-<html>
+<html>\r
<head>\r
<title>Mapping Between Different Sequences</title>\r
</head>\r
-<body>
+<body>\r
<p><strong>Mapping Between Different Sequences</strong></p>\r
-<p>A new feature in Jalview 2.8 is the ability to map \r
-between sequences in different domains, based on alignment, \r
-or by the use of explicit mappings provided by databases.\r
-</p>\r
+<p>A new feature in Jalview 2.3 is the ability to map between sequences in different \r
+ domains, based on alignment, or by the use of explicit mappings provided by \r
+ databases. </p>\r
<p>The most familiar mapping is the one used to identify\r
the coordinates corresponding to a displayed sequence when\r
viewing a PDB file associated with a sequence (see \r
can be imported directly from EMBL and EMBLCDS database records \r
retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>,\r
or by the definition of <a href="codingfeatures.html">coding regions</a>. \r
-</body>
+</body>\r
</html>
\ No newline at end of file
-<html>
-<head><title>PDB Viewing</title></head>
-<body>
-<p><strong>Viewing PDB Structures</strong></p>
-<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which can visualize polypeptide backbone
- structures associated with a sequence in a particular alignment view. It is
- accessed via the <strong>"Sequence→View PDB
- entry:"</strong> entry from the sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.</p>
-<p>To associate PDB files with a sequence, right click on a sequence ID and select
- "Associate Structure with Sequence", and one of the submenus:</p>
-<ul>
- <li>From File - You can load a PDB file from the local machine or network and
- associate it with the selected sequence. PDB files associated in this way
- will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>
- </li>
- <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch
- the PDB file with the entered Id.<br>
- </li>
- <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover
- PDB ids for all the sequences in the alignment which have valid Uniprot names
- / accession ids. </li>
-</ul>
-<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this
- service are automatically associated with their source database entry. For PDB
- sequences, simply select PDB as the database and enter your known PDB id (appended
- with ':' and a chain code, if desired).</p>
- <p>Sequences which have PDB File associations are annotated with sequence features
- from the group 'PDBFile' giving the corresponding PDB Residue Number for each
- mapped residue in the seuqence. The display of these features is controlled through
- the <strong>"View→Sequence Features"</strong> menu item and the
- <a href="featuresettings.html">Feature Settings dialog box</a>.</p>
-<p>See the <a
-href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>
-</body>
-</html>
+<html>\r
+<head><title>PDB Viewing</title></head>\r
+<body>\r
+<p><strong>Viewing PDB Structures</strong></p>\r
+<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which \r
+ can visualize polypeptide backbone structures associated with a sequence in \r
+ a particular alignment view. It is accessed via the <strong>"Sequence→View \r
+ PDB entry:"</strong> entry from the sequence's <a\r
+ href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
+<p>Since Jalview 2.3, Jmol has been integrated into the application and will also \r
+ run in the applet in all latest web browsers. For more help using Jmol, see \r
+ <a href="http://jmol.sourceforge.net/docs/JmolUserGuide/">http://jmol.sourceforge.net/docs/JmolUserGuide/</a> \r
+</p>\r
+<p>To associate PDB files with a sequence, right click on a sequence ID and select \r
+ "Associate Structure with Sequence", and one of the submenus:</p>\r
+<ul>\r
+ <li>From File - You can load a PDB file from the local machine or network and \r
+ associate it with the selected sequence. PDB files associated in this way \r
+ will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>\r
+ </li>\r
+ <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch \r
+ the PDB file with the entered Id.<br>\r
+ </li>\r
+ <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover \r
+ PDB ids for all the sequences in the alignment which have valid Uniprot names \r
+ / accession ids. </li>\r
+</ul>\r
+<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a\r
+ href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this \r
+ service are automatically associated with their source database entry. For PDB \r
+ sequences, simply select PDB as the database and enter your known PDB id (appended \r
+ with ':' and a chain code, if desired).</p>\r
+ <p>Sequences which have PDB File associations are annotated with sequence features \r
+ from the group 'PDBFile' giving the corresponding PDB Residue Number for each \r
+ mapped residue in the seuqence. The display of these features is controlled through\r
+ the <strong>"View→Sequence Features"</strong> menu item and the \r
+ <a href="featuresettings.html">Feature Settings dialog box</a>.</p> \r
+<p>See the <a\r
+href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>\r
+</body>\r
+</html>\r
-<html>
-<head><title>Key Strokes</title></head>
-<body>
-<p><strong>Key Strokes</strong></p>
-<p>
-Jalview has two distinct modes of keyboard operation - in 'Normal'
- mode, single keystrokes (including those shown next to menu items)
- provide short cuts to common commands. In <a
- href="features/cursorMode.html">'Cursor'</a> mode (enabled by
- <em>F2</em>), some of these are disabled and more complex 'Compound
- Keystrokes' can be entered to perform precise navigation, selection
- and editing operations.
