X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=b63d20bcc86d42cb7642405485ec97d674eba959;hb=dde303bc73617ab4eb3e681e67cf899e6a971318;hp=d13afe452521c229b02ad236ad32a6515baeb543;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index d13afe4..b63d20b 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -39,31 +39,31 @@
     <strong>Types of annotation</strong>
   <ul>
     <li><a name="seqannots"><strong>Sequence
-          associated annotation.</strong></a><br/>Data displayed on sequence annotation
-      rows are associated with the positions of a sequence. Often this
-      is 'Reference annotation' such as secondary structure information
-      derived from 3D structure data, or from the results of sequence
-      based prediction of <a href="../webServices/jnet.html">secondary
+          associated annotation.</strong></a><br />Data displayed on sequence
+      annotation rows are associated with the positions of a sequence.
+      Often this is 'Reference annotation' such as secondary structure
+      information derived from 3D structure data, or from the results of
+      sequence based prediction of <a href="../webServices/jnet.html">secondary
         structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
       If reference annotation is available for a the currently selected
       sequences, it can be shown by selecting the <strong>Add
         Reference Annotation</strong> option in the sequence or selection popup
       menu.</li>
-    <li><strong>Group associated annotation.</strong><br/>Data can be associated with
-      groups defined on the alignment.     If sequence groups are defined, <a
-      href="../calculations/conservation.html">Conservation</a> and <a
-      href="../calculations/consensus.html">Consensus</a> annotation can
-    be enabled for each group from the <a
+    <li><strong>Group associated annotation.</strong><br />Data can
+      be associated with groups defined on the alignment. If sequence
+      groups are defined, <a href="../calculations/conservation.html">Conservation</a>
+      and <a href="../calculations/consensus.html">Consensus</a>
+      annotation can be enabled for each group from the <a
       href="../menus/alwannotation.html">Annotations menu</a>, or can be
-    imported from a Jalview <a href="annotationsFormat.html">Annotations
-      file</a>.</li>
-    <li><strong>Alignment associated annotation.</strong><br />Annotation rows
-      associated with columns on the alignment are simply 'alignment
-      annotation'. Controls allow you to <a href="#iaannot">interactively create
-        alignment annotation</a> to add labels and symbols to alignment columns.
-      Jalview's consensus, conservation and quality calculations also
-      create histogram and sequence logo annotations on the alignment.
-    </li>
+      imported from a Jalview <a href="annotationsFormat.html">Annotations
+        file</a>.</li>
+    <li><strong>Alignment associated annotation.</strong><br />Annotation
+      rows associated with columns on the alignment are simply
+      'alignment annotation'. Controls allow you to <a href="#iaannot">interactively
+        create alignment annotation</a> to add labels and symbols to
+      alignment columns. Jalview's consensus, conservation and quality
+      calculations also create histogram and sequence logo annotations
+      on the alignment.</li>
   </ul>
   <p>
     <strong>Importing and exporting annotation</strong><br />
@@ -78,17 +78,15 @@
     groups of annotation rows can be shown or hidden using the pop-up
     menu obtained by right-clicking the label. You can also reorder them
     by dragging the label to a new position with the left mouse button.
-    The
-    <strong>Annotations</strong> menu provides settings controlling the
-    ordering and display of sequence, group and alignment associated
-    annotation. The
-    <strong>Colour by annotation</strong> option in the colour menu
-    allows annotation to be used to
-    <a href="../colourSchemes/annotationColouring.html">shade the
-      alignment</a>. Annotations can also be used to
-    <a href="../features/columnFilterByAnnotation.html">select or
-      hide columns</a> via the dialog opened from the
-    <strong>Selection</strong> menu.
+    The <strong>Annotations</strong> menu provides settings controlling
+    the ordering and display of sequence, group and alignment associated
+    annotation. The <strong>Colour by annotation</strong> option in the
+    colour menu allows annotation to be used to <a
+      href="../colourSchemes/annotationColouring.html">shade the
+      alignment</a>. Annotations can also be used to <a
+      href="../features/columnFilterByAnnotation.html">select or
+      hide columns</a> via the dialog opened from the <strong>Selection</strong>
+    menu.
   </p>
   <p>
     <strong>Sequence Highlighting and Selection from Annotation</strong>
@@ -148,32 +146,32 @@
         using the view's standard font size.</em></li>
   </ul>
   <p>
-    <strong>Editing labels and secondary structure annotation rows</strong>
+    <strong>Editing labels and secondary structure annotation
+      rows</strong>
   </p>
   <p>
     Use the <strong>left mouse button</strong> to select a position
     along the row that are to be annotated - these regions will be
-    coloured red. Press <strong>Control</strong> or <strong>shift</strong> in
-    combination with the left-click to either select an additional position,
-    or a range of positions on the alignment.
