE/processor, generous allowance here  
      */
-    System.gc();
-    waitFor(1500);
-
-    /*
-     * a second gc() call should not be necessary - but it is!
-     * the test passes with it, and fails without it
-     */
-    System.gc();
-    waitFor(1500);
-
-    /*
-     * check used memory is 'reasonably low'
-     */
-    long usedMemory = getUsedMemory();
-    /*
-     * sanity check - fails if any frame was added after
-     * closeAll_actionPerformed
-     */
-    assertEquals(Desktop.instance.getAllFrames().length, 0);
+    long usedMemory = 0L;
+    Long minUsedMemory = null;
+    int gcCount = 0;
+    while (gcCount < 3)
+    {
+      gcCount++;
+      System.gc();
+      waitFor(1500);
+      usedMemory = getUsedMemory();
+      if (minUsedMemory == null || usedMemory < minUsedMemory)
+      {
+        minUsedMemory = usedMemory;
+      }
+      if (usedMemory < expectedMax)
+      {
+        break;
+      }
+    }
 
     /*
-     * if this assertion fails
-     * - set a breakpoint here
-     * - run jvisualvm to inspect a heap dump of Jalview
-     * - identify large objects in the heap and their referers
+     * if this assertion fails (reproducibly!)
+     * - set a breakpoint here, conditional on (usedMemory > expectedMax)
+     * - run VisualVM to inspect the heap usage, and run GC from VisualVM to check 
+     *   it is not simply delayed garbage collection causing the test failure 
+     * - take a heap dump and identify large objects in the heap and their referers
      * - fix code as necessary to null the references on close
      */
-    System.out.println("Used memory after gc = " + usedMemory + "MB");
-    assertTrue(usedMemory < expectedMax, String.format(
+    System.out.println("(Minimum) Used memory after " + gcCount
+            + " call(s) to gc() = " + minUsedMemory + "MB (should be <="
+            + expectedMax + ")");
+    assertTrue(usedMemory <= expectedMax, String.format(
             "Used memory %d should be less than %d (Recommend running test manually to verify)",
-            usedMemory,
-            expectedMax));
+            usedMemory, expectedMax));
   }
 
   /**
@@ -193,7 +241,7 @@ public class FreeUpMemoryTest
      * wait until Tree and PCA have been computed
      */
     while (af.viewport.getCurrentTree() == null
-            && dialog.getPcaPanel().isWorking())
+            || dialog.getPcaPanel().isWorking())
     {
       waitFor(10);
     }
@@ -237,6 +285,7 @@ public class FreeUpMemoryTest
     int width = 100000;
     int height = 100;
     ag.generate(width, height, 0, 10, 15);
+    ps.close();
     return f;
   }
 }
diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 73aeb79..213a1c9 100644
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -21,8 +21,14 @@
 package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 
@@ -338,4 +344,27 @@ public class SeqCanvasTest
             "wrappedRepeatHeightPx");
     assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
   }
+
+  @Test(groups = "Functional")
+  public void testClear_HighlightAndSelection()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignViewport av = af.getViewport();
+    SearchResultsI highlight = new SearchResults();
+    highlight.addResult(
+            av.getAlignment().getSequenceAt(1).getDatasetSequence(), 50,
+            80);
+    af.alignPanel.highlightSearchResults(highlight);
+    af.avc.markHighlightedColumns(false, false, false);
+    assertNotNull(av.getSearchResults(),
+            "No highlight was created on alignment");
+    assertFalse(av.getColumnSelection().isEmpty(),
+            "No selection was created from highlight");
+    af.deselectAllSequenceMenuItem_actionPerformed(null);
+    assertTrue(av.getColumnSelection().isEmpty(),
+            "No Selection should be present after deselecting all.");
+    assertNull(av.getSearchResults(),
+            "No higlighted search results should be present after deselecting all.");
+  }
 }
diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java
index 64cf902..1386bfe 100644
--- a/test/jalview/io/BackupFilesTest.java
+++ b/test/jalview/io/BackupFilesTest.java
@@ -209,6 +209,7 @@ public class BackupFilesTest
           boolean noMax)
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.initLogger();
 
