Menus

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 00bca80..280cce9 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -25,7 +25,8 @@
           Postscript</a> file from your alignment.</em></li>\r
         <li><strong>PNG<br>\r
           </strong><em>Create a <a href="../io/index.html#export">Portable Network \r
-          Graphics</a> file from your alignment.</em></li>\r
+          Graphics</a> file from your alignment.<br>\r
+          </em></li>\r
       </ul>\r
     </li>\r
     <li><strong>Output to Textbox<br>\r
@@ -48,11 +49,13 @@
       coloursof your alignment. If the alignment has annotations visible, these \r
       will be printed below the alignment. If the alignment is wrapped the number \r
       of residues per line of your alignment will depend on the paper width or \r
-      your alignment window width, whichever is the smaller. </em></li>\r
+      your alignment window width, whichever is the smaller. <br>\r
+      </em></li>\r
     <li><strong>Load Associated Tree<br>\r
       </strong><em>Jalview can load in trees which are in the Newick file format \r
       and associate them with a particular alignment. Note: the ids of the tree \r
-      file and your alignment MUST be the same.</em></li>\r
+      file and your alignment MUST be the same.<br>\r
+      </em></li>\r
     <li><strong>Close<br>\r
       </strong><em>Close the alignment window. Be aware that changes to your alignment \r
       will not be save unless specifically actioned from the &quot;Save As&quot; \r
@@ -65,37 +68,108 @@
   <ul>\r
     <li><strong>Undo</strong><em><br>\r
       This will undo any edits you make to the alignment. This applies to insertion \r
-      or deletion of gaps, cutting residues or sequences from the alignment, pasting \r
+      or deletion of gaps, cutting residues or sequences from the alignment or \r
+      pasting sequences to the current alignment or sorting the alignment. It \r
+      DOES NOT undo colour changes or adjustments to group sizes affect the annotation \r
+      panel. <br>\r
       </em></li>\r
     <li><strong>Redo<br>\r
-      </strong></li>\r
-    <li><strong>Cut</strong></li>\r
-    <li><strong>Copy</strong></li>\r
+      </strong><em>Any actions which you undo can be redone using redo. <br>\r
+      </em></li>\r
+    <li><strong>Cut<br>\r
+      </strong><em>This will make a copy of the currently selected residues before \r
+      removing them from your alignment. Click on a sequence name if you wish \r
+      to select a whole sequence. <br>\r
+      Use &lt;CTRL&gt; and X (&lt;APPLE&gt; and X on MacOSX) to cut.<br>\r
+      </em></li>\r
+    <li><strong>Copy</strong><br>\r
+      <em>Copies the currently selected residues to the system clipboard. The \r
+      format of copied residues is NAME&lt;tab&gt;START_RES&lt;tab&gt;END_RES&lt;tab&gt;SEQUENCE \r
+      <br>\r
+      Use &lt;CTRL&gt; and C (&lt;APPLE&gt; and C on MacOSX) to copy.<br>\r
+      </em></li>\r
     <li><strong>Paste </strong> \r
       <ul>\r
-        <li><strong>To New Alignment</strong></li>\r
-        <li><strong>Add To This Alignment</strong></li>\r
+        <li><strong>To New Alignment<br>\r
+          </strong><em>A new alignment window will be created from sequences previously \r
+          copied or cut to the system clipboard. <br>\r
+          Use &lt;CTRL&gt; and V(&lt;APPLE&gt; and V on MacOSX) to paste.</em></li>\r
+        <li><strong>Add To This Alignment<br>\r
+          </strong><em>Copied sequences from another alignment window can be added \r
+          to the current Jalview alignment. <br>\r
+          </em><strong> </strong></li>\r
       </ul>\r
     </li>\r
-    <li><strong>Delete</strong></li>\r
-    <li><strong>Select All</strong></li>\r
-    <li><strong>Deselect All</strong></li>\r
-    <li><strong>Invert Selection</strong></li>\r
-    <li><strong>Undefine Groups</strong></li>\r
-    <li><strong>Remove Left</strong></li>\r
-    <li><strong>Remove Right</strong></li>\r
-    <li><strong>Remove Empty Columns</strong></li>\r
-    <li><strong>Remove All Gaps</strong></li>\r
-    <li><strong>Remove Redundancy</strong></li>\r
-    <li><strong>Pad Gaps</strong></li>\r