+    coloured red. Press <strong>Control</strong> or <strong>shift</strong>
+    in combination with the left-click to either select an additional
+    position, or a range of positions on the alignment.
   </p>
   <p>
     Once positions have been selected, use the <strong>right
-      mouse button</strong> and select one of the following from the <strong>annotation menu</strong>:
+      mouse button</strong> and select one of the following from the <strong>annotation
+      menu</strong>:
   </p>
   <ul>
-    <li>Helix<br>
-    <em>Marks selected positions with a helix glyph (a red oval),
-        and optional text label (see below). A dialog box will open for
-        you to enter the text. Consecutive ovals will be rendered as an
-        unbroken red line.</em>
+    <li>Helix<br> <em>Marks selected positions with a
+        helix glyph (a red oval), and optional text label (see below). A
+        dialog box will open for you to enter the text. Consecutive
+        ovals will be rendered as an unbroken red line.</em>
     </li>
-    <li>Sheet<br>
-    <em>Marks selected positions with a sheet glyph (a green arrow
-        oriented from left to right), and optional text label (see
-        below). A dialog box will open for you to enter the text.
-        Consecutive arrows will be joined together to form a single
-        green arrow.</em>
+    <li>Sheet<br> <em>Marks selected positions with a
+        sheet glyph (a green arrow oriented from left to right), and
+        optional text label (see below). A dialog box will open for you
+        to enter the text. Consecutive arrows will be joined together to
+        form a single green arrow.</em>
     </li>
     <li><a name="rna">RNA Helix</a> (only shown when working with
       nucleotide sequences)<br> <em>Marks selected positions
@@ -183,23 +181,22 @@
         region pairs with bases to the left of the highlighted columns.
         Other kinds of base-pair annotation are also supported (e.g. 'A'
         and 'a', or '&lt;' and '&gt;'), and Jalview will suggest an
-        appropriate symbol based on the closest unmatched
-        parenthesis to the left.<br />If any brackets do not match up, then an
-        orange square will highlight the first position where a bracket
-        was found not to match.
+        appropriate symbol based on the closest unmatched parenthesis to
+        the left.<br />If any brackets do not match up, then an orange
+        square will highlight the first position where a bracket was
+        found not to match.
     </em></li>
-    <li>Label<br>
-    <em>Set the text label at the selected positions. A dialog box
-        will open for you to enter the text. If more than one
-        consecutive position is marked with the same label, only the
-        first position's label will be rendered.</em>
+    <li>Label<br> <em>Set the text label at the selected
+        positions. A dialog box will open for you to enter the text. If
+        more than one consecutive position is marked with the same
+        label, only the first position's label will be rendered.</em>
     </li>
-    <li>Colour<br>
-    <em>Changes the colour of the annotation text label.</em>
+    <li>Colour<br> <em>Changes the colour of the
+        annotation text label.</em>
     </li>
-    <li>Remove Annotation<br>
-    <em>Blanks any annotation at the selected positions on the row.
-        Note: <strong>This cannot be undone</strong>
+    <li>Remove Annotation<br> <em>Blanks any annotation
+        at the selected positions on the row. Note: <strong>This
+          cannot be undone</strong>
     </em>
     </li>
   </ul>
@@ -211,14 +208,14 @@
     <em>Current Limitations</em>
   </p>
   <p>
-    The Jalview user interface does not support interactive
-    creation and editing of quantitative annotation (histograms and line
-    graphs), or to create annotation associated with a specific
-    sequence or group. It is also incapable of annotation grouping or changing
-    the style of existing annotation (e.g. to change between line or bar
-    charts, or to make multiple line graphs). These annotation
-    capabilities are only possible by the import of an <a
-      href="annotationsFormat.html">Annotation file</a>.<br>
+    The Jalview user interface does not support interactive creation and
+    editing of quantitative annotation (histograms and line graphs), or
+    to create annotation associated with a specific sequence or group.
+    It is also incapable of annotation grouping or changing the style of
+    existing annotation (e.g. to change between line or bar charts, or
+    to make multiple line graphs). These annotation capabilities are
+    only possible by the import of an <a href="annotationsFormat.html">Annotation
+      file</a>.<br>
   </p>
 </body>
 </html>