From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 27 May 2014 15:07:39 +0000 (+0100)
Subject: Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
X-Git-Tag: Release_2_8_1~4^2~8
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4456d786f0bd69dba5782fcd55a2d18b54747853;hp=faca912eeba088b058939b879f845f97b92c002e

Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
---

diff --git a/build.xml b/build.xml
index 82cbabb..ba538c2 100755
--- a/build.xml
+++ b/build.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html
index 97083e8..5556629 100644
--- a/doc/AddingGroovySupport.html
+++ b/doc/AddingGroovySupport.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html
index 62764df..e068f3b 100644
--- a/doc/JalviewRNASupport.html
+++ b/doc/JalviewRNASupport.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/building.html b/doc/building.html
index f07e2d8..04639d5 100755
--- a/doc/building.html
+++ b/doc/building.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/developing.html b/doc/developing.html
index 3715094..330a156 100644
--- a/doc/developing.html
+++ b/doc/developing.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/index.html b/doc/index.html
index 5e43906..7d3a278 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/doc/newdmobj.html b/doc/newdmobj.html
index 056665c..e564371 100644
--- a/doc/newdmobj.html
+++ b/doc/newdmobj.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/assets/css/ie6.css b/examples-jbake/assets/css/ie6.css
index d89b6c3..f333ebc 100644
--- a/examples-jbake/assets/css/ie6.css
+++ b/examples-jbake/assets/css/ie6.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/assets/css/ie7.css b/examples-jbake/assets/css/ie7.css
index 17c20e2..159d07e 100644
--- a/examples-jbake/assets/css/ie7.css
+++ b/examples-jbake/assets/css/ie7.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/assets/css/reset.css b/examples-jbake/assets/css/reset.css
index ef8e5bc..17a8f7b 100644
--- a/examples-jbake/assets/css/reset.css
+++ b/examples-jbake/assets/css/reset.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/assets/css/style.css b/examples-jbake/assets/css/style.css
index 466d507..344182b 100644
--- a/examples-jbake/assets/css/style.css
+++ b/examples-jbake/assets/css/style.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/assets/exampleFeatures.txt b/examples-jbake/assets/exampleFeatures.txt
index 210aab2..c16c3d8 100755
--- a/examples-jbake/assets/exampleFeatures.txt
+++ b/examples-jbake/assets/exampleFeatures.txt
@@ -1,5 +1,5 @@
 #-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/examples-jbake/assets/javascript/deployJava.js b/examples-jbake/assets/javascript/deployJava.js
index b0e9559..8aa7a65 100644
--- a/examples-jbake/assets/javascript/deployJava.js
+++ b/examples-jbake/assets/javascript/deployJava.js
@@ -1,81 +1 @@
-/*********
- * downloaded from http://java.com/js/deployJava.js
- * Probably copyright Oracle nee Sun 2011,2010,2009.
- */
-var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}
-if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}
-return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}
-return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}
-return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}
-location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}
-return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}
-var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}
-if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+
-minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}
-if(parameters!='undefined'&&parameters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}
-if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}
-params+='<param name="'+parameter+'" value="'+
-parameters[parameter]+'"/>';}
-if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}
-if(addCodeAttribute){startApplet+=(' code="dummy"');}
-startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)
-{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}
-if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}
-var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}
-return false;}else{alert('Invalid versionPattern passed to versionCheck: '+
-versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}
-if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}
-var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}
-retval=deployJava.versionCheck('1.4.2+');}
-return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}
-var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}
-if(jnlpDocbase==null){jnlpDocbase=document.URL;}
-var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+
-deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}
-if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}
-var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}
-var url='javascript:'+'if (!deployJava.isWebStartInstalled(&quot;'+
-minimumVersion+'&quot;)) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch(&quot;'+jnlp+'&quot;)) {}'+'}'+'} else {'+'if (deployJava.launch(&quot;'+jnlp+'&quot;)) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}
-return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}
-return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}
-return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}
-return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}
-return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}
-return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))
-{result[index]=matchData[i];index++;}}
-var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}
-return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}
-return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}
-if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}
-if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}
-return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}
-return false;}
-try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}
-return false;}
-for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}
-return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}
-var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}
-if(deployJava.compareVersions("1.5.0",version)){return true;}
-return false;},IEInstall:function(){location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}
-for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}
-if(a.length==2){a[2]=0;}
-if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}
-if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+
-deployJava.mimeType+'" hidden="true" />');written=true;}}}
-if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+
-deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}
-if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}
-if(loc==null)try{loc=navigator.language;}catch(err){}
-if(loc!=null){loc.replace("-","_")
-deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
+var deployJava=function(){var l={core:["id","class","title","style"],i18n:["lang","dir"],events:["onclick","ondblclick","onmousedown","onmouseup","onmouseover","onmousemove","onmouseout","onkeypress","onkeydown","onkeyup"],applet:["codebase","code","name","archive","object","width","height","alt","align","hspace","vspace"],object:["classid","codebase","codetype","data","type","archive","declare","standby","height","width","usemap","name","tabindex","align","border","hspace","vspace"]};var b=l.object.concat(l.core,l.i18n,l.events);var m=l.applet.concat(l.core);function g(o){if(!d.debug){return}if(console.log){console.log(o)}else{alert(o)}}function k(p,o){if(p==null||p.length==0){return true}var r=p.charAt(p.length-1);if(r!="+"&&r!="*"&&(p.indexOf("_")!=-1&&r!="_")){p=p+"*";r="*"}p=p.substring(0,p.length-1);if(p.length>0){var q=p.charAt(p.length-1);if(q=="."||q=="_"){p=p.substring(0,p.length-1)}}if(r=="*"){return(o.indexOf(p)==0)}else{if(r=="+"){return p<=o}}return false}function e(){var o="//java.com/js/webstart.png";try{return document.location.protocol.indexOf("http")!=-1?o:"http:"+o}catch(p){return"http:"+o}}function n(p){var o="http://java.com/dt-redirect";if(p==null||p.length==0){return o}if(p.charAt(0)=="&"){p=p.substring(1,p.length)}return o+"?"+p}function j(q,p){var o=q.length;for(var r=0;r<o;r++){if(q[r]===p){return true}}return false}function c(o){return j(m,o.toLowerCase())}function i(o){return j(b,o.toLowerCase())}function a(o){if("MSIE"!=deployJava.browserName){return true}if(deployJava.compareVersionToPattern(deployJava.getPlugin().version,["10","0","0"],false,true)){return true}if(o==null){return false}return !k("1.6.0_33+",o)}var d={debug:null,version:"20120801",firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,oldMimeType:"application/npruntime-scriptable-plugin;DeploymentToolkit",mimeType:"application/java-deployment-toolkit",launchButtonPNG:e(),browserName:null,browserName2:null,getJREs:function(){var t=new Array();if(this.isPluginInstalled()){var r=this.getPlugin();var o=r.jvms;for(var q=0;q<o.getLength();q++){t[q]=o.get(q).version}}else{var p=this.getBrowser();if(p=="MSIE"){if(this.testUsingActiveX("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingActiveX("1.6.0")){t[0]="1.6.0"}else{if(this.testUsingActiveX("1.5.0")){t[0]="1.5.0"}else{if(this.testUsingActiveX("1.4.2")){t[0]="1.4.2"}else{if(this.testForMSVM()){t[0]="1.1"}}}}}}else{if(p=="Netscape Family"){this.getJPIVersionUsingMimeType();if(this.firefoxJavaVersion!=null){t[0]=this.firefoxJavaVersion}else{if(this.testUsingMimeTypes("1.7")){t[0]="1.7.0"}else{if(this.testUsingMimeTypes("1.6")){t[0]="1.6.0"}else{if(this.testUsingMimeTypes("1.5")){t[0]="1.5.0"}else{if(this.testUsingMimeTypes("1.4.2")){t[0]="1.4.2"}else{if(this.browserName2=="Safari"){if(this.testUsingPluginsArray("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingPluginsArray("1.6")){t[0]="1.6.0"}else{if(this.testUsingPluginsArray("1.5")){t[0]="1.5.0"}else{if(this.testUsingPluginsArray("1.4.2")){t[0]="1.4.2"}}}}}}}}}}}}}if(this.debug){for(var q=0;q<t.length;++q){g("[getJREs()] We claim to have detected Java SE "+t[q])}}return t},installJRE:function(r,p){var o=false;if(this.isPluginInstalled()&&this.isAutoInstallEnabled(r)){var q=false;if(this.isCallbackSupported()){q=this.getPlugin().installJRE(r,p)}else{q=this.getPlugin().installJRE(r)}if(q){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return q}else{return this.installLatestJRE()}},isAutoInstallEnabled:function(o){if(!this.isPluginInstalled()){return false}if(typeof o=="undefined"){o=null}return a(o)},isCallbackSupported:function(){return this.isPluginInstalled()&&this.compareVersionToPattern(this.getPlugin().version,["10","2","0"],false,true)},installLatestJRE:function(q){if(this.isPluginInstalled()&&this.isAutoInstallEnabled()){var r=false;if(this.isCallbackSupported()){r=this.getPlugin().installLatestJRE(q)}else{r=this.getPlugin().installLatestJRE()}if(r){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return r}else{var p=this.getBrowser();var o=navigator.platform.toLowerCase();if((this.EAInstallEnabled=="true")&&(o.indexOf("win")!=-1)&&(this.EarlyAccessURL!=null)){this.preInstallJREList=this.getJREs();if(this.returnPage!=null){this.myInterval=setInterval("deployJava.poll()",3000)}location.href=this.EarlyAccessURL;return false}else{if(p=="MSIE"){return this.IEInstall()}else{if((p=="Netscape Family")&&(o.indexOf("win32")!=-1)){return this.FFInstall()}else{location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""))}}return false}}},runApplet:function(p,u,r){if(r=="undefined"||r==null){r="1.1"}var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(this.returnPage==null){this.returnPage=document.location}if(o!=null){var q=this.getBrowser();if(q!="?"){if(this.versionCheck(r+"+")){this.writeAppletTag(p,u)}else{if(this.installJRE(r+"+")){this.refresh();location.href=document.location;this.writeAppletTag(p,u)}}}else{this.writeAppletTag(p,u)}}else{g("[runApplet()] Invalid minimumVersion argument to runApplet():"+r)}},writeAppletTag:function(r,w){var o="<"+"applet ";var q="";var t="<"+"/"+"applet"+">";var x=true;if(null==w||typeof w!="object"){w=new Object()}for(var p in r){if(!c(p)){w[p]=r[p]}else{o+=(" "+p+'="'+r[p]+'"');if(p=="code"){x=false}}}var v=false;for(var u in w){if(u=="codebase_lookup"){v=true}if(u=="object"||u=="java_object"||u=="java_code"){x=false}q+='<param name="'+u+'" value="'+w[u]+'"/>'}if(!v){q+='<param name="codebase_lookup" value="false"/>'}if(x){o+=(' code="dummy"')}o+=">";document.write(o+"\n"+q+"\n"+t)},versionCheck:function(p){var v=0;var x="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var y=p.match(x);if(y!=null){var r=false;var u=false;var q=new Array();for(var t=1;t<y.length;++t){if((typeof y[t]=="string")&&(y[t]!="")){q[v]=y[t];v++}}if(q[q.length-1]=="+"){u=true;r=false;q.length--}else{if(q[q.length-1]=="*"){u=false;r=true;q.length--}else{if(q.length<4){u=false;r=true}}}var w=this.getJREs();for(var t=0;t<w.length;++t){if(this.compareVersionToPattern(w[t],q,r,u)){return true}}return false}else{var o="Invalid versionPattern passed to versionCheck: "+p;g("[versionCheck()] "+o);alert(o);return false}},isWebStartInstalled:function(r){var q=this.getBrowser();if(q=="?"){return true}if(r=="undefined"||r==null){r="1.4.2"}var p=false;var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(o!=null){p=this.versionCheck(r+"+")}else{g("[isWebStartInstaller()] Invalid minimumVersion argument to isWebStartInstalled(): "+r);p=this.versionCheck("1.4.2+")}return p},getJPIVersionUsingMimeType:function(){for(var p=0;p<navigator.mimeTypes.length;++p){var q=navigator.mimeTypes[p].type;var o=q.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(o!=null){this.firefoxJavaVersion=o[1];if("Opera"!=this.browserName2){break}}}},launchWebStartApplication:function(r){var o=navigator.userAgent.toLowerCase();this.getJPIVersionUsingMimeType();if(this.isWebStartInstalled("1.7.0")==false){if((this.installJRE("1.7.0+")==false)||((this.isWebStartInstalled("1.7.0")==false))){return false}}var u=null;if(document.documentURI){u=document.documentURI}if(u==null){u=document.URL}var p=this.getBrowser();var q;if(p=="MSIE"){q="<"+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+"<"+'PARAM name="launchjnlp" value="'+r+'"'+">"+"<"+'PARAM name="docbase" value="'+u+'"'+">"+"<"+"/"+"object"+">"}else{if(p=="Netscape Family"){q="<"+'embed type="application/x-java-applet;jpi-version='+this.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+r+'"'+'docbase="'+u+'"'+" />"}}if(document.body=="undefined"||document.body==null){document.write(q);document.location=u}else{var t=document.createElement("div");t.id="div1";t.style.position="relative";t.style.left="-10000px";t.style.margin="0px auto";t.className="dynamicDiv";t.innerHTML=q;document.body.appendChild(t)}},createWebStartLaunchButtonEx:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:deployJava.launchWebStartApplication('"+q+"');";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},createWebStartLaunchButton:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:"+"if (!deployJava.isWebStartInstalled(&quot;"+p+"&quot;)) {"+"if (deployJava.installLatestJRE()) {"+"if (deployJava.launch(&quot;"+q+"&quot;)) {}"+"}"+"} else {"+"if (deployJava.launch(&quot;"+q+"&quot;)) {}"+"}";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},launch:function(o){document.location=o;return true},isPluginInstalled:function(){var o=this.getPlugin();if(o&&o.jvms){return true}else{return false}},isAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().isAutoUpdateEnabled()}return false},setAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().setAutoUpdateEnabled()}return false},setInstallerType:function(o){this.installType=o;if(this.isPluginInstalled()){return this.getPlugin().setInstallerType(o)}return false},setAdditionalPackages:function(o){if(this.isPluginInstalled()){return this.getPlugin().setAdditionalPackages(o)}return false},setEarlyAccess:function(o){this.EAInstallEnabled=o},isPlugin2:function(){if(this.isPluginInstalled()){if(this.versionCheck("1.6.0_10+")){try{return this.getPlugin().isPlugin2()}catch(o){}}}return false},allowPlugin:function(){this.getBrowser();var o=("Safari"!=this.browserName2&&"Opera"!=this.browserName2);return o},getPlugin:function(){this.refresh();var o=null;if(this.allowPlugin()){o=document.getElementById("deployJavaPlugin")}return o},compareVersionToPattern:function(v,p,r,t){if(v==undefined||p==undefined){return false}var w="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var x=v.match(w);if(x!=null){var u=0;var y=new Array();for(var q=1;q<x.length;++q){if((typeof x[q]=="string")&&(x[q]!="")){y[u]=x[q];u++}}var o=Math.min(y.length,p.length);if(t){for(var q=0;q<o;++q){if(y[q]<p[q]){return false}else{if(y[q]>p[q]){return true}}}return true}else{for(var q=0;q<o;++q){if(y[q]!=p[q]){return false}}if(r){return true}else{return(y.length==p.length)}}}else{return false}},getBrowser:function(){if(this.browserName==null){var o=navigator.userAgent.toLowerCase();g("[getBrowser()] navigator.userAgent.toLowerCase() -> "+o);if((o.indexOf("msie")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("trident")!=-1||o.indexOf("Trident")!=-1){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("iphone")!=-1){this.browserName="Netscape Family";this.browserName2="iPhone"}else{if((o.indexOf("firefox")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Firefox"}else{if(o.indexOf("chrome")!=-1){this.browserName="Netscape Family";this.browserName2="Chrome"}else{if(o.indexOf("safari")!=-1){this.browserName="Netscape Family";this.browserName2="Safari"}else{if((o.indexOf("mozilla")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Other"}else{if(o.indexOf("opera")!=-1){this.browserName="Netscape Family";this.browserName2="Opera"}else{this.browserName="?";this.browserName2="unknown"}}}}}}}}g("[getBrowser()] Detected browser name:"+this.browserName+", "+this.browserName2)}return this.browserName},testUsingActiveX:function(o){var q="JavaWebStart.isInstalled."+o+".0";if(typeof ActiveXObject=="undefined"||!ActiveXObject){g("[testUsingActiveX()] Browser claims to be IE, but no ActiveXObject object?");return false}try{return(new ActiveXObject(q)!=null)}catch(p){return false}},testForMSVM:function(){var p="{08B0E5C0-4FCB-11CF-AAA5-00401C608500}";if(typeof oClientCaps!="undefined"){var o=oClientCaps.getComponentVersion(p,"ComponentID");if((o=="")||(o=="5,0,5000,0")){return false}else{return true}}else{return false}},testUsingMimeTypes:function(p){if(!navigator.mimeTypes){g("[testUsingMimeTypes()] Browser claims to be Netscape family, but no mimeTypes[] array?");return false}for(var q=0;q<navigator.mimeTypes.length;++q){s=navigator.mimeTypes[q].type;var o=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(o!=null){if(this.compareVersions(o[1],p)){return true}}}return false},testUsingPluginsArray:function(p){if((!navigator.plugins)||(!navigator.plugins.length)){return false}var o=navigator.platform.toLowerCase();for(var q=0;q<navigator.plugins.length;++q){s=navigator.plugins[q].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(this.compareVersions("1.5.0",p)){return true}}else{if(s.search(/^Java/)!=-1){if(o.indexOf("win")!=-1){if(this.compareVersions("1.5.0",p)||this.compareVersions("1.6.0",p)){return true}}}}}if(this.compareVersions("1.5.0",p)){return true}return false},IEInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""));return false},done:function(p,o){},FFInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):"")+((this.installType!=null)?("&type="+this.installType):""));return false},compareVersions:function(r,t){var p=r.split(".");var o=t.split(".");for(var q=0;q<p.length;++q){p[q]=Number(p[q])}for(var q=0;q<o.length;++q){o[q]=Number(o[q])}if(p.length==2){p[2]=0}if(p[0]>o[0]){return true}if(p[0]<o[0]){return false}if(p[1]>o[1]){return true}if(p[1]<o[1]){return false}if(p[2]>o[2]){return true}if(p[2]<o[2]){return false}return true},enableAlerts:function(){this.browserName=null;this.debug=true},poll:function(){this.refresh();var o=this.getJREs();if((this.preInstallJREList.length==0)&&(o.length!=0)){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}if((this.preInstallJREList.length!=0)&&(o.length!=0)&&(this.preInstallJREList[0]!=o[0])){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}},writePluginTag:function(){var o=this.getBrowser();if(o=="MSIE"){document.write("<"+'object classid="clsid:CAFEEFAC-DEC7-0000-0001-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+"<"+"/"+"object"+">")}else{if(o=="Netscape Family"&&this.allowPlugin()){this.writeEmbedTag()}}},refresh:function(){navigator.plugins.refresh(false);var o=this.getBrowser();if(o=="Netscape Family"&&this.allowPlugin()){var p=document.getElementById("deployJavaPlugin");if(p==null){this.writeEmbedTag()}}},writeEmbedTag:function(){var o=false;if(navigator.mimeTypes!=null){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.mimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.mimeType+'" hidden="true" />');o=true}}}if(!o){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.oldMimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.oldMimeType+'" hidden="true" />')}}}}}}};d.writePluginTag();if(d.locale==null){var h=null;if(h==null){try{h=navigator.userLanguage}catch(f){}}if(h==null){try{h=navigator.systemLanguage}catch(f){}}if(h==null){try{h=navigator.language}catch(f){}}if(h!=null){h.replace("-","_");d.locale=h}}return d}();
