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<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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* This file is part of Jalview.
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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* This file is part of Jalview.
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
-# 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<title>Jalview Command Line Arguments</title>
+<title>Jalview Command Line Arguments
+</title>
<body>
-<p><strong>The Jalview Executable's Command Line Arguments</strong></p>
-See
-<a href="commandline.html">running Jalview from the command line</a>
-for more information.
-<br>
-<table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td width="27%">
- <div align="center">-nodisplay</div>
- </td>
- <td width="73%">
- <div align="left">Run Jalview without User Interface.
- (automatically disables questionnaire, version and usage stats checks)</div>
- </td>
- </tr>
+ <p><strong>The Jalview Executable's Command Line
+ Arguments</strong></p>
+ See <a href="commandline.html">running Jalview from the command
+ line</a> for more information.<br>
+ <table width="100%" border="1" cellspacing="0" cellpadding="0">
+ <tr >
+ <td width="27%"><div align="center">-nodisplay</div></td>
+ <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
+ </tr>
- <tr>
- <td>
- <div align="center">-props FILE</div>
- </td>
- <td>
- <div align="left">Use the given Jalview properties file instead
- of users default.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-features FILE</div>
- </td>
- <td>
- <div align="left">
- <p>Use the given file to add sequence features to an alignment.
- See <a href="featuresFormat.html" target="NEW">Features File</a>
- (Known as Groups file prior to 2.08) description.</p>
+ <tr>
+ <td><div align="center">-props FILE</div></td>
+ <td><div align="left">Use the given Jalview properties file instead
+ of users default.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-features FILE</div></td>
+ <td><div align="left">
+ <p>Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features
+ File</a> (Known as Groups file prior to 2.08) description. </p>
</div>
</td>
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).</td>
- </tr>
+ </tr>
<tr>
<td>
<div align="center">-annotations FILE</div>
<div align="left">Turn off questionnaire check</div>
</td>
</tr>
- <tr>
- <td>
+ <tr><td>
<div align="center">-nousagestats</div>
<td>
<div align="left">Turn off google analytics usage tracking</div>
</td>
</tr>
- <tr>
- <td>
- <div align="center">-[no]sortbytree</div>
+ <tr><td>
+ <div align="center">-[no]sortbytree</div>
<td>
- <div align="left">Enable or disable automatic sorting of
- associated view when a new tree is displayed</div>
+ <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
</td>
</tr>
<tr>
<td>
<div align="center">-dasserver nickname=URL</div>
<td>
- <div align="left">Add and enable a <a href="dassettings.html">DAS
- server</a> with given nickname (alphanumeric or underscores only) for
- retrieval of features for all alignments<br>
- Sources that also support the sequence command may be specified by
- prepending the URL with 'sequence:'<br>
+ <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
+ nickname (alphanumeric or underscores only) for retrieval of features
+ for all alignments<br>
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
<em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
</td>
</tr>
<td>
<div align="center">-fetchfrom nickname</div>
<td>
- <div align="left">Query a <a href="dassettings.html">DAS
- source</a> called nickname for features for the alignments and display
- them</div>
+ <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
+ and display them</div>
</td>
</tr>
<tr>
<td>
<div align="center">-groovy FILE</div>
<td>
- <div align="left">Execute groovy script in FILE (where FILE may
- be 'STDIN' to read from the standard input) after all other arguments
- have been processed</div>
+ <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed</div>
</td>
</tr>
<tr>
- <td>
+ <td>
<div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
<td>
- <div align="left">Import the given vamsas document into a new
- session.<br>
- <em>New in 2.5</em></div>
+ <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
</td>
</tr>
<tr>
<td>
<div align="center">-vsess VAMSAS SESSION URL</div>
<td>
- <div align="left">Join the given vamsas session<br>
- 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!).<em>New in 2.5</em></div>
- </div>
+ <div align="left">Join the given vamsas session<br>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!).<em>New in 2.5</em></div></div>
</td>
</tr>
<tr>
<td>
<div align="center">-groovy FILE</div>
<td>
- <div align="left">Execute groovy script in FILE (where FILE may
- be 'STDIN' to read from the standard input) after all other arguments
- have been processed</div>
+ <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed</div>
</td>
</tr>
<tr>
<div align="left">Create alignment file FILE in Fasta format.</div>
</td>
</tr>
- <tr>
- <td>
- <div align="center">-clustal FILE</div>
- </td>
- <td>
- <div align="left">Create alignment file FILE in Clustal format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-msf FILE</div>
- </td>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
- <td>
- <div align="left">Create alignment file FILE in MSF format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-pileup FILE</div>
- </td>
- <td>
- <div align="left">Create alignment file FILE in Pileup format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-pir FILE</div>
- </td>
+ <td><div align="left">Create alignment file FILE in MSF format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
- <td>
- <div align="left">Create alignment file FILE in PIR format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-pfam FILE</div>
