Jalview Command Line Arguments

From c42bc457ef9b3a5606f309268d4a644ef113c390 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 14 Jun 2010 11:40:48 +0000 Subject: [PATCH] 2.5.1 release branding --- doc/AddingGroovySupport.html | 19 +- doc/building.html | 19 +- doc/developing.html | 19 +- doc/index.html | 19 +- doc/newdmobj.html | 19 +- help/html/calculations/consensus.html | 19 +- help/html/calculations/conservation.html | 19 +- help/html/calculations/pairwise.html | 19 +- help/html/calculations/pca.html | 19 +- help/html/calculations/quality.html | 19 +- help/html/calculations/recoverInputdata.html | 19 +- help/html/calculations/redundancy.html | 19 +- help/html/calculations/sorting.html | 19 +- help/html/calculations/tree.html | 19 +- help/html/calculations/treeviewer.html | 19 +- help/html/colourSchemes/abovePID.html | 19 +- help/html/colourSchemes/annotationColouring.html | 19 +- help/html/colourSchemes/blosum.html | 19 +- help/html/colourSchemes/buried.html | 19 +- help/html/colourSchemes/clustal.html | 19 +- help/html/colourSchemes/conservation.html | 19 +- help/html/colourSchemes/helix.html | 19 +- help/html/colourSchemes/hydrophobic.html | 19 +- help/html/colourSchemes/index.html | 19 +- help/html/colourSchemes/nucleotide.html | 19 +- help/html/colourSchemes/pid.html | 19 +- help/html/colourSchemes/strand.html | 19 +- help/html/colourSchemes/taylor.html | 19 +- help/html/colourSchemes/textcolour.html | 19 +- help/html/colourSchemes/turn.html | 19 +- help/html/colourSchemes/user.html | 19 +- help/html/colourSchemes/zappo.html | 19 +- help/html/editing/index.html | 19 +- help/html/features/annotation.html | 19 +- help/html/features/annotationsFormat.html | 19 +- help/html/features/clarguments.html | 248 ++--- help/html/features/codingfeatures.html | 19 +- help/html/features/commandline.html | 19 +- help/html/features/creatinFeatures.html | 19 +- help/html/features/cursorMode.html | 19 +- help/html/features/dasfeatures.html | 19 +- help/html/features/dassettings.html | 19 +- help/html/features/editingFeatures.html | 19 +- help/html/features/featuresFormat.html | 19 +- help/html/features/featureschemes.html | 19 +- help/html/features/featuresettings.html | 19 +- help/html/features/groovy.html | 19 +- help/html/features/hiddenRegions.html | 19 +- help/html/features/jalarchive.html | 19 +- help/html/features/jmol.html | 19 +- help/html/features/multipleViews.html | 19 +- help/html/features/newkeystrokes.html | 19 +- help/html/features/overview.html | 19 +- help/html/features/pdbviewer.html | 19 +- help/html/features/preferences.html | 19 +- help/html/features/search.html | 19 +- help/html/features/seqfeatures.html | 19 +- help/html/features/seqfetch.html | 19 +- help/html/features/seqmappings.html | 19 +- help/html/features/viewingpdbs.html | 19 +- help/html/features/wrap.html | 19 +- help/html/index.html | 19 +- help/html/io/export.html | 19 +- help/html/io/fileformats.html | 19 +- help/html/io/index.html | 19 +- help/html/io/modellerpir.html | 19 +- help/html/jalviewjnlp.html | 19 +- help/html/keys.html | 19 +- help/html/memory.html | 19 +- help/html/menus/alignmentMenu.html | 19 +- help/html/menus/alwannotations.html | 19 +- help/html/menus/alwcalculate.html | 19 +- help/html/menus/alwcolour.html | 19 +- help/html/menus/alwedit.html | 19 +- help/html/menus/alwfile.html | 19 +- help/html/menus/alwformat.html | 19 +- help/html/menus/alwselect.html | 19 +- help/html/menus/alwview.html | 19 +- help/html/menus/desktopMenu.html | 19 +- help/html/menus/index.html | 19 +- help/html/menus/popupMenu.html | 19 +- help/html/menus/wsmenu.html | 19 +- help/html/misc/aaproperties.html | 19 +- help/html/misc/aminoAcids.html | 19 +- help/html/misc/geneticCode.html | 19 +- help/html/privacy.html | 19 +- help/html/releases.html | 1293 +++++++++++----------- help/html/vamsas/index.html | 19 +- help/html/webServices/clustalw.html | 19 +- help/html/webServices/dbreffetcher.html | 19 +- help/html/webServices/index.html | 20 +- help/html/webServices/jnet.html | 19 +- help/html/webServices/mafft.html | 19 +- help/html/webServices/msaclient.html | 19 +- help/html/webServices/muscle.html | 19 +- help/html/webServices/urllinks.html | 19 +- help/html/whatsNew.html | 142 +-- 97 files changed, 859 insertions(+), 2611 deletions(-) diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index becc431..7f5adb1 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,23 +1,6 @@ -#------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) -# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle -# -# 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 . -#------------------------------------------------------------------------------- -Jalview Command Line Arguments +Jalview Command Line Arguments + -

