From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 3 Feb 2014 17:17:52 +0000 (+0000)
Subject: Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
X-Git-Tag: Jalview_2_9~204^2~4^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
updating 2.8.1 with source formatting, branding, and new examples build mechanism
Conflicts:
	build.xml
	examples/linkedapplets_ng.html
	help/helpTOC.xml
	src/jalview/appletgui/AlignFrame.java
	src/jalview/schemabinding/version2/AnnotationColours.java
	src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
---

2f4f1d8fb6878271b64f327bc58c895f458137af
diff --cc build.xml
index d11047e,6eab52a..82cbabb
--- a/build.xml
+++ b/build.xml
@@@ -15,38 -15,39 +15,39 @@@
   * PURPOSE.  See the GNU General Public License for more details.
   * 
   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
  -->
  <project name="jalviewX" default="usage" basedir=".">
 -  <!-- we use jalopy to format our sources -->
 -  <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
 -    <classpath>
 -      <fileset dir="utils/jalopy/lib">
 -        <include name="*.jar" />
 -      </fileset>
 -    </classpath>
 -  </taskdef>
 -
 -  <target name="help" depends="usage" />
 -  <target name="usage">
 -    <echo message="~~~Jalview Ant build.xml Usage~~~~" />
 -    <echo message="Targets include:" />
 -    <echo message="usage - default target, displays this message" />
 -    <echo message="buildindices - generates JavaHelpSearch from the help files" />
 -    <echo message="build - compiles all necessary files for Application" />
 -    <echo message="makedist - compiles and places all necessary jar files into directory dist" />
 -    <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
 -    <echo message="              this needs a keystore and key. See docs/building.html for more information." />
 -    <echo message="compileApplet - compiles all necessary files for Applet" />
 -    <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
 -    <echo message="See docs/building.html and the comments in build file for other targets." />
 -    <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
 -    <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
 -  </target>
 -
 -
 -  <!-- utils is a class path to additional utilities needed for
 +	<!-- we use jalopy to format our sources -->
 +	<taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
 +		<classpath>
 +			<fileset dir="utils/jalopy/lib">
 +				<include name="*.jar" />
 +			</fileset>
 +		</classpath>
 +	</taskdef>
 +
 +	<target name="help" depends="usage" />
 +	<target name="usage">
 +		<echo message="~~~Jalview Ant build.xml Usage~~~~" />
 +		<echo message="Targets include:" />
 +		<echo message="usage - default target, displays this message" />
 +		<echo message="buildindices - generates JavaHelpSearch from the help files" />
 +		<echo message="build - compiles all necessary files for Application" />
 +		<echo message="makedist - compiles and places all necessary jar files into directory dist" />
 +		<echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
 +		<echo message="              this needs a keystore and key. See docs/building.html for more information." />
 +		<echo message="compileApplet - compiles all necessary files for Applet" />
 +		<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
 +		<echo message="See docs/building.html and the comments in build file for other targets." />
 +		<echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
 +		<echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
 +	</target>
 +
 +
 +	<!-- utils is a class path to additional utilities needed for
      building docs, jars and webstart stuff -->
 -  <!--
 +	<!--
          Userdefined build property defaults
  
          wsdl.server list (plus namespace mapping info ???)  - also want
@@@ -291,9 -294,10 +292,10 @@@
  			
  			
  			-->
 -    <!--
 +					<!--
  				<association mime-type="application-x/ext-file" extensions="fa"/>
          <association mime-type="application-x/ext-file" extensions="fasta"/>
+         <association mime-type="application-x/ext-file" extensions="mfa"/>
          <association mime-type="application-x/ext-file" extensions="fastq"/>
          <association mime-type="application-x/ext-file" extensions="blc"/>
          <association mime-type="application-x/ext-file" extensions="msf"/>
@@@ -698,12 -684,14 +701,13 @@@
          <include name="ap_${jmolJar}" />
        </fileset>
      </signjar>
- 	</target>
- 	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- 	 <javadoc destdir="${javadocDir}">
- 	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- 	 	</packageset>
- 	 	</javadoc>
- 	</target>
- 	
+     <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+     <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+   </target>
+   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+     <javadoc destdir="${javadocDir}">
+       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+       </packageset>
+     </javadoc>
+   </target>
 -
  </project>
diff --cc examples/linkedapplets_ng.html
index 6aa5479,97941f8..1ad5423
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@@ -1,7 -1,7 +1,7 @@@
 -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 +<!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)
-  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+  * Copyright (C) 2014 The Jalview Authors
   * 
   * This file is part of Jalview.