     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
             reverse, noMax, rollMax, false);
diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
new file mode 100644
index 0000000..5d8ef21
--- /dev/null
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -0,0 +1,347 @@
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.fail;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class EmblFlatFileTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.initLogger();
+  }
+
+  /**
+   * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+   * one of them reverse strand
+   * 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testParse() throws MalformedURLException, IOException
+  {
+    File dataFile = new File("test/jalview/io/J03321.embl.txt");
+    FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE);
+    EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+    parser.parse();
+    List<SequenceI> seqs = parser.getSeqs();
+
+    assertEquals(seqs.size(), 1);
+    SequenceI seq = seqs.get(0);
+    assertEquals(seq.getName(), "EmblTest|J03321");
+    assertEquals(seq.getLength(), 7502);
+    assertEquals(seq.getDescription(),
+            "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+    /*
+     * should be 9 CDS features (one is a 'join' of two exons)
+     */
+    Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+    assertEquals(featureTypes.size(), 1);
+    assertTrue(featureTypes.contains("CDS"));
+
+    /*
+     * inspect some features (sorted just for convenience of test assertions)
+     */
+    List<SequenceFeature> features = seq.getFeatures()
+            .getAllFeatures("CDS");
+    SequenceFeatures.sortFeatures(features, true);
+    assertEquals(features.size(), 9);
+
+    SequenceFeature sf = features.get(0);
+    assertEquals(sf.getBegin(), 1);
+    assertEquals(sf.getEnd(), 437);
+    assertEquals(sf.getDescription(),
+            "Exon 2 for protein EMBLCDS:AAA91567.1");
+    assertEquals(sf.getFeatureGroup(), "EmblTest");
+    assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+    assertEquals(sf.getPhase(), "0");
+    assertEquals(sf.getStrand(), 1);
+    assertEquals(sf.getValue("note"), "pGP7-D");
+    // this is the second exon of circular CDS!
+    assertEquals(sf.getValue("exon number"), 2);
+    assertEquals(sf.getValue("product"), "hypothetical protein");
+    assertEquals(sf.getValue("transl_table"), "11");
+
+    sf = features.get(1);
+    assertEquals(sf.getBegin(), 488);
+    assertEquals(sf.getEnd(), 1480);
+    assertEquals(sf.getDescription(),
+            "Exon 1 for protein EMBLCDS:AAA91568.1");
+    assertEquals(sf.getFeatureGroup(), "EmblTest");
+    assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+    assertEquals(sf.getPhase(), "0");
+    assertEquals(sf.getStrand(), -1); // reverse strand!
+    assertEquals(sf.getValue("note"), "pGP8-D");
+    assertEquals(sf.getValue("exon number"), 1);
+    assertEquals(sf.getValue("product"), "hypothetical protein");
+
+    sf = features.get(7);
+    assertEquals(sf.getBegin(), 6045);
+    assertEquals(sf.getEnd(), 6788);
+    assertEquals(sf.getDescription(),
+            "Exon 1 for protein EMBLCDS:AAA91574.1");
+    assertEquals(sf.getFeatureGroup(), "EmblTest");
+    assertEquals(sf.getEnaLocation(), "6045..6788");
+    assertEquals(sf.getPhase(), "0");
+    assertEquals(sf.getStrand(), 1);
+    assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+    assertEquals(sf.getValue("exon number"), 1);
+    assertEquals(sf.getValue("product"), "hypothetical protein");
+
+    /*
+     * CDS at 7022-7502 is the first exon of the circular CDS
+     */
+    sf = features.get(8);
+    assertEquals(sf.getBegin(), 7022);
+    assertEquals(sf.getEnd(), 7502);
+    assertEquals(sf.getDescription(),
+            "Exon 1 for protein EMBLCDS:AAA91567.1");
+    assertEquals(sf.getFeatureGroup(), "EmblTest");
+    assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+    assertEquals(sf.getPhase(), "0");
+    assertEquals(sf.getStrand(), 1);
+    assertEquals(sf.getValue("note"), "pGP7-D");
+    assertEquals(sf.getValue("exon number"), 1);
+    assertEquals(sf.getValue("product"), "hypothetical protein");
+
+    /*
+     * Verify DBRefs, whether declared in the file or added by Jalview.
+     * There are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries 
+     * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
+     * Sample a few here. Note DBRefEntry constructor capitalises source.
+     */
+    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+
+    assertEquals(dbrefs.size(), 32);
+    // xref to 'self':
+    DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
+    int[] range = new int[] { 1, seq.getLength() };
+    selfRef.setMap(new Mapping(null, range, range, 1, 1));
+    assertTrue(dbrefs.contains(selfRef));
+
+    // 1st DR line; note trailing period is removed
+    assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
+            "d4c4942a634e3df4995fd5ac75c26a61")));
+    // the 4th DR line:
+    assertTrue(
+            dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941")));
+    // from the first CDS feature
+    assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
+    // from the last CDS feature
+    assertTrue(
+            dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350")));
+
+    /*
+     * verify mappings to, and sequences for, UNIPROT proteins
+     */
+    int uniprotCount = 0;
+    List<int[]> ranges;
+    for (DBRefEntry dbref : dbrefs)
+    {
+      if ("UNIPROT".equals(dbref.getSource()))
+      {
+        uniprotCount++;
+        Mapping mapping = dbref.getMap();
+        assertNotNull(mapping);
+        MapList map = mapping.getMap();
+        String mappedToName = mapping.getTo().getName();
+        if ("UNIPROT|P0CE16".equals(mappedToName))
+        {
+          assertEquals((ranges = map.getFromRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1579);
+          assertEquals(ranges.get(0)[1], 2934);
+          assertEquals((ranges = map.getToRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1);
+          assertEquals(ranges.get(0)[1], 451);
+          // CDS /product carries over as protein product description
+          assertEquals(mapping.getTo().getDescription(),
+                  "hypothetical protein");
+        }
+        else if ("UNIPROT|P0CE17".equals(mappedToName))
+        {
+          assertEquals((ranges = map.getFromRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 2928);