- </td>
- <td>
- <div align="left">Create alignment file FILE in PFAM format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-blc FILE</div>
- </td>
- <td>
- <div align="left">Create alignment file FILE in BLC format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-jalview FILE</div>
- </td>
+ <td><div align="left">Create alignment file FILE in PIR format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
- <td>
- <div align="left">Create alignment file FILE in Jalview format.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-png FILE</div>
- </td>
- <td>
- <div align="left">Create PNG image FILE from alignment.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-imgMap FILE</div>
- </td>
+ <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
- <td>
- <div align="left">Create HTML file FILE with image map of PNG
- image.</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-eps FILE</div>
- </td>
- <td>
- <div align="left">Create EPS file FILE from alignment.</div>
- </td>
- </tr>
-</table>
+ <td><div align="left">Create HTML file FILE with image map of PNG
+ image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from alignment.</div></td>
+ </tr>
+ </table>
</body>
</html>
-#-------------------------------------------------------------------------------\r
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
-# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
-# \r
-# This file is part of Jalview.\r
-# \r
-# Jalview is free software: you can redistribute it and/or\r
-# modify it under the terms of the GNU General Public License \r
-# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
-# \r
-# Jalview is distributed in the hope that it will be useful, but \r
-# WITHOUT ANY WARRANTY; without even the implied warranty \r
-# of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
-# PURPOSE. See the GNU General Public License for more details.\r
-# \r
-# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
-#-------------------------------------------------------------------------------\r
<html>\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
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* \r
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-#-------------------------------------------------------------------------------
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<html>\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<html>\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
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<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------\r
<html>\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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-#-------------------------------------------------------------------------------
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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-#-------------------------------------------------------------------------------
<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
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-#-------------------------------------------------------------------------------
<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
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-#-------------------------------------------------------------------------------
<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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-#-------------------------------------------------------------------------------
<html>
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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-# 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/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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 - 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 <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
<div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
<em>30/4/2010</em></div>
</td>
- <td><em>New Capabilities</em>
+ <td>
+ <em>New Capabilities</em>
<ul>
<li>URL links generated from description line for
regular-expression based URL links (applet and application)
<li>Linked viewing of nucleic acid sequences and structures</li>
<li>Automatic Scrolling option in View menu to display the
currently highlighted region of an alignment.</li>
- <li>Order an alignment by sequence length, or using the average
- score or total feature count for each sequence.</li>
+ <li>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
<li>Shading features by score or associated description</li>
- <li>Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).</li>
- <li>New hide/show options including Shift+Control+H to hide
- everything but the currently selected region.</li>
+ <li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
<!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
- </ul>
- <em>Application</em>
- <ul>
- <li>Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the command line
- or via the Add local source dialog box.</li>
- <li>DAS Dbref and DbxRef feature types are parsed as database
- references and protein_name is parsed as description line (BioSapiens
- terms).</li>
- <li>Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.</li>
- <!-- <li>New hidden columns and rows and representatives capabilities
+</ul>
+<em>Application</em>
+<ul>
+ <li>Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line
+ or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as database
+ references and protein_name is parsed as description line (BioSapiens
+ terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
in annotations file (in progress - not yet fully implemented)</li> -->
- <li>Group-associated consensus, sequence logos and conservation