The Jalview Executable's Command Line Arguments

-See -running Jalview from the command line -for more information. -
- - - - - +

The Jalview Executable's Command Line + Arguments

+ See running Jalview from the command + line for more information.
+

-nodisplay

Run Jalview without User Interface. - (automatically disables questionnaire, version and usage stats checks)

+ + + + - - - - - - - + + + + + + @@ -81,7 +52,7 @@ for more information. the built-in colourschemes, a name of a predefined colourscheme (defined in the jalview properties file), or an 'inline' colourscheme (see the applet's colour parameter for more information). - + - - - - @@ -144,47 +111,38 @@ for more information. - @@ -196,91 +154,51 @@ for more information.

Create alignment file FILE in Fasta format.

- - - - - - + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - -

-nodisplay	Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)
- -props FILE -	- Use the given Jalview properties file instead - of users default. -
- -features FILE -	- - Use the given file to add sequence features to an alignment. - See Features File - (Known as Groups file prior to 2.08) description. +
-props FILE	Use the given Jalview properties file instead + of users default.
-features FILE	+ Use the given file to add sequence features to an alignment. + See Features + File (Known as Groups file prior to 2.08) description.
-annotations FILE @@ -113,30 +84,26 @@ for more information. Turn off questionnaire check
+
-nousagestats	Turn off google analytics usage tracking
- -[no]sortbytree +
+ -[no]sortbytree	- Enable or disable automatic sorting of - associated view when a new tree is displayed + Enable or disable automatic sorting of associated view when a new tree is displayed
-dasserver nickname=URL	- Add and enable a DAS - server with given nickname (alphanumeric or underscores only) for - retrieval of features for all alignments - Sources that also support the sequence command may be specified by - prepending the URL with 'sequence:' + Add and enable a DAS server with given + nickname (alphanumeric or underscores only) for retrieval of features + for all alignments + Sources that also support the sequence command may be specified by prepending the URL with 'sequence:' e.g. sequence:http://localdas.somewhere.org/das/source
-fetchfrom nickname	- Query a DAS - source called nickname for features for the alignments and display - them + Query a DAS source called nickname for features for the alignments + and display them
-groovy FILE	- Execute groovy script in FILE (where FILE may - be 'STDIN' to read from the standard input) after all other arguments - have been processed + Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other + arguments have been processed
+	-vdoc VAMSAS DOCUMENT FILE or URL	- Import the given vamsas document into a new - session. - New in 2.5 + Import the given vamsas document into a new session. New in 2.5
-vsess VAMSAS SESSION URL	- Join the given vamsas session - If a document was also specified, this will be imported first and then - committed as new data from Jalview to the specified session - (Experimental - not yet enabled!).New in 2.5 - + Join the given vamsas session If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).New in 2.5
-groovy FILE	- Execute groovy script in FILE (where FILE may - be 'STDIN' to read from the standard input) after all other arguments - have been processed + Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other + arguments have been processed
- -clustal FILE -	- Create alignment file FILE in Clustal format. -
- -msf FILE -
-clustal FILE	Create alignment file FILE in Clustal format.
-msf FILE	- Create alignment file FILE in MSF format. -
- -pileup FILE -	- Create alignment file FILE in Pileup format. -
- -pir FILE -	Create alignment file FILE in MSF format.
-pileup FILE	Create alignment file FILE in Pileup format.
-pir FILE	- Create alignment file FILE in PIR format. -
- -pfam FILE -	- Create alignment file FILE in PFAM format. -
- -blc FILE -	- Create alignment file FILE in BLC format. -
- -jalview FILE -	Create alignment file FILE in PIR format.
-pfam FILE	Create alignment file FILE in PFAM format.
-blc FILE	Create alignment file FILE in BLC format.
-jalview FILE	- Create alignment file FILE in Jalview format. -
- -png FILE -	- Create PNG image FILE from alignment. -
- -imgMap FILE -	Create alignment file FILE in Jalview format.
-png FILE	Create PNG image FILE from alignment.
-imgMap FILE	- Create HTML file FILE with image map of PNG - image. -
- -eps FILE -	- Create EPS file FILE from alignment. -

Create HTML file FILE with image map of PNG + image.