+          assertEquals(ranges.get(0)[1], 3992);
+          assertEquals((ranges = map.getToRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1);
+          assertEquals(ranges.get(0)[1], 354);
+        }
+        else if ("UNIPROT|P0CE18".equals(mappedToName))
+        {
+          assertEquals((ranges = map.getFromRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 4054);
+          assertEquals(ranges.get(0)[1], 4848);
+          assertEquals((ranges = map.getToRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1);
+          assertEquals(ranges.get(0)[1], 264);
+        }
+        else if ("UNIPROT|P0CE19".equals(mappedToName))
+        {
+          // join(7022..7502,1..437)
+          assertEquals((ranges = map.getFromRanges()).size(), 2);
+          assertEquals(ranges.get(0)[0], 7022);
+          assertEquals(ranges.get(0)[1], 7502);
+          assertEquals(ranges.get(1)[0], 1);
+          assertEquals(ranges.get(1)[1], 437);
+          assertEquals((ranges = map.getToRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1);
+          assertEquals(ranges.get(0)[1], 305);
+        }
+        else if ("UNIPROT|P0CE20".equals(mappedToName))
+        {
+          // complement(488..1480)
+          assertEquals((ranges = map.getFromRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1480);
+          assertEquals(ranges.get(0)[1], 488);
+          assertEquals((ranges = map.getToRanges()).size(), 1);
+          assertEquals(ranges.get(0)[0], 1);
+          assertEquals(ranges.get(0)[1], 330);
+        }
+        else if (!"UNIPROT|P0CE23".equals(mappedToName)
+                && !"UNIPROT|P10559".equals(mappedToName)
+                && !"UNIPROT|P10560".equals(mappedToName))
+        {
+          fail("Unexpected UNIPROT dbref to " + mappedToName);
+        }
+      }
+    }
+    assertEquals(uniprotCount, 8);
+  }
+
+  @Test(groups = "Functional")
+  public void testParse_codonStartNot1()
+  {
+    // TODO verify CDS-to-protein mapping for CDS with /codon_start=2
+    // example: https://www.ebi.ac.uk/ena/browser/api/embl/EU498516
+  }
+
+  /**
+   * Test for the case that the EMBL CDS has no UNIPROT xref. In this case
+   * Jalview should synthesize an xref to EMBLCDSPROTEIN in the hope this will
+   * allow Get Cross-References.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testParse_noUniprotXref() throws IOException
+  {
+    // MN908947 cut down to 40BP, one CDS, length 5 peptide for test purposes
+    // plus an additional (invented) test case:
+    // - multi-line /product qualifier including escaped quotes
+    String data = "ID   MN908947; SV 3; linear; genomic RNA; STD; VRL; 20 BP.\n"
+            + "DE   Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,\n"
+            + "FT   CDS             3..17\n"
+            + "FT                   /protein_id=\"QHD43415.1\"\n"
+            + "FT                   /product=\"orf1ab polyprotein\n"
+            + "FT                   \"\"foobar\"\" \"\n"
+            + "FT                   /translation=\"MRKLD\n"
+            + "SQ   Sequence 7496 BP; 2450 A; 1290 C; 1434 G; 2322 T; 0 other;\n"
+            + "     ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga        40\n";
+    FileParse fp = new FileParse(data, DataSourceType.PASTE);
+    EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+    parser.parse();
+    List<SequenceI> seqs = parser.getSeqs();
+    assertEquals(seqs.size(), 1);
+    SequenceI seq = seqs.get(0);
+    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+
+    /*
+     * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
+     */
+    assertEquals(dbrefs.size(), 2);
+    
+    // dbref to self
+    DBRefEntry dbref = dbrefs.get(0);
+    assertEquals(dbref.getSource(), "EMBLTEST");
+    assertEquals(dbref.getAccessionId(), "MN908947");
+    Mapping mapping = dbref.getMap();
+    assertNull(mapping.getTo());
+    MapList map = mapping.getMap();
+    assertEquals(map.getFromLowest(), 1);
+    assertEquals(map.getFromHighest(), 40);
+    assertEquals(map.getToLowest(), 1);
+    assertEquals(map.getToHighest(), 40);
+    assertEquals(map.getFromRatio(), 1);
+    assertEquals(map.getToRatio(), 1);
+    
+    // dbref to inferred EMBLCDSPROTEIN:
+    dbref = dbrefs.get(1);
+    assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+    assertEquals(dbref.getAccessionId(), "QHD43415.1");
+    mapping = dbref.getMap();
+    SequenceI mapTo = mapping.getTo();
+    assertEquals(mapTo.getName(), "QHD43415.1");
+    // the /product qualifier transfers to protein product description
+    assertEquals(mapTo.getDescription(), "orf1ab polyprotein \"foobar\"");
+    assertEquals(mapTo.getSequenceAsString(), "MRKLD");
+    map = mapping.getMap();
+    assertEquals(map.getFromLowest(), 3);
+    assertEquals(map.getFromHighest(), 17);
+    assertEquals(map.getToLowest(), 1);
+    assertEquals(map.getToHighest(), 5);
+    assertEquals(map.getFromRatio(), 3);
+    assertEquals(map.getToRatio(), 1);
+  }
+
+  @Test(groups = "Functional")
+  public void testAdjustForProteinLength()
+  {
+    int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+    // exact length match:
+    assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
+
+    // match if we assume exons include stop codon not in protein:
+    assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
+
+    // truncate last exon by 6bp
+    int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+
+    // remove last exon and truncate preceding by 1bp (so 3bp in total)
+    truncated = EmblFlatFile.adjustForProteinLength(3, exons);
+    assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+
+    // exact removal of exon case:
+    exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+    truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+
+    // what if exons are too short for protein?
+    truncated = EmblFlatFile.adjustForProteinLength(7, exons);
+    assertSame(exons, truncated);
+  }
+
+  @Test(groups = "Functional")
+  public void testRemoveQuotes()
+  {
+    assertNull(EmblFlatFile.removeQuotes(null));
+    assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here");
+    assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes");
+    assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example");
+  }
+}
diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index f6480a6..04d01b0 100644
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -20,16 +20,23 @@
  */
 package jalview.io;
 