- plots</li>
- <li>Symbol distributions for each column can be exported and
- visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit within
- each column of annotation row<!-- todo for applet --></li>
- <li>Optional automatic sort of associated alignment view when a
- new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving between
- different screens.</li>
- <li>New preference items for sequence ID tooltip and consensus
- annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows</li>
- <li><em>Vamsas Capabilities</em>
- <ul>
- <li>Improved VAMSAS synchronization (jalview archive used to
- preserve views, structures, and tree display settings)</li>
- <li>Import of vamsas documents from disk or URL via command
- line</li>
- <li>Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
- </ul>
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
- <ul>
- <li>sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide branch
- lengths (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if
- unassociated nodes should be highlighted in the tree view</li>
- <li>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.</li>
- </ul>
- </li>
- <li>Non-positional features displayed in sequence ID tooltip</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Features format: graduated colour definitions and
- specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display
- properties (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.</li>
- </td>
- <td>
- <ul>
- <li>Source field in GFF files parsed as feature source rather
- than description</li>
- <li>Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
- documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in
- peptide product</li>
- <li>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.</li>
- <li>AMSA files only contain first column of multi-character
- column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly name</li>
- <li>Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.</li>
- <li>Application:
- <ul>
- <li>Better handling of exceptions during sequence retrieval</li>
- <li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled when
- fetch or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- <li>Ensured that command line das feature retrieval completes
- before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for first
- time.</li>
- <li>isAligned check prior to calculating tree, PCA or
- submitting an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered from Jalview
- projects.</li>
- </ul>
- </li>
- </ul>
- </td>
+ <li>Group-associated consensus, sequence logos and conservation
+ plots</li>
+ <li>Symbol distributions for each column can be exported and
+ visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit within
+ each column of annotation row<!-- todo for applet --></li>
+ <li>Optional automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving between different screens.</li>
+ <li>New preference items for sequence ID tooltip and consensus
+ annotation</li>
+ <li>Client to submit sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows</li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (jalview archive used to
+ preserve views, structures, and tree display settings)</li>
+ <li>Import of vamsas documents from disk or URL via command line</li>
+ <li>Sharing of selected regions between views and with other
+ VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul>
+ </li>
+</ul>
+<em>Applet</em>
+<ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the associated
+ alignment view by the tree when a new tree is opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide branch
+ bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide branch lengths
+ (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated
+ nodes should be highlighted in the tree view</li>
+ <li>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.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID tooltip</li>
+</ul>
+<em>Other</em>
+<ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display properties
+ (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile visualization
+ settings.</li>
+ </td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source rather
+ than description</li>
+ <li>Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product</li>
+ <li>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.</li>
+ <li>AMSA files only contain first column of multi-character
+ column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence retrieval</li>
+ <li>Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled when fetch
+ or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all data
+ sources</li>
+ <li>Ensured that command line das feature retrieval completes
+ before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for first time.</li>
+ <li>isAligned check prior to calculating tree, PCA or submitting
+ an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered from Jalview projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
</tr>
<tr>
<li>Sequence Group colour can be specified in Annotation File</li>
<li>Ad-hoc colouring of group in Annotation File using RGB
triplet as name of colourscheme</li>
- </ul>
- <em>VAMSAS Client capabilities (Experimental)</em>
- <ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS alignments
- (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
- </ul>
- <em>Application command line</em>
- <ul>
- <li>-tree parameter to open trees (introduced for passing from
- applet)</li>
- <li>-fetchfrom command line argument to specify nicknames of DAS
- servers to query for alignment features</li>
- <li>-dasserver command line argument to add new servers that are
- also automatically queried for features</li>
- <li>-groovy command line argument executes a given groovy script
- after all input data has been loaded and parsed</li>