+ + +

-eps FILE

Create EPS file FILE from alignment.

+ + diff --git a/help/html/features/codingfeatures.html b/help/html/features/codingfeatures.html index 2b37cad..d9fe2c4 100644 --- a/help/html/features/codingfeatures.html +++ b/help/html/features/codingfeatures.html @@ -1,23 +1,6 @@ -#------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) -# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle -# -# 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 . -#------------------------------------------------------------------------------- - - Application -

Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources
Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box.
DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms).
Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application.
Group-associated consensus, sequence logos and conservation - plots
Symbol distributions for each column can be exported and - visualized as sequence logos
Optionally scale multi-character column labels to fit within - each column of annotation row
Optional automatic sort of associated alignment view when a - new tree is opened.
Jalview Java Console
Better placement of desktop window when moving between - different screens.
New preference items for sequence ID tooltip and consensus - annotation
Client to submit sequences and IDs to Envision2 Workflows
Vamsas Capabilities -
- Improved VAMSAS synchronization (jalview archive used to - preserve views, structures, and tree display settings)
- Import of vamsas documents from disk or URL via command - line
- Sharing of selected regions between views and with other - VAMSAS applications (Experimental feature!)
- Updated API to VAMSAS version 0.2
-

- Applet -

Middle button resizes annotation row height
New Parameters -
- sortByTree (true/false) - automatically sort the associated - alignment view by the tree when a new tree is opened.
- showTreeBootstraps (true/false) - show or hide branch - bootstraps (default is to show them if available)
- showTreeDistances (true/false) - show or hide branch - lengths (default is to show them if available)
- showUnlinkedTreeNodes (true/false) - indicate if - unassociated nodes should be highlighted in the tree view
- heightScale and widthScale (1.0 or more) - increase the - height or width of a cell in the alignment grid relative to the - current font size.
-
Non-positional features displayed in sequence ID tooltip

- Other -

Features format: graduated colour definitions and - specification of feature scores
Alignment Annotations format: new keywords for group - associated annotation (GROUP_REF) and annotation row display - properties (ROW_PROPERTIES)
XML formats extended to support graduated feature - colourschemes, group associated annotation, and profile visualization - settings.

Source field in GFF files parsed as feature source rather - than description
Non-positional features are now included in sequence feature - and gff files (controlled via non-positional feature visibility in - tooltip).
URL links generated for all feature links (bugfix)
Added URL embedding instructions to features file - documentation.
Codons containing ambiguous nucleotides translated as 'X' in - peptide product
Match case switch in find dialog box works for both sequence - ID and sequence string and query strings do not have to be in upper - case to match case-insensitively.
AMSA files only contain first column of multi-character - column annotation labels
Jalview Annotation File generation/parsing consistent with - documentation (e.g. Stockholm annotation can be exported and - re-imported)
PDB files without embedded PDB IDs given a friendly name
Find incrementally searches ID string matches as well as - subsequence matches, and correctly reports total number of both.
Application: -
- Better handling of exceptions during sequence retrieval
- Dasobert generated non-positional feature URL link text - excludes the start_end suffix
- DAS feature and source retrieval buttons disabled when - fetch or registry operations in progress.
- PDB files retrieved from URLs are cached properly
- Sequence description lines properly shared via VAMSAS
- Sequence fetcher fetches multiple records for all data - sources
- Ensured that command line das feature retrieval completes - before alignment figures are generated.
- Reduced time taken when opening file browser for first - time.
- isAligned check prior to calculating tree, PCA or - submitting an MSA to JNet now excludes hidden sequences.
- User defined group colours properly recovered from Jalview - projects.
-

Group-associated consensus, sequence logos and conservation + plots
Symbol distributions for each column can be exported and + visualized as sequence logos
Optionally scale multi-character column labels to fit within + each column of annotation row
Optional automatic sort of associated alignment view when a + new tree is opened.
Jalview Java Console
Better placement of desktop window when moving between different screens.
New preference items for sequence ID tooltip and consensus + annotation
Client to submit sequences and IDs to Envision2 Workflows
Vamsas Capabilities +
- Improved VAMSAS synchronization (jalview archive used to + preserve views, structures, and tree display settings)
- Import of vamsas documents from disk or URL via command line
- Sharing of selected regions between views and with other + VAMSAS applications (Experimental feature!)
- Updated API to VAMSAS version 0.2
+