-</p>
-<table border="1">
- <tr>
- <td><strong>Key</strong></td>
- <td><strong>Which Mode</strong></td>
- <td><strong>Action</strong></td>
- </tr>
- <!--<tr>
-<td><strong>Escape</strong></td><td>Both</td>
-<td>The Panic button.</td></tr>
-<tr> -->
- <tr><td><strong> Escape</strong></td>
- <td>Normal</td>
- <td>Clears the current selection region, highlighted columns and highlghted
- residues. </td>
- </tr>
- <tr>
- <td><strong>Escape</strong></td>
- <td>Cursor</td>
- <td>As in normal mode, but also cancels any partially entered commands</td></tr>
- <tr>
- <td><strong><em>F1</em></strong></td>
- <td>Both</td>
- <td>Show Help Documentation</td></tr>
- <tr>
- <td><strong><em>F2</em></strong></td>
- <td></td>
- <td>Toggle Cursor mode on / off</td>
- </tr>
- <tr>
- <td><strong>Control 'Z'</strong></td>
- <td>Both</td>
- <td>Undoes the last sequence edit</td>
- </tr>
- <tr>
- <td><strong>Control 'Y'</strong></td>
- <td>Both</td>
- <td>Redo the last sequence edit undone.</td>
- </tr>
- <tr>
- <td><strong>Up Arrow</strong></td>
- <td>Normal</td>
- <td>Moves selected sequence(s) up the alignment</td></tr>
- <tr>
- <td><strong>Down Arrow</strong></td>
- <td>Normal</td>
- <td>Moves selected sequence(s) down the alignment.</td></tr>
- <tr><td><strong>Cursor Keys<br>
- (Arrow Keys)</strong></td>
- <td>Cursor</td>
- <td>Move cursor around alignment</td>
- </tr>
- <tr><td><strong>Page Up</strong></td><td>Both</td><td>Scroll up the alignment view</td></tr>
- <tr><td><strong>Page Down</strong></td><td>Both</td><td>Scroll down the alignment view</td></tr>
- <tr>
- <td><strong>Control 'A'</strong></td>
- <td>Both</td>
- <td>Selects all sequences in the alignment</td>
- </tr>
- <tr>
- <td><strong>Control 'I'</strong></td>
- <td>Both
- </td>
- <td>Invert sequence selection.
- </td>
- </tr>
- <tr>
- <td><strong>Control Alt 'I'</strong></td>
- <td>Both
- </td>
- <td>Invert column selection.
- </td>
- </tr>
- <tr>
- <td><strong>Control 'C'</strong></td>
- <td>Both</td>
- <td>Copies the selected region into the clipboard as a Fasta format file<br>
- <em>nb. not available in applet, as no clipboard is available</em></td>
- </tr>
- <tr>
- <td><strong>Control 'V'</strong></td>
- <td>Both</td>
- <td>
- Paste the contents of the clipboard to the current alignment
- window. (Alignment Window->Edit->Paste->Add to this Alignment)<br>
- <em>nb. if the paste is from a Jalview alignment, any sequence and alignment
- annotations will also be copied over.</em></td></tr>
- <tr>
- <td><strong>Control Shift 'V'</strong></td>
- <td>Both</td>
- <td>Paste the contents of the clipboard to a new alignment
- window. (Alignment Window->Edit->Paste->To New Alignment)</td>
- </tr>
- <tr>
- <td><strong>Control 'X'</strong></td>
- <td>Both</td>
- <td>Cuts the (fully) selected sequences from the alignment.