\ No newline at end of file
diff --git a/examples-jbake/assets/javascript/jalview.js b/examples-jbake/assets/javascript/jalview.js
index f827db5..293b73a 100644
--- a/examples-jbake/assets/javascript/jalview.js
+++ b/examples-jbake/assets/javascript/jalview.js
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples-jbake/templates/header.ftl b/examples-jbake/templates/header.ftl
index 1c3e9fc..d42b314 100644
--- a/examples-jbake/templates/header.ftl
+++ b/examples-jbake/templates/header.ftl
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index fe29b2e..7eaf9f7 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/applets.html b/examples/applets.html
index bb6bb10..d715a4d 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/css/ie6.css b/examples/css/ie6.css
index d89b6c3..f333ebc 100644
--- a/examples/css/ie6.css
+++ b/examples/css/ie6.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/css/ie7.css b/examples/css/ie7.css
index 17c20e2..159d07e 100644
--- a/examples/css/ie7.css
+++ b/examples/css/ie7.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/css/reset.css b/examples/css/reset.css
index ef8e5bc..17a8f7b 100644
--- a/examples/css/reset.css
+++ b/examples/css/reset.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/css/style.css b/examples/css/style.css
index 466d507..344182b 100644
--- a/examples/css/style.css
+++ b/examples/css/style.css
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/embedded.html b/examples/embedded.html
index 7bae979..6072294 100644
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index af4df17..77ac6e7 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index 210aab2..c16c3d8 100755
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -1,5 +1,5 @@
 #-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/examples/formComplete.html b/examples/formComplete.html
index f4e96ce..f4833a6 100644
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html
index 3f1c752..2b8a29d 100644
--- a/examples/jalviewLiteJs.html
+++ b/examples/jalviewLiteJs.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/javascript/deployJava.js b/examples/javascript/deployJava.js
index b0e9559..8aa7a65 100644
--- a/examples/javascript/deployJava.js
+++ b/examples/javascript/deployJava.js
@@ -1,81 +1 @@
-/*********
- * downloaded from http://java.com/js/deployJava.js
- * Probably copyright Oracle nee Sun 2011,2010,2009.
- */
-var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}
-if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}
-return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}
-return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}
-return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}
-location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}
-return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}
-var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}
-if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+
-minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}
-if(parameters!='undefined'&&parameters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}
-if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}
-params+='<param name="'+parameter+'" value="'+
-parameters[parameter]+'"/>';}
-if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}
-if(addCodeAttribute){startApplet+=(' code="dummy"');}
-startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)
-{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}
-if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}
-var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}
-return false;}else{alert('Invalid versionPattern passed to versionCheck: '+
-versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}
-if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}
-var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}
-retval=deployJava.versionCheck('1.4.2+');}
-return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}
-var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}
-if(jnlpDocbase==null){jnlpDocbase=document.URL;}
-var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+
-deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}
-if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}
-var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}
-var url='javascript:'+'if (!deployJava.isWebStartInstalled(&quot;'+
-minimumVersion+'&quot;)) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch(&quot;'+jnlp+'&quot;)) {}'+'}'+'} else {'+'if (deployJava.launch(&quot;'+jnlp+'&quot;)) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}
-return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}
-return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}
-return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}
-return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}
-return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}
-return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))
-{result[index]=matchData[i];index++;}}
-var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}
-return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}
-return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}
-if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}
-if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}
-return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}
-return false;}
-try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}
-return false;}
-for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}
-return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}
-var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}
-if(deployJava.compareVersions("1.5.0",version)){return true;}
-return false;},IEInstall:function(){location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+
-((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+
-((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+
-((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+
-((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}
-for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}
-if(a.length==2){a[2]=0;}
-if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}
-if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+
-deployJava.mimeType+'" hidden="true" />');written=true;}}}
-if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+
-deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}
-if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}
-if(loc==null)try{loc=navigator.language;}catch(err){}
-if(loc!=null){loc.replace("-","_")
-deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
+var deployJava=function(){var l={core:["id","class","title","style"],i18n:["lang","dir"],events:["onclick","ondblclick","onmousedown","onmouseup","onmouseover","onmousemove","onmouseout","onkeypress","onkeydown","onkeyup"],applet:["codebase","code","name","archive","object","width","height","alt","align","hspace","vspace"],object:["classid","codebase","codetype","data","type","archive","declare","standby","height","width","usemap","name","tabindex","align","border","hspace","vspace"]};var b=l.object.concat(l.core,l.i18n,l.events);var m=l.applet.concat(l.core);function g(o){if(!d.debug){return}if(console.log){console.log(o)}else{alert(o)}}function k(p,o){if(p==null||p.length==0){return true}var r=p.charAt(p.length-1);if(r!="+"&&r!="*"&&(p.indexOf("_")!=-1&&r!="_")){p=p+"*";r="*"}p=p.substring(0,p.length-1);if(p.length>0){var q=p.charAt(p.length-1);if(q=="."||q=="_"){p=p.substring(0,p.length-1)}}if(r=="*"){return(o.indexOf(p)==0)}else{if(r=="+"){return p<=o}}return false}function e(){var o="//java.com/js/webstart.png";try{return document.location.protocol.indexOf("http")!=-1?o:"http:"+o}catch(p){return"http:"+o}}function n(p){var o="http://java.com/dt-redirect";if(p==null||p.length==0){return o}if(p.charAt(0)=="&"){p=p.substring(1,p.length)}return o+"?"+p}function j(q,p){var o=q.length;for(var r=0;r<o;r++){if(q[r]===p){return true}}return false}function c(o){return j(m,o.toLowerCase())}function i(o){return j(b,o.toLowerCase())}function a(o){if("MSIE"!=deployJava.browserName){return true}if(deployJava.compareVersionToPattern(deployJava.getPlugin().version,["10","0","0"],false,true)){return true}if(o==null){return false}return !k("1.6.0_33+",o)}var d={debug:null,version:"20120801",firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,oldMimeType:"application/npruntime-scriptable-plugin;DeploymentToolkit",mimeType:"application/java-deployment-toolkit",launchButtonPNG:e(),browserName:null,browserName2:null,getJREs:function(){var t=new Array();if(this.isPluginInstalled()){var r=this.getPlugin();var o=r.jvms;for(var q=0;q<o.getLength();q++){t[q]=o.get(q).version}}else{var p=this.getBrowser();if(p=="MSIE"){if(this.testUsingActiveX("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingActiveX("1.6.0")){t[0]="1.6.0"}else{if(this.testUsingActiveX("1.5.0")){t[0]="1.5.0"}else{if(this.testUsingActiveX("1.4.2")){t[0]="1.4.2"}else{if(this.testForMSVM()){t[0]="1.1"}}}}}}else{if(p=="Netscape Family"){this.getJPIVersionUsingMimeType();if(this.firefoxJavaVersion!=null){t[0]=this.firefoxJavaVersion}else{if(this.testUsingMimeTypes("1.7")){t[0]="1.7.0"}else{if(this.testUsingMimeTypes("1.6")){t[0]="1.6.0"}else{if(this.testUsingMimeTypes("1.5")){t[0]="1.5.0"}else{if(this.testUsingMimeTypes("1.4.2")){t[0]="1.4.2"}else{if(this.browserName2=="Safari"){if(this.testUsingPluginsArray("1.7.0")){t[0]="1.7.0"}else{if(this.testUsingPluginsArray("1.6")){t[0]="1.6.0"}else{if(this.testUsingPluginsArray("1.5")){t[0]="1.5.0"}else{if(this.testUsingPluginsArray("1.4.2")){t[0]="1.4.2"}}}}}}}}}}}}}if(this.debug){for(var q=0;q<t.length;++q){g("[getJREs()] We claim to have detected Java SE "+t[q])}}return t},installJRE:function(r,p){var o=false;if(this.isPluginInstalled()&&this.isAutoInstallEnabled(r)){var q=false;if(this.isCallbackSupported()){q=this.getPlugin().installJRE(r,p)}else{q=this.getPlugin().installJRE(r)}if(q){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return q}else{return this.installLatestJRE()}},isAutoInstallEnabled:function(o){if(!this.isPluginInstalled()){return false}if(typeof o=="undefined"){o=null}return a(o)},isCallbackSupported:function(){return this.isPluginInstalled()&&this.compareVersionToPattern(this.getPlugin().version,["10","2","0"],false,true)},installLatestJRE:function(q){if(this.isPluginInstalled()&&this.isAutoInstallEnabled()){var r=false;if(this.isCallbackSupported()){r=this.getPlugin().installLatestJRE(q)}else{r=this.getPlugin().installLatestJRE()}if(r){this.refresh();if(this.returnPage!=null){document.location=this.returnPage}}return r}else{var p=this.getBrowser();var o=navigator.platform.toLowerCase();if((this.EAInstallEnabled=="true")&&(o.indexOf("win")!=-1)&&(this.EarlyAccessURL!=null)){this.preInstallJREList=this.getJREs();if(this.returnPage!=null){this.myInterval=setInterval("deployJava.poll()",3000)}location.href=this.EarlyAccessURL;return false}else{if(p=="MSIE"){return this.IEInstall()}else{if((p=="Netscape Family")&&(o.indexOf("win32")!=-1)){return this.FFInstall()}else{location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""))}}return false}}},runApplet:function(p,u,r){if(r=="undefined"||r==null){r="1.1"}var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(this.returnPage==null){this.returnPage=document.location}if(o!=null){var q=this.getBrowser();if(q!="?"){if(this.versionCheck(r+"+")){this.writeAppletTag(p,u)}else{if(this.installJRE(r+"+")){this.refresh();location.href=document.location;this.writeAppletTag(p,u)}}}else{this.writeAppletTag(p,u)}}else{g("[runApplet()] Invalid minimumVersion argument to runApplet():"+r)}},writeAppletTag:function(r,w){var o="<"+"applet ";var q="";var t="<"+"/"+"applet"+">";var x=true;if(null==w||typeof w!="object"){w=new Object()}for(var p in r){if(!c(p)){w[p]=r[p]}else{o+=(" "+p+'="'+r[p]+'"');if(p=="code"){x=false}}}var v=false;for(var u in w){if(u=="codebase_lookup"){v=true}if(u=="object"||u=="java_object"||u=="java_code"){x=false}q+='<param name="'+u+'" value="'+w[u]+'"/>'}if(!v){q+='<param name="codebase_lookup" value="false"/>'}if(x){o+=(' code="dummy"')}o+=">";document.write(o+"\n"+q+"\n"+t)},versionCheck:function(p){var v=0;var x="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var y=p.match(x);if(y!=null){var r=false;var u=false;var q=new Array();for(var t=1;t<y.length;++t){if((typeof y[t]=="string")&&(y[t]!="")){q[v]=y[t];v++}}if(q[q.length-1]=="+"){u=true;r=false;q.length--}else{if(q[q.length-1]=="*"){u=false;r=true;q.length--}else{if(q.length<4){u=false;r=true}}}var w=this.getJREs();for(var t=0;t<w.length;++t){if(this.compareVersionToPattern(w[t],q,r,u)){return true}}return false}else{var o="Invalid versionPattern passed to versionCheck: "+p;g("[versionCheck()] "+o);alert(o);return false}},isWebStartInstalled:function(r){var q=this.getBrowser();if(q=="?"){return true}if(r=="undefined"||r==null){r="1.4.2"}var p=false;var t="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var o=r.match(t);if(o!=null){p=this.versionCheck(r+"+")}else{g("[isWebStartInstaller()] Invalid minimumVersion argument to isWebStartInstalled(): "+r);p=this.versionCheck("1.4.2+")}return p},getJPIVersionUsingMimeType:function(){for(var p=0;p<navigator.mimeTypes.length;++p){var q=navigator.mimeTypes[p].type;var o=q.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(o!=null){this.firefoxJavaVersion=o[1];if("Opera"!=this.browserName2){break}}}},launchWebStartApplication:function(r){var o=navigator.userAgent.toLowerCase();this.getJPIVersionUsingMimeType();if(this.isWebStartInstalled("1.7.0")==false){if((this.installJRE("1.7.0+")==false)||((this.isWebStartInstalled("1.7.0")==false))){return false}}var u=null;if(document.documentURI){u=document.documentURI}if(u==null){u=document.URL}var p=this.getBrowser();var q;if(p=="MSIE"){q="<"+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+"<"+'PARAM name="launchjnlp" value="'+r+'"'+">"+"<"+'PARAM name="docbase" value="'+u+'"'+">"+"<"+"/"+"object"+">"}else{if(p=="Netscape Family"){q="<"+'embed type="application/x-java-applet;jpi-version='+this.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+r+'"'+'docbase="'+u+'"'+" />"}}if(document.body=="undefined"||document.body==null){document.write(q);document.location=u}else{var t=document.createElement("div");t.id="div1";t.style.position="relative";t.style.left="-10000px";t.style.margin="0px auto";t.className="dynamicDiv";t.innerHTML=q;document.body.appendChild(t)}},createWebStartLaunchButtonEx:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:deployJava.launchWebStartApplication('"+q+"');";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},createWebStartLaunchButton:function(q,p){if(this.returnPage==null){this.returnPage=q}var o="javascript:"+"if (!deployJava.isWebStartInstalled(&quot;"+p+"&quot;)) {"+"if (deployJava.installLatestJRE()) {"+"if (deployJava.launch(&quot;"+q+"&quot;)) {}"+"}"+"} else {"+"if (deployJava.launch(&quot;"+q+"&quot;)) {}"+"}";document.write("<"+'a href="'+o+"\" onMouseOver=\"window.status=''; "+'return true;"><'+"img "+'src="'+this.launchButtonPNG+'" '+'border="0" /><'+"/"+"a"+">")},launch:function(o){document.location=o;return true},isPluginInstalled:function(){var o=this.getPlugin();if(o&&o.jvms){return true}else{return false}},isAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().isAutoUpdateEnabled()}return false},setAutoUpdateEnabled:function(){if(this.isPluginInstalled()){return this.getPlugin().setAutoUpdateEnabled()}return false},setInstallerType:function(o){this.installType=o;if(this.isPluginInstalled()){return this.getPlugin().setInstallerType(o)}return false},setAdditionalPackages:function(o){if(this.isPluginInstalled()){return this.getPlugin().setAdditionalPackages(o)}return false},setEarlyAccess:function(o){this.EAInstallEnabled=o},isPlugin2:function(){if(this.isPluginInstalled()){if(this.versionCheck("1.6.0_10+")){try{return this.getPlugin().isPlugin2()}catch(o){}}}return false},allowPlugin:function(){this.getBrowser();var o=("Safari"!=this.browserName2&&"Opera"!=this.browserName2);return o},getPlugin:function(){this.refresh();var o=null;if(this.allowPlugin()){o=document.getElementById("deployJavaPlugin")}return o},compareVersionToPattern:function(v,p,r,t){if(v==undefined||p==undefined){return false}var w="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var x=v.match(w);if(x!=null){var u=0;var y=new Array();for(var q=1;q<x.length;++q){if((typeof x[q]=="string")&&(x[q]!="")){y[u]=x[q];u++}}var o=Math.min(y.length,p.length);if(t){for(var q=0;q<o;++q){if(y[q]<p[q]){return false}else{if(y[q]>p[q]){return true}}}return true}else{for(var q=0;q<o;++q){if(y[q]!=p[q]){return false}}if(r){return true}else{return(y.length==p.length)}}}else{return false}},getBrowser:function(){if(this.browserName==null){var o=navigator.userAgent.toLowerCase();g("[getBrowser()] navigator.userAgent.toLowerCase() -> "+o);if((o.indexOf("msie")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("trident")!=-1||o.indexOf("Trident")!=-1){this.browserName="MSIE";this.browserName2="MSIE"}else{if(o.indexOf("iphone")!=-1){this.browserName="Netscape Family";this.browserName2="iPhone"}else{if((o.indexOf("firefox")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Firefox"}else{if(o.indexOf("chrome")!=-1){this.browserName="Netscape Family";this.browserName2="Chrome"}else{if(o.indexOf("safari")!=-1){this.browserName="Netscape Family";this.browserName2="Safari"}else{if((o.indexOf("mozilla")!=-1)&&(o.indexOf("opera")==-1)){this.browserName="Netscape Family";this.browserName2="Other"}else{if(o.indexOf("opera")!=-1){this.browserName="Netscape Family";this.browserName2="Opera"}else{this.browserName="?";this.browserName2="unknown"}}}}}}}}g("[getBrowser()] Detected browser name:"+this.browserName+", "+this.browserName2)}return this.browserName},testUsingActiveX:function(o){var q="JavaWebStart.isInstalled."