- </ul>
- <em>Applet-Application data exchange</em>
- <ul>
- <li>Trees passed as applet parameters can be passed to
- application (when using "View in full application")</li>
- </ul>
- <em>Applet Parameters</em>
- <ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
- <li>showbutton parameter</li>
- </ul>
- <em>Applet API methods</em>
- <ul>
- <li>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
- <li>get list of currently selected sequences</li>
- </ul>
- <em>New Jalview distribution features</em>
- <ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
- <li>RELEASE file gives build properties for the latest Jalview
- release.</li>
- <li>Java 1.1 Applet build made easier and donotobfuscate
- property controls execution of obfuscator</li>
- <li>Build target for generating source distribution</li>
- <li>Debug flag for javacc</li>
- <li>.jalview_properties file is documented (slightly) in
- jalview.bin.Cache</li>
- <li>Continuous Build Integration for stable and development
- version of Application, Applet and source distribution</li>
- </ul>
+</ul>
+<em>VAMSAS Client capabilities (Experimental)</em>
+<ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS alignments
+ (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+</ul>
+<em>Application command line</em>
+<ul>
+ <li>-tree parameter to open trees (introduced for passing from
+ applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames of DAS
+ servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers that are
+ also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy script
+ after all input data has been loaded and parsed</li>
+</ul>
+<em>Applet-Application data exchange</em>
+<ul>
+ <li>Trees passed as applet parameters can be passed to application
+ (when using "View in full application")</li>
+</ul>
+<em>Applet Parameters</em>
+<ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+</ul>
+<em>Applet API methods</em>
+<ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+</ul>
+<em>New Jalview distribution features</em>
+<ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest Jalview
+ release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate property
+ controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution</li>
+</ul>
- </td>
- <td>
- <ul>
- <li>selected region output includes visible annotations (for
- certain formats)</li>
- <li>edit label/displaychar contains existing label/char for
- editing</li>
- <li>update PDBEntries when DBRefEntries change (vamsas)</li>
- <li>shorter peptide product names from EMBL records</li>
- <li>Newick string generator makes compact representations</li>
- <li>bootstrap values parsed correctly for tree files with
- comments</li>
- <li>pathological filechooser bug avoided by not allowing
- filenames containing a ':'</li>
- <li>Fixed exception when parsing GFF files containing global
- sequence features</li>
- <li>Alignment datasets are finalized only when number of
- references from alignment sequences goes to zero</li>
- <li>Close of tree branch colour box without colour selection
- causes cascading exceptions</li>
- <li>occasional negative imgwidth exceptions</li>
- <li>better reporting of non-fatal warnings to user when file
- parsing fails.</li>
- <li>Save works when Jalview project is default format</li>
- <li>Save as dialog opened if current alignment format is not a
- valid output format</li>
- <li>Uniprot canonical names introduced for both das and vamsas</li>
- <li>Histidine should be midblue (not pink!) in Zappo</li>
- <li>error messages passed up and output when data read fails</li>
- <li>edit undo recovers previous dataset sequence when sequence
- is edited</li>
- <li>allow PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) to be read in properly</li>
- <li>allow reading of JPred concise files as a normal filetype</li>
- <li>Stockholm annotation parsing and alignment properties import
- fixed for PFAM records</li>
- <li>Structure view windows have correct name in Desktop window
- list</li>
- <li>annotation consisting of sequence associated scores can be
- read and written correctly to annotation file</li>
- <li>Aligned cDNA translation to aligned peptide works correctly</li>
- <li>Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet</li>
- <li>Applet Menus are always embedded in applet window on Macs.</li>
- <li>Newly shown features appear at top of stack (in Applet)</li>
- <li>Annotations added via parameter not drawn properly due to
- null pointer exceptions</li>
- <li>Secondary structure lines are drawn starting from first
- column of alignment</li>
- <li>Uniprot XML import updated for new schema release in July
- 2008</li>
- <li>Sequence feature to sequence ID match for Features file is
- case-insensitive</li>
- <li>Sequence features read from Features file appended to all
- sequences with matching IDs</li>
- <li>PDB structure coloured correctly for associated views
- containing a sub-sequence</li>
- <li>PDB files can be retrieved by applet from Jar files</li>
- <li>feature and annotation file applet parameters referring to
- different directories are retrieved correctly</li>
- <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
- <li>Fixed application hang whilst waiting for splash-screen
- version check to complete</li>
- <li>Applet properly URLencodes input parameter values when
- passing them to the launchApp service</li>
- <li>display name and local features preserved in results
- retrieved from web service</li>
- <li>Visual delay indication for sequence retrieval and sequence
- fetcher initialisation</li>
- <li>updated Application to use DAS 1.53e version of dasobert DAS
- client</li>
- <li>Re-instated Full AMSA support and .amsa file association</li>
- <li>Fixed parsing of JNet Concise annotation <em>sans</em>
- sequences</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.3</strong><br>
- 9/5/07</div>
