<p><strong>Search</strong></p>\r
<p>The search box is displayed by pressing Control and F or\r
selecting "Find..." from the "Search" menu.</p>\r
-<img src="search.gif" width="339" height="111">\r
+<img src="search.gif" width="339" height="110">\r
<p>"Find next" will find the next occurence of the specified and adjust \r
the alignment window view to show it, and "Find all" highlights all \r
matches for a pattern. The "New Feature" is a quick way to highlight \r
and group residues matching the specified search pattern throughout the alignment. \r
<ul>\r
-<li>The search uses regular expressions. (understands a mixture of\r
- posix and perl style regex - see below for a summary)</li>\r
-<li>Gaps are ignored when matching the query to the sequences in the\r
- alignment.</li>\r
-<li>The search is applied to both sequences and their IDs but the "Find next"\r
- and "Find all" buttons only count the sequence matches.</li>\r
- <li>If a region is selected, then search will <strong>only</strong>\r
- be performed on that region. </li>\r
+ <li>The search uses regular expressions. (understands a mixture of posix and \r
+ perl style regex - see below for a summary)</li>\r
+ <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>\r
+ <li>The search is applied to both sequences and their IDs but the "Find \r
+ next" and "Find all" buttons only count the sequence matches.</li>\r
+ <li>If a region is selected, then search will <strong>only</strong> be performed \r
+ on that region. </li>\r
<li>To quickly clear the current selection, press the "Escape" key.</li>\r
+ <li>Tick the "Match Case" box to perform a case sensitive search.</li>\r
</ul>\r
<p><strong>Creating Features from Search Results</strong></p>\r
<p>\r
on the alignment or on a selected sequence name. It may not be\r
accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>\r
<ul>\r
- <li><strong>Define </strong> \r
+ <li><strong>Define</strong> \r
<ul>\r
<li><strong>Group<br>\r
</strong><em>This will display a window asking for the name of the currently \r
</strong></li>\r
<li><strong>Border Colour <br>\r
</strong><em>Selecting this will display a "Colour Chooser" \r
- window. Select a colour than press OK to set the border colour of a group.</em><strong><br>\r
+ window. Select a colour than press OK to set the border colour of a group.<br>\r
+ </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Edit </strong> \r
+ <ul>\r
+ <li><strong>Copy</strong><br>\r
+ <em>Copys the selected region. In the applet version, the copied sequences \r
+ are not available to the system clipboard.</em> <br>\r
+ </li>\r
+ <li><strong>Cut<br>\r
+ </strong><em>Cuts the selected region from the alignment. In the applet \r
+ version, the copied sequences are not available to the system clipboard.</em> \r
+ <em><br>\r
+ </em></li>\r
+ <li><strong>To Lower Case<br>\r
+ </strong><em>Changes the case of selected region to upper case.</em><strong><br>\r
</strong></li>\r
+ <li><strong>To Upper Case<br>\r
+ </strong><em>Changes the case of selected region to lower case.</em><strong><br>\r
+ </strong></li>\r
+ <li><strong>Toggle Case</strong><br>\r
+ <em>Switches the case of all residues within the selected region.</em> \r
+ <br>\r
+ <br>\r
+ </li>\r
</ul>\r
</li>\r
<li><strong>Sequence <br>\r
you must save in Fasta, PIR or Jalview File format.</em><strong><br>\r
</strong></li>\r
<li><strong>View PDB Structure<br>\r
- </strong><em>\r
- If the sequence has a PDB file associated with it Jalview will display \r
- a 3D interactive viewer of the file.<br>\r
-This entry is only present if the sequence has an\r
- <a href="../features/viewingpdbs.html">associated PDB structure</a>.\r
- If you can't see this entry for your sequence, and the sequence name\r
- is a uniprot identifier, then try enabling the "View \r
- -> Sequence Features" and opening the popup menu again.</em>\r
- </li>\r
+ </strong><em> If the sequence has a PDB file associated with it Jalview \r
+ will display a 3D interactive viewer of the file.<br>\r
+ This entry is only present if the sequence has an <a href="../features/viewingpdbs.html">associated \r
+ PDB structure</a>. If you can't see this entry for your sequence, and \r
+ the sequence name is a uniprot identifier, then try enabling the "View \r
+ -> Sequence Features" and opening the popup menu again.</em> </li>\r
</ul>\r
</li>\r
<li><strong><em>Link</em></strong><br>\r
<td ><div align="center"><em><strong>Issues Resolved</strong></em></div></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 movemnet 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