+o+".0";if(typeof ActiveXObject=="undefined"||!ActiveXObject){g("[testUsingActiveX()] Browser claims to be IE, but no ActiveXObject object?");return false}try{return(new ActiveXObject(q)!=null)}catch(p){return false}},testForMSVM:function(){var p="{08B0E5C0-4FCB-11CF-AAA5-00401C608500}";if(typeof oClientCaps!="undefined"){var o=oClientCaps.getComponentVersion(p,"ComponentID");if((o=="")||(o=="5,0,5000,0")){return false}else{return true}}else{return false}},testUsingMimeTypes:function(p){if(!navigator.mimeTypes){g("[testUsingMimeTypes()] Browser claims to be Netscape family, but no mimeTypes[] array?");return false}for(var q=0;q<navigator.mimeTypes.length;++q){s=navigator.mimeTypes[q].type;var o=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(o!=null){if(this.compareVersions(o[1],p)){return true}}}return false},testUsingPluginsArray:function(p){if((!navigator.plugins)||(!navigator.plugins.length)){return false}var o=navigator.platform.toLowerCase();for(var q=0;q<navigator.plugins.length;++q){s=navigator.plugins[q].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(this.compareVersions("1.5.0",p)){return true}}else{if(s.search(/^Java/)!=-1){if(o.indexOf("win")!=-1){if(this.compareVersions("1.5.0",p)||this.compareVersions("1.6.0",p)){return true}}}}}if(this.compareVersions("1.5.0",p)){return true}return false},IEInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):""));return false},done:function(p,o){},FFInstall:function(){location.href=n(((this.returnPage!=null)?("&returnPage="+this.returnPage):"")+((this.locale!=null)?("&locale="+this.locale):"")+((this.brand!=null)?("&brand="+this.brand):"")+((this.installType!=null)?("&type="+this.installType):""));return false},compareVersions:function(r,t){var p=r.split(".");var o=t.split(".");for(var q=0;q<p.length;++q){p[q]=Number(p[q])}for(var q=0;q<o.length;++q){o[q]=Number(o[q])}if(p.length==2){p[2]=0}if(p[0]>o[0]){return true}if(p[0]<o[0]){return false}if(p[1]>o[1]){return true}if(p[1]<o[1]){return false}if(p[2]>o[2]){return true}if(p[2]<o[2]){return false}return true},enableAlerts:function(){this.browserName=null;this.debug=true},poll:function(){this.refresh();var o=this.getJREs();if((this.preInstallJREList.length==0)&&(o.length!=0)){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}if((this.preInstallJREList.length!=0)&&(o.length!=0)&&(this.preInstallJREList[0]!=o[0])){clearInterval(this.myInterval);if(this.returnPage!=null){location.href=this.returnPage}}},writePluginTag:function(){var o=this.getBrowser();if(o=="MSIE"){document.write("<"+'object classid="clsid:CAFEEFAC-DEC7-0000-0001-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+"<"+"/"+"object"+">")}else{if(o=="Netscape Family"&&this.allowPlugin()){this.writeEmbedTag()}}},refresh:function(){navigator.plugins.refresh(false);var o=this.getBrowser();if(o=="Netscape Family"&&this.allowPlugin()){var p=document.getElementById("deployJavaPlugin");if(p==null){this.writeEmbedTag()}}},writeEmbedTag:function(){var o=false;if(navigator.mimeTypes!=null){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.mimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.mimeType+'" hidden="true" />');o=true}}}if(!o){for(var p=0;p<navigator.mimeTypes.length;p++){if(navigator.mimeTypes[p].type==this.oldMimeType){if(navigator.mimeTypes[p].enabledPlugin){document.write("<"+'embed id="deployJavaPlugin" type="'+this.oldMimeType+'" hidden="true" />')}}}}}}};d.writePluginTag();if(d.locale==null){var h=null;if(h==null){try{h=navigator.userLanguage}catch(f){}}if(h==null){try{h=navigator.systemLanguage}catch(f){}}if(h==null){try{h=navigator.language}catch(f){}}if(h!=null){h.replace("-","_");d.locale=h}}return d}();
\ No newline at end of file
diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index f827db5..293b73a 100644
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -1,5 +1,5 @@
 /**
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index ea8619f..e7e7232 100644
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 1ad5423..553d8a4 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> 
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_applets.html b/examples/u_applets.html
index f34a702..378a895 100644
--- a/examples/u_applets.html
+++ b/examples/u_applets.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_embedded.html b/examples/u_embedded.html
index 39d9e58..6ec04e5 100644
--- a/examples/u_embedded.html
+++ b/examples/u_embedded.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_embeddedWJmol.html b/examples/u_embeddedWJmol.html
index 4aa7035..02a4f10 100644
--- a/examples/u_embeddedWJmol.html
+++ b/examples/u_embeddedWJmol.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_formComplete.html b/examples/u_formComplete.html
index a8daafd..15c473e 100644
--- a/examples/u_formComplete.html
+++ b/examples/u_formComplete.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_javascriptLaunch.html b/examples/u_javascriptLaunch.html
index 0e786c5..b34e195 100644
--- a/examples/u_javascriptLaunch.html
+++ b/examples/u_javascriptLaunch.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/examples/u_linkedapplets_ng.html b/examples/u_linkedapplets_ng.html
index 4e4b447..e605c1a 100644
--- a/examples/u_linkedapplets_ng.html
+++ b/examples/u_linkedapplets_ng.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/help.hs b/help/help.hs
index b791d35..c56ee9f 100755
--- a/help/help.hs
+++ b/help/help.hs
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1" ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/help.jhm b/help/help.jhm
index 3587079..08d3ca9 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1" ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c0e9b66..4ff36ba 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index 12d832f..aa619e6 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index b9d4b6f..e67c1fa 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html
index edd0ae4..52afe7c 100755
--- a/help/html/calculations/pairwise.html
+++ b/help/html/calculations/pairwise.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index db7be9b..0d6e85e 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html
index 6f5f000..dc27e97 100755
--- a/help/html/calculations/quality.html
+++ b/help/html/calculations/quality.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html
index bb640b7..7a40a44 100644
--- a/help/html/calculations/recoverInputdata.html
+++ b/help/html/calculations/recoverInputdata.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html
index 89d92f1..2dcc475 100755
--- a/help/html/calculations/redundancy.html
+++ b/help/html/calculations/redundancy.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 100e21c..fb3b0b2 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index bbbca5c..bf60b88 100755
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 4093777..af316ed 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 9591f39..ba3582b 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index dad8483..2f03d65 100755
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index 6ecaf98..30b9846 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 2d9fb10..ba9cbdd 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/blosum.html b/help/html/colourSchemes/blosum.html
index 35a8019..fdc3f19 100755
--- a/help/html/colourSchemes/blosum.html
+++ b/help/html/colourSchemes/blosum.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/buried.html b/help/html/colourSchemes/buried.html
index facc4ba..640b753 100755
--- a/help/html/colourSchemes/buried.html
+++ b/help/html/colourSchemes/buried.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
index 45125e5..1737280 100755
--- a/help/html/colourSchemes/clustal.html
+++ b/help/html/colourSchemes/clustal.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html
index 1ed1207..1b3d93a 100755
--- a/help/html/colourSchemes/conservation.html
+++ b/help/html/colourSchemes/conservation.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/helix.html b/help/html/colourSchemes/helix.html
index f447abf..1f1e1b8 100755
--- a/help/html/colourSchemes/helix.html
+++ b/help/html/colourSchemes/helix.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/hydrophobic.html b/help/html/colourSchemes/hydrophobic.html
index ade1ecf..dd5a334 100755
--- a/help/html/colourSchemes/hydrophobic.html
+++ b/help/html/colourSchemes/hydrophobic.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html
index a88c44f..b344330 100755
--- a/help/html/colourSchemes/index.html
+++ b/help/html/colourSchemes/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html
index c7c3f34..90e40ef 100755
--- a/help/html/colourSchemes/nucleotide.html
+++ b/help/html/colourSchemes/nucleotide.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/pid.html b/help/html/colourSchemes/pid.html
index d85dd4c..0839749 100755
--- a/help/html/colourSchemes/pid.html
+++ b/help/html/colourSchemes/pid.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/purinepyrimidine.html b/help/html/colourSchemes/purinepyrimidine.html
index 0e17e3f..2438416 100644
--- a/help/html/colourSchemes/purinepyrimidine.html
+++ b/help/html/colourSchemes/purinepyrimidine.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/rnahelicesColouring.html b/help/html/colourSchemes/rnahelicesColouring.html
index e683d8a..daca474 100644
--- a/help/html/colourSchemes/rnahelicesColouring.html
+++ b/help/html/colourSchemes/rnahelicesColouring.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/strand.html b/help/html/colourSchemes/strand.html
index d9bcb66..58f242e 100755
--- a/help/html/colourSchemes/strand.html
+++ b/help/html/colourSchemes/strand.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/taylor.html b/help/html/colourSchemes/taylor.html
index 1661b6e..6ff5c7f 100755
--- a/help/html/colourSchemes/taylor.html
+++ b/help/html/colourSchemes/taylor.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/textcolour.html b/help/html/colourSchemes/textcolour.html
index 1ddc66a..597f618 100644
--- a/help/html/colourSchemes/textcolour.html
+++ b/help/html/colourSchemes/textcolour.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/turn.html b/help/html/colourSchemes/turn.html
index e77e2b7..2860bc8 100755
--- a/help/html/colourSchemes/turn.html
+++ b/help/html/colourSchemes/turn.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html
index cf841a9..015fbe5 100755
--- a/help/html/colourSchemes/user.html
+++ b/help/html/colourSchemes/user.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/colourSchemes/zappo.html b/help/html/colourSchemes/zappo.html
index cfa75f3..362d98c 100755
--- a/help/html/colourSchemes/zappo.html
+++ b/help/html/colourSchemes/zappo.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index 0139be8..eddea18 100755
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index e2d471e..0da3a88 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 1820c6a..a0a6dae 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index fe5c801..ac44c46 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/codingfeatures.html b/help/html/features/codingfeatures.html
index 7343620..7b15ef6 100644
--- a/help/html/features/codingfeatures.html
+++ b/help/html/features/codingfeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
index 7a4be57..da47ca5 100644
--- a/help/html/features/commandline.html
+++ b/help/html/features/commandline.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/creatinFeatures.html b/help/html/features/creatinFeatures.html
index bdee259..ad9cdc2 100644
--- a/help/html/features/creatinFeatures.html
+++ b/help/html/features/creatinFeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/cursorMode.html b/help/html/features/cursorMode.html
index ccb84ee..34fe0e1 100755
--- a/help/html/features/cursorMode.html
+++ b/help/html/features/cursorMode.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html
index d97d7a2..7e2e7e2 100644
--- a/help/html/features/dasfeatures.html
+++ b/help/html/features/dasfeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html
index 0170a8f..45d150e 100644
--- a/help/html/features/dassettings.html
+++ b/help/html/features/dassettings.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/editingFeatures.html b/help/html/features/editingFeatures.html
index 0d0dd72..2856e70 100644
--- a/help/html/features/editingFeatures.html
+++ b/help/html/features/editingFeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index 0f63b33..d1337eb 100755
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/featureschemes.html b/help/html/features/featureschemes.html
index 8b88fc3..64a4c53 100644
--- a/help/html/features/featureschemes.html
+++ b/help/html/features/featureschemes.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index ed18ae7..9526ed5 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -37,15 +37,30 @@ they are currently being displayed (only the ticked features and groups
 are displayed). <strong><em>You can change the colour or
 shading style used for a feature in the associated alignment by clicking
 on its colour box.</em></strong></p>
-  <p>
-    <strong><em>Selecting alignment columns by feature</em></strong><br>
-    <strong>Double-click</strong> a feature to add all the columns where
-    that feature is found to the current column selection. <strong>Shift+Double-click</strong>
-    will add all the columns where that feature is <strong>not</strong>
-    found. You can also find these options in the feature's pop-up menu
-    (see below). <br />
-    <em>Select columns by feature was added in Jalview 2.8.1</em>
-  </p>
+	<p>
+		<a name="selectbyfeature"><strong><em>Selecting
+					alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+			a feature type</strong> allows you to select columns in the alignment that
+		contain (or do not contain) features of that type. If a region of the
+		alignment is currently selected, then only features in the current
+		selection will be searched. The following keys affect the way in which
+		selections are made:
+	
+	<ul>
+		<li>Hold down <strong>Alt</strong> to select columns not
+			containing features of a particular type.
+		</li>
+		<li>Hold down <strong>Shift</strong> to add columns to the
+			current selection.
+		</li>
+		<li>Press <strong>Command/Windows key</strong> to toggle column
+			selection state (XOR)
+		</li>
+	</ul>
+	Options are also provided in the feature's pop-up menu (see below).
+	<br />
+	<em>Select columns by feature was added in Jalview 2.8.1</em>
+	</p>
   <p><strong><em>Feature settings pop-up menu</em></strong><br>
 <strong>Right-click</strong> on a feature to open a pop-up menu that
 allows you to sort the alignment or current selection using that feature
diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index 56ec86c..d4b9f7f 100644
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 7d2d88f..540a961 100644
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/jalarchive.html b/help/html/features/jalarchive.html
index cef3a69..f820523 100755
--- a/help/html/features/jalarchive.html
+++ b/help/html/features/jalarchive.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index b3c3570..21241d3 100644
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -24,14 +24,33 @@
 <p><strong>The Jmol PDB Viewer</strong></p>
 <p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
 has been integrated into Jalview for interactively viewing structures
-opened by selecting the <strong>&quot;Structure&#8594;View PDB
-entry:&quot;</strong> option in the <a href="../menus/popupMenu.html">sequence
+opened by entries in the <strong>&quot;Structure&quot;</strong> submenu in the <a href="../menus/popupMenu.html">sequence
 id pop-up menu</a> (if you can't see this, then you need to <a
 	href="viewingpdbs.html">associate a PDB structure</a> with the
 sequence). Jmol is available from the Jalview desktop and should also
 run in the JalviewLite applet, providing the browser supports Java 1.5.
 If Jmol is not available, then the original <a href="pdbviewer.html">internal
 pdb viewer</a> will be used as a fallback.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+  <ul>
+    <li>The <strong>&quot;Structure&#8594;View
+        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
+      for display from the available structures for a sequence.
+    </li>
+    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        structures
+    </strong> option will open a new window containing all structures associated
+      with the current selection.
+    </li>
+    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures
+    </strong> option will open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    <em>The View representative structures option was introduced in
+        Jalview 2.8.1</em></li>
+  </ul>
+  <br> 
+</p>
 <p><a name="align"><strong>Superposing structures based
 on their aligned sequences</strong></a><br>
 If several structures are available on the alignment, you may add
diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html
index 6d20d30..f726507 100644
--- a/help/html/features/multipleViews.html
+++ b/help/html/features/multipleViews.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/newkeystrokes.html b/help/html/features/newkeystrokes.html
index 8830bb1..f17c278 100644
--- a/help/html/features/newkeystrokes.html
+++ b/help/html/features/newkeystrokes.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/overview.html b/help/html/features/overview.html
index dcd625a..7d05848 100755
--- a/help/html/features/overview.html
+++ b/help/html/features/overview.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index 10924a5..bfed174 100755
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -29,9 +29,11 @@ PDB viewer, which is only used in situations where Jmol is unavailable
 or cannot operate.</p>
 <p><strong>The PDB Viewer Window</strong>
 <p>This interactive structure viewing window is opened by selecting
-the <strong>&quot;Sequence&#8594;View PDB entry:&quot;</strong> entry in
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This
-can only be done for sequences which have an <a href="viewingpdbs.html">associated
+entries from the <strong>&quot;Structure&#8594;&quot;</strong> submenu
+		of the <a href="../menus/popupMenu.html">sequence
+			id pop-up menu</a>. The internal PDB viewer is not able to show
+		superpositions, so no other options are provided. Structures can only
+		be viewed for sequences which have an <a href="viewingpdbs.html">associated
 PDB structure</a>, and the PDB Viewer will only be associated with the
 particular alignment view from which it was opened.</p>
 <p><strong>Controls</strong></p>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index e68e44e..259b0f4 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/search.html b/help/html/features/search.html
index 509316b..6845be9 100755
--- a/help/html/features/search.html
+++ b/help/html/features/search.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index fe8de4e..0b14348 100755
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index 424841e..212605e 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html
index b34e1b8..157a591 100644
--- a/help/html/features/seqmappings.html
+++ b/help/html/features/seqmappings.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/varna.html b/help/html/features/varna.html
index 69c3e36..5b7fed1 100644
--- a/help/html/features/varna.html
+++ b/help/html/features/varna.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 6c10e98..048f0ef 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -24,8 +24,31 @@
 <p><strong>Viewing PDB Structures</strong></p>
 