+Applet +

Middle button resizes annotation row height
New Parameters +
- sortByTree (true/false) - automatically sort the associated + alignment view by the tree when a new tree is opened.
- showTreeBootstraps (true/false) - show or hide branch + bootstraps (default is to show them if available)
- showTreeDistances (true/false) - show or hide branch lengths + (default is to show them if available)
- showUnlinkedTreeNodes (true/false) - indicate if unassociated + nodes should be highlighted in the tree view
- heightScale and widthScale (1.0 or more) - increase the + height or width of a cell in the alignment grid relative to the + current font size.
+
Non-positional features displayed in sequence ID tooltip

+Other +

Features format: graduated colour definitions and + specification of feature scores
Alignment Annotations format: new keywords for group + associated annotation (GROUP_REF) and annotation row display properties + (ROW_PROPERTIES)
XML formats extended to support graduated feature + colourschemes, group associated annotation, and profile visualization + settings.

Source field in GFF files parsed as feature source rather + than description
Non-positional features are now included in sequence feature + and gff files (controlled via non-positional feature visibility in + tooltip).
URL links generated for all feature links (bugfix)
Added URL embedding instructions to features file + documentation.
Codons containing ambiguous nucleotides translated as 'X' in + peptide product
Match case switch in find dialog box works for both sequence + ID and sequence string and query strings do not have to be in upper + case to match case-insensitively.
AMSA files only contain first column of multi-character + column annotation labels
Jalview Annotation File generation/parsing consistent with + documentation (e.g. Stockholm annotation can be exported and + re-imported)
PDB files without embedded PDB IDs given a friendly name
Find incrementally searches ID string matches as well as + subsequence matches, and correctly reports total number of both.
Application: +
- Better handling of exceptions during sequence retrieval
- Dasobert generated non-positional feature URL link text + excludes the start_end suffix
- DAS feature and source retrieval buttons disabled when fetch + or registry operations in progress.
- PDB files retrieved from URLs are cached properly
- Sequence description lines properly shared via VAMSAS
- Sequence fetcher fetches multiple records for all data + sources
- Ensured that command line das feature retrieval completes + before alignment figures are generated.
- Reduced time taken when opening file browser for first time.
- isAligned check prior to calculating tree, PCA or submitting + an MSA to JNet now excludes hidden sequences.
- User defined group colours properly recovered from Jalview projects.
+

Sequence Group colour can be specified in Annotation File
Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme

- VAMSAS Client capabilities (Experimental) -

treenode binding for VAMSAS tree exchange
local editing and update of sequences in VAMSAS alignments - (experimental)
Create new or select existing session to join
load and save of vamsas documents

- Application command line -

-tree parameter to open trees (introduced for passing from - applet)
-fetchfrom command line argument to specify nicknames of DAS - servers to query for alignment features
-dasserver command line argument to add new servers that are - also automatically queried for features
-groovy command line argument executes a given groovy script - after all input data has been loaded and parsed

- Applet-Application data exchange -

Trees passed as applet parameters can be passed to - application (when using "View in full application")

- Applet Parameters -

feature group display control parameter
debug parameter
showbutton parameter

- Applet API methods -

newView public method
Window (current view) specific get/set public methods
Feature display control methods
get list of currently selected sequences

- New Jalview distribution features -

InstallAnywhere Installer upgraded to IA 2008 VP1
RELEASE file gives build properties for the latest Jalview - release.
Java 1.1 Applet build made easier and donotobfuscate - property controls execution of obfuscator
Build target for generating source distribution
Debug flag for javacc
.jalview_properties file is documented (slightly) in - jalview.bin.Cache
Continuous Build Integration for stable and development - version of Application, Applet and source distribution

+ +VAMSAS Client capabilities (Experimental) +

treenode binding for VAMSAS tree exchange
local editing and update of sequences in VAMSAS alignments + (experimental)
Create new or select existing session to join
load and save of vamsas documents

+Application command line +

-tree parameter to open trees (introduced for passing from + applet)
-fetchfrom command line argument to specify nicknames of DAS + servers to query for alignment features
-dasserver command line argument to add new servers that are + also automatically queried for features
-groovy command line argument executes a given groovy script + after all input data has been loaded and parsed

+Applet-Application data exchange +

Trees passed as applet parameters can be passed to application + (when using "View in full application")

+Applet Parameters +

feature group display control parameter
debug parameter
showbutton parameter

+Applet API methods +

newView public method
Window (current view) specific get/set public methods
Feature display control methods
get list of currently selected sequences

+New Jalview distribution features +

InstallAnywhere Installer upgraded to IA 2008 VP1
RELEASE file gives build properties for the latest Jalview + release.
Java 1.1 Applet build made easier and donotobfuscate property + controls execution of obfuscator
Build target for generating source distribution
Debug flag for javacc
.jalview_properties file is documented (slightly) in + jalview.bin.Cache
Continuous Build Integration for stable and development + version of Application, Applet and source distribution