+    <li><strong>Delete<br>\r
+      </strong><em>This will delete the currently selected residues without making \r
+      a copy of them first.<br>\r
+      </em></li>\r
+    <li><strong>Select All<br>\r
+      </strong><em>Selects all the sequences and residues in the alignment. <br>\r
+      Use &lt;CTRL&gt; and A (&lt;APPLE&gt; and A on a MacOSX) to select all.<br>\r
+      </em></li>\r
+    <li><strong>Deselect All<br>\r
+      </strong><em>Removes the current selection box (red dashed box) from the \r
+      alignment window. All selected sequences, residues and marked columns will \r
+      be deselected. </em><em> <br>\r
+      Use &lt;ESCAPE&gt; to deselect all.<br>\r
+      </em></li>\r
+    <li><strong>Invert Selection<br>\r
+      </strong><em>Any sequence ids currently not selected will replace the current \r
+      selection. <br>\r
+      </em><strong> </strong></li>\r
+    <li><strong>Undefine Groups<br>\r
+      </strong><em>The alignment will be reset with no defined groups. WARNING: \r
+      This cannot be undone.<br>\r
+      </em></li>\r
+    <li><strong>Remove Left<br>\r
+      </strong><em>If the alignment has marked columns, the alignment will be \r
+      trimmed to the left of the leftmost marked column. To mark a column, mouse \r
+      click the scale bar above the alignment. Click again to unmark a column, \r
+      or select &quot;Deselect All&quot; to deselect all columns.<br>\r
+      </em></li>\r
+    <li><strong>Remove Right<br>\r
+      </strong><em>If the alignment has marked columns, the alignment will be \r
+      trimmed to the left of the leftmost marked column. To mark a column, mouse \r
+      click the scale bar above the alignment. Click again to unmark a column, \r
+      or select &quot;Deselect All&quot; to deselect all columns.<br>\r
+      </em></li>\r
+    <li><strong>Remove Empty Columns<br>\r
+      </strong><em>All columns which contain purely gap characters (&quot;-&quot;, \r
+      &quot;.&quot;) will be deleted.<br>\r
+      You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+      </em><em><br>\r
+      </em></li>\r
+    <li><strong>Remove All Gaps</strong><br>\r
+      <em>All gap characters (&quot;-&quot;, &quot;.&quot;) will be deleted from \r
+      the alignment.<br>\r
+      You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+      <br>\r
+      </em> </li>\r
+    <li><strong>Remove Redundancy<br>\r
+      </strong><em>Selecting this option brings up a window asking you to select \r
+      a threshold. If the percentage identity between two sequences exceeds this \r
+      value one of the sequences (the shorter) is discarded. Press the &quot;Apply&quot; \r
+      button to reomove redundant sequences.<br>\r
+      </em></li>\r
+    <li><strong>Pad Gaps<br>\r
+      </strong><em>If the sequences in an alignment window are not all the same \r
+      length they can all be set to the length of the longest sequence by selecting \r
+      &quot;Pad Gaps.&quot; Any sequences which are shorter than the longest sequence \r
+      in an alignment will have gap characters (&quot;-&quot; or &quot;.&quot;) \r
+      appended to the beginning or end to make them equal length. <br>\r
+      You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+      </em></li>\r
   </ul>\r
 </blockquote>\r
 <ul>\r
   <li><strong>Search</strong></li>\r
 </ul>\r
-<blockquote>\r
+<blockquote> \r
   <ul>\r
-    <li><strong>Find</strong></li>\r
+    <li><strong>Find<br>\r
+      </strong><em>Select this to <a href="../features/search.html">search</a> \r
+      for residues, sequence name or residue position within the alignment. </em></li>\r
   </ul>\r
 </blockquote>\r
 <ul>\r
@@ -103,16 +177,63 @@
 </ul>\r
 <blockquote> \r
   <ul>\r
-    <li><strong>Font</strong></li>\r
-    <li><strong>Wrap</strong></li>\r
-    <li><strong>Show Full Sequence ID</strong></li>\r
-    <li><strong>Boxes</strong></li>\r
-    <li><strong>Text</strong></li>\r
-    <li><strong>Colour Text</strong></li>\r
-    <li><strong>Show Gaps</strong></li>\r
-    <li><strong>Show Annotations</strong></li>\r
-    <li><strong>Sequence Features</strong></li>\r
-    <li><strong>Overview Window</strong></li>\r
