From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 2 May 2006 12:24:48 +0000 (+0000)
Subject: 2.08.1
X-Git-Tag: Release_2_08_1~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=caad315933db2600eaca9bf111932d5767ccb78b;p=jalview.git

2.08.1
---

diff --git a/help/html/features/search.gif b/help/html/features/search.gif
index d571085..1c0ffb0 100755
Binary files a/help/html/features/search.gif and b/help/html/features/search.gif differ
diff --git a/help/html/features/search.html b/help/html/features/search.html
index c1ad561..3d60858 100755
--- a/help/html/features/search.html
+++ b/help/html/features/search.html
@@ -13,21 +13,21 @@ td {
 <p><strong>Search</strong></p>
 <p>The search box is displayed by pressing Control and F or
   selecting &quot;Find...&quot; from the &quot;Search&quot; menu.</p>
-<img src="search.gif" width="339" height="111">
+<img src="search.gif" width="339" height="110">
 <p>&quot;Find next&quot; will find the next occurence of the specified and adjust 
   the alignment window view to show it, and &quot;Find all&quot; highlights all 
   matches for a pattern. The &quot;New Feature&quot; is a quick way to highlight 
   and group residues matching the specified search pattern throughout the alignment. 
 <ul>
-<li>The search uses regular expressions. (understands a mixture of
-  posix and perl style regex - see below for a summary)</li>
-<li>Gaps are ignored when matching the query to the sequences in the
-  alignment.</li>
-<li>The search is applied to both sequences and their IDs but the &quot;Find next&quot;
-  and &quot;Find all&quot; buttons only count the sequence matches.</li>
-  <li>If a region is selected, then search will <strong>only</strong>
-  be performed on that region. </li>
+  <li>The search uses regular expressions. (understands a mixture of posix and 
+    perl style regex - see below for a summary)</li>
+  <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>
+  <li>The search is applied to both sequences and their IDs but the &quot;Find 
+    next&quot; and &quot;Find all&quot; buttons only count the sequence matches.</li>
+  <li>If a region is selected, then search will <strong>only</strong> be performed 
+    on that region. </li>
   <li>To quickly clear the current selection, press the &quot;Escape&quot; key.</li>
+  <li>Tick the &quot;Match Case&quot; box to perform a case sensitive search.</li>
 </ul>
 <p><strong>Creating Features from Search Results</strong></p>
 <p>
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index faf98e9..940e3cf 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -7,7 +7,7 @@
   on the alignment or on a selected sequence name. It may not be
   accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
-  <li><strong>Define </strong> 
+  <li><strong>Define</strong> 
     <ul>
       <li><strong>Group<br>
         </strong><em>This will display a window asking for the name of the currently 
@@ -35,8 +35,32 @@
         </strong></li>
       <li><strong>Border Colour <br>
         </strong><em>Selecting this will display a &quot;Colour Chooser&quot; 
-        window. Select a colour than press OK to set the border colour of a group.</em><strong><br>
+        window. Select a colour than press OK to set the border colour of a group.<br>
+        </em></li>
+    </ul>
+  </li>
+  <li><strong>Edit </strong> 
+    <ul>
+      <li><strong>Copy</strong><br>
+        <em>Copys the selected region. In the applet version, the copied sequences 
+        are not available to the system clipboard.</em> <br>
+      </li>
+      <li><strong>Cut<br>
+        </strong><em>Cuts the selected region from the alignment. In the applet 
+        version, the copied sequences are not available to the system clipboard.</em> 
+        <em><br>
+        </em></li>
+      <li><strong>To Lower Case<br>
+        </strong><em>Changes the case of selected region to upper case.</em><strong><br>
         </strong></li>
+      <li><strong>To Upper Case<br>
+        </strong><em>Changes the case of selected region to lower case.</em><strong><br>
+        </strong></li>
+      <li><strong>Toggle Case</strong><br>
+        <em>Switches the case of all residues within the selected region.</em> 
+        <br>
+        <br>
+      </li>
     </ul>
   </li>
   <li><strong>Sequence <br>
@@ -50,15 +74,12 @@
         you must save in Fasta, PIR or Jalview File format.</em><strong><br>
         </strong></li>
       <li><strong>View PDB Structure<br>
-        </strong><em>
-        If the sequence has a PDB file associated with it Jalview will display 
-        a 3D interactive viewer of the file.<br>
-This entry is only present if the sequence has an
-  <a href="../features/viewingpdbs.html">associated PDB structure</a>.
-  If you can't see this entry for your sequence, and the sequence name
-  is a uniprot identifier, then try enabling the &quot;View 
-        -&gt; Sequence Features&quot; and opening the popup menu again.</em>
-        </li>
+        </strong><em> If the sequence has a PDB file associated with it Jalview 
+        will display a 3D interactive viewer of the file.<br>
+        This entry is only present if the sequence has an <a href="../features/viewingpdbs.html">associated 
+        PDB structure</a>. If you can't see this entry for your sequence, and 
+        the sequence name is a uniprot identifier, then try enabling the &quot;View 
+        -&gt; Sequence Features&quot; and opening the popup menu again.</em> </li>
     </ul>
   </li>
   <li><strong><em>Link</em></strong><br>
diff --git a/help/html/releases.html b/help/html/releases.html
index eeae226..e37c5b5 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -9,6 +9,28 @@
     <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></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 movemnet 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>&nbsp;</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>