- </td>
- <td>
- <ul>
- <li>Jmol 11.0.2 integration</li>
- <li>PDB views stored in Jalview XML files</li>
- <li>Slide sequences</li>
- <li>Edit sequence in place</li>
- <li>EMBL CDS features</li>
- <li>DAS Feature mapping</li>
- <li>Feature ordering</li>
- <li>Alignment Properties</li>
- <li>Annotation Scores</li>
- <li>Sort by scores</li>
- <li>Feature/annotation editing in applet</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Headless state operation in 2.2.1</li>
- <li>Incorrect and unstable DNA pairwise alignment</li>
- <li>Cut and paste of sequences with annotation</li>
- <li>Feature group display state in XML</li>
- <li>Feature ordering in XML</li>
- <li>blc file iteration selection using filename # suffix</li>
- <li>Stockholm alignment properties</li>
- <li>Stockhom alignment secondary structure annotation</li>
- <li>2.2.1 applet had no feature transparency</li>
- <li>Number pad keys can be used in cursor mode</li>
- <li>Structure Viewer mirror image resolved</li>
- </ul>
- </td>
+</td>
+<td>
+<ul>
+ <li>selected region output includes visible annotations (for
+ certain formats)</li>
+ <li>edit label/displaychar contains existing label/char for
+ editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with comments</li>
+ <li>pathological filechooser bug avoided by not allowing filenames
+ containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing global
+ sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour selection
+ causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when file
+ parsing fails.</li>
+ <li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is not a
+ valid output format</li>
+ <li>Uniprot canonical names introduced for both das and vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read fails</li>
+ <li>edit undo recovers previous dataset sequence when sequence is
+ edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like those
+ generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal filetype</li>
+ <li>Stockholm annotation parsing and alignment properties import
+ fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop window
+ list</li>
+ <li>annotation consisting of sequence associated scores can be
+ read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works correctly</li>
+ <li>Fixed display of hidden sequence markers and non-italic font
+ for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on Macs.</li>
+ <li>Newly shown features appear at top of stack (in Applet)</li>
+ <li>Annotations added via parameter not drawn properly due to null
+ pointer exceptions</li>
+ <li>Secondary structure lines are drawn starting from first column
+ of alignment</li>
+ <li>Uniprot XML import updated for new schema release in July 2008</li>
+ <li>Sequence feature to sequence ID match for Features file is
+ case-insensitive</li>
+ <li>Sequence features read from Features file appended to all
+ sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters referring to
+ different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for splash-screen
+ version check to complete</li>
+ <li>Applet properly URLencodes input parameter values when passing
+ them to the launchApp service</li>
+ <li>display name and local features preserved in results retrieved
+ from web service</li>
+ <li>Visual delay indication for sequence retrieval and sequence
+ fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of dasobert DAS
+ client</li>
+ <li>Re-instated Full AMSA support and .amsa file association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences</li>
+</ul>
+</td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.3</strong><br>
+ 9/5/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2.1</strong><br>
- 12/2/07</div>
- </td>
- <td>
- <ul>
- <li>Non standard characters can be read and displayed
- <li>Annotations/Features can be imported/exported to the applet
- via textbox
- <li>Applet allows editing of sequence/annotation/group name
- & description
- <li>Preference setting to display sequence name in italics
- <li>Annotation file format extended to allow Sequence_groups to
- be defined
- <li>Default opening of alignment overview panel can be specified
- in preferences
- <li>PDB residue numbering annotation added to associated
- sequences
- </ul>
- </td>
- <td>
- <ul>
- <li>Applet crash under certain Linux OS with Java 1.6 installed
- <li>Annotation file export / import bugs fixed
- <li>PNG / EPS image output bugs fixed
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.2</strong><br>
- 27/11/06</div>
- </td>
- <td>
- <ul>
- <li>Multiple views on alignment
- <li>Sequence feature editing
- <li>"Reload" alignment
- <li>"Save" to current filename
- <li>Background dependent text colour
- <li>Right align sequence ids
- <li>User-defined lower case residue colours
- <li>Format Menu
- <li>Select Menu
- <li>Menu item accelerator keys
- <li>Control-V pastes to current alignment
- <li>Cancel button for DAS Feature Fetching
- <li>PCA and PDB Viewers zoom via mouse roller
- <li>User-defined sub-tree colours and sub-tree selection
- <li>'New Window' button on the 'Output to Text box'
- </ul>
- </td>
- <td>
- <ul>
- <li>New memory efficient Undo/Redo System
- <li>Optimised symbol lookups and conservation/consensus
- calculations
- <li>Region Conservation/Consensus recalculated after edits
- <li>Fixed Remove Empty Columns Bug (empty columns at end of
- alignment)
- <li>Slowed DAS Feature Fetching for increased robustness.
- <li>Made angle brackets in ASCII feature descriptions display
- correctly
- <li>Re-instated Zoom function for PCA
- <li>Sequence descriptions conserved in web service analysis
- results
- <li>Uniprot ID discoverer uses any word separated by ∣
- <li>WsDbFetch query/result association resolved
- <li>Tree leaf to sequence mapping improved
- <li>Smooth fonts switch moved to FontChooser dialog box.
