This commit was manufactured by cvs2svn to create tag 'Release_2_1_1'.

This commit was manufactured by cvs2svn to create tag 'Release_2_1_1'.

Sprout from master 2006-09-12 10:01:52 UTC andrew 'Copy consensus'
Cherrypick from master 2007-02-09 18:02:17 UTC jprocter 'running jalview from the command line.':
    doc/AddingGroovySupport.html
    help/html/align.jpg
    help/html/colourSchemes/textcolour.gif
    help/html/colourSchemes/textcolour.html
    help/html/features/amendfeature.gif
    help/html/features/clarguments.html
    help/html/features/codingfeatures.html
    help/html/features/commandline.html
    help/html/features/creatinFeatures.html
    help/html/features/crnewfeature.gif
    help/html/features/das.gif
    help/html/features/editingFeatures.html
    help/html/features/multipleViews.html
    help/html/features/newkeystrokes.html
    help/html/features/seqmappings.html
    help/html/menus/alwformat.html
    help/html/menus/alwselect.html
    lib/vamsas-client.jar
    src/jalview/analysis/Finder.java
    src/jalview/appletgui/EditNameDialog.java
    src/jalview/commands/ChangeCaseCommand.java
    src/jalview/commands/CommandI.java
    src/jalview/commands/EditCommand.java
    src/jalview/commands/OrderCommand.java
    src/jalview/commands/RemoveGapColCommand.java
    src/jalview/commands/RemoveGapsCommand.java
    src/jalview/commands/TrimRegionCommand.java
    src/jalview/gui/EditNameDialog.java
    src/jalview/gui/TextColourChooser.java
    src/jalview/gui/UserQuestionnaireCheck.java
    src/jalview/gui/VamsasClient.java
    src/jalview/io/AMSAFile.java
    src/jalview/io/VamsasDatastore.java
    src/jalview/schemes/ScoreMatrix.java
    src/jalview/util/MapList.java
    src/jalview/ws/JPredThread.java