- - -

selected region output includes visible annotations (for - certain formats)
edit label/displaychar contains existing label/char for - editing
update PDBEntries when DBRefEntries change (vamsas)
shorter peptide product names from EMBL records
Newick string generator makes compact representations
bootstrap values parsed correctly for tree files with - comments
pathological filechooser bug avoided by not allowing - filenames containing a ':'
Fixed exception when parsing GFF files containing global - sequence features
Alignment datasets are finalized only when number of - references from alignment sequences goes to zero
Close of tree branch colour box without colour selection - causes cascading exceptions
occasional negative imgwidth exceptions
better reporting of non-fatal warnings to user when file - parsing fails.
Save works when Jalview project is default format
Save as dialog opened if current alignment format is not a - valid output format
Uniprot canonical names introduced for both das and vamsas
Histidine should be midblue (not pink!) in Zappo
error messages passed up and output when data read fails
edit undo recovers previous dataset sequence when sequence - is edited
allow PDB files without pdb ID HEADER lines (like those - generated by MODELLER) to be read in properly
allow reading of JPred concise files as a normal filetype
Stockholm annotation parsing and alignment properties import - fixed for PFAM records
Structure view windows have correct name in Desktop window - list
annotation consisting of sequence associated scores can be - read and written correctly to annotation file
Aligned cDNA translation to aligned peptide works correctly
Fixed display of hidden sequence markers and non-italic font - for representatives in Applet
Applet Menus are always embedded in applet window on Macs.
Newly shown features appear at top of stack (in Applet)
Annotations added via parameter not drawn properly due to - null pointer exceptions
Secondary structure lines are drawn starting from first - column of alignment
Uniprot XML import updated for new schema release in July - 2008
Sequence feature to sequence ID match for Features file is - case-insensitive
Sequence features read from Features file appended to all - sequences with matching IDs
PDB structure coloured correctly for associated views - containing a sub-sequence
PDB files can be retrieved by applet from Jar files
feature and annotation file applet parameters referring to - different directories are retrieved correctly
Fixed application hang whilst waiting for splash-screen - version check to complete
Applet properly URLencodes input parameter values when - passing them to the launchApp service
display name and local features preserved in results - retrieved from web service
Visual delay indication for sequence retrieval and sequence - fetcher initialisation
updated Application to use DAS 1.53e version of dasobert DAS - client
Re-instated Full AMSA support and .amsa file association
Fixed parsing of JNet Concise annotation sans - sequences

- - - - -

2.3
- 9/5/07

- - -

Jmol 11.0.2 integration
PDB views stored in Jalview XML files
Slide sequences
Edit sequence in place
EMBL CDS features
DAS Feature mapping
Feature ordering
Alignment Properties
Annotation Scores
Sort by scores
Feature/annotation editing in applet

- - -

Headless state operation in 2.2.1
Incorrect and unstable DNA pairwise alignment
Cut and paste of sequences with annotation
Feature group display state in XML
Feature ordering in XML
blc file iteration selection using filename # suffix
Stockholm alignment properties
Stockhom alignment secondary structure annotation
2.2.1 applet had no feature transparency
Number pad keys can be used in cursor mode
Structure Viewer mirror image resolved

- + + +

selected region output includes visible annotations (for + certain formats)
edit label/displaychar contains existing label/char for + editing
update PDBEntries when DBRefEntries change (vamsas)
shorter peptide product names from EMBL records
Newick string generator makes compact representations
bootstrap values parsed correctly for tree files with comments
pathological filechooser bug avoided by not allowing filenames + containing a ':'
Fixed exception when parsing GFF files containing global + sequence features
Alignment datasets are finalized only when number of + references from alignment sequences goes to zero
Close of tree branch colour box without colour selection + causes cascading exceptions
occasional negative imgwidth exceptions
better reporting of non-fatal warnings to user when file + parsing fails.
Save works when Jalview project is default format
Save as dialog opened if current alignment format is not a + valid output format
Uniprot canonical names introduced for both das and vamsas
Histidine should be midblue (not pink!) in Zappo
error messages passed up and output when data read fails
edit undo recovers previous dataset sequence when sequence is + edited
allow PDB files without pdb ID HEADER lines (like those + generated by MODELLER) to be read in properly
allow reading of JPred concise files as a normal filetype
Stockholm annotation parsing and alignment properties import + fixed for PFAM records
Structure view windows have correct name in Desktop window + list
annotation consisting of sequence associated scores can be + read and written correctly to annotation file
Aligned cDNA translation to aligned peptide works correctly
Fixed display of hidden sequence markers and non-italic font + for representatives in Applet
Applet Menus are always embedded in applet window on Macs.
Newly shown features appear at top of stack (in Applet)
Annotations added via parameter not drawn properly due to null + pointer exceptions
Secondary structure lines are drawn starting from first column + of alignment
Uniprot XML import updated for new schema release in July 2008
Sequence feature to sequence ID match for Features file is + case-insensitive
Sequence features read from Features file appended to all + sequences with matching IDs
PDB structure coloured correctly for associated views + containing a sub-sequence
PDB files can be retrieved by applet from Jar files
feature and annotation file applet parameters referring to + different directories are retrieved correctly
Fixed application hang whilst waiting for splash-screen + version check to complete
Applet properly URLencodes input parameter values when passing + them to the launchApp service
display name and local features preserved in results retrieved + from web service
Visual delay indication for sequence retrieval and sequence + fetcher initialisation
updated Application to use DAS 1.53e version of dasobert DAS + client
Re-instated Full AMSA support and .amsa file association
Fixed parsing of JNet Concise annotation sans + sequences