   * 
diff --cc help/helpTOC.xml
index e27d41a,3c5b9c2..aa10130
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@@ -19,24 -20,10 +20,14 @@@
  <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
  <toc version="1.0">
  <tocitem text="Jalview Documentation" target="home" expand="true" >
- 	<tocitem text="What's new" target="new" expand="true">
-     <tocitem text="Protein Disorder Prediction" target="disorder"/>
-     <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-     	<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- 		<tocitem text="Viewing RNA structure" target="varna" />
- 		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- 		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- 		<tocitem text="HTML annotation report" target="io.seqreport"/>
- 		<tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
- 		<tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
- 	  <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
- 	  <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
- 	  <tocitem text="DNA or Protein PCA calculation" target="pca"/>
- 	  <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
- 	</tocitem>
-     <tocitem text="Editing Alignments" target ="edit"/>	
-     <tocitem text="Cursor Mode" target="cursor"/>
- 	<tocitem text="Key Strokes" target="keys"/>
 -	<tocitem text="What's new" target="new" expand="false"/>
++ <tocitem text="What's new" target="new" expand="true">
++ <tocitem text="Protein Disorder Prediction" target="disorder"/>
++   <tocitem text="Alignment Conservation Analysis" target="aacon"/>
++  <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
++  </tocitem>
+   <tocitem text="Editing Alignments" target ="edit"/>	
+   <tocitem text="Cursor Mode" target="cursor"/>
 -	<tocitem text="Key Strokes" target="keys"/>
++  <tocitem text="Key Strokes" target="keys"/>
  	<tocitem text="Input / Output" target="io"/>
    	<tocitem text="Making Figures" target="export"/>
  	<tocitem text="Hidden Regions" target="hiddenRegions"/>
diff --cc resources/lang/Messages.properties
index 53a05dd,0000000..f9356ce
mode 100644,000000..100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1,389 -1,0 +1,389 @@@
 +action.cancel = Cancel
 +action.create = Create
 +action.update = Update
 +action.delete = Delete
 +action.snapshot = Snapshot
 +action.clear = Clear
 +action.accept = Accept
 +action.select_ddbb = --- Select Database ---
 +action.undo = Undo
 +action.redo = Redo
 +action.reset = Reset
 +action.remove_left = Remove left
 +action.remove_right = Remove right
 +action.remove_empty_columns = Remove Empty Columns
 +action.remove_all_gaps = Remove All Gaps
 +action.boxes = Boxes
 +action.text = Text
 +action.by_pairwise_id = by Pairwise Identity
 +action.by_id = by Id
 +action.by_length = by Length
 +action.by_group = by Group
 +action.remove_redundancy = Remove Redundancy...
 +action.pairwise_alignment = Pairwise Alignments...
 +action.by_rna_helixes = by RNA Helices
 +action.user_defined = User Defined...
 +action.by_conservation = By Conservation
 +action.wrap = Wrap
 +action.show_gaps = Show Gaps
 +action.find = Find...
 +action.undefine_groups = Undefine Groups
 +action.make_groups_selection = Make Groups For Selection
 +action.copy = Copy
 +action.cut = Cut
 +action.paste = Paste
 +action.font = Font...
 +action.scale_above = Scale Above
 +action.scale_left = Scale Left
 +action.scale_right = Scale Right
 +action.by_tree_order = By Tree Order
 +action.sort = Sort
 +action.calculate_tree = Calculate Tree
 +action.help = Help
 +action.by_annotation = by Annotation...