- <!-- not yet in this version
-This will not happen if only some
-columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
- </td>
- </tr>
- <tr>
- <td><strong>Control 'F'</strong></td>
- <td>Both</td>
- <td>Launches the search window</td>
- </tr>
- <tr>
- <td><strong>H</strong></td>
- <td>Both</td>
- <td>Hides / Reveals selected columns and sequences</td>
- </tr>
- <tr>
- <td><strong>Control 'H'</strong></td>
- <td>Both</td>
- <td>Hides / Reveals selected columns</td>
- </tr>
- <tr>
- <td><strong>Shift 'H'</strong></td>
- <td>Both</td>
- <td>Hides / Reveals selected sequences</td>
- </tr>
- <tr>
- <td><strong>Control 'O'</strong></td>
- <td>Both</td>
- <td>Input new alignment from file</td>
- </tr>
- <tr>
- <td><strong>Control 'S'</strong></td>
- <td>Both</td>
- <td>Save alignment with current filename and format</td>
- </tr>
- <tr>
- <td><strong>Control Shift 'S'</strong></td>
- <td>Both</td>
- <td>Save alignment as a new file or with a different format</td>
- </tr>
- <tr>
- <td><strong>Control 'P'</strong></td>
- <td>Both</td>
- <td>Opens the print dialog box to print the current view</td>
- </tr>
- <tr>
- <td><strong>Control 'W'</strong></td>
- <td>Both</td>
- <td>Closes the current view or the current alignment</td>
- </tr>
- <tr>
- <td><strong>Backspace</strong></td>
- <td>Normal</td>
- <td>Delete the currently selected rows or columns from the alignment.</td>
- </tr>
- <tr>
- <td><strong>Control 'L'</strong></td>
- <td>Left</td>
- <td>Remove columns to left of left-most column marker.</td>
- </tr>
- <tr>
- <td><strong>Control 'R'</strong></td>
- <td>Both</td>
- <td>Remove columns to right of right-most column marker.</td>
- </tr>
- <tr>
- <td><strong>Control 'E'</strong></td>
- <td>Both</td>
- <td>Remove gapped columns</td>
- </tr>
- <tr>
- <td><strong>Control Shift 'E'</strong></td>
- <td>Both</td>
- <td>Remove all gaps</td>
- </tr>
- <tr>
- <td><strong>Control 'D'</strong></td>
- <td>Both</td>
- <td>Open the 'Remove redundancy' Dialog box.</td>
- </tr>
-
- <tr>
- <td><strong></strong></td>
- <td>Normal</td>
- <td></td>
- </tr>
-
-
-</table>
-<p>The compound commands available in the Cursor mode are summarised
-below. Single letter commands can be prefixed by digits to specify a repetition
-number, and some more complex commands take one or more numeric
-parameters (prefixing the command key and separated by commas).</p>
-<table border=1><tr><td><strong>Compound
-Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
-<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
-numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
-command.</td></tr>
-<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
-more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
-<tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>
-<tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>
-<tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>
-<tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>
-<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
-<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
-<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
-one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
-<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
-one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
-<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
-one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>
-<p> </p>
-<p> </p>
-</body>
-</html>
+<html>\r
+<head><title>Key Strokes</title></head>\r
+<body>\r
+<p><strong>Key Strokes</strong></p>\r
+<p>\r
+Jalview has two distinct modes of keyboard operation - in 'Normal'\r
+ mode, single keystrokes (including those shown next to menu items)\r
+ provide short cuts to common commands. In <a\r
+ href="features/cursorMode.html">'Cursor'</a> mode (enabled by\r
+ <em>F2</em>), some of these are disabled and more complex 'Compound\r
+ Keystrokes' can be entered to perform precise navigation, selection\r
+ and editing operations.\r
+</p>\r
+<table border="1">\r
+ <tr> \r
+ <td><strong>Key</strong></td>\r
+ <td><strong>Which Mode</strong></td>\r
+ <td><strong>Action</strong></td>\r
+ </tr>\r
+ <!--<tr>\r
+<td><strong>Escape</strong></td><td>Both</td>\r
+<td>The Panic button.</td></tr>\r
+<tr> -->\r
+ <tr> \r
+ <td><strong> Escape</strong></td>\r
+ <td>Normal</td>\r
+ <td>Clears the current selection region, highlighted columns and highlghted \r