 <p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure&rarr;View PDB entry:"</strong> entries from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+via the <strong>"Structure&rarr;"</strong> submenu from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+  <ul>
+    <li>The <strong>&quot;Structure&#8594;View
+        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
+      for display from the available structures for a sequence.
+    </li>
+    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        structures
+    </strong> option will open a new window containing all structures associated
+      with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
+      capability was added in Jalview 2.7</em>
+    </li>
+    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures
+    </strong> option will open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    <em>The View representative structures option was introduced in
+        Jalview 2.8.1</em></li>
+  </ul>
+  <br> 
+</p>
+
+<p>If a single pdb
 structure is selected, one of the following will happen:</p>
 
 <ul>
@@ -44,17 +67,6 @@ structure is selected, one of the following will happen:</p>
 	<li style="list-style: none">See the <a href="jmol.html">Jmol
 	PDB viewer</a> help page for more information about the display.</li>
 </ul>
-	<p>
-		<em>Opening structures associated with the current selection</em><br />
-		If one or more of the sequences in the alignment are selected, then
-		the Structure submenu of the <a href="../menus/popupMenu.html">Sequence
-			ID popup menu</a> will contain will include either a 'View all <em>X</em>
-		structures' entry in the submenu or a 'View structure for <em>Sequence</em>'
-		entry. Both these options will open a new Jmol view containing one, or
-		all the structures available for all selected sequences, superimposed
-		using the currently selected region of the alignment. (<em>This
-			capability was added in Jalview 2.7</em>)
-	</p>
 	<p><strong>Associating PDB files with Sequences</strong></p>
 	<p>To associate PDB files with a sequence, right click on a sequence
 ID and select "Structure<strong>&rarr;</strong> Associate Structure with
diff --git a/help/html/features/wrap.html b/help/html/features/wrap.html
index a7bec32..4835317 100755
--- a/help/html/features/wrap.html
+++ b/help/html/features/wrap.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/index.html b/help/html/index.html
index 7fc5ba2..ae12479 100755
--- a/help/html/index.html
+++ b/help/html/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/export.html b/help/html/io/export.html
index 9dae0bd..a452615 100755
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/exportseqreport.html b/help/html/io/exportseqreport.html
index c497571..837164b 100644
--- a/help/html/io/exportseqreport.html
+++ b/help/html/io/exportseqreport.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index 517da1a..6138203 100755
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/index.html b/help/html/io/index.html
index 5794a7a..d803fb0 100755
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/modellerpir.html b/help/html/io/modellerpir.html
index 42a480c..56d0cfc 100755
--- a/help/html/io/modellerpir.html
+++ b/help/html/io/modellerpir.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/tcoffeescores.html b/help/html/io/tcoffeescores.html
index aa72b10..9a507c8 100644
--- a/help/html/io/tcoffeescores.html
+++ b/help/html/io/tcoffeescores.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html
index bddd331..191f6b1 100755
--- a/help/html/jalviewjnlp.html
+++ b/help/html/jalviewjnlp.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/keys.html b/help/html/keys.html
index 1c0ffc8..9bc7095 100755
--- a/help/html/keys.html
+++ b/help/html/keys.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/memory.html b/help/html/memory.html
index b07c885..eec75d3 100755
--- a/help/html/memory.html
+++ b/help/html/memory.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index f4ad784..d4ffc50 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 4e1d844..3a1afc3 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index f459c04..93652af 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index 92e78a0..3e93057 100755
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html
index 5362838..e5ae321 100755
--- a/help/html/menus/alwedit.html
+++ b/help/html/menus/alwedit.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index 9e6e40a..bc6c9b1 100755
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
index 17cf8a0..0bdbe91 100644
--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index 133f89f..9738e47 100644
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 7be8170..4248f9a 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index b2a2f47..59b521a 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/index.html b/help/html/menus/index.html
index 0fa72ce..ce4825d 100755
--- a/help/html/menus/index.html
+++ b/help/html/menus/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6ceccee..2be6000 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -148,11 +148,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
           <li><strong>From File<br>
             </strong><em>Load a PDB file from local disk which will be associated 
             with this sequence. This file will be used if the user subsequently 
-            clicks on &quot;View PDB Structure&quot; menu item.</em></li>
+            clicks on &quot;View Structure&quot; menu item.</em></li>
           <li><strong>Enter PDB id<br>
             </strong><em>Enter the PDB id from an input window. This PDB id will 
             be used by the service WSDBFetch, provided by the EBI, to fetch the 
-            PDB file if the user subsequently clicks on &quot;View PDB Structure&quot; 
+            PDB file if the user subsequently clicks on its &quot;View Structure&quot; 
             menu item. </em></li>
           <li><strong>Discover PDB ids<br>
             </strong><em>This will use the service WSDBFetch, provided by the 
@@ -169,6 +169,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 			href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
 			If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
       </li>
+      <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
+  <ul>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        structures<br/>
+    </strong><em>Opens a new window containing all structures associated
+      with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
+      capability was added in Jalview 2.7)</em>
+    </li>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures<br/>
+    </strong><em>Open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    (The View representative structures option was introduced in
+        Jalview 2.8.1)</em></li>
+  </ul>
+  <br> <li>
+      
+      </li>
     </ul>
   </li>
   <li><strong>Hide Sequences</strong><br>
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 1997101..f3a4102 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/misc/aaproperties.html b/help/html/misc/aaproperties.html
index f2b57ad..e6a2199 100755
--- a/help/html/misc/aaproperties.html
+++ b/help/html/misc/aaproperties.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -26,7 +26,7 @@
   <table width="295" border="1" cellspacing="0" cellpadding="0">
     <tr>
       <td width="291"><pre><font size="4" face="Courier New, Courier, mono"><strong>ILVCAGMFYWHKREQDNSTPBZX-</strong>
-XXXXXXXXXXX&middot;·&middot;&middot;&middot;&middot;&middot;X&middot;&middot;&middot;XX Hydrophobic
+XXXXXXXXXXX&middot;&middot;&middot;&middot;&middot;&middot;&middot;X&middot;&middot;&middot;XX Hydrophobic
 &middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;XXXXXXXXXX&middot;XXXXX Polar
 &middot;&middot;XXXX&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;XXXXX&middot;&middot;XX Small
 &middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;&middot;X&middot;&middot;XX Proline
diff --git a/help/html/misc/aminoAcids.html b/help/html/misc/aminoAcids.html
index bbf3b3a..14650eb 100755
--- a/help/html/misc/aminoAcids.html
+++ b/help/html/misc/aminoAcids.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/misc/geneticCode.html b/help/html/misc/geneticCode.html
index f047abf..1ca1026 100755
--- a/help/html/misc/geneticCode.html
+++ b/help/html/misc/geneticCode.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/na/index.html b/help/html/na/index.html
index 6bac556..366e357 100644
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/privacy.html b/help/html/privacy.html
index 0d2f828..f86b6a6 100644
--- a/help/html/privacy.html
+++ b/help/html/privacy.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/releases.html b/help/html/releases.html
index d436b34..b6fb83c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -34,6 +34,52 @@
 		<div align="center"><em><strong>Issues Resolved</strong></em></div>
 		</td>
 	</tr>
+  <tr>
+  <td><div align="center">
+  <strong><a name="Jalview.2.8.1">2.8.1</a><br/><em>20/5/2014</em></strong>
+  </div>
+  </td>
+      <td> <!--  New features -->
+      <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+      <ul>
+      <li>i18n Internationalisation of user interface and translation for Spanish locale</li>
+      </ul>
+      <em>Application</em><ul>
+        <li>Define/Undefine group on current selection with Ctrl-G</li>
+ <li>Select columns containing particular features from Feature Settings dialog</li>
+<li>View all 'representative' PDB structures for selected sequences</li>
+<li>Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service</li>
+<li></li>
+      <li>Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows) </li>
+        </ul>
+      <em>Applet</em><ul>
+      
+        </ul> <em>Other improvements</em>
+        <ul>
+        </ul>
+      </td>
+      <td><!--  issues resolved -->
+        <em>Application</em><ul>
+					<li>Newly created RNA secondary structure line doesn't have
+						'display all symbols' flag set</li>
+				  <li>T-COFFEE alignment score shading scheme not saved in
+						jalview project</li>
+					<li>Local file cannot be loaded in freshly downloaded Jalview</li>
+					<li>??? unresolved ??? Jalview icon not shown on dock in
+						Mountain Lion/Webstart</li>
+					<li>Load file from desktop file browser fails</li>
+					<li>Occasional NPE thrown when calculating large trees</li>
+				</ul>
+        <em>Applet</em>
+			<ul>
+					<li>Apply to all groups ticked but colourscheme changes don't
+						affect groups</li>
+				</ul> 
+				<em>Other</em><ul>
+        <li></li>
+        </ul>
+      </td>
+    </tr>
 	<tr>
 	<td><div align="center">
 	<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
@@ -137,7 +183,7 @@
      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
     </div></td>
    <td><em>Application</em>
-    <li>Support for JABAWS 2.0 Services (AACon alignment
+    <ul><li>Support for JABAWS 2.0 Services (AACon alignment
      conservation, protein disorder and Clustal Omega)</li>
     <li>JABAWS server status indicator in Web Services preferences
    </li>
diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html
index a177601..f2794b6 100644
--- a/help/html/vamsas/index.html
+++ b/help/html/vamsas/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html
index 61f2f9f..8652e0f 100644
--- a/help/html/webServices/AACon.html
+++ b/help/html/webServices/AACon.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index ac93813..467f8d7 100644
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html
index 2dff2bc..90bd87d 100644
--- a/help/html/webServices/dbreffetcher.html
+++ b/help/html/webServices/dbreffetcher.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index c3d83fa..efbe3b1 100755
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 9b715c2..70c57ea 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index b04e047..775eec8 100644
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/newsreader.html b/help/html/webServices/newsreader.html
index 498520a..953e121 100644
--- a/help/html/webServices/newsreader.html
+++ b/help/html/webServices/newsreader.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html
index 77bdc01..a91de0e 100644
--- a/help/html/webServices/proteinDisorder.html
+++ b/help/html/webServices/proteinDisorder.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html
index d3f0bf3..ad12579 100755
--- a/help/html/webServices/shmr.html
+++ b/help/html/webServices/shmr.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 75346d6..ef77c7e 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/webServicesParams.html b/help/html/webServices/webServicesParams.html
index ba1df32..690fb0f 100644
--- a/help/html/webServices/webServicesParams.html
+++ b/help/html/webServices/webServicesParams.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html
index 4dff124..8ef6e5d 100644
--- a/help/html/webServices/webServicesPrefs.html
+++ b/help/html/webServices/webServicesPrefs.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 55e94ef..a016a35 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -26,9 +26,24 @@
 		highlights below, and the comprehensive list is given in the <a
 			href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
 	</p>
-  <strong>Enhancements and new features</strong>
+	<strong>Internationalisation</strong>
+	<p>
+		In August 2013, David RÃ³ldan-Martinez took on the task of
+		internationalising Jalview's user interface. He also recruited Sara
+		HernÃ¡ndez DÃ­az and Laura Ferrandis Martinez who created Jalview's
+		first spanish user interface translation.<br /> If you notice any
+		problems, or would like to help translate Jalview's user interface
+		into other languages, head over to <a href="http://issues.jalview.org">issues.jalview.org</a>
+		and put in a feature request describing the translations you can
+		provide to the <a
+			href="http://issues.jalview.org/browse/JAL/component/10682">i18n
+			component</a>.<br/>
+			David has also put together some documentation about getting started with i18n translations
+	</p>
+	<strong>Enhancements and new features</strong>
 	<ul>
-  <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
+	<li>
+  <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
 	</ul>
 	<strong>Bug fixes</strong>
 	<ul>
diff --git a/jalview-jalopy.xml b/jalview-jalopy.xml
index 054ce99..e9c493c 100755
--- a/jalview-jalopy.xml
+++ b/jalview-jalopy.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/nbbuild.xml b/nbbuild.xml
index d4b2979..95674ff 100644
--- a/nbbuild.xml
+++ b/nbbuild.xml
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/nbproject/project.xml b/nbproject/project.xml
index 9511664..ac09730 100644
--- a/nbproject/project.xml
+++ b/nbproject/project.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml
index 92e483c..1b38efb 100644
--- a/resources/embl_mapping.xml
+++ b/resources/embl_mapping.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 906db68..6736791 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -463,8 +463,8 @@ label.jalview_cut = Cut (Jalview Only)
 label.to_upper_case = To Upper Case
 label.to_lower_case = To Lower Case
 label.toggle_case = Toggle Case
-label.edit_name_description = Edit Name/Description
-label.create_sequence_feature = Create Sequence Feature
+label.edit_name_description = Edit Name/Description ...
+label.create_sequence_feature = Create Sequence Feature ...
 label.edit_sequence = Edit Sequence
 label.edit_sequences = Edit Sequences
 label.sequence_details = Sequence Details
@@ -629,7 +629,7 @@ label.edit_name_and_description_current_group = Edit name and description of cur
 label.view_structure_for = View structure for {0}
 label.view_all_structures = View all {0} structures.
 label.view_all_representative_structures = View all {0} representative structures.
-label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = "Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment."
+label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment.
 label.associate_structure_with_sequence = Associate Structure with Sequence
 label.from_file = from file
 label.enter_pdb_id = Enter PDB Id
diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index db6fa20..3392d54 100755
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/JalviewWsParamSet.xsd b/schemas/JalviewWsParamSet.xsd
index 23457d4..32696df 100644
--- a/schemas/JalviewWsParamSet.xsd
+++ b/schemas/JalviewWsParamSet.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/castor-mapping.xsd b/schemas/castor-mapping.xsd
index 09fc99c..2f30f89 100644
--- a/schemas/castor-mapping.xsd
+++ b/schemas/castor-mapping.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/jalview.nodesc.properties b/schemas/jalview.nodesc.properties
index baa0ddc..8f0dd45 100644
--- a/schemas/jalview.nodesc.properties
+++ b/schemas/jalview.nodesc.properties
@@ -1,5 +1,5 @@
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/schemas/jalview.properties b/schemas/jalview.properties
index c174b5e..2016960 100644
--- a/schemas/jalview.properties
+++ b/schemas/jalview.properties
@@ -1,5 +1,5 @@
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index ab893bd..3fdf20c 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/jalviewJvV1.xsd b/schemas/jalviewJvV1.xsd
index 8685d9f..f222379 100644
--- a/schemas/jalviewJvV1.xsd
+++ b/schemas/jalviewJvV1.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index dfee914..9f6ebea 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/schemas/vamsasJvV1.xsd b/schemas/vamsasJvV1.xsd
index 4b12299..bd6b196 100644
--- a/schemas/vamsasJvV1.xsd
+++ b/schemas/vamsasJvV1.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 212f0f3..e5d8487 100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index d550326c..8a1c430 100644
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 8b844d7..6140ed0 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 6517c7a..fdfb3d0 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 0bef874..d409312 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 11caf98..8c16aad 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 8338c63..823e02c 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index fc52c08..dc53855 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index caa2501..aab4081 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index 3a8c979..2efbefe 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 0e7a271..72e28b9 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/castor.properties b/src/castor.properties
index 673fe47..f1176f8 100644
--- a/src/castor.properties
+++ b/src/castor.properties
@@ -1,5 +1,5 @@
 ###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/src/ext/vamsas/IRegistry.java b/src/ext/vamsas/IRegistry.java
index 7290a1a..23ed3f4 100755
--- a/src/ext/vamsas/IRegistry.java
+++ b/src/ext/vamsas/IRegistry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/IRegistryService.java b/src/ext/vamsas/IRegistryService.java
index 13210ad..b0ffe9e 100755
--- a/src/ext/vamsas/IRegistryService.java
+++ b/src/ext/vamsas/IRegistryService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java
index 3ced73d..d411513 100755
--- a/src/ext/vamsas/IRegistryServiceLocator.java
+++ b/src/ext/vamsas/IRegistryServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/Jpred.java b/src/ext/vamsas/Jpred.java
index 561789e..59dadcc 100755
--- a/src/ext/vamsas/Jpred.java
+++ b/src/ext/vamsas/Jpred.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/JpredService.java b/src/ext/vamsas/JpredService.java
index b0f14c3..cc7a008 100755
--- a/src/ext/vamsas/JpredService.java
+++ b/src/ext/vamsas/JpredService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java
index 8b7161b..7a23737 100755
--- a/src/ext/vamsas/JpredServiceLocator.java
+++ b/src/ext/vamsas/JpredServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index 7d407ad..b35eabe 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java
index eb55004..ef9f1f7 100755
--- a/src/ext/vamsas/MuscleWS.java
+++ b/src/ext/vamsas/MuscleWS.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/MuscleWSService.java b/src/ext/vamsas/MuscleWSService.java
index 18701bd..31bfd22 100755
--- a/src/ext/vamsas/MuscleWSService.java
+++ b/src/ext/vamsas/MuscleWSService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java
index 9cec16e..a79dd27 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java
index 8b55ad1..7054d6f 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
index e6020e8..b3fdb09 100755
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/SeqSearchI.java b/src/ext/vamsas/SeqSearchI.java
index fd7f477..63b3fec 100644
--- a/src/ext/vamsas/SeqSearchI.java
+++ b/src/ext/vamsas/SeqSearchI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java
index e9e2560..a5708fe 100644
--- a/src/ext/vamsas/SeqSearchServiceLocator.java
+++ b/src/ext/vamsas/SeqSearchServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/SeqSearchServiceService.java b/src/ext/vamsas/SeqSearchServiceService.java
index 37bd8e0..e8d145d 100644
--- a/src/ext/vamsas/SeqSearchServiceService.java
+++ b/src/ext/vamsas/SeqSearchServiceService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
index 9e51321..fba1287 100644
--- a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
+++ b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java
index 4fa31ca..bb27197 100755
--- a/src/ext/vamsas/ServiceHandle.java
+++ b/src/ext/vamsas/ServiceHandle.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java
index 0edb9f9..250f8bc 100755
--- a/src/ext/vamsas/ServiceHandles.java
+++ b/src/ext/vamsas/ServiceHandles.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 75a777f..d028ade 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 573c545..5b37934 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b5a0be8..cdb7dbe 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 8641629..f0dc860 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 17658b3..8d52caf 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index e74d4b5..3b41a8e 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 06d75ac..0494896 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index bca85df..29b9323 100644
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 41d599e..4a5f762 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 979968f..733e7f9 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index ccae429..b55542f 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index be7105a..835ead3 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index e46848b..4fc54b8 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index cc2b458..a502523 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 6409413..f56a70b 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/analysis/WUSSParseException.java b/src/jalview/analysis/WUSSParseException.java
index cbe0f0e..b7bf231 100644
--- a/src/jalview/analysis/WUSSParseException.java
+++ b/src/jalview/analysis/WUSSParseException.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/AlignCalcManagerI.java b/src/jalview/api/AlignCalcManagerI.java
index c2e7b14..2641c96 100644
--- a/src/jalview/api/AlignCalcManagerI.java
+++ b/src/jalview/api/AlignCalcManagerI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/AlignCalcWorkerI.java b/src/jalview/api/AlignCalcWorkerI.java
index 2227b10..c8dc96d 100644
--- a/src/jalview/api/AlignCalcWorkerI.java
+++ b/src/jalview/api/AlignCalcWorkerI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 1d1e5fb..cac3776 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -21,6 +21,14 @@ public interface AlignViewControllerI<ViewportI>
 
   public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
 
-  boolean markColumnsContainingFeatures(boolean invert, String featureType);
+  /**
+   * Mark columns in the current column selection according to positions of sequence features
+   * @param invert - when set, mark all but columns containing given type
+   * @param extendCurrent - when set, do not clear existing column selection
+   * @param toggle - rather than explicitly set, toggle selection state
+   * @param featureType - feature type string
+   * @return true if operation affected state
+   */
+  boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean clearColumns, String featureType);
 