 +action.invert_sequence_selection = Invert Sequence Selection
 +action.invert_column_selection = Invert Column Selection
 +action.show = Show
 +action.hide = Hide
 +action.ok = OK
 +action.set_defaults = Defaults
 +action.create_group = Create Group
 +action.remove_group = Remove Group
 +action.edit_group = Edit Group
 +action.edit_new_group = Edit New Group
 +action.hide_sequences = Hide Sequences
 +action.reveal_all = Reveal All
 +action.reveal_sequences = Reveal Sequences
 +action.find_all = Find all
 +action.find_next = Find next
 +action.file = File
 +action.view = View
 +action.change_params = Change Parameters
 +action.apply = Apply
 +action.apply_threshold_all_groups = Apply threshold to all groups
 +action.apply_all_groups = Apply to all Groups
 +action.by_chain = By chain
 +action.by_sequence = By Sequence
 +action.paste_annotations = Paste Annotations
 +action.format = Format
 +action.select = Select
 +action.new_view = New View
 +action.close = Close
 +action.add = Add
 +action.save_as_default = Save as default
 +action.cancel_fetch = Cancel Fetch
 +action.save_omit_hidden_columns = Save / Omit Hidden Columns
 +action.change_font = Change Font
 +action.colour = Colour
 +action.calculate = Calculate
 +action.select_all = Select all
 +action.deselect_all = Deselect all
 +action.invert_selection = Invert selection
 +action.using_jmol = Using Jmol
 +action.link = Link
 +action.show_chain = Show Chain
 +label.str = Str:
 +label.seq = Seq:
 +label.structures_manager = Structures Manager
 +label.nickname = Nickname:
 +label.url = URL:
 +label.input_file_url = Enter URL or Input File
 +label.select_feature = Select feature:
 +label.name = Name:
 +label.name_param = Name: {0}
 +label.group = Group:
 +label.colour = Colour:
 +label.description = Description:
 +label.start = Start:
 +label.end = End:
 +label.current_parameter_set_name = Current parameter set name:
 +label.service_action = Service Action:
 +label.post_url = POST URL:
 +label.url_suffix = URL Suffix
 +label.sequence_source = Sequence Source
 +label.per_seq = per Sequence
 +label.result_vertically_separable = Results are vertically separable
 +label.amend = Amend
 +label.undo_command = Undo {0}
 +label.redo_command = Redo {0}
 +label.principal_component_analysis = Principal Component Analysis
 +label.average_distance_identity = Average Distance Using % Identity
 +label.neighbour_joining_identity = Neighbour Joining Using % Identity
 +label.status_bar = Status bar
 +label.out_to_textbox = Output to Textbox
 +label.clustalx = Clustalx
 +label.zappo = Zappo
 +label.taylor = Taylor
 +label.hydrophobicity = Hydrophobicity
 +label.helix_propensity = Helix Propensity
 +label.strand_propensity = Strand Propensity
 +label.turn_propensity = Turn Propensity
 +label.buried_index = Buried Index
 +label.purine_pyrimidine = Purine/Pyrimidine
 +label.percentage_identity = Percentage Identity
 +label.blosum62_score = BLOSUM62 Score
 +label.tcoffee_scores = T-Coffee Scores
 +label.average_distance_bloslum62 = Average Distance Using BLOSUM62
 +label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
 +label.show_annotations = Show annotations
 +label.colour_text = Colour Text
 +label.show_non_conversed = Show nonconserved
 +label.overview_window = Overview Window
 +label.none = None
 +label.above_identity_threshold = Above Identity Threshold
 +label.nucleotide = Nucleotide
 +label.to_new_alignment = To New Alignment
 +label.to_this_alignment = Add To This Alignment
 +label.apply_colour_to_all_groups = Apply Colour To All Groups
 +label.modify_identity_thereshold = Modify Identity Threshold...
 +label.modify_conservation_thereshold = Modify Conservation Threshold...
 +label.input_from_textbox = Input from textbox
 +label.centre_column_labels = Centre column labels
 +label.automatic_scrolling = Automatic Scrolling
 +label.documentation = Documentation
 +label.about = About...
 +label.show_sequence_limits = Show Sequence Limits
 +label.feature_settings = Feature Settings...