+ residues. </td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Escape</strong></td>\r
+ <td>Cursor</td>\r
+ <td>As in normal mode, but also cancels any partially entered commands</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong><em>F1</em></strong></td>\r
+ <td>Both</td>\r
+ <td>Show Help Documentation</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong><em>F2</em></strong></td>\r
+ <td></td>\r
+ <td>Toggle Cursor mode on / off</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'Z'</strong></td>\r
+ <td>Both</td>\r
+ <td>Undoes the last sequence edit</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'Y'</strong></td>\r
+ <td>Both</td>\r
+ <td>Redo the last sequence edit undone.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Up Arrow</strong></td>\r
+ <td>Normal</td>\r
+ <td>Moves selected sequence(s) up the alignment</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Down Arrow</strong></td>\r
+ <td>Normal</td>\r
+ <td>Moves selected sequence(s) down the alignment.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Left Arrow</strong></td>\r
+ <td>Normal </td>\r
+ <td>Slides selected sequence(s) left. Press Alt key to slide in cursor mode</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Right Arrow</strong></td>\r
+ <td>Normal</td>\r
+ <td>Slides selected sequence(s) right. Press Alt key to slide in cursor mode</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Cursor Keys<br>\r
+ (Arrow Keys)</strong></td>\r
+ <td>Cursor</td>\r
+ <td>Move cursor around alignment</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Page Up</strong></td>\r
+ <td>Both</td>\r
+ <td>Scroll up the alignment view</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Page Down</strong></td>\r
+ <td>Both</td>\r
+ <td>Scroll down the alignment view</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'A'</strong></td>\r
+ <td>Both</td>\r
+ <td>Selects all sequences in the alignment</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'I'</strong></td>\r
+ <td>Both </td>\r
+ <td>Invert sequence selection. </td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control Alt 'I'</strong></td>\r
+ <td>Both </td>\r
+ <td>Invert column selection. </td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'C'</strong></td>\r
+ <td>Both</td>\r
+ <td>Copies the selected region into the clipboard as a Fasta format file<br> \r
+ <em>nb. not available in applet, as no clipboard is available</em></td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'V'</strong></td>\r
+ <td>Both</td>\r
+ <td> Paste the contents of the clipboard to the current alignment window. \r
+ (Alignment Window->Edit->Paste->Add to this Alignment)<br> <em>nb. if the \r
+ paste is from a Jalview alignment, any sequence and alignment annotations \r
+ will also be copied over.</em></td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control Shift 'V'</strong></td>\r
+ <td>Both</td>\r
+ <td>Paste the contents of the clipboard to a new alignment window. (Alignment \r
+ Window->Edit->Paste->To New Alignment)</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'X'</strong></td>\r
+ <td>Both</td>\r
+ <td>Cuts the (fully) selected sequences from the alignment. \r
+ <!-- not yet in this version \r
+This will not happen if only some\r
+columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->\r
+ </td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'F'</strong></td>\r
+ <td>Both</td>\r
+ <td>Launches the search window</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>H</strong></td>\r
+ <td>Both</td>\r
+ <td>Hides / Reveals selected columns and sequences</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'H'</strong></td>\r
+ <td>Both</td>\r
+ <td>Hides / Reveals selected columns</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Shift 'H'</strong></td>\r
+ <td>Both</td>\r
+ <td>Hides / Reveals selected sequences</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'O'</strong></td>\r
+ <td>Both</td>\r
+ <td>Input new alignment from file</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'S'</strong></td>\r
+ <td>Both</td>\r
+ <td>Save alignment with current filename and format</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control Shift 'S'</strong></td>\r
+ <td>Both</td>\r
+ <td>Save alignment as a new file or with a different format</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'P'</strong></td>\r
+ <td>Both</td>\r
+ <td>Opens the print dialog box to print the current view</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'W'</strong></td>\r