-import jalview.gui.JvOptionPane;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
 
+import java.io.BufferedInputStream;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 
 import org.testng.AssertJUnit;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+
 /**
  * @author jimp
  * 
@@ -50,6 +57,7 @@ public class FileIOTester
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    Cache.initLogger();
   }
 
   /**
@@ -88,8 +96,9 @@ public class FileIOTester
   public void testStarsInFasta1() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = STARS_FA_FILE1.getAbsoluteFile()
-            .toString(), DataSourceType.FILE);
+    FileParse fp = new FileParse(
+            uri = STARS_FA_FILE1.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
     assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
@@ -97,8 +106,9 @@ public class FileIOTester
   public void testStarsInFasta2() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = STARS_FA_FILE2.getAbsoluteFile()
-            .toString(), DataSourceType.FILE);
+    FileParse fp = new FileParse(
+            uri = STARS_FA_FILE2.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
     assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
@@ -106,8 +116,9 @@ public class FileIOTester
   public void testGzipIo() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = ALIGN_FILE.getAbsoluteFile().toURI()
-            .toString(), DataSourceType.URL);
+    FileParse fp = new FileParse(
+            uri = ALIGN_FILE.getAbsoluteFile().toURI().toString(),
+            DataSourceType.URL);
     assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
@@ -115,17 +126,36 @@ public class FileIOTester
   public void testGziplocalFileIO() throws IOException
   {
     String filepath;
-    FileParse fp = new FileParse(filepath = ALIGN_FILE.getAbsoluteFile()
-            .toString(), DataSourceType.FILE);
+    FileParse fp = new FileParse(
+            filepath = ALIGN_FILE.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
     assertValidFormat(FileFormat.Fasta, filepath, fp);
   }
 