 +label.sequence_features = Sequence Features
 +label.all_columns = All Columns
 +label.all_sequences = All Sequences
 +label.selected_columns = Selected Columns 
 +label.selected_sequences = Selected Sequences
 +label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H)
 +label.selected_region = Selected Region
 +label.all_sequences_columns = All Sequences and Columns
 +label.group_consensus = Group Consensus
 +label.group_conservation = Group Conservation
 +label.show_consensus_histogram = Show Consensus Histogram
 +label.show_consensus_logo = Show Consensus Logo
 +label.norm_consensus_logo = Normalise Consensus Logo
 +label.apply_all_groups = Apply to all groups
 +label.autocalculated_annotation = Autocalculated Annotation
 +label.min_colour = Min Colour
 +label.max_colour = Max Colour
 +label.use_original_colours = Use Original Colours
 +label.threshold_minmax = Threshold is min/max
 +label.represent_group_with = Represent Group with
 +label.selection = Selection
 +label.group_colour = Group Colour
 +label.sequence = Sequence
 +label.view_pdb_structure = View PDB Structure
 +label.min = Min:
 +label.max = Max:
 +label.colour_by_label = Colour by label
 +label.new_feature = New Feature
 +label.match_case = Match Case
 +label.view_alignment_editor = View in alignment editor
 +label.labels = Labels
 +label.output_values = Output Values...
 +label.input_data = Input Data...
 +label.nucleotide_matrix = Nucleotide matrix
 +label.protein_matrix = Protein matrix
 +label.show_bootstrap_values = Show Bootstrap Values
 +label.show_distances = Show distances
 +label.mark_unassociated_leaves = Mark Unassociated Leaves
 +label.fit_to_window = Fit To Window
 +label.newick_format = Newick Format
 +label.colours = Colours
 +label.view_mapping = View Mapping
 +label.wireframe = Wireframe
 +label.depthcue = Depthcue
 +label.z_buffering = Z Buffering
 +label.charge_cysteine = Charge & Cysteine
 +label.all_chains_visible = All Chains Visible
 +label.successfully_added_features_alignment = Successfully added features to alignment
 +label.keyboard_editing_mode = Keyboard editing mode is {0}
 +label.paste_features_annotations_Tcoffee_here = Paste your features / annotations / T-coffee score file here.
 +label.removed_columns = Removed {0} columns.
 +label.removed_empty_columns = Removed {0} empty columns.
 +label.paste_newick_tree_file = Paste your Newick tree file here.
 +label.order_by_params = Order by {0}
 +label.html_content = <html>{0}</html>
 +label.paste_pdb_file= Paste your PDB file here.
 +label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0}
 +label.could_not_parse_newick_file  = Could not parse Newick file\!\n {0}
 +label.successfully_pasted_tcoffee_scores_to_alignment= Successfully pasted T-Coffee scores to alignment.
 +label.failed_add_tcoffee_scores = Failed to add T-Coffee scores: 
 +label.successfully_pasted_annotation_to_alignment= Successfully pasted annotation to alignment.
 +label.successfully_pasted_alignment_file = Successfully pasted alignment file
 +label.paste_your_alignment_file = Paste your alignment file here
 +label.paste_your = Paste your
 +label.finished_searching = Finished searching
 +label.search_results= Search results {0} : {1}
 +label.found_match_for = Found match for {0}
 +label.font = Font:
 +label.size = Size:
 +label.style = Style:
 +label.enter_redundancy_threshold = Enter the redundancy threshold
 +label.calculating = Calculating....
 +label.modify_conservation_visibility = Modify conservation visibility
 +label.colour_residues_above_occurence = Colour residues above % occurence
 +label.set_this_label_text = set this label text
 +label.sequences_from = Sequences from {0}
 +label.successfully_loaded_file  = Successfully loaded file {0}
 +label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
 +label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
 +label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
 +label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file
 +label.source_to_target = {0} to '{1}'
 +label.per_sequence_only= Per-sequence only
 +label.to_file = to File
 +label.to_textbox = to Textbox
 +label.jalview = Jalview
 +label.csv_spreadsheet = CSV (Spreadsheet)
 +label.status =  [Status]
 +label.channels = Channels
 +label.channel_title_item_count = {0} ({1})
 +label.blog_item_published_on_date = {0} {1} 
 +label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
 +label.session_update = Session Update
 +label.new_vamsas_session = New Vamsas Session
 +label.groovy_console = Groovy Console...