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1.1</strong><br>
- 12/9/06</div>
- </td>
- <td>
- <ul>
- <li>Copy consensus sequence to clipboard</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Image output - rightmost residues are rendered if sequence
- id panel has been resized</li>
- <li>Image output - all offscreen group boundaries are rendered</li>
- <li>Annotation files with sequence references - all elements in
- file are relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.1</strong><br>
- 22/8/06</div>
- </td>
- <td>
- <ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2 required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08.1</strong><br>
- 2/5/06</div>
- </td>
- <td>
- <ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress / expand
- the visible width and height of the alignment</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Annotation Panel displays complete JNet results</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08b</strong><br>
- 18/4/06</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct value</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.08</strong><br>
- 10/4/06</div>
- </td>
- <td>
- <ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence
- descriptions saved.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.07</strong><br>
- 12/12/05</div>
- </td>
- <td>
- <ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence name for
- file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be used for
- HTML form input</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.06</strong><br>
- 28/9/05</div>
- </td>
- <td>
- <ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td height="63">
- <div align="center"><strong>2.05b</strong><br>
- 15/9/05</div>
- </td>
- <td>
- <ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.05</strong><br>
- 30/8/05</div>
- </td>
- <td>
- <ul>
- <li>Edit and annotate in "Wrapped" view</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Several GUI bugs resolved</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.04</strong><br>
- 24/8/05</div>
- </td>
- <td>
- <ul>
- <li>Hold down mouse wheel & scroll to change font size</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.03</strong><br>
- 18/8/05</div>
- </td>
- <td>
- <ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added to
- Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.02</strong><br>
- 18/7/05</div>
- </td>
- <td> </td>
- <td>
- <ul>
- <li>Copy & Paste order of sequences maintains alignment
- order.</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.01</strong><br>
- 12/7/05</div>
- </td>
- <td>
- <ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment
- annotations.</li>
- <li>Version and build date written to build properties file.</li>
- <li>InstallAnywhere installation will check for updates at
- launch of Jalview.</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching. Return key
- will initiate a search.<br>
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center"><strong>2.0</strong><br>
- 20/6/05</div>
- </td>
- <td>
- <ul>
- <li>New codebase</li>
- </ul>
- </td>
- <td> </td>
- </tr>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.2.1</strong><br>
+ 12/2/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the applet
+ via textbox
+ <li>Applet allows editing of sequence/annotation/group name &
+ description
+ <li>Preference setting to display sequence name in italics
+ <li>Annotation file format extended to allow Sequence_groups to
+ be defined
+ <li>Default opening of alignment overview panel can be specified
+ in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6 installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.2</strong><br>
+ 27/11/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+ <li>'New Window' button on the 'Output to Text box'
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end of
+ alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+ <li>Made angle brackets in ASCII feature descriptions display
+ correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service analysis
+ results
+ <li>Uniprot ID discoverer uses any word separated by ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.1.1</strong><br>
+ 12/9/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Image output - rightmost residues are rendered if sequence id
+ panel has been resized</li>
+ <li>Image output - all offscreen group boundaries are rendered</li>
+ <li>Annotation files with sequence references - all elements in
+ file are relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.1</strong><br>
+ 22/8/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2 required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.08.1</strong><br>
+ 2/5/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress / expand
+ the visible width and height of the alignment</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.08b</strong><br>
+ 18/4/06</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct value</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.08</strong><br>
+ 10/4/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence
+ descriptions saved.</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.07</strong><br>
+ 12/12/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence name for
+ file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be used for
+ HTML form input</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.06</strong><br>
+ 28/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td height="63">
+ <div align="center"><strong>2.05b</strong><br>
+ 15/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.05</strong><br>
+ 30/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.04</strong><br>
+ 24/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Hold down mouse wheel & scroll to change font size</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.03</strong><br>
+ 18/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added to
+ Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.02</strong><br>
+ 18/7/05</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Copy & Paste order of sequences maintains alignment
+ order.</li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.01</strong><br>
+ 12/7/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment
+ annotations.</li>
+ <li>Version and build date written to build properties file.</li>
+ <li>InstallAnywhere installation will check for updates at launch
+ of Jalview.</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching. Return key
+ will initiate a search.<br>
+ </li>
+ </ul>
+ </td>
+</tr>
+<tr>
+ <td>
+ <div align="center"><strong>2.0</strong><br>
+ 20/6/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>New codebase</li>
+ </ul>
+ </td>
+ <td> </td>
+</tr>
</table>
<p> </p>
</body>
-#-------------------------------------------------------------------------------
-# 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.