+ + + + +

2.3
+ 9/5/07

+ + +

Jmol 11.0.2 integration
PDB views stored in Jalview XML files
Slide sequences
Edit sequence in place
EMBL CDS features
DAS Feature mapping
Feature ordering
Alignment Properties
Annotation Scores
Sort by scores
Feature/annotation editing in applet

+ + +

Headless state operation in 2.2.1
Incorrect and unstable DNA pairwise alignment
Cut and paste of sequences with annotation
Feature group display state in XML
Feature ordering in XML
blc file iteration selection using filename # suffix
Stockholm alignment properties
Stockhom alignment secondary structure annotation
2.2.1 applet had no feature transparency
Number pad keys can be used in cursor mode
Structure Viewer mirror image resolved

+ - - - -

2.2.1
- 12/2/07

- - -

Non standard characters can be read and displayed -
Annotations/Features can be imported/exported to the applet - via textbox -
Applet allows editing of sequence/annotation/group name - & description -
Preference setting to display sequence name in italics -
Annotation file format extended to allow Sequence_groups to - be defined -
Default opening of alignment overview panel can be specified - in preferences -
PDB residue numbering annotation added to associated - sequences -

- - -

Applet crash under certain Linux OS with Java 1.6 installed -
Annotation file export / import bugs fixed -
PNG / EPS image output bugs fixed -

- - - - -

2.2
- 27/11/06

- - -

Multiple views on alignment -
Sequence feature editing -
"Reload" alignment -
"Save" to current filename -
Background dependent text colour -
Right align sequence ids -
User-defined lower case residue colours -
Format Menu -
Select Menu -
Menu item accelerator keys -
Control-V pastes to current alignment -
Cancel button for DAS Feature Fetching -
PCA and PDB Viewers zoom via mouse roller -
User-defined sub-tree colours and sub-tree selection -
'New Window' button on the 'Output to Text box' -

- - -

New memory efficient Undo/Redo System -
Optimised symbol lookups and conservation/consensus - calculations -
Region Conservation/Consensus recalculated after edits -
Fixed Remove Empty Columns Bug (empty columns at end of - alignment) -
Slowed DAS Feature Fetching for increased robustness. -
Made angle brackets in ASCII feature descriptions display - correctly -
Re-instated Zoom function for PCA -
Sequence descriptions conserved in web service analysis - results -
Uniprot ID discoverer uses any word separated by ∣ -
WsDbFetch query/result association resolved -
Tree leaf to sequence mapping improved -
Smooth fonts switch moved to FontChooser dialog box. -

- - - - -

2.1.1
- 12/9/06

- - -

Copy consensus sequence to clipboard

- - -

Image output - rightmost residues are rendered if sequence - id panel has been resized
Image output - all offscreen group boundaries are rendered
Annotation files with sequence references - all elements in - file are relative to sequence position
Mac Applet users can use Alt key for group editing

- - - - -

2.1
- 22/8/06

- - -

MAFFT Multiple Alignment in default Web Service list
DAS Feature fetching
Hide sequences and columns
Export Annotations and Features
GFF file reading / writing
Associate structures with sequences from local PDB files
Add sequences to exisiting alignment
Recently opened files / URL lists
Applet can launch the full application
Applet has transparency for features (Java 1.2 required)
Applet has user defined colours parameter
Applet can load sequences from parameter "sequencex"

- - -

Redundancy Panel reinstalled in the Applet
Monospaced font - EPS / rescaling bug fixed
Annotation files with sequence references bug fixed