+    <li><strong>Font<br>\r
+      </strong><em>Change the font of the display. The default font can be set \r
+      from the &quot;Choose Font&quot; window, which is shown when the &quot;Font \r
+      Menu&quot; is selected. <br>\r
+      </em></li>\r
+    <li><strong>Wrap<br>\r
+      </strong><em>The default alignment display shows sequences in a single horizontal \r
+      row. If your alignment has only a few sequences you may wish to &quot;Wrap&quot; \r
+      the alignment so that the sequences are shown on multiple horizontal rows. \r
+      Options are available to show the residue numbering at the start and/or \r
+      end of an alignment as well as showing the alignment position above each \r
+      sequence row. <br>\r
+      NOTE: In the current version the wrap alignment should be used for viewing, \r
+      not editing. <br>\r
+      </em><strong> </strong></li>\r
+    <li><strong>Show Full Sequence ID<br>\r
+      </strong><em>If this box is selected the sequence name will have the start \r
+      and end position of the sequence appended to the name, in the format NAME/START-END<br>\r
+      </em></li>\r
+    <li><strong>Boxes</strong><em><br>\r
+      If this is selected the background of a residue will be coloured using the \r
+      selected background colour. Useful if used in conjunction with &quot;Colour \r
+      Text.&quot; <br>\r
+      </em></li>\r
+    <li><strong>Text<br>\r
+      </strong><em>If this is selected the residues will be displayed using the \r
+      standard 1 character amino acid alphabet.<br>\r
+      </em></li>\r
+    <li><strong>Colour Text<br>\r
+      </strong><em>If this is selected the residues will be coloured according \r
+      to the background colour associated with that residue. The colour is slightly \r
+      darker than background to enable the residue to be read. <br>\r
+      </em></li>\r
+    <li><strong>Show Gaps<br>\r
+      </strong><em>If this is selected gap characters will be displayed as &quot;.&quot; \r
+      or &quot;-&quot;. If unselected gap characters will appear as blank spaces. \r
+      <br>\r
+      You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
+      </em></li>\r
+    <li><strong>Show Annotations<br>\r
+      </strong><em>If this is selected the &quot;Annotation Panel&quot; will be \r
+      displayed below the alignment. The default setting is to display the conservation \r
+      calulation, quality calculation and consensus values as bar charts. </em><br>\r
+    </li>\r
+    <li><strong>Sequence Features<br>\r
+      </strong><em>If the sequence names are Swissprot entries Jalview will use \r
+      the names to retrieve sequence features from the EBI. Features which are \r
+      1 residue in length are coloured red, sequences longer than 1 residue are \r
+      coloured blue. Move the mouse over a coloured feature to display the details \r
+      of the feature. <br>\r
+      Note: The retrieved information will update the sequence start and end labels \r
+      if they are incorrect. <br>\r
+      </em></li>\r
+    <li><strong>Overview Window<br>\r
+      </strong><em>A scaled version of the alignment will be displayed in a small \r
+      window. A red box will indicate the currently visible area of the alignment. \r
+      Move the visible region using the mouse. </em><strong> </strong></li>\r
   </ul>\r
 </blockquote>\r
 <ul>\r
@@ -120,24 +241,30 @@
 </ul>\r
 <blockquote> \r
   <ul>\r
-    <li><strong>Apply Colour To All Groups</strong></li>\r
-    <li><strong>None</strong></li>\r
-    <li><strong>ClustalX</strong></li>\r
-    <li><strong>Blosum62 Score</strong></li>\r
-    <li><strong>Percentage Identity</strong></li>\r
-    <li><strong>Zappo</strong></li>\r
-    <li><strong>Taylor</strong></li>\r
-    <li><strong>Hydrophobicity</strong></li>\r
-    <li><strong>Helix Propensity</strong></li>\r
-    <li><strong>Strand Propensity</strong></li>\r
-    <li><strong>Turn Propensity</strong></li>\r
-    <li><strong>Buried Index</strong></li>\r
-    <li><strong>Nucleotide</strong></li>\r
-    <li><strong>User Defined</strong></li>\r
-    <li><strong>By Conservation</strong></li>\r