 +label.lineart = Lineart
 +label.dont_ask_me_again = Don't ask me again
 +label.select_eps_character_rendering_style = Select EPS character rendering style
 +label.invert_selection = Invert Selection
 +label.optimise_order = Optimise Order
 +label.seq_sort_by_score = Seq sort by Score
 +label.load_colours = Load Colours
 +label.save_colours = Save Colours
 +label.fetch_das_features = Fetch DAS Features
 +label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} 
 +label.database_param = Database: {0}
 +label.example_param = Example: {0}
 +label.select_file_format_before_saving = You must select a file format before saving!
 +label.file_format_not_specified = File format not specified
 +label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?
 +label.couldnt_save_file = Couldn't save file: {0}
 +label.error_saving_file = Error Saving File
 +label.remove_from_default_list = Remove from default list?
 +label.remove_user_defined_colour = Remove user defined colour
 +label.you_must_select_least_two_sequences = You must select at least 2 sequences.
 +label.invalid_selection = Invalid Selection
 +label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
 +label.sequence_selection_insufficient = Sequence selection insufficient
 +label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
 +label.not_enough_sequences = Not enough sequences
 +label.selected_region_to_tree_may_only_contain_residues_or_gaps =  The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
 +label.sequences_selection_not_aligned = Sequences in selection are not aligned
 +label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.
 +label.sequences_not_aligned = Sequences not aligned
 +label.problem_reading_tree_file =  Problem reading tree file
 +label.possible_problem_with_tree_file = Possible problem with tree file
 +label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
 +label.translation_failed = Translation Failed
 +label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
 +label.implementation_error  = Implementation error:
 +label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
 +label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
 +label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
 +label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
 +label.enter_view_name = Enter View Name
 +label.enter_label = Enter label
 +label.enter_label_for_the_structure = Enter a label for the structure?
 +label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?
 +label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
 +label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n
 +label.align_to_existing_structure_view = Align to existing structure view
 +label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.
 +label.couldnt_load_file = Couldn't load file
 +label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
 +label.no_pdb_id_in_file = No PDB Id in File
 +label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
 +label.error_parsing_text = Error parsing text
 +label.enter_local_das_source = Enter Nickname & URL of Local DAS Source
 +label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!
 +label.public_das_source = Public DAS source - not editable
 +label.input_alignment_from_url = Input Alignment From URL
 +label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session.
 +label.vamsas_document_import_failed = Vamsas Document Import Failed
 +label.couldnt_locate = Couldn't locate {0}
 +label.url_not_found = URL not found
 +label.no_link_selected = No link selected
 +label.new_sequence_url_link = New sequence URL link
 +label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
 +label.wrapped_view_no_edit = Wrapped view - no edit
 +label.error_retrieving_data = Error Retrieving Data
 +label.user_colour_scheme_must_have_name = User colour scheme must have a name
 +label.no_name_colour_scheme = No name for colour scheme
 +label.invalid_url = Invalid URL !
 +label.error_loading_file = Error loading file
 +label.problems_opening_file = Encountered problems opening {0}!!
 +label.file_open_error = File open error
 +label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.
 +label.no_das_sources_selected_title = No DAS Sources Selected
 +label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"
 +label.duplicate_scheme_name = Duplicate scheme name
 +label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n
 +label.jalview_user_survey = Jalview User Survey
 +label.alignment_properties = Alignment Properties: {0}
 +label.alignment_props = Alignment Properties
 +label.input_cut_paste = Cut & Paste Input
 +label.alignment_output_command = Alignment output - {0}
 +label.annotations = Annotations
 +label.features = Features
 +label.overview_params = Overview {0}
 +label.paste_newick_file = Paste Newick file
 +label.load_tree_from_file = From File - 
 +label.colour_by_annotation = Colour by Annotation
 +label.selection_output_command = Selection output - {0}
 +label.annotation_for_displayid = <p><h2>Annotation for {0} </h2></p><p>
 +label.pdb_sequence_mapping = PDB - Sequence Mapping
 +label.pca_details = PCA details
 +label.redundancy_threshold_selection = Redundancy threshold selection
 +label.user_defined_colours = User defined colours
 +label.jalviewLite_release = JalviewLite - Release {0}
 +label.jaview_build_date = Build date: {0}
- label.jalview_authors_1 = Authors:  Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,
- label.jalview_authors_2 = Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
++label.jalview_authors_1 = Authors: :  Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,
++label.jalview_authors_2 = Daniel Barton, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.