- - - - -

2.08.1
- 2/5/06

- - -

Change case of selected region from Popup menu
Choose to match case when searching
Middle mouse button and mouse movement can compress / expand - the visible width and height of the alignment

- - -

Annotation Panel displays complete JNet results

- - - - -

2.08b
- 18/4/06

- - - -

Java 1.5 bug - InternalMessageDialog fix for threads
Righthand label on wrapped alignments shows correct value

- - - - -

2.08
- 10/4/06

- - -

Editing can be locked to the selection area
Keyboard editing
Create sequence features from searches
Precalculated annotations can be loaded onto alignments
Features file allows grouping of features
Annotation Colouring scheme added
Smooth fonts off by default - Faster rendering
Choose to toggle Autocalculate Consensus On/Off

- - -

Drag & Drop fixed on Linux
Jalview Archive file faster to load/save, sequence - descriptions saved.

- - - - -

2.07
- 12/12/05

- - -

PDB Structure Viewer enhanced
Sequence Feature retrieval and display enhanced
Choose to output sequence start-end after sequence name for - file output
Sequence Fetcher WSDBFetch@EBI
Applet can read feature files, PDB files and can be used for - HTML form input

- - -

HTML output writes groups and features
Group editing is Control and mouse click
File IO bugs

- - - - -

2.06
- 28/9/05

- - -

View annotations in wrapped mode
More options for PCA viewer

- - -

GUI bugs resolved
Runs with -nodisplay from command line

- - - - -

2.05b
- 15/9/05

- - -

Choose EPS export as lineart or text
Jar files are executable
Can read in Uracil - maps to unknown residue

- - -

Known OutOfMemory errors give warning message
Overview window calculated more efficiently
Several GUI bugs resolved

- - - - -

2.05
- 30/8/05

- - -

Edit and annotate in "Wrapped" view

- - -

Several GUI bugs resolved

- - - - -

2.04
- 24/8/05

- - -

Hold down mouse wheel & scroll to change font size

- - -

Improved JPred client reliability
Improved loading of Jalview files

- - - - -

2.03
- 18/8/05

- - -

Set Proxy server name and port in preferences
Multiple URL links from sequence ids
User Defined Colours can have a scheme name and added to - Colour Menu
Choose to ignore gaps in consensus calculation
Unix users can set default web browser
Runs without GUI for batch processing
Dynamically generated Web Service Menus

- - -

InstallAnywhere download for Sparc Solaris

- - - - -

2.02
- 18/7/05

- - - -

Copy & Paste order of sequences maintains alignment - order.

- - - - -

2.01
- 12/7/05

- - -

Use delete key for deleting selection.
Use Mouse wheel to scroll sequences.
Help file updated to describe how to add alignment - annotations.
Version and build date written to build properties file.
InstallAnywhere installation will check for updates at - launch of Jalview.

- - -

Delete gaps bug fixed.
FileChooser sorts columns.
Can remove groups one by one.
Filechooser icons installed.
Finder ignores return character when searching. Return key - will initiate a search.
-

- - - - -

2.0
- 20/6/05

- - -

New codebase

- - - + + + +

2.2.1
+ 12/2/07

+ + +

Non standard characters can be read and displayed +
Annotations/Features can be imported/exported to the applet + via textbox +
Applet allows editing of sequence/annotation/group name & + description +
Preference setting to display sequence name in italics +
Annotation file format extended to allow Sequence_groups to + be defined +
Default opening of alignment overview panel can be specified + in preferences +
PDB residue numbering annotation added to associated + sequences +

+ + +

Applet crash under certain Linux OS with Java 1.6 installed +
Annotation file export / import bugs fixed +
PNG / EPS image output bugs fixed +

+ + + + +

2.2
+ 27/11/06

+ + +

Multiple views on alignment +
Sequence feature editing +
"Reload" alignment +
"Save" to current filename +
Background dependent text colour +
Right align sequence ids +
User-defined lower case residue colours +
Format Menu +
Select Menu +
Menu item accelerator keys +
Control-V pastes to current alignment +
Cancel button for DAS Feature Fetching +
PCA and PDB Viewers zoom via mouse roller +
User-defined sub-tree colours and sub-tree selection +
'New Window' button on the 'Output to Text box' +

+ + +

New memory efficient Undo/Redo System +
Optimised symbol lookups and conservation/consensus + calculations +
Region Conservation/Consensus recalculated after edits +
Fixed Remove Empty Columns Bug (empty columns at end of + alignment) +
Slowed DAS Feature Fetching for increased robustness. +
Made angle brackets in ASCII feature descriptions display + correctly +
Re-instated Zoom function for PCA +
Sequence descriptions conserved in web service analysis + results +
Uniprot ID discoverer uses any word separated by ∣ +
WsDbFetch query/result association resolved +
Tree leaf to sequence mapping improved +
Smooth fonts switch moved to FontChooser dialog box. +