   @Test(groups = { "Functional" })
+  public void testIsGzipInputStream() throws IOException
+  {
+    InputStream is = new FileInputStream(ALIGN_FILE);
+    
+    /*
+     * first try fails - FileInputStream does not support mark/reset
+     */
+    assertFalse(FileParse.isGzipStream(is));
+    
+    /*
+     * wrap in a BufferedInputStream and try again
+     */
+    is = new BufferedInputStream(is, 16);
+    assertTrue(FileParse.isGzipStream(is));
+  }
+
+  @Test(groups = { "Functional" })
   public void testNonGzipURLIO() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = NOTGZALIGN_FILE.getAbsoluteFile()
-            .toURI().toString(), DataSourceType.URL);
+    FileParse fp = new FileParse(
+            uri = NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),
+            DataSourceType.URL);
     assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
@@ -133,8 +163,9 @@ public class FileIOTester
   public void testNonGziplocalFileIO() throws IOException
   {
     String filepath;
-    FileParse fp = new FileParse(filepath = NOTGZALIGN_FILE
-            .getAbsoluteFile().toString(), DataSourceType.FILE);
+    FileParse fp = new FileParse(
+            filepath = NOTGZALIGN_FILE.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
     assertValidFormat(FileFormat.Fasta, filepath, fp);
   }
 }
diff --git a/test/jalview/io/J03321.embl.txt b/test/jalview/io/J03321.embl.txt
new file mode 100644
index 0000000..b0bc512
--- /dev/null
+++ b/test/jalview/io/J03321.embl.txt
@@ -0,0 +1,306 @@
+ID   J03321; SV 1; circular; genomic DNA; STD; PRO; 7502 BP.
+XX
+AC   J03321;
+XX
+DT   27-JUL-1990 (Rel. 24, Created)
+DT   10-APR-2020 (Rel. 144, Last updated, Version 9)
+XX
+DE   Chlamydia trachomatis plasmid pCHL1, complete sequence.
+XX
+KW   .
+XX
+OS   Chlamydia trachomatis
+OC   Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae;
+OC   Chlamydia/Chlamydophila group; Chlamydia.
+OG   Plasmid pCHL1
+XX
+RN   [1]
+RP   1-7502
+RX   DOI; 10.1016/0147-619X(90)90034-A.
+RX   PUBMED; 2194229.
+RA   Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT   "Diversity of the Chlamydia trachomatis common plasmid in biovars with
+RT   different pathogenicity";
+RL   Plasmid 23(2):149-154(1990).
+XX
+RN   [2]
+RP   1-7502
+RA   Comanducci M., Ricci S., Cevenini R., Ratti G.;
+RT   ;
+RL   Submitted (23-JUN-2010) to the INSDC.
+RL   Sclavo Research Centre, Siena, Italy
+XX
+DR   MD5; d4c4942a634e3df4995fd5ac75c26a61.
+DR   BioSample; SAMN14225621.
+DR   EuropePMC; PMC4450983; 26031715.
+DR   EuropePMC; PMC87941; 11283058.
+XX
+CC   Draft entry and computer-readable sequence kindly submitted by
+CC   G.Ratti, 28-MAR-1990.
+XX
+XX   ! first CDS location below split across two lines for test purposes !
+FH   Key             Location/Qualifiers
+FH
+FT   source          1..7502
+FT                   /organism="Chlamydia trachomatis"
+FT                   /plasmid="pCHL1"
+FT                   /isolate="G0/86"
+FT                   /serotype="D"
+FT                   /mol_type="genomic DNA"
+FT                   /isolation_source="trachoma"
+FT                   /db_xref="taxon:813"
+FT   CDS             join(7022..7502,
+FT                   1..437)
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP7-D"
+FT                   /db_xref="GOA:P0CE19"
+FT                   /db_xref="InterPro:IPR002104"
+FT                   /db_xref="InterPro:IPR011010"
+FT                   /db_xref="InterPro:IPR013762"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE19"
+FT                   /protein_id="AAA91567.1"
+FT                   /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSLE
+FT                   ILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLTKG
+FT                   YIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQGIR
+FT                   KLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNGRVFV
+FT                   SKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMRISCLS
+FT                   SRQSVCSYCSGEEVIPLVQTPTIL"
+FT   CDS             complement(488..1480)
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP8-D"
+FT                   /db_xref="GOA:P0CE20"
+FT                   /db_xref="InterPro:IPR002104"
+FT                   /db_xref="InterPro:IPR011010"
+FT                   /db_xref="InterPro:IPR013762"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE20"
+FT                   /protein_id="AAA91568.1"
+FT                   /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEVI
+FT                   MHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKTSW
+FT                   TEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSLQTA
+FT                   SFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQTEKRI
+FT                   IITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKITPHVL
+FT                   RATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI"
+FT   CDS             1579..2934
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP1-D"
+FT                   /db_xref="GOA:P0CE16"
+FT                   /db_xref="InterPro:IPR003593"
+FT                   /db_xref="InterPro:IPR007693"
+FT                   /db_xref="InterPro:IPR007694"
+FT                   /db_xref="InterPro:IPR027417"
+FT                   /db_xref="InterPro:IPR036185"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE16"
+FT                   /protein_id="AAA91569.1"
+FT                   /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCSH
+FT                   HKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVSHT
+FT                   VFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSIRSA
+FT                   RGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKGNFVI
+FT                   IAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGEKLQRG
+FT                   DLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFIDYLQLI
+FT                   NSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSDLRDSGQI
+FT                   EQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKVW"
+FT   CDS             2928..3992
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP2-D"
+FT                   /db_xref="InterPro:IPR040719"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE17"
+FT                   /protein_id="AAA91570.1"
+FT                   /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVIG
+FT                   LDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLEAY
+FT                   GVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTLSPI
+FT                   IRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPANVYQ
+FT                   EIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYILRMNRY
+FT                   ICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERFEEITKK
+FT                   SKEQMEQLEQESIN"
+FT   CDS             4054..4848
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP3-D"
+FT                   /db_xref="InterPro:IPR008444"
+FT                   /db_xref="InterPro:IPR033758"
+FT                   /db_xref="InterPro:IPR038264"
+FT                   /db_xref="PDB:6GJT"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE18"
+FT                   /protein_id="AAA91571.1"
+FT                   /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVAA
+FT                   KMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQDI
+FT                   LDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSGSMF
+FT                   LVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTPTTYS
+FT                   LRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA"
+FT   CDS             4918..5226
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP4-D"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P0CE23"
+FT                   /protein_id="AAA91572.1"
+FT                   /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLEL
+FT                   YHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE"
+FT   CDS             5317..6048
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP5-D (gtg start codon)"
+FT                   /db_xref="GOA:P10559"
+FT                   /db_xref="InterPro:IPR025669"
+FT                   /db_xref="InterPro:IPR027417"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P10559"
+FT                   /protein_id="AAA91573.1"
+FT                   /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVYT
+FT                   SNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICIID
+FT                   TPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIALSFW
+FT                   DDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAEDILKL
+FT                   THEIANILHIEYERDYSQRTT"
+FT   CDS             6045..6788
+FT                   /codon_start=1
+FT                   /transl_table=11
+FT                   /product="hypothetical protein"
+FT                   /note="pGP6-D (gtg start codon)"
+FT                   /db_xref="InterPro:IPR005350"
+FT                   /db_xref="UniProtKB/Swiss-Prot:P10560"
+FT                   /protein_id="AAA91574.1"
+FT                   /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQSL
+FT                   DRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDHFS
+FT                   STTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKGDLK
+FT                   TKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEILRIM
+FT                   CSGVSLSSYNENLLQQLFELFKQKS"
+FT   repeat_region   6857..6945