 }
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 44fef0e..7463187 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/AlignmentViewPanel.java b/src/jalview/api/AlignmentViewPanel.java
index 1705995..e3d8d66 100644
--- a/src/jalview/api/AlignmentViewPanel.java
+++ b/src/jalview/api/AlignmentViewPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index ea7f55a..d46d684 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/OOMHandlerI.java b/src/jalview/api/OOMHandlerI.java
index 6effadf..0c4dda8 100644
--- a/src/jalview/api/OOMHandlerI.java
+++ b/src/jalview/api/OOMHandlerI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/RotatableCanvasI.java b/src/jalview/api/RotatableCanvasI.java
index 32a1b8a..f00ffa4 100644
--- a/src/jalview/api/RotatableCanvasI.java
+++ b/src/jalview/api/RotatableCanvasI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/SequenceRenderer.java b/src/jalview/api/SequenceRenderer.java
index 4118844..7f47848 100644
--- a/src/jalview/api/SequenceRenderer.java
+++ b/src/jalview/api/SequenceRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/SequenceStructureBinding.java b/src/jalview/api/SequenceStructureBinding.java
index 829da37..99be87a 100644
--- a/src/jalview/api/SequenceStructureBinding.java
+++ b/src/jalview/api/SequenceStructureBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/api/StructureSelectionManagerProvider.java b/src/jalview/api/StructureSelectionManagerProvider.java
index d08ae7c..c287142 100644
--- a/src/jalview/api/StructureSelectionManagerProvider.java
+++ b/src/jalview/api/StructureSelectionManagerProvider.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 13dcd05..a955176 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 40999c6..f902f24 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -3362,7 +3362,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       fileMenu.remove(closeMenuItem);
       fileMenu.remove(3); // Remove Seperator
       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
-              Font.PLAIN, 10, false); // use our own fonts.
+              Font.PLAIN, 11, false); // use our own fonts.
       // and actually add the components to the applet area
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2ced8da..42aae94 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 5a49281..3214e70 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -433,6 +433,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationPanelHolder.setVisible(b);
+    } else {
+      annotationSpaceFillerHolder.setVisible(false);
+      annotationPanelHolder.setVisible(false);
     }
     validate();
     repaint();
@@ -512,7 +515,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     alabels.setSize(new Dimension(e.width, height));
     annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
     annotationPanelHolder.setSize(new Dimension(d.width, height));
-    seqPanelHolder.setSize(d.width, seqandannot - height);
+    // seqPanelHolder.setSize(d.width, seqandannot - height);
     seqPanel.seqCanvas
             .setSize(d.width, seqPanel.seqCanvas.getSize().height);
     int s = apvscroll.getValue();
@@ -521,8 +524,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       s = 0;
     }
     apvscroll.setValues(s, height, 0, mheight);
-    annotationPanel.setScrollOffset(apvscroll.getValue());
-    alabels.setScrollOffset(apvscroll.getValue());
+    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+    alabels.setScrollOffset(apvscroll.getValue(), false);
   }
 
   public void setWrapAlignment(boolean wrap)
@@ -544,12 +547,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       annotationPanelHolder.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
-
+    
     idSpaceFillerPanel1.setVisible(!wrap);
 
     fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
+    sequenceHolderPanel.revalidate();
     repaint();
 
   }
@@ -686,8 +690,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (evt == null || evt.getSource() == apvscroll)
     {
-      annotationPanel.setScrollOffset(apvscroll.getValue());
-      alabels.setScrollOffset(apvscroll.getValue());
+      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+      alabels.setScrollOffset(apvscroll.getValue(), false);
       // annotationPanel.image=null;
       // alabels.image=null;
       // alabels.repaint();
@@ -817,12 +821,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    alabels.repaint();
-
     seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
     idPanel.idCanvas.repaint();
+    if (!av.wrapAlignment) 
+    {
+      if (av.showAnnotation)
+      {
+        alabels.repaint();
+        annotationPanel.repaint();
+      }
+      scalePanel.repaint();
+    }
+    
   }
 
   protected Panel sequenceHolderPanel = new Panel();
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index db928b7..99ddc50 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 858c055..5900b67 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -93,10 +93,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
     this.av = av;
   }
 
-  public void setScrollOffset(int y)
+  public void setScrollOffset(int y, boolean repaint)
   {
     scrollOffset = y;
-    repaint();
+    if (repaint)
+    {
+      repaint();
+    }
   }
 
   /**
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 250d222..a343bcf 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -636,10 +636,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   int scrollOffset = 0;
 
-  public void setScrollOffset(int value)
+  public void setScrollOffset(int value, boolean repaint)
   {
     scrollOffset = value;
-    repaint();
+    if (repaint)
+    {
+      repaint();
+    }
   }
 
   @Override
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f2a769..b88bb94 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index edf2d45..923f3b2 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 756fa81..ff05547 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java
index 4eb3aa3..44aa229 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index 0f20ad6..9d893d6 100644
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -92,7 +92,7 @@ public class EmbmenuFrame extends Frame implements MouseListener
     {
       // Build the embedded menu panel
       embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, "Arial", Font.PLAIN,
-              10, true); // try to pickup system font.
+              11, true); // try to pickup system font.
       setMenuBar(null);
       // add the components to the TreePanel area.
       add(embeddedMenu, BorderLayout.NORTH);
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index a4ae58c..ae6b5ab 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 4968688..66929d4 100644
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 0a40439..0478a76 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index df2ec15..004125d 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index ad99983..b27dfc5 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index d3351e7..a9fee20 100644
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 140f5f9..aa3a578 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d73668b..e427f42 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 095a592..dc3fdba 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/JVDialog.java b/src/jalview/appletgui/JVDialog.java
index 3443cad..60df71d 100644
--- a/src/jalview/appletgui/JVDialog.java
+++ b/src/jalview/appletgui/JVDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 4d2aeed..954f777 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 78f950b..f592404 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 506ace4..e2f9756 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 2df0eac..589a664 100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index b5f507f..3d7c80f 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 1c38c56..9ab487b 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 41e9acd..58f4d69 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 58e6caa..34ef556 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 429183d..9e2c86f 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 154bea4..aec564b 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 1bd5fd8..fc33c42 100644
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java
index 9cda080..37066a5 100755
--- a/src/jalview/appletgui/Tooltip.java
+++ b/src/jalview/appletgui/Tooltip.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index fc1e464..a2626e7 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 62fa99d..ee070a9 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 225cfc7..1cf12f5 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index b07593d..a395093 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5dc6c81..859b6f5 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 68a85f3..631c7fe 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -61,6 +61,7 @@ import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import netscape.javascript.JSException;
 import netscape.javascript.JSObject;
 
 /**
@@ -1479,7 +1480,36 @@ public class JalviewLite extends Applet implements
       callInitCallback();
     }
   }
-
+  private void initLiveConnect()
+  {
+    // try really hard to get the liveConnect thing working
+    boolean notFailed=false;
+    int tries=0;
+    while (notFailed && tries<10) {
+      if (tries>0)
+      {
+        System.err.println("LiveConnect request thread going to sleep.");
+      }
+      try {
+        Thread.sleep(700*(1+tries));
+      }
+      catch (InterruptedException q) {};
+      if (tries++>0)
+      {
+        System.err.println("LiveConnect request thread woken up.");
+      }
+      try {
+        JSObject scriptObject = JSObject.getWindow(this);
+        if (scriptObject.eval("navigator")!=null)
+        {
+          notFailed=true;
+        }
+      } catch (JSException jsex)
+      {
+        System.err.println("Attempt "+tries+" to access LiveConnect javascript failed.");
+      }
+    }
+  }
   private void callInitCallback()
   {
     String initjscallback = getParameter("oninit");
@@ -1498,6 +1528,9 @@ public class JalviewLite extends Applet implements
       {
       }
       ;
+      // try really hard to let the browser plugin know we want liveconnect 
+      initLiveConnect();
+
       if (scriptObject != null)
       {
         try
diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java
index 2eb1d91..67f3b67 100644
--- a/src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/src/jalview/bin/JalviewLiteURLRetrieve.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index b32ca97..fb696e7 100644
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index 1c6480f..ef2071d 100644
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index 9272234..cdd0c11 100644
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index 7802c35..e0d75e6 100644
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java
index 1a12502..28109e6 100644
--- a/src/jalview/binding/Feature.java
+++ b/src/jalview/binding/Feature.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
index 5628281..7f2d750 100644
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java
index ec22915..f8c1f18 100644
--- a/src/jalview/binding/Features.java
+++ b/src/jalview/binding/Features.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
index 5b7cbf3..080b146 100644
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index ba4ae36..9b3dfc2 100644
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java
index 9dbc5a5..21e8b36 100644
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 66b424f..f8940d3 100644
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index deb5bc7..d25dd59 100644
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
index 3aa6ad6..6464563 100644
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java
index 6fe9924..41edda3 100644
--- a/src/jalview/binding/PdbentryItem.java
+++ b/src/jalview/binding/PdbentryItem.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java
index 08d53f3..d848fa3 100644
--- a/src/jalview/binding/Pdbids.java
+++ b/src/jalview/binding/Pdbids.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java
index 6a0fbee..3a02d27 100644
--- a/src/jalview/binding/Property.java
+++ b/src/jalview/binding/Property.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java
index 7f63ef5..a7aaf4b 100644
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index cd4601a..611d49d 100644
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java
index 816b166..c653e30 100644
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
index 691dfde..c01fc35 100644
--- a/src/jalview/binding/Setting.java
+++ b/src/jalview/binding/Setting.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java
index 7af1853..a1cbf24 100644
--- a/src/jalview/binding/Tree.java
+++ b/src/jalview/binding/Tree.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index b7430e5..be41f1a 100644
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
index 77b1205..411c6be 100644
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 1362e34..ca813a1 100644
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index 288b71f..18ad533 100644
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index b9367da..9a78ced 100644
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index c026f37..138628a 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java
index d07e285..d35f290 100644
--- a/src/jalview/commands/CommandI.java
+++ b/src/jalview/commands/CommandI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ed9e551..ba66e82 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index 274e9e9..316d6ee 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 80a0dd5..d67df61 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 8754b51..c97d43a 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index a6b1480..5bdecc8 100644
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index e33e679..f98da94 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 1a1d219..329267e 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -8,7 +8,10 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -109,14 +112,16 @@ public class AlignViewController implements AlignViewControllerI
   }
    
   @Override
-  public boolean markColumnsContainingFeatures(boolean invert,
-          String featureType)
+  public boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean toggle, String featureType)
   {
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    List<SequenceI> seqs = viewport.getAlignment().getSequences();
-    int alw = viewport.getAlignment().getWidth();
+    int alw,alStart;
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport.getAlignment() : viewport.getSelectionGroup()); 
+    alStart = sqcol.getStartRes();
+    alw = sqcol.getEndRes()+1;
+    List<SequenceI> seqs = sqcol.getSequences();
     int nseq = 0;
     for (SequenceI sq : seqs)
     {
@@ -132,6 +137,13 @@ public class AlignViewController implements AlignViewControllerI
         SequenceFeature[] sf = dsq.getSequenceFeatures();
         if (sf != null)
         {
+          int ist = sq.findIndex(sq.getStart());
+          int iend = sq.findIndex(sq.getEnd());
+          if (iend < alStart || ist> alw)
+          {
+            // sequence not in region
+            continue;
+          }
           for (SequenceFeature sfpos : sf)
           {
             // future functionalty - featureType == null means mark columns
@@ -144,12 +156,19 @@ public class AlignViewController implements AlignViewControllerI
               // counting
 
               int i = sq.findIndex(sfpos.getBegin());
-              int ist = sq.findIndex(sq.getStart());
-              if (i < ist)
+              int j = sq.findIndex(sfpos.getEnd());
+              if (j<alStart || i>alw)
+              {
+                // feature is outside selected region
+                continue;
+              }
+              if (i < alStart)
               {
+                i = alStart;
+              }
+              if (i< ist) {
                 i = ist;
               }
-              int j = sq.findIndex(sfpos.getEnd());
               if (j > alw)
               {
                 j = alw;
@@ -168,21 +187,33 @@ public class AlignViewController implements AlignViewControllerI
         }
       }
     }
+    ColumnSelection cs = viewport.getColumnSelection();
     if (bs.cardinality() > 0 || invert)
     {
-      ColumnSelection cs = viewport.getColumnSelection();
       if (cs == null)
       {
         cs = new ColumnSelection();
+      } else {
+        if (!extendCurrent)
+        {
+          cs.clear();
+        }
       }
       if (invert)
       {
-        for (int i = bs.nextClearBit(0), ibs = bs.nextSetBit(0); i >= 0
-                && i < alw;)
+        // invert only in the currently selected sequence region
+        for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
+                && i < (alw);)
         {
           if (ibs < 0 || i < ibs)
           {
-            cs.addElement(i++);
+            if (toggle && cs.contains(i))
+              {
+                cs.removeElement(i++);
+              } else 
+              {
+                cs.addElement(i++);
+              }
           }
           else
           {
@@ -193,22 +224,33 @@ public class AlignViewController implements AlignViewControllerI
       }
       else
       {
-        for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs.nextSetBit(i + 1))
         {
-          cs.addElement(i);
+          if (toggle && cs.contains(i))
+          {
+            cs.removeElement(i);
+          } else 
+          {
+            cs.addElement(i);
+          }
         }
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus("Marked "
-              + (invert ? alw - bs.cardinality() : bs.cardinality())
-              + " columns containing features of type " + featureType
-              + " across " + nseq);
+      avcg.setStatus((toggle ? "Toggled ": "Marked ")
+              + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality())
+              + " columns "+(invert ? "not " : "") + "containing features of type " + featureType
+              + " across " + nseq + " sequence(s)");
       return true;
     }
     else
     {
       avcg.setStatus("No features of type " + featureType + " found.");
+      if (!extendCurrent && cs!=null)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
       return false;
     }
   }
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 9cfc4ba..d974eb2 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 35efe4f..5d97fe3 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8f5b63d..5145a4f 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2190fa8..975f9fa 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index e95ec39..a230717 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 273a685..c5019d1 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 0f856ee..7baf5f5 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 1c88c82..93b6ff6 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 177ebe7..47cd108 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 456b8b0..041ed44 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index a45efcd..8315166 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 15c600d..38ebdb1 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 7957d33..1a79b17 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java
index e68ed6f..0b422d8 100644
--- a/src/jalview/datamodel/CigarSimple.java
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index b87cd2b..5518588 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 6dc6641..0039dd5 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index d13f9c8..ceb11bf 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index dbe4ab4..fbf0740 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/GraphLine.java b/src/jalview/datamodel/GraphLine.java
index be475f4..ed4bd8d 100755
--- a/src/jalview/datamodel/GraphLine.java
+++ b/src/jalview/datamodel/GraphLine.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index d24f794..9f08b7e 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index c9c9170..2e374c6 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/NodeTransformI.java b/src/jalview/datamodel/NodeTransformI.java
index 72742c7..b5fc803 100644
--- a/src/jalview/datamodel/NodeTransformI.java
+++ b/src/jalview/datamodel/NodeTransformI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 7f6e77a..c41ea2e 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java
index 1da74a0..5988fb7 100755
--- a/src/jalview/datamodel/Provenance.java
+++ b/src/jalview/datamodel/Provenance.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/ProvenanceEntry.java b/src/jalview/datamodel/ProvenanceEntry.java
index 51de184..b943285 100755
--- a/src/jalview/datamodel/ProvenanceEntry.java
+++ b/src/jalview/datamodel/ProvenanceEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index bd1a375..dd021cf 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c81cc5e..0ceefd5 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cd817ab..910c86d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 11e8c67..73cf03f 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 66e59f1..24afbd3 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index a8b0ace..a01c0a5 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 285b7a8..8fc02cd 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 81f5e9b..d6770c0 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 3690b43..d38da0f 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java
index 5693555..f21591a 100755
--- a/src/jalview/datamodel/UniprotEntry.java
+++ b/src/jalview/datamodel/UniprotEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/UniprotFile.java b/src/jalview/datamodel/UniprotFile.java
index 2739e28..f68ffc6 100755
--- a/src/jalview/datamodel/UniprotFile.java
+++ b/src/jalview/datamodel/UniprotFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
index 4a96b0c..cb21789 100755
--- a/src/jalview/datamodel/UniprotProteinName.java
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/UniprotSequence.java b/src/jalview/datamodel/UniprotSequence.java
index 0480ec2..a5112c6 100755
--- a/src/jalview/datamodel/UniprotSequence.java
+++ b/src/jalview/datamodel/UniprotSequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/BasePosition.java b/src/jalview/datamodel/xdb/embl/BasePosition.java
index b3968c3..53d4341 100644
--- a/src/jalview/datamodel/xdb/embl/BasePosition.java
+++ b/src/jalview/datamodel/xdb/embl/BasePosition.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9661d12..0445046 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblError.java b/src/jalview/datamodel/xdb/embl/EmblError.java
index 5d8daa4..c7a59d8 100644
--- a/src/jalview/datamodel/xdb/embl/EmblError.java
+++ b/src/jalview/datamodel/xdb/embl/EmblError.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java
index 1aed0a1..c920f7b 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeature.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
index 63f0ac4..c5aad07 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index daef573..fd4de3c 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 78c4f5c..7e39a51 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java
index 42ca6a4..a997066 100644
--- a/src/jalview/datamodel/xdb/embl/EmblSequence.java
+++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/datamodel/xdb/embl/Qualifier.java b/src/jalview/datamodel/xdb/embl/Qualifier.java
index 9d0dbe0..c60c52a 100644
--- a/src/jalview/datamodel/xdb/embl/Qualifier.java
+++ b/src/jalview/datamodel/xdb/embl/Qualifier.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 46c94c4..8ee2296 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 8494b4b..17a622d 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ext/varna/JalviewVarnaBinding.java b/src/jalview/ext/varna/JalviewVarnaBinding.java
index 411e4fe..c0b6bec 100644
--- a/src/jalview/ext/varna/JalviewVarnaBinding.java
+++ b/src/jalview/ext/varna/JalviewVarnaBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 8ed7462..94899ca 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d475c91..d992233 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e9829bb..de8f310 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 6bfe4bd..cad4339 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index da7a176..60a0759 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 56c6e2d..a199c95 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index ae7596d..2178e37 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 3e9b38e..128110b 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 81b88ac..bf32dff 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 80a7b9e..2424f90 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 1de0cf2..f047199 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index b287b8e..d191212 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 1fa9e71..e9208e6 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 8326e35..566f1c7 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4fe45c8..7552dc9 100644
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index ca554a0..a2ebd0a 100644
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 6ccc5ff..c8901d3 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 340e134..a875bf9 100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d54c887..a0e45a6 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index 551129e..9cc1844 100644
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index cd440cd..5e69ac7 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index d6ddd16..6b28937 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index c07fdcf..970160e 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 9e0925b..3787efa 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -108,7 +108,7 @@ public class FeatureSettings extends JPanel
         else if (evt.getClickCount() == 2)
         {
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
-                  evt.isShiftDown(),
+                  evt.isAltDown(),evt.isShiftDown() || evt.isMetaDown(), evt.isMetaDown(),
                   (String) table.getValueAt(selectedRow, 0));
         }
       }
@@ -138,7 +138,8 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-
+    table.setToolTipText("<html>"+JvSwingUtils
+            .wrapTooltip("Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/>")+"</html>");
     scrollPane.setViewportView(table);
 