-#
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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*
* This file is part of Jalview.
history</a> for the bugs that this release resolves.</p>
<p><strong>Highlights in Jalview Version 2.5</strong></p>
<ul>
- Linked viewing of nucleic acid sequences and structures
- <br />
- Automatic Scrolling option in View menu to display the currently
- highlighted region of an alignment.
- <br />
- Order an alignment by sequence length, or using the average score or
- total feature count for each sequence.
- <br />
- Shading features by score or associated description
- <br />
- Subdivide alignment and groups based on identity of selected
- subsequence (Make Groups from Selection).
- <br />
- New hide/show options including Shift+Control+H to hide everything but
- the currently selected region.
- <br />
+ Linked viewing of nucleic acid sequences and structures<br/>
+ Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.<br/>
+ Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
+ Shading features by score or associated description<br/>
+ Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
+ New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
</ul>
<em>Jalview Desktop:</em>
<ul>
- Fetch DB References capabilities and UI expanded to support retrieval
- from DAS sequence sources
- <br />
- Enable or disable non-positional feature and database references in
- sequence ID tooltip from View menu in application.
- <br />
- Group-associated consensus, sequence logos and conservation plots
- <br />
- Symbol distributions for each column can be exported and visualized as
- sequence logos
- <br />
- Jalview Java Console
- <br />
- New webservice for submitting sequences and IDs to
- <a href="webServices/index.html#envision2">Envision2</a>
- Workflows
- <br />
- Improved VAMSAS synchronization and sharing of selections.
- <br />
+ Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources<br/>
+ Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.<br/>
+ Group-associated consensus, sequence logos and conservation
+ plots<br/>
+ Symbol distributions for each column can be exported and
+ visualized as sequence logos<br/>
+ Jalview Java Console<br/>
+ New webservice for submitting sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
+ Improved VAMSAS synchronization and sharing of selections.<br/>
</ul>
<em>JalviewLite:</em>
<ul>
- Middle button resizes annotation row height
- <br />
- New Parameters - including default tree display settings.
- <br />
- Non-positional features displayed in ID tooltip
- <br />
+ Middle button resizes annotation row height<br/>
+ New Parameters - including default tree display settings.<br/>
+ Non-positional features displayed in ID tooltip<br/>
</ul>
<p><strong>Issues Resolved (a select list)</strong></p>
<ul>
<ul>
- Source field in GFF files parsed as feature source rather than
- description
- <br />
- Non-positional features are now included in sequence feature and gff
- files (controlled via non-positional feature visibility in tooltip).
- <br />
- URL links generated for all feature links (bugfix)
- <br />
- Codons containing ambiguous nucleotides translated as 'X' in peptide
- product
- <br />
- 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.
- <br />
+ Source field in GFF files parsed as feature source rather
+ than description<br/>
+ Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).<br/>
+ URL links generated for all feature links (bugfix)<br/>
+ Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product<br/>
+ 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.<br/>
Jalview Annotation File generation/parsing consistent with
documentation (e.g. Stockholm annotation can be exported and
- re-imported)
- <br />
- Find incrementally searches ID string matches as well as subsequence
- matches, and correctly reports total number of both.
- <br />
+ re-imported)<br/>
+ Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.<br/>
</ul>
<em>Desktop Issues</em>
<ul>
- Better handling of exceptions during sequence retrieval
- <br />
- PDB files retrieved from URLs are cached properly
- <br />
- Sequence description lines properly shared via VAMSAS
- <br />
- Sequence fetcher fetches multiple records for all data sources
- <br />
- Ensured that command line das feature retrieval completes before
- alignment figures are generated.
- <br />
- Reduced time taken when opening file browser for first time.
- <br />
- User defined group colours properly recovered from Jalview projects.
- <br />
- </ul>
+ Better handling of exceptions during sequence retrieval<br/>
+ PDB files retrieved from URLs are cached properly<br/>
+ Sequence description lines properly shared via VAMSAS<br/>
+ Sequence fetcher fetches multiple records for all data
+ sources<br/>
+ Ensured that command line das feature retrieval completes
+ before alignment figures are generated.<br/>
+ Reduced time taken when opening file browser for first time.<br/>
+ User defined group colours properly recovered from Jalview projects.<br/>
+ </ul>
</ul>
<p> </p>
git://source.jalview.org / jalview.git / commitdiff