+FT                   /note="four tandem 22bp repeats"
+XX
+SQ   Sequence 7502 BP; 2460 A; 1285 C; 1433 G; 2324 T; 0 other;
+     ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca        60
+     atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat       120
+     ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat       180
+     ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg       240
+     cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt       300
+     tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt       360
+     catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa       420
+     cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac       480
+     ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt       540
+     acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc       600
+     accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa       660
+     aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca       720
+     ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta       780
+     gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct       840
+     taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta       900
+     agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg       960
+     cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg      1020
+     tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg      1080
+     ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg      1140
+     ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa      1200
+     tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg      1260
+     acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt      1320
+     tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt      1380
+     tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta      1440
+     acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac      1500
+     ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg      1560
+     gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc      1620
+     gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg      1680
+     cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa      1740
+     cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg      1800
+     cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca      1860
+     aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc      1920
+     gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca      1980
+     ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata      2040
+     gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag      2100
+     tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa      2160
+     aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc      2220
+     ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta      2280
+     gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct      2340
+     ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct      2400
+     ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct      2460
+     ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac      2520
+     ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc      2580
+     gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat      2640
+     atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc      2700
+     caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga      2760
+     gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg      2820
+     tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta      2880
+     ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata      2940
+     gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac      3000
+     ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag      3060
+     gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg      3120
+     caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc      3180
+     aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg      3240
+     gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa      3300
+     ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa      3360
+     ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta      3420
+     ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac      3480
+     cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct      3540
+     tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa      3600
+     aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag      3660
+     cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat      3720
+     taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa      3780
+     ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg      3840
+     gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag      3900
+     aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa      3960
+     tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt      4020
+     tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat      4080
+     aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc      4140
+     aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct      4200
+     tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt      4260
+     ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt      4320
+     gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa      4380
+     acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt      4440
+     caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata      4500
+     ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt      4560
+     attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag      4620
+     ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc      4680
+     agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa      4740
+     agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat      4800
+     acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt      4860
+     ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg      4920
+     caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat      4980
+     ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct      5040
+     cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa      5100
+     aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta      5160
+     aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct      5220
+     gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt      5280
+     aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt      5340
+     ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg      5400
+     ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat      5460
+     ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt      5520
+     tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta      5580
+     tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc      5640
+     ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact      5700
+     ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga      5760
+     aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg      5820
+     actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca      5880
+     aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat      5940
+     gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat      6000
+     attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa      6060
+     aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga      6120
+     cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg      6180
+     atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca      6240
+     tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc      6300
+     ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa      6360
+     caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc      6420
+     ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat      6480
+     cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg      6540
+     tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc      6600
+     aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag      6660
+     agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag      6720
+     tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa      6780
+     agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt      6840
+     tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga      6900
+     ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac      6960
+     ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa      7020
+     aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga      7080
+     aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt      7140
+     tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga      7200
+     ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc      7260
+     agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag      7320
+     attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt      7380
+     ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt      7440
+     ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca      7500
+     ag                                                                     7502
+//
diff --git a/test/jalview/io/cache/JvCacheableInputBoxTest.java b/test/jalview/io/cache/JvCacheableInputBoxTest.java
index 010a4b2..9b899e2 100644
--- a/test/jalview/io/cache/JvCacheableInputBoxTest.java
+++ b/test/jalview/io/cache/JvCacheableInputBoxTest.java
@@ -13,8 +13,8 @@ public class JvCacheableInputBoxTest
 