     dassourceBrowser = new DasSourceBrowser(this);
@@ -304,7 +305,7 @@ public class FeatureSettings extends JPanel
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, type);
+        fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, false, type);
       }
     });
     JMenuItem clearCols = new JMenuItem(MessageManager.getString("label.select_columns_not_containing"));
@@ -314,7 +315,7 @@ public class FeatureSettings extends JPanel
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, type);
+        fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, false, type);
       }
     });
     men.add(selCols);
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index f53af3f..3161271 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 5e1897d..ea84207 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/IProgressIndicator.java b/src/jalview/gui/IProgressIndicator.java
index a39d5f2..a1e4b2e 100644
--- a/src/jalview/gui/IProgressIndicator.java
+++ b/src/jalview/gui/IProgressIndicator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/IProgressIndicatorHandler.java b/src/jalview/gui/IProgressIndicatorHandler.java
index 183facf..c288abd 100644
--- a/src/jalview/gui/IProgressIndicatorHandler.java
+++ b/src/jalview/gui/IProgressIndicatorHandler.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c4c68c2..5216f0d 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 97e3366..2b87d21 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index c62ab91..632d4df 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index b7ec5a9..b2bbdef 100644
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b20e144..dcf65b7 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9d838f8..b470974 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/JalviewAppender.java b/src/jalview/gui/JalviewAppender.java
index 40a0ac4..eb86e58 100644
--- a/src/jalview/gui/JalviewAppender.java
+++ b/src/jalview/gui/JalviewAppender.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/JalviewChangeSupport.java b/src/jalview/gui/JalviewChangeSupport.java
index 050b02f..d4c1bc1 100644
--- a/src/jalview/gui/JalviewChangeSupport.java
+++ b/src/jalview/gui/JalviewChangeSupport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/JalviewDialog.java b/src/jalview/gui/JalviewDialog.java
index cfdf313..3f58769 100644
--- a/src/jalview/gui/JalviewDialog.java
+++ b/src/jalview/gui/JalviewDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java
index 641ac62..0e3ecd8 100644
--- a/src/jalview/gui/JvSwingUtils.java
+++ b/src/jalview/gui/JvSwingUtils.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java
index 261fae8..6ab5220 100644
--- a/src/jalview/gui/OOMWarning.java
+++ b/src/jalview/gui/OOMWarning.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 1dd848b..5df0174 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/OptsParametersContainerI.java b/src/jalview/gui/OptsParametersContainerI.java
index 841e99e..2d3f59e 100644
--- a/src/jalview/gui/OptsParametersContainerI.java
+++ b/src/jalview/gui/OptsParametersContainerI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 614326d..0b11189 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ccc4697..d1216b9 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index dabf8db..01a5f57 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6738556..e2f96f1 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 66cafc5..67bc00f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 20a136f..51138f2 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index c710a89..95b3fd4 100644
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 7b489a7..59ee1e7 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java
index 764f9c9..497bbe2 100644
--- a/src/jalview/gui/RestInputParamEditDialog.java
+++ b/src/jalview/gui/RestInputParamEditDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index 2507ceb..cfdea05 100644
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index dba5dae..7f31eb1 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 416b787..62f767d 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index 4c8ccd7..e9ffd6e 100644
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 77fc1fe..e7d9030 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2add218..904b856 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 435d218..45d944d 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 9023c4e..9ca3d83 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index f53204e..aa4aa64 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 1006782..652aa75 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 5eadc51..2f9422a 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 97cca4b..5bea550 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 7f85594..923d702 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a2dedd5..e1ff5e0 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index dc23978..cd102b6 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 5f585b6..5ee7e36 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/ViewSelectionMenu.java b/src/jalview/gui/ViewSelectionMenu.java
index e2bda4c..b90f742 100644
--- a/src/jalview/gui/ViewSelectionMenu.java
+++ b/src/jalview/gui/ViewSelectionMenu.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 760db66..723746c 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 9b02401..b905b63 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index 780b30f..5335b22 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index ab7e341..59e6309 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index ee3c18c..31f9b21 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7550a5b..93803c8 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index 37912be..86fa6a0 100644
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 5979a27..9a21fbb 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 6679a03..98037e4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index b95cf1f..6ce0d61 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/ClansFile.java b/src/jalview/io/ClansFile.java
index ad9daad..b7bfacc 100644
--- a/src/jalview/io/ClansFile.java
+++ b/src/jalview/io/ClansFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index bc6ca7f..b45e908 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java
index c24cbdd..c29294a 100644
--- a/src/jalview/io/DBRefFile.java
+++ b/src/jalview/io/DBRefFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 3a7197f..d8890af 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a87fd60..0c8e226 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9cc1e16..b578724 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 69e801c..b52fdfb 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6d77acc..bb1608d 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index d0fdd32..4b4dd93 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 93f9a98..7ed7cbd 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 155e236..a334b4f 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 46ecf41..a8aa8d4 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index 43dda7e..2f2499b 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index 27c6a07..0dcc7c2 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 51cd302..8ffcaf7 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 2d20a40..9b6fc89 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
index 42b9578..09e150c 100644
--- a/src/jalview/io/MatrixFile.java
+++ b/src/jalview/io/MatrixFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index a57cefa..fd28956 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 813ac78..b86c170 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 5af94e2..6db8cd4 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index ba1a9b9..6b617f8 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index f489d80..24c4239 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index fbcc436..74cfa86 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index b8d7569..70ccb26 100644
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 4566bac..9b5a5cd 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 602b0d0..274f532 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 34c61d9..8d1c275 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 732c072..df15b5e 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/packed/DataProvider.java b/src/jalview/io/packed/DataProvider.java
index 80fc0c0..c50c69a 100644
--- a/src/jalview/io/packed/DataProvider.java
+++ b/src/jalview/io/packed/DataProvider.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index b3f061c..40c80a6 100644
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 17e94e7..3130b9e 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/packed/SimpleDataProvider.java b/src/jalview/io/packed/SimpleDataProvider.java
index 4806f91..fdfd019 100644
--- a/src/jalview/io/packed/SimpleDataProvider.java
+++ b/src/jalview/io/packed/SimpleDataProvider.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 08e6288..841d357 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 0fae890..65ccec1 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/DatastoreRegistry.java b/src/jalview/io/vamsas/DatastoreRegistry.java
index 468cb7a..0d76285 100644
--- a/src/jalview/io/vamsas/DatastoreRegistry.java
+++ b/src/jalview/io/vamsas/DatastoreRegistry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index 68bc498..0f43bc3 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/LocalDocSyncObject.java b/src/jalview/io/vamsas/LocalDocSyncObject.java
index 881404d..2c7bfe0 100644
--- a/src/jalview/io/vamsas/LocalDocSyncObject.java
+++ b/src/jalview/io/vamsas/LocalDocSyncObject.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 281e8a4..fb16f55 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 5d04c4c..9cde411 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 241ff85..5dcf4e8 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 43febb4..27aacce 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index 4ed9a08..34d1d2e 100644
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 25eb3be..6878fac 100644
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/JsCallBack.java b/src/jalview/javascript/JsCallBack.java
index 7c86360..9320538 100644
--- a/src/jalview/javascript/JsCallBack.java
+++ b/src/jalview/javascript/JsCallBack.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/JsSelectionSender.java b/src/jalview/javascript/JsSelectionSender.java
index 66b1cac..7ecd675 100644
--- a/src/jalview/javascript/JsSelectionSender.java
+++ b/src/jalview/javascript/JsSelectionSender.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/MouseOverListener.java b/src/jalview/javascript/MouseOverListener.java
index cb3fee7..4115a9e 100644
--- a/src/jalview/javascript/MouseOverListener.java
+++ b/src/jalview/javascript/MouseOverListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 9d7e0cc..766393e 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index cf78585..6e98f74 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 4a20adb..6a7ab97 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index 38fe7a3..5f74844 100644
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index ecfe2af..4149c85 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
index e01d0c7..b16c013 100755
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 4ef6fdd..ab9a0a3 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index d811fee..08fdf39 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index 5f1748e..69859720 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 266bfc6..3fe76ac 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index 7a7392d..57e1348 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index a8626d8..d1df38d 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GRestInputParamEditDialog.java b/src/jalview/jbgui/GRestInputParamEditDialog.java
index 9580d43..f1ce039 100644
--- a/src/jalview/jbgui/GRestInputParamEditDialog.java
+++ b/src/jalview/jbgui/GRestInputParamEditDialog.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GRestServiceEditorPane.java b/src/jalview/jbgui/GRestServiceEditorPane.java
index 97ad295..50048aa 100644
--- a/src/jalview/jbgui/GRestServiceEditorPane.java
+++ b/src/jalview/jbgui/GRestServiceEditorPane.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java
index dd39080..9e72a13 100644
--- a/src/jalview/jbgui/GRnaStructureViewer.java
+++ b/src/jalview/jbgui/GRnaStructureViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index cb4d90f..d3b9c54 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 72224c3..4c5edf5 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index c60d732..720138a 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 47f94c5..1b35d51 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index e097d85..1f4fc9d 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index 21d9b47..0d99704 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/jbgui/GWsPreferences.java b/src/jalview/jbgui/GWsPreferences.java
index 3ad5bb1..cae8232 100644
--- a/src/jalview/jbgui/GWsPreferences.java
+++ b/src/jalview/jbgui/GWsPreferences.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 8d95203..87b0ef3 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index e2ed0c0..a4c2940 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index d951aba..5a53b71 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/renderer/AwtRenderPanelI.java b/src/jalview/renderer/AwtRenderPanelI.java
index 678233e..1d46ae3 100644
--- a/src/jalview/renderer/AwtRenderPanelI.java
+++ b/src/jalview/renderer/AwtRenderPanelI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java
index f423223..8fd8e28 100644
--- a/src/jalview/schemabinding/version2/AlcodMap.java
+++ b/src/jalview/schemabinding/version2/AlcodMap.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java
index f5654e9..fd16b40 100644
--- a/src/jalview/schemabinding/version2/Alcodon.java
+++ b/src/jalview/schemabinding/version2/Alcodon.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java
index d3fde76..cf48788 100644
--- a/src/jalview/schemabinding/version2/AlcodonFrame.java
+++ b/src/jalview/schemabinding/version2/AlcodonFrame.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 98c202e..1c0de1e 100644
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/AnnotationColourScheme.java b/src/jalview/schemabinding/version2/AnnotationColourScheme.java
index 8bf97d5..ca7fbc9 100644
--- a/src/jalview/schemabinding/version2/AnnotationColourScheme.java
+++ b/src/jalview/schemabinding/version2/AnnotationColourScheme.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index cbda218..9f2eada 100644
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index a558e86..26dbe15 100644
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/CalcIdParam.java b/src/jalview/schemabinding/version2/CalcIdParam.java
index aab1434..dd4b584 100644
--- a/src/jalview/schemabinding/version2/CalcIdParam.java
+++ b/src/jalview/schemabinding/version2/CalcIdParam.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 70409b6..4933206 100644
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index de43ff4..27e1018 100644
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index d7deeff..130d515 100644
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index 30afdb4..e975554 100644
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index cfcd531..d66d8e8 100644
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java
index f71c873..c16d352 100644
--- a/src/jalview/schemabinding/version2/Group.java
+++ b/src/jalview/schemabinding/version2/Group.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index 01ec035..811ad33 100644
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 44e8739..a1f62bc 100644
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 070ef7f..aa38064 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index 5ffff2a..6ab4caf 100644
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index 1e3095c..7fd186b 100644
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 2719ecd..ccb0963 100644
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java
index 2eeb726..2817fd6 100644
--- a/src/jalview/schemabinding/version2/MapListFrom.java
+++ b/src/jalview/schemabinding/version2/MapListFrom.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java
index 55c54a5..f185d87 100644
--- a/src/jalview/schemabinding/version2/MapListTo.java
+++ b/src/jalview/schemabinding/version2/MapListTo.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java
index d94d197..04de497 100644
--- a/src/jalview/schemabinding/version2/MapListType.java
+++ b/src/jalview/schemabinding/version2/MapListType.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java
index 69b7413..91d03d9 100644
--- a/src/jalview/schemabinding/version2/Mapping.java
+++ b/src/jalview/schemabinding/version2/Mapping.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java
index b0f49d0..614efba 100644
--- a/src/jalview/schemabinding/version2/MappingChoice.java
+++ b/src/jalview/schemabinding/version2/MappingChoice.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 7908828..2e5772d 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index a2584c2..f207ddc 100644
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 357c939..84aef38 100644
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 8c34216..5e3f13a 100644
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index e91bd35..34e0d57 100644
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 501c44e..50ca919 100644
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index e399ed4..568df1f 100644
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java
index b46fb1d..d01f875 100644
--- a/src/jalview/schemabinding/version2/SequenceSetProperties.java
+++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index 1a6dc08..157c83e 100644
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 9de7b21..58779c5 100644
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 428b3db..82e3e7b 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index 2e90527..5d5c376 100644
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index a2a13cb..a459edc 100644
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index da78647..3625d87 100644
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index 4c75230..2a223d4 100644
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 2d3e829..2c56862 100644
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index 7ea0a45..ffde324 100644
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index a3e20c6..8dbb94b 100644
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/WebServiceParameterSet.java b/src/jalview/schemabinding/version2/WebServiceParameterSet.java
index b645f0b..481c0ce 100644
--- a/src/jalview/schemabinding/version2/WebServiceParameterSet.java
+++ b/src/jalview/schemabinding/version2/WebServiceParameterSet.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
index 7adf1d0..f20ad7a 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
index 47d6e01..171b8af 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
index 1cebb2a..7ff61af 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
index 98f2855..870a90d 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 5eb3939..7ddb280 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index eac9bc7..fdb7d00 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
index 24a90b9..83a9941 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java b/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
index 007175c..7117178 100644
--- a/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/CalcIdParamDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index a8a2cf5..493347d 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
index 514e2d3..3b5f1dc 100644
--- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
index 403e432..4fd913f 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
index 75586b6..3f41d5d 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index 498d18d..cdc2b0a 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
index 0dad270..d2ffed1 100644
--- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
index ebcec89..a5fdfa0 100644
--- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index aec96ef..47917d6 100644
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 8be5479..ba1c904 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
index 31127fa..22d130f 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
index 01b416c..b1ff133 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index c70f679..34f4d98 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
index 9aa7542..05a7ccc 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
index efdf00f..96bfee6 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
index 8402449..a84177b 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
index 1d57dd5..4498c7a 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
index b192ad8..24520c8 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index 69ae032..057a804 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
index 001c3e5..afb41ba 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
index 5748515..5f823dc 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
index 2b0f360..24108d4 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
index eca975a..a231d17 100644
--- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
index 478f2cf..a4e83f4 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
index 09ffdfc..e9e0cb8 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
index e7b075d..06ee93d 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
index 904bd47..8e60014 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index dd318b3..38c5fcf 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 9d82b98..b687586 100644
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
index 671b60f..96cf9c7 100644
--- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index b24356e..6d92ec3 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index 919b3b6..b4253f6 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
index 7725ad1..0c27408 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
index 6148798..e35407c 100644
--- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index d9e97f5..60ab87e 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index 5485480..f995afa 100644
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
index ba75d45..396379f 100644
--- a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 8f0626f..301eb73 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index b43afec..8d8eba0 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 5caa275..f7b186f 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 77d7e5b..30addb0 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 536efe7..66be80d 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 76b1ff1..04ffbe9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 91e0fff..b5cfcc9 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index e410d50..62d0b7b 100644
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java
index caed820..665a78b 100644
--- a/src/jalview/schemes/GraduatedColor.java
+++ b/src/jalview/schemes/GraduatedColor.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index cb0079e..b060788 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 46d93eb..4674aed 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index c359382..6b1ac51 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index a500914..57a5023 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 094ee61..0a088c6 100644
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 06553f0..0a37052 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index bcac5c7..cfa20f4 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 8b3150b..4eefcda 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a277868..2050147 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 8198ff1..6eef929 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index ab603e1..8ef7930 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index 3303f12..6b4b597 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 1c8e469..cd2681b 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index 2274c22..80cb1fe 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index c3b436a..1cc297a 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index eb9f7b1..08b7abf 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index 6760a90..d2cdde9 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/AlignmentViewPanelListener.java b/src/jalview/structure/AlignmentViewPanelListener.java
index ceb8b73..2dcc4d0 100644
--- a/src/jalview/structure/AlignmentViewPanelListener.java
+++ b/src/jalview/structure/AlignmentViewPanelListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/SecondaryStructureListener.java b/src/jalview/structure/SecondaryStructureListener.java
index ad38657..c01e0dd 100644
--- a/src/jalview/structure/SecondaryStructureListener.java
+++ b/src/jalview/structure/SecondaryStructureListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/SelectionListener.java b/src/jalview/structure/SelectionListener.java
index e754035..7c5f450 100644
--- a/src/jalview/structure/SelectionListener.java
+++ b/src/jalview/structure/SelectionListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/SelectionSource.java b/src/jalview/structure/SelectionSource.java
index 43c5408..1e28bd4 100644
--- a/src/jalview/structure/SelectionSource.java
+++ b/src/jalview/structure/SelectionSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index 1a78f08..bf53258 100644
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index bf3ca2d..eef46a7 100644
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index c66b740..d28446f 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/StructureMappingcommandSet.java b/src/jalview/structure/StructureMappingcommandSet.java
index e3256f6..a0eaf7b 100644
--- a/src/jalview/structure/StructureMappingcommandSet.java
+++ b/src/jalview/structure/StructureMappingcommandSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index bbee3b7..bf14000 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/VamsasListener.java b/src/jalview/structure/VamsasListener.java
index f5fc84d..145d2d5 100644
--- a/src/jalview/structure/VamsasListener.java
+++ b/src/jalview/structure/VamsasListener.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/structure/VamsasSource.java b/src/jalview/structure/VamsasSource.java
index 01be511..cab0c23 100644
--- a/src/jalview/structure/VamsasSource.java
+++ b/src/jalview/structure/VamsasSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java
index cfcf396..3ac2927 100644
--- a/src/jalview/util/AWTConsole.java
+++ b/src/jalview/util/AWTConsole.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 634ffc7..cf898b7 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/ColorUtils.java b/src/jalview/util/ColorUtils.java
index 13adc7e..1ab6361 100644
--- a/src/jalview/util/ColorUtils.java
+++ b/src/jalview/util/ColorUtils.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index bd8abbd..4f2c0a7 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 96cd8db..884af30 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index ddc4ceb..5bab738 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 7224681..4642ad8 100644
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 4d11276..7c429f3 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index d712721..c7a32f7 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/ParseHtmlBodyAndLinks.java b/src/jalview/util/ParseHtmlBodyAndLinks.java
index b0b8ef8..102bead 100644
--- a/src/jalview/util/ParseHtmlBodyAndLinks.java
+++ b/src/jalview/util/ParseHtmlBodyAndLinks.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 8287ca3..8c406a9 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 20f1ac7..1d9d8ec 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 54a5218..3c0683a 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
index dcb5330..3352cbb 100755
--- a/src/jalview/util/TableSorter.java
+++ b/src/jalview/util/TableSorter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 80a4380..2936ac3 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/util/jarInputStreamProvider.java b/src/jalview/util/jarInputStreamProvider.java
index 8829118..76e612f 100644
--- a/src/jalview/util/jarInputStreamProvider.java
+++ b/src/jalview/util/jarInputStreamProvider.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 44ecf76..e25818e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 00cc94b..a9c8787 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index a9af5e7..6a2d6ee 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 7497e7a..18bff53 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 97d1236..735b97f 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index a8bc268..cae430f 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 9a8f2d8..1fc6d01 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 8a31587..37d064d 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/AWsJob.java b/src/jalview/ws/AWsJob.java
index 71c021c..91f9644 100644
--- a/src/jalview/ws/AWsJob.java
+++ b/src/jalview/ws/AWsJob.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 84eba02..7b06a71 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 2d8617a..08070db 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 792f150..edc7fb7 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/JobStateSummary.java b/src/jalview/ws/JobStateSummary.java
index 35fb0fc..dd68f93 100644
--- a/src/jalview/ws/JobStateSummary.java
+++ b/src/jalview/ws/JobStateSummary.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index ce3e952..ecaa57a 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index cfa81b8..c41a2f7 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java
index 2c5d4a2..e2aa3c7 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/WSMenuEntryProviderI.java b/src/jalview/ws/WSMenuEntryProviderI.java
index 2194144..0cfb238 100644
--- a/src/jalview/ws/WSMenuEntryProviderI.java
+++ b/src/jalview/ws/WSMenuEntryProviderI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index bc29a2d..9e1a848 100644
--- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
+++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 02e7f29..a317fa4 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 44427a5..5e54f1b 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index fe67b21..89d9f05 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index c8598db..77ff992 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 3dff679..af8676f 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 579a6fe..3f0ec11 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index e9c525e..162f1fa 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index ab19f57..71667ed 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 76f8b10..f5d77ab 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index d61d0f3..1eb3215 100644
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index 2d69480..47ba60d 100644
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 2abb605..1deb272 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/UnprotName.java b/src/jalview/ws/dbsources/UnprotName.java
index 23e0e7a..c45357c 100644
--- a/src/jalview/ws/dbsources/UnprotName.java
+++ b/src/jalview/ws/dbsources/UnprotName.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index a8ea3a8..756ca1b 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java b/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
index 5e8f6a8..7bd5bca 100644
--- a/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
+++ b/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
index 0f4a920..d23a1289 100644
--- a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
+++ b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index c677fdc..980dc81 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 52e8db5..04a1b60 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index daaf0ba..b48616b 100644
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 623a586..074b76c 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/io/mime/HttpContentHandler.java b/src/jalview/ws/io/mime/HttpContentHandler.java
index 7ceeaa9..72c858a 100644
--- a/src/jalview/ws/io/mime/HttpContentHandler.java
+++ b/src/jalview/ws/io/mime/HttpContentHandler.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
index 44a1c96..1b5965c 100644
--- a/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
+++ b/src/jalview/ws/io/mime/JalviewMimeContentHandler.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/io/mime/MimeTypes.java b/src/jalview/ws/io/mime/MimeTypes.java
index f2d8ad5..6c12b02 100644
--- a/src/jalview/ws/io/mime/MimeTypes.java
+++ b/src/jalview/ws/io/mime/MimeTypes.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 900d2e7..48ee9af 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index dccaf4a..4358fac 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 7fbe911..509e020 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/JWS1Thread.java b/src/jalview/ws/jws1/JWS1Thread.java
index 3797b53..4be4f83 100644
--- a/src/jalview/ws/jws1/JWS1Thread.java
+++ b/src/jalview/ws/jws1/JWS1Thread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index c6c6c8c..270b95c 100644
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index a919d2d..168a808 100644
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java
index 171c988..7d3976d 100644
--- a/src/jalview/ws/jws1/SeqSearchWSClient.java
+++ b/src/jalview/ws/jws1/SeqSearchWSClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 2021798..108a586 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/WS1Client.java b/src/jalview/ws/jws1/WS1Client.java
index ba03699..11e299a 100644
--- a/src/jalview/ws/jws1/WS1Client.java
+++ b/src/jalview/ws/jws1/WS1Client.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws1/WSJob.java b/src/jalview/ws/jws1/WSJob.java
index ecc0dbc..e25f0a7 100644
--- a/src/jalview/ws/jws1/WSJob.java
+++ b/src/jalview/ws/jws1/WSJob.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index ee64c1f..aba9222 100644
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index e158da7..e5a39a7 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/AWS2Thread.java b/src/jalview/ws/jws2/AWS2Thread.java
index f1f6bfe..a98da76 100644
--- a/src/jalview/ws/jws2/AWS2Thread.java
+++ b/src/jalview/ws/jws2/AWS2Thread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/JWs2Job.java b/src/jalview/ws/jws2/JWs2Job.java
index e33ccaa..23e131b 100644
--- a/src/jalview/ws/jws2/JWs2Job.java
+++ b/src/jalview/ws/jws2/JWs2Job.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index ed51f9a..7ce1115 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/JabaPreset.java b/src/jalview/ws/jws2/JabaPreset.java
index fd9bbb4..5df106d 100644
--- a/src/jalview/ws/jws2/JabaPreset.java
+++ b/src/jalview/ws/jws2/JabaPreset.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java
index a82d1b6..7248d7c 100644
--- a/src/jalview/ws/jws2/JabaWsServerQuery.java
+++ b/src/jalview/ws/jws2/JabaWsServerQuery.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 0494d1f..6bfeddf 100644
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 0a3db0d..fa43e7c 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 0782d57..66179a0 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 278501f..7bc0ece 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 08accba..e5c3752 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index 1ecb3fb..be90458 100644
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index a590470..fb5f823 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index 49c8aa9..eff2128 100644
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/dm/JabaOption.java b/src/jalview/ws/jws2/dm/JabaOption.java
index a227f4f..f6202e1 100644
--- a/src/jalview/ws/jws2/dm/JabaOption.java
+++ b/src/jalview/ws/jws2/dm/JabaOption.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/dm/JabaParameter.java b/src/jalview/ws/jws2/dm/JabaParameter.java
index 2d6dda5..02cc167 100644
--- a/src/jalview/ws/jws2/dm/JabaParameter.java
+++ b/src/jalview/ws/jws2/dm/JabaParameter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/dm/JabaValueConstrain.java b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
index 2367a85..dd07c9d 100644
--- a/src/jalview/ws/jws2/dm/JabaValueConstrain.java
+++ b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/dm/JabaWsParamSet.java b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
index 118e932..5cd93e6 100644
--- a/src/jalview/ws/jws2/dm/JabaWsParamSet.java
+++ b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 0ac1df4..f21c29d 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/ArgumentI.java b/src/jalview/ws/params/ArgumentI.java
index 05c8ce4..7d13d8b 100644
--- a/src/jalview/ws/params/ArgumentI.java
+++ b/src/jalview/ws/params/ArgumentI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/AutoCalcSetting.java b/src/jalview/ws/params/AutoCalcSetting.java
index 84a79b7..1a28326 100644
--- a/src/jalview/ws/params/AutoCalcSetting.java
+++ b/src/jalview/ws/params/AutoCalcSetting.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/InvalidArgumentException.java b/src/jalview/ws/params/InvalidArgumentException.java
index 8da77e0..ac5e135 100644
--- a/src/jalview/ws/params/InvalidArgumentException.java
+++ b/src/jalview/ws/params/InvalidArgumentException.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/OptionI.java b/src/jalview/ws/params/OptionI.java
index 12b5af8..2aca4b9 100644
--- a/src/jalview/ws/params/OptionI.java
+++ b/src/jalview/ws/params/OptionI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/ParamDatastoreI.java b/src/jalview/ws/params/ParamDatastoreI.java
index 247bfe2..3074ad4 100644
--- a/src/jalview/ws/params/ParamDatastoreI.java
+++ b/src/jalview/ws/params/ParamDatastoreI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/ParamManager.java b/src/jalview/ws/params/ParamManager.java
index d37dd88..e067228 100644
--- a/src/jalview/ws/params/ParamManager.java
+++ b/src/jalview/ws/params/ParamManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/ParameterI.java b/src/jalview/ws/params/ParameterI.java
index d3d3c35..678047c 100644
--- a/src/jalview/ws/params/ParameterI.java
+++ b/src/jalview/ws/params/ParameterI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/ValueConstrainI.java b/src/jalview/ws/params/ValueConstrainI.java
index 5c8b139..ed4080b 100644
--- a/src/jalview/ws/params/ValueConstrainI.java
+++ b/src/jalview/ws/params/ValueConstrainI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/WsParamSetI.java b/src/jalview/ws/params/WsParamSetI.java
index efccbd4..c1be913 100644
--- a/src/jalview/ws/params/WsParamSetI.java
+++ b/src/jalview/ws/params/WsParamSetI.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/simple/BooleanOption.java b/src/jalview/ws/params/simple/BooleanOption.java
index cbb1233..d4076ff 100644
--- a/src/jalview/ws/params/simple/BooleanOption.java
+++ b/src/jalview/ws/params/simple/BooleanOption.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/simple/IntegerParameter.java b/src/jalview/ws/params/simple/IntegerParameter.java
index 3464ced..94a054b 100644
--- a/src/jalview/ws/params/simple/IntegerParameter.java
+++ b/src/jalview/ws/params/simple/IntegerParameter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/simple/Option.java b/src/jalview/ws/params/simple/Option.java
index aebf384..0ce9f09 100644
--- a/src/jalview/ws/params/simple/Option.java
+++ b/src/jalview/ws/params/simple/Option.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/simple/Parameter.java b/src/jalview/ws/params/simple/Parameter.java
index 9d7c74f..40bf6fa 100644
--- a/src/jalview/ws/params/simple/Parameter.java
+++ b/src/jalview/ws/params/simple/Parameter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/params/simple/StringChoiceParameter.java b/src/jalview/ws/params/simple/StringChoiceParameter.java
index 4396403..3f3a3cf 100644
--- a/src/jalview/ws/params/simple/StringChoiceParameter.java
+++ b/src/jalview/ws/params/simple/StringChoiceParameter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/AlignmentProcessor.java b/src/jalview/ws/rest/AlignmentProcessor.java
index eabbd2f..df7573b 100644
--- a/src/jalview/ws/rest/AlignmentProcessor.java
+++ b/src/jalview/ws/rest/AlignmentProcessor.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/HttpResultSet.java b/src/jalview/ws/rest/HttpResultSet.java
index ed77736..3654620 100644
--- a/src/jalview/ws/rest/HttpResultSet.java
+++ b/src/jalview/ws/rest/HttpResultSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index 2047632..a0ef868 100644
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/NoValidInputDataException.java b/src/jalview/ws/rest/NoValidInputDataException.java
index 1e0fd0c..a332c40 100644
--- a/src/jalview/ws/rest/NoValidInputDataException.java
+++ b/src/jalview/ws/rest/NoValidInputDataException.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 046871e..ceb2809 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index 7bd9f49..d41cfc0 100644
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 5000fdc..2aa071d 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index aae2255..02c0bbf 100644
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index f78788b..d6af1c4 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index ed9383e..9aeeb9a 100644
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/JobConstant.java b/src/jalview/ws/rest/params/JobConstant.java
index b975fe4..968011c 100644
--- a/src/jalview/ws/rest/params/JobConstant.java
+++ b/src/jalview/ws/rest/params/JobConstant.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 124c789..87a1d9a 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/SeqIdVector.java b/src/jalview/ws/rest/params/SeqIdVector.java
index b3bffa2..05acb23 100644
--- a/src/jalview/ws/rest/params/SeqIdVector.java
+++ b/src/jalview/ws/rest/params/SeqIdVector.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index 6e1563a..8dd5dfd 100644
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/rest/params/Tree.java b/src/jalview/ws/rest/params/Tree.java
index 3487cb4..db4ce8b 100644
--- a/src/jalview/ws/rest/params/Tree.java
+++ b/src/jalview/ws/rest/params/Tree.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index cf60b63..8b63184 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index af72f16..3a50fb5 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index da7e09a..bdd21fd 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/picr/model/CrossReference.java b/src/uk/ac/ebi/picr/model/CrossReference.java
index ca6d66d..2469db5 100644
--- a/src/uk/ac/ebi/picr/model/CrossReference.java
+++ b/src/uk/ac/ebi/picr/model/CrossReference.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
index 7ea0783..65a1092 100644
--- a/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
+++ b/src/uk/ac/ebi/picr/model/CrossReference_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/picr/model/UPEntry.java b/src/uk/ac/ebi/picr/model/UPEntry.java
index 5bfa02c..8a82575 100644
--- a/src/uk/ac/ebi/picr/model/UPEntry.java
+++ b/src/uk/ac/ebi/picr/model/UPEntry.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
index 59e1012..54da470 100644
--- a/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
+++ b/src/uk/ac/ebi/picr/model/UPEntry_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/Data.java b/src/uk/ac/ebi/www/Data.java
index ad6b546..29206cc 100755
--- a/src/uk/ac/ebi/www/Data.java
+++ b/src/uk/ac/ebi/www/Data.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/InputParams.java b/src/uk/ac/ebi/www/InputParams.java
index bbaf521..a6a57f5 100755
--- a/src/uk/ac/ebi/www/InputParams.java
+++ b/src/uk/ac/ebi/www/InputParams.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/WSFile.java b/src/uk/ac/ebi/www/WSFile.java
index e22c43f..1cb0841 100755
--- a/src/uk/ac/ebi/www/WSFile.java