+ <td>Both</td>\r
+ <td>Closes the current view or the current alignment</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Backspace</strong></td>\r
+ <td>Normal</td>\r
+ <td>Delete the currently selected rows or columns from the alignment.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'L'</strong></td>\r
+ <td>Left</td>\r
+ <td>Remove columns to left of left-most column marker.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'R'</strong></td>\r
+ <td>Both</td>\r
+ <td>Remove columns to right of right-most column marker.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'E'</strong></td>\r
+ <td>Both</td>\r
+ <td>Remove gapped columns</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control Shift 'E'</strong></td>\r
+ <td>Both</td>\r
+ <td>Remove all gaps</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong>Control 'D'</strong></td>\r
+ <td>Both</td>\r
+ <td>Open the 'Remove redundancy' Dialog box.</td>\r
+ </tr>\r
+ <tr> \r
+ <td><strong></strong></td>\r
+ <td>Normal</td>\r
+ <td></td>\r
+ </tr>\r
+</table>\r
+<p>The compound commands available in the Cursor mode are summarised\r
+below. Single letter commands can be prefixed by digits to specify a repetition\r
+number, and some more complex commands take one or more numeric\r
+parameters (prefixing the command key and separated by commas).</p>\r
+<table border=1><tr><td><strong>Compound\r
+Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>\r
+<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a\r
+numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit\r
+command.</td></tr>\r
+<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or\r
+more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>\r
+<tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
+<tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>\r
+<tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>\r
+<tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>\r
+<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>\r
+<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>\r
+<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts\r
+one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes\r
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
+<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes\r
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>\r
+<p> </p>\r
+<p> </p>\r
+</body>\r
+</html>\r
-<html>
-<head><title>Release History</title></head>
-<body>
-<p><strong>Release History</strong> </p>
-<table border="1">
- <tr>
- <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>
- <td ><div align="center"><em><strong>New Features</strong></em></div></td>
- <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>
- </tr>
- <tr>
- <td><div align="center"><strong>2.3</strong><br>
- 2/5/07</div></td>
- <td><ul>
- <li>Jmol 11 integration</li>
- <li>PDB views in Jalview XML</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>
- </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>
-</table>
-<p> </p>
-</body>
-</html>
+<html>\r
+<head><title>Release History</title></head>\r
+<body>\r
+<p><strong>Release History</strong> </p>\r
+<table border="1">\r
+ <tr> \r
+ <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>\r
+ <td ><div align="center"><em><strong>New Features</strong></em></div></td>\r
+ <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
+ </tr>\r
+ <tr>\r
+ <td><div align="center"><strong>2.3</strong><br>\r
+ 8/5/07</div></td>\r
+ <td><ul>\r
+ <li>Jmol 11 integration</li>\r
+ <li>PDB views stored in Jalview XML files</li>\r
+ <li>Slide sequences</li>\r
+ <li>Edit sequence in place</li>\r
+ <li>EMBL CDS features</li>\r
+ <li>DAS Feature mapping</li>\r
+ <li>Feature ordering</li>\r
+ <li>Alignment Properties</li>\r
+ <li>Annotation Scores</li>\r
+ <li>Sort by scores</li>\r
+ <li>Feature/annotation editing in applet</li>\r
+</ul></td><td>\r
+ <ul>\r
+ <li>Headless state operation in 2.2.1</li>\r
+ <li>Incorrect and unstable DNA pairwise alignment</li>\r
+ <li>Cut and paste of sequences with annotation</li>\r
+ <li>Feature group display state in XML</li>\r
+ <li>Feature ordering in XML</li>\r
+ <li>blc file iteration selection using filename # suffix</li>\r
+ <li>Stockholm alignment properties</li>\r
+ <li>Stockhom alignment secondary structure annotation</li>\r
+ <li>2.2.1 applet had no feature transparency</li>\r