   private static final String TEST_CACHE_KEY = "CACHE.UNIT_TEST";
 
-  private JvCacheableInputBox<String> cacheBox = new JvCacheableInputBox<String>(
-          TEST_CACHE_KEY);
+  private JvCacheableInputBox<String> cacheBox = new JvCacheableInputBox<>(
+          TEST_CACHE_KEY, 20);
 
   @BeforeClass(alwaysRun = true)
   private void setUpCache()
diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 097ccd4..dd789d6 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
@@ -1284,4 +1285,33 @@ public class MappingUtilsTest
     assertEquals(1, ranges.size());
     assertEquals(9, ranges.get(0)[1]);
   }
+  
+  @Test(groups = "Functional")
+  public void testListToArray()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    
+    int[] result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 0);
+    ranges.add(new int[] {24, 12});
+    result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 2);
+    assertEquals(result[0], 24);
+    assertEquals(result[1], 12);
+    ranges.add(new int[] {-7, 30});
+    result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 4);
+    assertEquals(result[0], 24);
+    assertEquals(result[1], 12);
+    assertEquals(result[2], -7);
+    assertEquals(result[3], 30);
+    try
+    {
+      MappingUtils.listToArray(null);
+      fail("Expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+  }
 }
diff --git a/test/jalview/ws/dbsources/EmblSourceTest.java b/test/jalview/ws/dbsources/EmblXmlSourceTest.java
similarity index 93%
rename from test/jalview/ws/dbsources/EmblSourceTest.java
rename to test/jalview/ws/dbsources/EmblXmlSourceTest.java
index d450495..5f288a8 100644
--- a/test/jalview/ws/dbsources/EmblSourceTest.java
+++ b/test/jalview/ws/dbsources/EmblXmlSourceTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -40,9 +41,10 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-public class EmblSourceTest
+public class EmblXmlSourceTest
 {
 
   // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
@@ -95,16 +97,49 @@ public class EmblSourceTest
           + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
           + "</sequence></entry></ROOT>";
 
+  private EmblXmlSource testee;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    testee = new EmblXmlSource()
+    {
+
+      @Override
+      public String getDbSource()
+      {
+        return null;
+      }
+
+      @Override
+      public String getDbName()
+      {
+        return null;
+      }
+
+      @Override
+      public String getTestQuery()
+      {
+        return null;
+      }
+
+      @Override
+      public AlignmentI getSequenceRecords(String queries) throws Exception
+      {
+        return null;
+      }
+    };
+  }
+
   @Test(groups = "Functional")
   public void testGetCdsRanges()
   {
-    EmblSource testee = new EmblSource();
-
     /*
      * Make a (CDS) Feature with 5 locations
      */
     Feature cds = new Feature();
-    cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
+    cds.setLocation(
+            "join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
 
     int[] exons = testee.getCdsRanges("EMBL", cds);
     assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
@@ -116,10 +151,9 @@ public class EmblSourceTest
   {
     // not the whole sequence but enough for this test...
     List<SequenceI> peptides = new ArrayList<>();
-    List<EntryType> entries = EmblSourceTest.getEmblEntries();
+    List<EntryType> entries = getEmblEntries();
     assertEquals(1, entries.size());
     EntryType entry = entries.get(0);
-    EmblSource testee = new EmblSource();
     String sourceDb = "EMBL";
     SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
 
@@ -165,8 +199,9 @@ public class EmblSourceTest
             3, 1);
     MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
             3, 1);
-    MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
-        1, 3 }, 3, 1);
+    MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 },
+            new int[]
+            { 1, 3 }, 3, 1);
 
     DBRefEntry[] dbrefs = dna.getDBRefs();
     assertEquals(7, dbrefs.length);
@@ -222,10 +257,12 @@ public class EmblSourceTest
      * - to EMBLCDS (with 1:3 mapping)
      * - direct (no mapping) to other protein accessions
      */
-    MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
-        1, 12 }, 1, 3);
-    MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
-        1, 9 }, 1, 3);
+    MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 },
+            new int[]
+            { 1, 12 }, 1, 3);
+    MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 },
+            new int[]
+            { 1, 9 }, 1, 3);
 
     // dbrefs for first CDS EMBL product CAA30420.1
     dbrefs = peptides.get(0).getDBRefs();
@@ -339,10 +376,10 @@ public class EmblSourceTest
   @Test(groups = { "Functional" })
   public void testGetEmblEntries()
   {
-    List<EntryType> entries = EmblSourceTest.getEmblEntries();
+    List<EntryType> entries = getEmblEntries();
     assertEquals(1, entries.size());
     EntryType entry = entries.get(0);
-  
+
     assertEquals("X07547", entry.getAccession());
     assertEquals("C. trachomatis plasmid", entry.getDescription());
     assertEquals("STD", entry.getDataClass());
@@ -359,7 +396,7 @@ public class EmblSourceTest
     assertEquals(2, entry.getKeyword().size());
     assertEquals("plasmid", entry.getKeyword().get(0));
     assertEquals("unidentified reading frame", entry.getKeyword().get(1));
-  
+
     /*
      * dbrefs
      */
@@ -372,7 +409,7 @@ public class EmblSourceTest
     assertEquals("MD5", dbref.getDb());
     assertEquals("ac73317", dbref.getId());
     assertNull(dbref.getSecondaryId());
-  
+
     /*
      * three sequence features for CDS
      */
@@ -403,7 +440,7 @@ public class EmblSourceTest
     q = ef.getQualifier().get(2);
     assertEquals("translation", q.getName());
     assertEquals("MLCF", q.getValue());
-  
+
     /*
      * second CDS
      */
@@ -422,7 +459,7 @@ public class EmblSourceTest
     q = ef.getQualifier().get(1);
     assertEquals("translation", q.getName());
     assertEquals("MSSS", q.getValue());
-  
+
     /*
      * third CDS
      */
@@ -438,16 +475,14 @@ public class EmblSourceTest
     q = ef.getQualifier().get(1);
     assertEquals("translation", q.getName());
     assertEquals("MSS", q.getValue());
-  
+
     /*
      * Sequence - raw data before removal of newlines
      */
     String seq = entry.getSequence();
-    assertEquals(
-            "GGTATGTCCTCTAGTACAAAC\n"
-                    + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
-            seq);
-  
+    assertEquals("GGTATGTCCTCTAGTACAAAC\n"
+            + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT", seq);
+
     /*
      * getSequence() converts empty DBRefEntry.version to "0"
      */
@@ -455,9 +490,9 @@ public class EmblSourceTest
     assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
   }
 