+ + + + +

2.1.1
+ 12/9/06

+ + +

Copy consensus sequence to clipboard

+ + +

Image output - rightmost residues are rendered if sequence id + panel has been resized
Image output - all offscreen group boundaries are rendered
Annotation files with sequence references - all elements in + file are relative to sequence position
Mac Applet users can use Alt key for group editing

+ + + + +

2.1
+ 22/8/06

+ + +

MAFFT Multiple Alignment in default Web Service list
DAS Feature fetching
Hide sequences and columns
Export Annotations and Features
GFF file reading / writing
Associate structures with sequences from local PDB files
Add sequences to exisiting alignment
Recently opened files / URL lists
Applet can launch the full application
Applet has transparency for features (Java 1.2 required)
Applet has user defined colours parameter
Applet can load sequences from parameter "sequencex"

+ + +

Redundancy Panel reinstalled in the Applet
Monospaced font - EPS / rescaling bug fixed
Annotation files with sequence references bug fixed

+ + + + +

2.08.1
+ 2/5/06

+ + +

Change case of selected region from Popup menu
Choose to match case when searching
Middle mouse button and mouse movement can compress / expand + the visible width and height of the alignment

+ + +

Annotation Panel displays complete JNet results

+ + + + +

2.08b
+ 18/4/06

+ + + +

Java 1.5 bug - InternalMessageDialog fix for threads
Righthand label on wrapped alignments shows correct value

+ + + + +

2.08
+ 10/4/06

+ + +

Editing can be locked to the selection area
Keyboard editing
Create sequence features from searches
Precalculated annotations can be loaded onto alignments
Features file allows grouping of features
Annotation Colouring scheme added
Smooth fonts off by default - Faster rendering
Choose to toggle Autocalculate Consensus On/Off

+ + +

Drag & Drop fixed on Linux
Jalview Archive file faster to load/save, sequence + descriptions saved.

+ + + + +

2.07
+ 12/12/05

+ + +

PDB Structure Viewer enhanced
Sequence Feature retrieval and display enhanced
Choose to output sequence start-end after sequence name for + file output
Sequence Fetcher WSDBFetch@EBI
Applet can read feature files, PDB files and can be used for + HTML form input

+ + +

HTML output writes groups and features
Group editing is Control and mouse click
File IO bugs

+ + + + +

2.06
+ 28/9/05

+ + +

View annotations in wrapped mode
More options for PCA viewer

+ + +

GUI bugs resolved
Runs with -nodisplay from command line

+ + + + +

2.05b
+ 15/9/05

+ + +

Choose EPS export as lineart or text
Jar files are executable
Can read in Uracil - maps to unknown residue

+ + +

Known OutOfMemory errors give warning message
Overview window calculated more efficiently
Several GUI bugs resolved

+ + + + +

2.05
+ 30/8/05

+ + +

Edit and annotate in "Wrapped" view

+ + +

Several GUI bugs resolved

+ + + + +

2.04
+ 24/8/05

+ + +

Hold down mouse wheel & scroll to change font size

+ + +

Improved JPred client reliability
Improved loading of Jalview files

+ + + + +

2.03
+ 18/8/05

+ + +

Set Proxy server name and port in preferences
Multiple URL links from sequence ids
User Defined Colours can have a scheme name and added to + Colour Menu
Choose to ignore gaps in consensus calculation
Unix users can set default web browser
Runs without GUI for batch processing
Dynamically generated Web Service Menus

+ + +

InstallAnywhere download for Sparc Solaris

+ + + + +

2.02
+ 18/7/05

+ + + +

Copy & Paste order of sequences maintains alignment + order.

+ + + + +

2.01
+ 12/7/05

+ + +

Use delete key for deleting selection.
Use Mouse wheel to scroll sequences.
Help file updated to describe how to add alignment + annotations.
Version and build date written to build properties file.
InstallAnywhere installation will check for updates at launch + of Jalview.

+ + +

Delete gaps bug fixed.
FileChooser sorts columns.
Can remove groups one by one.
Filechooser icons installed.
Finder ignores return character when searching. Return key + will initiate a search.
+

+ + + + +

2.0
+ 20/6/05

+ + +

New codebase

+ + +

diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index b51e072..c082c3f 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -1,23 +1,6 @@ -#------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) -# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle -# -# 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 . -#-------------------------------------------------------------------------------