+++ b/src/uk/ac/ebi/www/WSFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/WSWUBlast.java b/src/uk/ac/ebi/www/WSWUBlast.java
index 32a6073..9b891a8 100755
--- a/src/uk/ac/ebi/www/WSWUBlast.java
+++ b/src/uk/ac/ebi/www/WSWUBlast.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/WSWUBlastService.java b/src/uk/ac/ebi/www/WSWUBlastService.java
index ee7f068..5bb0475 100755
--- a/src/uk/ac/ebi/www/WSWUBlastService.java
+++ b/src/uk/ac/ebi/www/WSWUBlastService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
index dd53a7e..5e5ba13 100755
--- a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
+++ b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
index 69005fb..5059842 100755
--- a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
+++ b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
index d3e19d5..235508b 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
index 9b9ddff..b199ee8 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
index 7386401..02ea047 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
index dda7ade..1336c78 100644
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java
index 7438a34..9c05ef5 100755
--- a/src/vamsas/IMsaWS.java
+++ b/src/vamsas/IMsaWS.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index b875b56..e03b768 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
index b3e820d..0c9e127 100755
--- a/src/vamsas/objects/simple/Alignment_Helper.java
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/JpredResult.java b/src/vamsas/objects/simple/JpredResult.java
index 12e05da..a6f3877 100755
--- a/src/vamsas/objects/simple/JpredResult.java
+++ b/src/vamsas/objects/simple/JpredResult.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/JpredResult_Helper.java b/src/vamsas/objects/simple/JpredResult_Helper.java
index 1244535..b2baf3f 100755
--- a/src/vamsas/objects/simple/JpredResult_Helper.java
+++ b/src/vamsas/objects/simple/JpredResult_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index be3214a..939c4c4 100755
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java
index fb9fd2c..c9f5ea1 100755
--- a/src/vamsas/objects/simple/MsaResult_Helper.java
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java
index ba18a9a..5aaf0db 100755
--- a/src/vamsas/objects/simple/Msfalignment.java
+++ b/src/vamsas/objects/simple/Msfalignment.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Msfalignment_Helper.java b/src/vamsas/objects/simple/Msfalignment_Helper.java
index 66ed53b..c50c5be 100755
--- a/src/vamsas/objects/simple/Msfalignment_Helper.java
+++ b/src/vamsas/objects/simple/Msfalignment_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
index 77eceb0..5e491d6 100755
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
index 2755f3f..a45718b 100755
--- a/src/vamsas/objects/simple/Object_Helper.java
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
index 60ede6f..d0ac976 100755
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java
index 4c2d744..d2d4960 100755
--- a/src/vamsas/objects/simple/Result_Helper.java
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Secstructpred.java b/src/vamsas/objects/simple/Secstructpred.java
index ea335df..1a14efb 100755
--- a/src/vamsas/objects/simple/Secstructpred.java
+++ b/src/vamsas/objects/simple/Secstructpred.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Secstructpred_Helper.java b/src/vamsas/objects/simple/Secstructpred_Helper.java
index a085900..b7f059b 100755
--- a/src/vamsas/objects/simple/Secstructpred_Helper.java
+++ b/src/vamsas/objects/simple/Secstructpred_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/SeqSearchResult.java b/src/vamsas/objects/simple/SeqSearchResult.java
index 6673fff..058830d 100644
--- a/src/vamsas/objects/simple/SeqSearchResult.java
+++ b/src/vamsas/objects/simple/SeqSearchResult.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/SeqSearchResult_Helper.java b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
index 8328383..7076c33 100644
--- a/src/vamsas/objects/simple/SeqSearchResult_Helper.java
+++ b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
index 04122cd..2f6d742 100755
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index e8865da..9aaca58 100755
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
index 1c820e4..181be98 100755
--- a/src/vamsas/objects/simple/SequenceSet_Helper.java
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java
index 43c444c..9f56351 100755
--- a/src/vamsas/objects/simple/Sequence_Helper.java
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
index 14f34ba..476df91 100755
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
index 2521c4b..5d9f216 100755
--- a/src/vamsas/objects/simple/WsJobId_Helper.java
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/test/jalview/analysis/DnaTranslation.java b/test/jalview/analysis/DnaTranslation.java
index a26495c..da2fac4 100644
--- a/test/jalview/analysis/DnaTranslation.java
+++ b/test/jalview/analysis/DnaTranslation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/InstallAnywhere/jalview_buildinstaller.xml b/utils/InstallAnywhere/jalview_buildinstaller.xml
index 1873087..ee21e74 100644
--- a/utils/InstallAnywhere/jalview_buildinstaller.xml
+++ b/utils/InstallAnywhere/jalview_buildinstaller.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/eclipse/JalviewCodeStyle.xml b/utils/eclipse/JalviewCodeStyle.xml
index c778599..a73f116 100644
--- a/utils/eclipse/JalviewCodeStyle.xml
+++ b/utils/eclipse/JalviewCodeStyle.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/getJavaVersion.java b/utils/getJavaVersion.java
index 6bec144..f3b12d4 100644
--- a/utils/getJavaVersion.java
+++ b/utils/getJavaVersion.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/gff2annot.pl b/utils/gff2annot.pl
index 73d5579..6d90f70 100755
--- a/utils/gff2annot.pl
+++ b/utils/gff2annot.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/utils/help2Website.java b/utils/help2Website.java
index 875d5b9..e2e79ac 100755
--- a/utils/help2Website.java
+++ b/utils/help2Website.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/acknowledge.html b/utils/jalopy/docs/acknowledge.html
index 6fc8a5d..71ff9e4 100755
--- a/utils/jalopy/docs/acknowledge.html
+++ b/utils/jalopy/docs/acknowledge.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/bi01.html b/utils/jalopy/docs/bi01.html
index eca896a..24a6ec4 100755
--- a/utils/jalopy/docs/bi01.html
+++ b/utils/jalopy/docs/bi01.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/build.html b/utils/jalopy/docs/build.html
index d5418b4..b4bc167 100755
--- a/utils/jalopy/docs/build.html
+++ b/utils/jalopy/docs/build.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/comments.html b/utils/jalopy/docs/comments.html
index 8554aa8..5eceab4 100755
--- a/utils/jalopy/docs/comments.html
+++ b/utils/jalopy/docs/comments.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/contact.html b/utils/jalopy/docs/contact.html
index c2fa66f..38afa69 100755
--- a/utils/jalopy/docs/contact.html
+++ b/utils/jalopy/docs/contact.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/contributors.html b/utils/jalopy/docs/contributors.html
index f0a376a..75d4324 100755
--- a/utils/jalopy/docs/contributors.html
+++ b/utils/jalopy/docs/contributors.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/dedication.html b/utils/jalopy/docs/dedication.html
index 8d1440f..662188e 100755
--- a/utils/jalopy/docs/dedication.html
+++ b/utils/jalopy/docs/dedication.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/dependencies.html b/utils/jalopy/docs/dependencies.html
index 826efb0..9a95c1d 100755
--- a/utils/jalopy/docs/dependencies.html
+++ b/utils/jalopy/docs/dependencies.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/docs.html b/utils/jalopy/docs/docs.html
index 6399e53..c5c3cb9 100755
--- a/utils/jalopy/docs/docs.html
+++ b/utils/jalopy/docs/docs.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/download.html b/utils/jalopy/docs/download.html
index e19df02..168dd00 100755
--- a/utils/jalopy/docs/download.html
+++ b/utils/jalopy/docs/download.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/environment.html b/utils/jalopy/docs/environment.html
index f9241b8..d7377f8 100755
--- a/utils/jalopy/docs/environment.html
+++ b/utils/jalopy/docs/environment.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/faq.html b/utils/jalopy/docs/faq.html
index b6d6a5b..c0bb742 100755
--- a/utils/jalopy/docs/faq.html
+++ b/utils/jalopy/docs/faq.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/features.html b/utils/jalopy/docs/features.html
index 11abe49..b8d3aa5 100755
--- a/utils/jalopy/docs/features.html
+++ b/utils/jalopy/docs/features.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/footer.html b/utils/jalopy/docs/footer.html
index dc35661..f2de4ce 100755
--- a/utils/jalopy/docs/footer.html
+++ b/utils/jalopy/docs/footer.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/header.html b/utils/jalopy/docs/header.html
index 8f8bea0..6e39c0c 100755
--- a/utils/jalopy/docs/header.html
+++ b/utils/jalopy/docs/header.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/history.html b/utils/jalopy/docs/history.html
index e8a9ba9..8537730 100755
--- a/utils/jalopy/docs/history.html
+++ b/utils/jalopy/docs/history.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/imports.html b/utils/jalopy/docs/imports.html
index bdfbd92..85ed7f0 100755
--- a/utils/jalopy/docs/imports.html
+++ b/utils/jalopy/docs/imports.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/indentation.html b/utils/jalopy/docs/indentation.html
index 422722c..b2de732 100755
--- a/utils/jalopy/docs/indentation.html
+++ b/utils/jalopy/docs/indentation.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/index.html b/utils/jalopy/docs/index.html
index 01d892d..a8f9b1c 100755
--- a/utils/jalopy/docs/index.html
+++ b/utils/jalopy/docs/index.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/inspector-naming.html b/utils/jalopy/docs/inspector-naming.html
index 932d675..98fd625 100755
--- a/utils/jalopy/docs/inspector-naming.html
+++ b/utils/jalopy/docs/inspector-naming.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/inspector.html b/utils/jalopy/docs/inspector.html
index 5d12e1d..75d5bf3 100755
--- a/utils/jalopy/docs/inspector.html
+++ b/utils/jalopy/docs/inspector.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/installation.html b/utils/jalopy/docs/installation.html
index 946de99..f95ea66 100755
--- a/utils/jalopy/docs/installation.html
+++ b/utils/jalopy/docs/installation.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/introduction.html b/utils/jalopy/docs/introduction.html
index 999231a..a9d1724 100755
--- a/utils/jalopy/docs/introduction.html
+++ b/utils/jalopy/docs/introduction.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/ix01.html b/utils/jalopy/docs/ix01.html
index 96bf741..1eb057d 100755
--- a/utils/jalopy/docs/ix01.html
+++ b/utils/jalopy/docs/ix01.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/javadoc.html b/utils/jalopy/docs/javadoc.html
index 7010dbb..9e4814b 100755
--- a/utils/jalopy/docs/javadoc.html
+++ b/utils/jalopy/docs/javadoc.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/license-antlr.html b/utils/jalopy/docs/license-antlr.html
index 6c8139f..5214ba5 100755
--- a/utils/jalopy/docs/license-antlr.html
+++ b/utils/jalopy/docs/license-antlr.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/license-apache.html b/utils/jalopy/docs/license-apache.html
index 8be355f..840e7fd 100755
--- a/utils/jalopy/docs/license-apache.html
+++ b/utils/jalopy/docs/license-apache.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/license-common-public.html b/utils/jalopy/docs/license-common-public.html
index bea5670..8ee409c 100755
--- a/utils/jalopy/docs/license-common-public.html
+++ b/utils/jalopy/docs/license-common-public.html
@@ -1,5 +1,5 @@
 <!--
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index fa40bf3..0d0b93d 100755
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@@ -1,5 +1,5 @@
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diff --git a/utils/jalopy/docs/license-gnu.html b/utils/jalopy/docs/license-gnu.html
index c1bdb10..3c7420c 100755
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@@ -1,5 +1,5 @@
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diff --git a/utils/jalopy/docs/license-sun-public.html b/utils/jalopy/docs/license-sun-public.html
index 656b918..5c7c644 100755
--- a/utils/jalopy/docs/license-sun-public.html
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@@ -1,5 +1,5 @@
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index 533b326..fb8bddc 100755
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@@ -1,5 +1,5 @@
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index 6849685..ab4e694 100755
--- a/utils/jalopy/docs/manual.html
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@@ -1,5 +1,5 @@
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index 05e6657..b0b1b7a 100755
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@@ -1,5 +1,5 @@
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diff --git a/utils/jalopy/docs/misc.html b/utils/jalopy/docs/misc.html
index 2a1d4ff..e7c7431 100755
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@@ -1,5 +1,5 @@
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index 40281a1..189a6b6 100755
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@@ -1,5 +1,5 @@
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index 1ad987b..9453a47 100755
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@@ -1,5 +1,5 @@
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index 113b61e..974a6c8 100755
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index 76ea7de..8ffc273 100755
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index 699b054..6b39254 100755
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index 70354ed..53b36fa 100755
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diff --git a/utils/jalopy/docs/plugin-console-license.html b/utils/jalopy/docs/plugin-console-license.html
index e469866..757b901 100755
--- a/utils/jalopy/docs/plugin-console-license.html
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@@ -1,5 +1,5 @@
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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diff --git a/utils/jalopy/docs/plugin-console-usage.html b/utils/jalopy/docs/plugin-console-usage.html
index 20a8cea..f8c0722 100755
--- a/utils/jalopy/docs/plugin-console-usage.html
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@@ -1,5 +1,5 @@
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index 697d410..f8275cb 100755
--- a/utils/jalopy/docs/plugin-console.html
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@@ -1,5 +1,5 @@
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index 964ad32..d7e3a18 100755
--- a/utils/jalopy/docs/plugin-eclipse-integration.html
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@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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index 473f1f1..8c5676e 100755
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@@ -1,5 +1,5 @@
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index 26db561..8ef0d4e 100755
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@@ -1,5 +1,5 @@
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diff --git a/utils/jalopy/docs/plugin-jbuilder-integration.html b/utils/jalopy/docs/plugin-jbuilder-integration.html
index cf8dd8f..0fca529 100755
--- a/utils/jalopy/docs/plugin-jbuilder-integration.html
+++ b/utils/jalopy/docs/plugin-jbuilder-integration.html
@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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diff --git a/utils/jalopy/docs/plugin-jbuilder-license.html b/utils/jalopy/docs/plugin-jbuilder-license.html
index e1d8f10..24771fa 100755
--- a/utils/jalopy/docs/plugin-jbuilder-license.html
+++ b/utils/jalopy/docs/plugin-jbuilder-license.html
@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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diff --git a/utils/jalopy/docs/plugin-jbuilder.html b/utils/jalopy/docs/plugin-jbuilder.html
index 91847e8..ad854be 100755
--- a/utils/jalopy/docs/plugin-jbuilder.html
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@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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index 50a21f9..5708a8a 100755
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@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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  * 
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diff --git a/utils/jalopy/docs/plugin-jdev-license.html b/utils/jalopy/docs/plugin-jdev-license.html
index 0d7b467..acaa975 100755
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@@ -1,5 +1,5 @@
 <!--
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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  * 
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diff --git a/utils/jalopy/docs/plugin-jdev.html b/utils/jalopy/docs/plugin-jdev.html
index b111757..aece616 100755
--- a/utils/jalopy/docs/plugin-jdev.html
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@@ -1,5 +1,5 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
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diff --git a/utils/jalopy/docs/plugin-jedit-integration.html b/utils/jalopy/docs/plugin-jedit-integration.html
index b5083ae..91bb923 100755
--- a/utils/jalopy/docs/plugin-jedit-integration.html
+++ b/utils/jalopy/docs/plugin-jedit-integration.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugin-jedit-license.html b/utils/jalopy/docs/plugin-jedit-license.html
index 1ca9201..a376cdb 100755
--- a/utils/jalopy/docs/plugin-jedit-license.html
+++ b/utils/jalopy/docs/plugin-jedit-license.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugin-jedit.html b/utils/jalopy/docs/plugin-jedit.html
index 31e08be..ced3833 100755
--- a/utils/jalopy/docs/plugin-jedit.html
+++ b/utils/jalopy/docs/plugin-jedit.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugin-netbeans-integration.html b/utils/jalopy/docs/plugin-netbeans-integration.html
index 9dc4da0..983270d 100755
--- a/utils/jalopy/docs/plugin-netbeans-integration.html
+++ b/utils/jalopy/docs/plugin-netbeans-integration.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugin-netbeans-license.html b/utils/jalopy/docs/plugin-netbeans-license.html
index 4224ce7..c0a0c5a 100755
--- a/utils/jalopy/docs/plugin-netbeans-license.html
+++ b/utils/jalopy/docs/plugin-netbeans-license.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugin-netbeans.html b/utils/jalopy/docs/plugin-netbeans.html
index 41b8db2..e653198 100755
--- a/utils/jalopy/docs/plugin-netbeans.html
+++ b/utils/jalopy/docs/plugin-netbeans.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/plugins.html b/utils/jalopy/docs/plugins.html
index 5051318..7aae9b8 100755
--- a/utils/jalopy/docs/plugins.html
+++ b/utils/jalopy/docs/plugins.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/printer.html b/utils/jalopy/docs/printer.html
index e43d274..15f5c78 100755
--- a/utils/jalopy/docs/printer.html
+++ b/utils/jalopy/docs/printer.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/project.html b/utils/jalopy/docs/project.html
index d93e417..ee00723 100755
--- a/utils/jalopy/docs/project.html
+++ b/utils/jalopy/docs/project.html
@@ -1,5 +1,5 @@
 <!--
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
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index 3eb56f2..20f1a68 100755
--- a/utils/jalopy/docs/separation.html
+++ b/utils/jalopy/docs/separation.html
@@ -1,5 +1,5 @@
 <!--
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/settings.html b/utils/jalopy/docs/settings.html
index 64d7e2d..797f5a8 100755
--- a/utils/jalopy/docs/settings.html
+++ b/utils/jalopy/docs/settings.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/site.css b/utils/jalopy/docs/site.css
index c5adfa8..9dffb8e 100755
--- a/utils/jalopy/docs/site.css
+++ b/utils/jalopy/docs/site.css
@@ -1,5 +1,5 @@
 #-------------------------------------------------------------------------------
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/utils/jalopy/docs/sorting.html b/utils/jalopy/docs/sorting.html
index be41bda..50d93d1 100755
--- a/utils/jalopy/docs/sorting.html
+++ b/utils/jalopy/docs/sorting.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/usage.html b/utils/jalopy/docs/usage.html
index 32e8ebf..dfa82d3 100755
--- a/utils/jalopy/docs/usage.html
+++ b/utils/jalopy/docs/usage.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/whitespace.html b/utils/jalopy/docs/whitespace.html
index 2ceb9ee..81dfe99 100755
--- a/utils/jalopy/docs/whitespace.html
+++ b/utils/jalopy/docs/whitespace.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/docs/wrapping.html b/utils/jalopy/docs/wrapping.html
index 453d3c4..e5dccad 100755
--- a/utils/jalopy/docs/wrapping.html
+++ b/utils/jalopy/docs/wrapping.html
@@ -1,5 +1,5 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jalopy/readme.html b/utils/jalopy/readme.html
index f8912d7..3182984 100755
--- a/utils/jalopy/readme.html
+++ b/utils/jalopy/readme.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
diff --git a/utils/jarunsigner.pl b/utils/jarunsigner.pl
index 36ecb87..f8a810b 100755
--- a/utils/jarunsigner.pl
+++ b/utils/jarunsigner.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/utils/patchGt.pl b/utils/patchGt.pl
index ff3e621..bc9d2da 100644
--- a/utils/patchGt.pl
+++ b/utils/patchGt.pl
@@ -1,6 +1,6 @@
 #!/bin/perl
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
diff --git a/utils/splitstockholm.pl b/utils/splitstockholm.pl
index 0b698c5..9654057 100644
--- a/utils/splitstockholm.pl
+++ b/utils/splitstockholm.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/perl
 ##
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
 # Copyright (C) 2014 The Jalview Authors
 # 
 # This file is part of Jalview.