-  static List<EntryType> getEmblEntries()
+  List<EntryType> getEmblEntries()
   {
-    return new EmblSource()
+    return testee
             .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
   }
 }
diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java
index f5cc640..23cceb2 100644
--- a/test/jalview/ws/dbsources/PfamFullTest.java
+++ b/test/jalview/ws/dbsources/PfamFullTest.java
@@ -38,7 +38,7 @@ public class PfamFullTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "pfam.xfam.org/family/ABC/alignment/full";
+    String path = "pfam.xfam.org/family/ABC/alignment/full/gzipped";
 
     // with default value for domain
     String url = new PfamFull().getURL(" abc ");
diff --git a/test/jalview/ws/dbsources/PfamSeedTest.java b/test/jalview/ws/dbsources/PfamSeedTest.java
index 355ef0c..451810b 100644
--- a/test/jalview/ws/dbsources/PfamSeedTest.java
+++ b/test/jalview/ws/dbsources/PfamSeedTest.java
@@ -38,7 +38,7 @@ public class PfamSeedTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "pfam.xfam.org/family/ABC/alignment/seed";
+    String path = "pfam.xfam.org/family/ABC/alignment/seed/gzipped";
 
     // with default value for domain
     String url = new PfamSeed().getURL(" abc ");
diff --git a/test/jalview/ws/dbsources/RfamFullTest.java b/test/jalview/ws/dbsources/RfamFullTest.java
index 2d1497f..87b963f 100644
--- a/test/jalview/ws/dbsources/RfamFullTest.java
+++ b/test/jalview/ws/dbsources/RfamFullTest.java
@@ -38,7 +38,7 @@ public class RfamFullTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "rfam.xfam.org/family/ABC/alignment/full";
+    String path = "rfam.xfam.org/family/ABC/alignment/full?gzip=1&download=1";
 
     // with default value for domain
     String url = new RfamFull().getURL(" abc ");
diff --git a/test/jalview/ws/dbsources/RfamSeedTest.java b/test/jalview/ws/dbsources/RfamSeedTest.java
index 745ba2e..1165d1f 100644
--- a/test/jalview/ws/dbsources/RfamSeedTest.java
+++ b/test/jalview/ws/dbsources/RfamSeedTest.java
@@ -38,7 +38,7 @@ public class RfamSeedTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "rfam.xfam.org/family/ABC/alignment/stockholm";
+    String path = "rfam.xfam.org/family/ABC/alignment/stockholm?gzip=1&download=1";
 
     // with default value for domain
     String url = new RfamSeed().getURL(" abc ");
diff --git a/test/jalview/ws/ebi/EBIFetchClientTest.java b/test/jalview/ws/ebi/EBIFetchClientTest.java
index c559966..c3fae6c 100644
--- a/test/jalview/ws/ebi/EBIFetchClientTest.java
+++ b/test/jalview/ws/ebi/EBIFetchClientTest.java
@@ -47,13 +47,13 @@ public class EBIFetchClientTest
     /*
      * EMBL
      */
-    assertEquals("https://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
+    assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
 
     /*
      * EMBLCDS
      */
-    assertEquals("https://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
+    assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
 
     /*
diff --git a/utils/clover/lib/clover-ant-4.4.1.jar b/utils/clover/lib/clover-ant-4.4.1.jar
new file mode 100644
index 0000000..4f92395
Binary files /dev/null and b/utils/clover/lib/clover-ant-4.4.1.jar differ
diff --git a/utils/cmd-nox.sh b/utils/cmd-nox.sh
new file mode 100755
index 0000000..bd615bd
--- /dev/null
+++ b/utils/cmd-nox.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+CMD=$(basename $0)
+CMD=${CMD%-nox.sh}
+
+echo "Running '$CMD' headlessly"
+
+xvfb-run -s "-screen 0 1280x800x16" -e /dev/stdout -a $CMD ${@}
diff --git a/utils/gradle-nox.sh b/utils/gradle-nox.sh
new file mode 120000
index 0000000..4abb9a2
--- /dev/null
+++ b/utils/gradle-nox.sh
@@ -0,0 +1 @@
+cmd-nox.sh
\ No newline at end of file