+ <li>Number pad keys can be used in cursor mode</li>\r
+ </ul>\r
+ </td>\r
+\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.2.1</strong><br>\r
+ 12/2/07</div></td>\r
+ <td><ul>\r
+ <li>Non standard characters can be read and displayed\r
+ <li>Annotations/Features can be imported/exported to the applet via textbox\r
+ <li>Applet allows editing of sequence/annotation/group name & description\r
+ <li>Preference setting to display sequence name in italics\r
+ <li>Annotation file format extended to allow Sequence_groups\r
+ to be defined\r
+ <li>Default opening of alignment overview panel can be specified in\r
+ preferences\r
+ <li>PDB residue numbering annotation added to associated sequences\r
+ </ul></td>\r
+ <td> <ul>\r
+ <li>Applet crash under certain Linux OS with Java 1.6 installed\r
+ <li>Annotation file export / import bugs fixed\r
+ <li>PNG / EPS image output bugs fixed</ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.2</strong><br>\r
+ 27/11/06</div></td>\r
+ <td><ul>\r
+ <li>Multiple views on alignment \r
+ <li>Sequence feature editing \r
+ <li>"Reload" alignment \r
+ <li>"Save" to current filename \r
+ <li>Background dependent text colour \r
+ <li>Right align sequence ids \r
+ <li>User-defined lower case residue colours \r
+ <li>Format Menu \r
+ <li>Select Menu \r
+ <li>Menu item accelerator keys \r
+ <li>Control-V pastes to current alignment \r
+ <li>Cancel button for DAS Feature Fetching \r
+ <li>PCA and PDB Viewers zoom via mouse roller \r
+ <li>User-defined sub-tree colours and sub-tree selection \r
+ <li>'New Window' button on the 'Output to Text box' </ul></td>\r
+ <td> <ul>\r
+ <li>New memory efficient Undo/Redo System \r
+ <li>Optimised symbol lookups and conservation/consensus calculations \r
+ <li>Region Conservation/Consensus recalculated after edits \r
+ <li>Fixed Remove Empty Columns Bug (empty columns at end of alignment) \r
+ <li>Slowed DAS Feature Fetching for increased robustness. \r
+ <li>Made angle brackets in ASCII feature descriptions display correctly \r
+ <li>Re-instated Zoom function for PCA \r
+ <li>Sequence descriptions conserved in web service analysis results \r
+ <li>Uniprot ID discoverer uses any word separated by ∣ \r
+ <li>WsDbFetch query/result association resolved \r
+ <li>Tree leaf to sequence mapping improved \r
+ <li>Smooth fonts switch moved to FontChooser dialog box. </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td> <div align="center"><strong>2.1.1</strong><br>\r
+ 12/9/06</div></td>\r
+ <td><ul>\r
+ <li>Copy consensus sequence to clipboard</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Image output - rightmost residues are rendered if sequence id panel \r
+ has been resized</li>\r
+ <li>Image output - all offscreen group boundaries are rendered </li>\r
+ <li>Annotation files with sequence references - all elements in file are \r
+ relative to sequence position</li>\r
+ <li>Mac Applet users can use Alt key for group editing</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.1</strong><br>\r
+ 22/8/06</div></td>\r
+ <td><ul>\r
+ <li>MAFFT Multiple Alignment in default Web Service list</li>\r
+ <li>DAS Feature fetching</li>\r
+ <li>Hide sequences and columns</li>\r
+ <li>Export Annotations and Features</li>\r
+ <li>GFF file reading / writing</li>\r
+ <li>Associate structures with sequences from local PDB files</li>\r
+ <li>Add sequences to exisiting alignment</li>\r
+ <li>Recently opened files / URL lists</li>\r
+ <li>Applet can launch the full application</li>\r
+ <li>Applet has transparency for features (Java 1.2 required)</li>\r
+ <li>Applet has user defined colours parameter</li>\r
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Redundancy Panel reinstalled in the Applet</li>\r
+ <li>Monospaced font - EPS / rescaling bug fixed</li>\r
+ <li>Annotation files with sequence references bug fixed</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.08.1</strong><br>\r
+ 2/5/06</div></td>\r
+ <td><ul>\r
+ <li>Change case of selected region from Popup menu</li>\r
+ <li>Choose to match case when searching</li>\r
+ <li>Middle mouse button and mouse movement can compress / expand the visible \r
+ width and height of the alignment</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Annotation Panel displays complete JNet results</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.08b</strong><br>\r
+ 18/4/06</div></td>\r
+ <td> </td>\r
+ <td><ul>\r
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>\r