 +label.jalview_dev_managers = Development managed by The Barton Group, University of Dundee, Scotland, UK.
 +label.jalview_distribution_lists = For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list
 +label.jalview_please_cite = If  you use Jalview, please cite:
 +label.jalview_cite_1_authors = Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 +label.jalview_cite_1_title = Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
 +label.jalview_cite_1_ref = Bioinformatics doi: 10.1093/bioinformatics/btp033
 +label.right_click = Right click
 +label.to_add_annotation = to add annotation
 +label.alignment_has_no_annotations = Alignment has no annotations
 +label.retrieving_pdb_data = Retrieving PDB data...
 +label.label = Label
 +label.no_features_added_to_this_alignment = No Features added to this alignment!!
 +label.features_can_be_added_from_searches_1 = (Features can be added from searches or
 +label.features_can_be_added_from_searches_2 = from Jalview / GFF features files)
 +label.calculating_pca= Calculating PCA
 +label.reveal_columns = Reveal Columns
 +label.jalview_cannot_open_file = Jalview can't open file
 +label.jalview_applet = Jalview applet
 +label.loading_data = Loading data
 +label.memory_stats = Total Free Memory: {0} MB; Max Memory: {1} MB; {2} %
 +label.calculating_tree = Calculating tree
 +label.state_queueing = queuing
 +label.state_running = running
 +label.state_complete = complete
 +label.state_job_cancelled = job cancelled!!
 +label.state_job_error = job error!
 +label.server_error_try_later = Server Error! (try later)
 +label.error_loading_pdb_data = Error loading PDB data!!
 +label.fetching_pdb_data = Fetching PDB data...
 +label.structure_type = Structure_type
 +label.settings_for_type = Settings for {0}
 +label.view_full_application = View in Full Application
 +label.load_associated_tree = Load Associated Tree ...
 +label.load_features_annotations = Load Features/Annotations ...
 +label.export_features = Export Features ...
 +label.export_annotations = Export Annotations ...
 +label.jalview_copy = Copy (Jalview Only)
 +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_sequence = Edit Sequence
 +label.sequence_details = Sequence Details
 +label.jmol_help = Jmol Help
 +label.all = All
 +label.sort_by_score = Sort by Score
 +label.sort_by_density = Sort by Density
 +label.reveal = Reveal
 +label.hide_columns = Hide Columns
diff --cc src/MCview/AppletPDBViewer.java
index b2e1187,f01a7e3..d550326c
mode 100644,100755..100644
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
diff --cc src/jalview/appletgui/APopupMenu.java
index c51653d,35fe48b..1bb4049
mode 100644,100755..100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
diff --cc src/jalview/appletgui/AnnotationColourChooser.java
index 3c0f704,33c0bb8..27d5497
mode 100644,100755..100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
diff --cc src/jalview/appletgui/CutAndPasteTransfer.java
index 8e758e6,eccfc52..6bfe6b0
mode 100644,100755..100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
diff --cc src/jalview/appletgui/FeatureRenderer.java
index a14c321,e2e9fe2..0a40439
mode 100644,100755..100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
diff --cc src/jalview/appletgui/Finder.java
index 93ab314,11bf1ac..ad99983
mode 100644,100755..100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
diff --cc src/jalview/appletgui/FontChooser.java
index 7de8789,85537bf..34b014c
mode 100644,100755..100644
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
diff --cc src/jalview/appletgui/PCAPanel.java
index bcd3634,46343ce..78f950b
mode 100644,100755..100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
diff --cc src/jalview/appletgui/PairwiseAlignPanel.java
index a377892,6e3f8ed..2df0eac
mode 100644,100755..100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
diff --cc src/jalview/appletgui/RedundancyPanel.java
index d91e53b,5712390..345c906
mode 100644,100755..100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
diff --cc src/jalview/appletgui/SliderPanel.java
index 886c194,68d2b2f..340bb64
mode 100644,100755..100644
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
diff --cc src/jalview/appletgui/UserDefinedColours.java
index 55f7c65,b245565..225cfc7
mode 100644,100755..100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
diff --cc src/jalview/gui/AlignFrame.java
index 62fd29d,7975671..57ff660
mode 100644,100755..100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
diff --cc src/jalview/gui/AnnotationColourChooser.java
index 5ee69f2,7c9a118..69b54ea
mode 100644,100755..100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
diff --cc src/jalview/gui/AnnotationExporter.java
index 02758fa,9b812af..bcf29cd
mode 100644,100755..100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
diff --cc src/jalview/gui/CutAndPasteTransfer.java
index 2a555d0,7e55f38..5c397f4
mode 100644,100755..100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
diff --cc src/jalview/gui/DasSourceBrowser.java
index 293f9db,3b5e8f9..340e134
mode 100644,100755..100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
diff --cc src/jalview/gui/EPSOptions.java
index 89e34f7,da85114..551129e
mode 100644,100755..100644
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
diff --cc src/jalview/gui/FeatureRenderer.java
index 587c12f,a5b5029..84d2284
mode 100644,100755..100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
diff --cc src/jalview/gui/FeatureSettings.java
index 106ced9,9f73873..4e9db60
mode 100644,100755..100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
diff --cc src/jalview/gui/PCAPanel.java
index 663c262,e59005f..538b245
mode 100644,100755..100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
diff --cc src/jalview/gui/WebserviceInfo.java
index ea2bacb,27cbfe4..760db66
mode 100644,100755..100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
diff --cc src/jalview/schemabinding/version2/AnnotationColours.java
index 9eef6f0,f9cd7e5..a8a10c6
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@@ -1,14 -1,25 +1,26 @@@
  /*
-  * This class was automatically generated with 
-  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
-  * Schema.
-  * $Id$
+  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+  * Copyright (C) 2014 The Jalview Authors
+  * 
+  * This file is part of Jalview.
+  * 
+  * Jalview is free software: you can redistribute it and/or
+  * modify it under the terms of the GNU General Public License 
+  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+  *  
+  * Jalview is distributed in the hope that it will be useful, but 
+  * WITHOUT ANY WARRANTY; without even the implied warranty 
+  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+  * PURPOSE.  See the GNU General Public License for more details.
+  * 
+  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
   */
 +
  package jalview.schemabinding.version2;
  
 -//---------------------------------/
 -//- Imported classes and packages -/
 +  //---------------------------------/
 + //- Imported classes and packages -/
  //---------------------------------/
  
  import org.exolab.castor.xml.Marshaller;
diff --cc src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 196ad60,a142283..627ecde
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@@ -1,14 -1,25 +1,26 @@@
  /*
-  * This class was automatically generated with 
-  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
-  * Schema.
-  * $Id$
+  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+  * Copyright (C) 2014 The Jalview Authors
+  * 
+  * This file is part of Jalview.
+  * 
+  * Jalview is free software: you can redistribute it and/or
+  * modify it under the terms of the GNU General Public License 
+  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+  *  
+  * Jalview is distributed in the hope that it will be useful, but 
+  * WITHOUT ANY WARRANTY; without even the implied warranty 
+  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+  * PURPOSE.  See the GNU General Public License for more details.
+  * 
+  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+  * The Jalview Authors are detailed in the 'AUTHORS' file.
   */
 +
  package jalview.schemabinding.version2.descriptors;
  
 -//---------------------------------/
 -//- Imported classes and packages -/
 +  //---------------------------------/
 + //- Imported classes and packages -/
  //---------------------------------/
  
  import jalview.schemabinding.version2.AnnotationColours;