-    <li><strong>Modify Conservation Threshold</strong></li>\r
-    <li><strong>Above Identity Threshold</strong></li>\r
-    <li><strong>Modify Identity Threshold</strong></li>\r
+    <li><strong>Apply Colour To All Groups<br>\r
+      </strong><em>If this is selected, any changes made to the background colour \r
+      will be applied to all currently defined groups.<br>\r
+      </em></li>\r
+    <li><strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, \r
+      Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried \r
+      Index, Nucleotide, User Defined<br>\r
+      </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for \r
+      a description of all colour schemes.</em><br>\r
+    </li>\r
+    <li><strong>By Conservation<br>\r
+      </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
+      by Conservation</a>.</em><br>\r
+    </li>\r
+    <li><strong>Modify Conservation Threshold<br>\r
+      </strong><em>Use this to display the conservation threshold slider window. \r
+      Useful if the window has been closed. </em></li>\r
+    <li><strong>Above Identity Threshold<br>\r
+      </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
+      Identity</a></em><strong>.<br>\r
+      </strong></li>\r
+    <li><strong>Modify Identity Threshold<br>\r
+      </strong><em>Use this to set the threshold value for colouring above Identity. \r
+      Useful if the window has been closed. </em></li>\r
   </ul>\r
 </blockquote>\r
 <ul>\r
@@ -147,9 +274,21 @@
   <ul>\r
     <li><strong>Sort </strong> \r
       <ul>\r
-        <li><strong>by ID</strong></li>\r
-        <li><strong>by Group</strong></li>\r
-        <li><strong>by Pairwise Identity</strong></li>\r
+        <li><strong>by ID<br>\r
+          </strong><em>This will sort the sequences according to sequence name. \r
+          If the sort is repeated, the order of the sorted sequences will be inverted. \r
+          </em><strong><br>\r
+          </strong></li>\r
+        <li><strong>by Group</strong><strong><br>\r
+          </strong><em>This will sort the sequences according to sequence name. \r
+          If the sort is repeated, the order of the sorted sequences will be inverted. \r
+          </em><strong></strong><strong><br>\r
+          </strong></li>\r
+        <li><strong>by Pairwise Identity<br>\r
+          </strong><em>This will sort the selected sequences by their percentage \r
+          identity to the consensus sequence. The most similar sequence is put \r
+          at the top. </em><strong><br>\r
+          </strong></li>\r
       </ul>\r
     </li>\r
     <li><strong>Calculate Tree </strong> \r
@@ -157,14 +296,28 @@
         <li><strong>Average Distance Using % Identity</strong></li>\r
         <li><strong>Neighbour Joining Using % Identity</strong></li>\r
         <li><strong>Average Distance Using Blosum62</strong></li>\r
-        <li><strong>Neighbour Joining Using Blosum62</strong></li>\r
+        <li><strong>Neighbour Joining Using Blosum62<br>\r
+          </strong><em>See <a href="../calculations/tree.html">calculating trees</a>.</em><strong> \r
+          <br>\r
+          </strong></li>\r
       </ul>\r
     </li>\r
-    <li><strong>Paiwise Alignments</strong></li>\r
-    <li><strong>Principal Component Analysis</strong></li>\r
-    <li><strong>Web Service </strong> \r
+    <li><strong>Paiwise Alignments</strong><br>\r
+      <em>See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
+    </li>\r
+    <li><strong>Principal Component Analysis</strong><br>\r
+      <em>See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em> \r
+      <br>\r
+    </li>\r
+    <li><strong>Web Service <br>\r
+      </strong> \r
       <ul>\r
+        <em>Selecting one of the following menu items will start a remote service \r
+        on the high powered computing faciltiy at the University of Dundee. You \r
+        will need a continuous network connection in order to use these services. \r
+        </em> \r
         <li><strong>Clustal Alignment</strong></li>\r
+        <li><strong>Clustal Realign</strong></li>\r
         <li><strong>JPred</strong></li>\r
         <li><strong>Muscle Alignment</strong></li>\r
       </ul>\r

diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 29857b9..e1ef461 100755 (executable)
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -40,12 +40,21 @@
   </li>\r
   <li><strong>Help </strong> \r
     <ul>\r
-      <li><strong>About, </strong></li>\r
+      <li><strong>About<br>\r
+        </strong><em>Displays the version and creation date of the application, \r
+        as well as acknowledgements and a citation reference. </em></li>\r
       <li><strong>Documentation<br>\r
+        </strong><em>Displays help files as a browseable, searchable set of pages \r
+        with a table of contents. </em><strong><br>\r
         </strong></li>\r
     </ul>\r
   </li>\r
-  <li><strong>Window</strong></li>\r
+  <li><strong>Window<br>\r
+    </strong><em>Each time a new window is added to the Jalview Desktop a new \r
+    menu item will be added to the &quot;Window&quot; menu. If you are working \r
+    with several alignments, trees or other types of windows use the &quot;Window&quot; \r
+    menu to bring your window of choice to the top of the pile if it has been \r
+    hidden by other windows. </em></li>\r
 </ul>\r
 </body>\r
 </html>\r

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 10f8072..14dc178 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -2,21 +2,61 @@
 <head><title>Popup Menu</title></head>\r
 \r
 <body>\r
-<p><strong>Popup Menu</strong></p>\r
-<p><em>Define </em></p>\r
+<p><strong>Popup Menu</strong><br>\r
+  <em>This menu is visible when right clicking either within a selected region \r
+  on the alignment or on a selected sequence name.</em></p>\r
 <ul>\r
-  <li>Group, </li>\r
-  <li>Remove Group</li>\r
-  <li>Group Colour</li>\r
-  <li>Boxes</li>\r
-  <li> Text</li>\r
-  <li>Colour Text</li>\r
-  <li>Border Colour </li>\r
-</ul>\r
-<p><em>Sequence</em> </p>\r
-<ul>\r
-  <li>Edit Name</li>\r
-  <li>View PDB Structure</li>\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
+        selected group. Click OK to set the name, cancel to use the default group \r
+        name. </em><strong><br>\r
+        </strong></li>\r
+      <li><strong>Remove Group<br>\r
+        </strong><em>This will undefine the selected group. </em><strong> <br>\r
+        </strong></li>\r
+      <li><strong>Group Colour<br>\r
+        </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
+        of the group.</em><strong> <br>\r
+        </strong></li>\r
+      <li><strong>Boxes<br>\r
+        </strong><em>If selected the background of a residue within the selected \r
+        group will be coloured according to the assigned colour scheme.</em><strong> \r
+        <br>\r
+        </strong></li>\r
+      <li><strong> Text<br>\r
+        </strong><em>If selected the selected group will display text. </em><strong><br>\r
+        </strong></li>\r
+      <li><strong>Colour Text<br>\r
+        </strong><em>If selected the selected group will display text in a colour \r
+        slightly darker than the background colour of that residue.</em><strong><br>\r
+        </strong></li>\r
+      <li><strong>Border Colour <br>\r
+        </strong><em>Selecting this will display a &quot;Colour Chooser&quot; \r
+        window. Select a colour than press OK to set the border colour of a group.</em><strong><br>\r
+        </strong></li>\r
+    </ul>\r
+  </li>\r
+  <li><strong>Sequence <br>\r
+    </strong><em>This menu is only visible if you right-click on a sequence name. \r
+    </em> \r
+    <ul>\r
+      <li><strong>Edit Name<br>\r
+        </strong><em>You may edit the name of each sequence. A window will be \r
+        displayed asking for a new sequence name to be entered. Press OK to accept \r
+        your edit.</em><strong><br>\r
+        </strong></li>\r
+      <li><strong>View PDB Structure<br>\r
+        </strong><em>In the current version you will first need to select &quot;View \r
+        -&gt; Sequence Features&quot; before associating a PDB file with a sequence. \r
+        <br>\r
+        If the sequence has a PDB file associated with it Jalview will display \r
+        a 3D interactive viewer of the file. </em><strong><br>\r
+        <br>\r
+        </strong></li>\r
+    </ul>\r
+  </li>\r
 </ul>\r
 </body>\r
 </html>\r