+ <li>Righthand label on wrapped alignments shows correct value</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.08</strong><br>\r
+ 10/4/06</div></td>\r
+ <td><ul>\r
+ <li>Editing can be locked to the selection area</li>\r
+ <li>Keyboard editing</li>\r
+ <li>Create sequence features from searches</li>\r
+ <li>Precalculated annotations can be loaded onto alignments</li>\r
+ <li>Features file allows grouping of features</li>\r
+ <li>Annotation Colouring scheme added</li>\r
+ <li>Smooth fonts off by default - Faster rendering</li>\r
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Drag & Drop fixed on Linux</li>\r
+ <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
+ </li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.07</strong><br>\r
+ 12/12/05</div></td>\r
+ <td><ul>\r
+ <li>PDB Structure Viewer enhanced</li>\r
+ <li>Sequence Feature retrieval and display enhanced</li>\r
+ <li>Choose to output sequence start-end after sequence name for file output</li>\r
+ <li>Sequence Fetcher WSDBFetch@EBI</li>\r
+ <li>Applet can read feature files, PDB files and can be used for HTML \r
+ form input</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>HTML output writes groups and features</li>\r
+ <li>Group editing is Control and mouse click</li>\r
+ <li>File IO bugs</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.06</strong><br>\r
+ 28/9/05</div></td>\r
+ <td><ul>\r
+ <li>View annotations in wrapped mode</li>\r
+ <li>More options for PCA viewer</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>GUI bugs resolved</li>\r
+ <li>Runs with -nodisplay from command line</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td height="63"> <div align="center"><strong>2.05b</strong><br>\r
+ 15/9/05</div></td>\r
+ <td><ul>\r
+ <li>Choose EPS export as lineart or text</li>\r
+ <li>Jar files are executable</li>\r
+ <li>Can read in Uracil - maps to unknown residue</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Known OutOfMemory errors give warning message</li>\r
+ <li>Overview window calculated more efficiently</li>\r
+ <li>Several GUI bugs resolved</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.05</strong><br>\r
+ 30/8/05</div></td>\r
+ <td><ul>\r
+ <li>Edit and annotate in "Wrapped" view</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Several GUI bugs resolved</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.04</strong><br>\r
+ 24/8/05</div></td>\r
+ <td><ul>\r
+ <li>Hold down mouse wheel & scroll to change font size</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Improved JPred client reliability</li>\r
+ <li>Improved loading of Jalview files</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td> <div align="center"><strong>2.03</strong><br>\r
+ 18/8/05</div></td>\r
+ <td><ul>\r
+ <li>Set Proxy server name and port in preferences</li>\r
+ <li>Multiple URL links from sequence ids</li>\r
+ <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
+ <li>Choose to ignore gaps in consensus calculation</li>\r
+ <li>Unix users can set default web browser</li>\r
+ <li>Runs without GUI for batch processing</li>\r
+ <li>Dynamically generated Web Service Menus</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>InstallAnywhere download for Sparc Solaris</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td> <div align="center"><strong>2.02</strong><br>\r
+ 18/7/05</div></td>\r
+ <td> </td>\r
+ <td><ul>\r
+ <li>Copy & Paste order of sequences maintains alignment order.</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.01</strong><br>\r
+ 12/7/05</div></td>\r
+ <td><ul>\r
+ <li>Use delete key for deleting selection.</li>\r
+ <li>Use Mouse wheel to scroll sequences.</li>\r
+ <li>Help file updated to describe how to add alignment annotations.</li>\r
+ <li>Version and build date written to build properties file.</li>\r
+ <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>Delete gaps bug fixed.</li>\r
+ <li>FileChooser sorts columns.</li>\r
+ <li>Can remove groups one by one.</li>\r
+ <li>Filechooser icons installed.</li>\r
+ <li>Finder ignores return character when searching. Return key will initiate \r
+ a search.<br>\r
+ </li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
+ <td> <div align="center"><strong>2.0</strong><br>\r
+ 20/6/05</div></td>\r
+ <td ><ul>\r
+ <li> New codebase</li>\r
+ </ul></td>\r
+ <td > </td>\r
+ </tr>\r
+</table>\r
+<p> </p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff