updated helpTOC to include recently added features, updated menus and outdated screen...

diff --git a/help/help.jhm b/help/help.jhm
index a450473..fe465ec 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -107,7 +107,6 @@
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
    <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>  
    <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>   
-   <mapID target="calcs.annotation" url="html/calculations/columnFilterByAnnotation.html"/>
    
    <mapID target="nucleicAcids" url="html/na/index.html"/>
    
@@ -138,6 +137,11 @@
    <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
    <mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
    
+   <mapID target="biojson" url="html/features/bioJsonFormat.html" />
+   <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+   <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+   <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
+   
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />
    <mapID target="homeIcon" url="icons/Home.png" />

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 4ce9892..75ff4c4 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -31,7 +31,11 @@
                <tocitem text="Multiple Views" target="multipleviews" />
                <tocitem text="Split Frame View" target="splitframe" />
                <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
-               <tocitem text="Fetching Sequences" target="seqfetch" />
+               <tocitem text="Fetching Sequences" target="seqfetch" />         
+               <tocitem text="BioJSON v1.0" target="biojson" />
+               <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+               <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+               <tocitem text="Select columns by annotation" target="selectcolbyannot" />
                <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
                        <tocitem text="Viewing RNA structure" target="varna" />
                        <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />

diff --git a/help/html/calculations/AnnotationColumnSelectionWithSM.gif b/help/html/features/AnnotationColumnSelectionWithSM.gif
similarity index 100%
rename from help/html/calculations/AnnotationColumnSelectionWithSM.gif
rename to help/html/features/AnnotationColumnSelectionWithSM.gif

diff --git a/help/html/calculations/AnnotationColumnSelectionWithoutSM.gif b/help/html/features/AnnotationColumnSelectionWithoutSM.gif
similarity index 100%
rename from help/html/calculations/AnnotationColumnSelectionWithoutSM.gif
rename to help/html/features/AnnotationColumnSelectionWithoutSM.gif

diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html
similarity index 100%
rename from help/html/calculations/columnFilterByAnnotation.html
rename to help/html/features/columnFilterByAnnotation.html

diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png
index dc5aa93..f551c50 100644 (file)
Binary files a/help/html/features/schooser_enter-id.png and b/help/html/features/schooser_enter-id.png differ

diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png
index fe9e5dc..ab69427 100644 (file)
Binary files a/help/html/features/schooser_main.png and b/help/html/features/schooser_main.png differ

diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index 1bf9f32..7db8083 100644 (file)
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -32,7 +32,7 @@
        selecting PDB structures to view in Jalview by querying readily
        available meta-data of structures. The Interface  can be invoked by selecting
        the
-       <strong>"View Structure"</strong> option from a sequence's
+       <strong>"3D Structure Data.."</strong> option from a sequence's
        <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
        features it provides are listed below:
        <ul>

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 44a07cc..3586083 100755 (executable)
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -104,7 +104,7 @@ structure is selected, one of the following will happen:</p>
 
 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
 You can retrieve sequences from the PDB using the <a
-       href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
+       href="pdbsequencefetcher.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).<br>

diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index 9d2ad33..87582f8 100755 (executable)
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -64,7 +64,8 @@
                <li><strong>PileUp</strong></li>
                <li><strong>AMSA</strong></li>
                <li><strong>STH</strong></li>
-               <li><strong>Phylip</strong></li>
+               <li><strong>PHYLIP</strong></li>
+               <li><strong>JSON</strong></li>
        </ul>
        </li>
        <li><strong>Page Setup ...</strong><br>
@@ -94,6 +95,8 @@
                Graphics</a> file from your alignment.</em></li>
                <li><strong>SVG<br>
                </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
+               <li><strong>BioJS<br>
+               </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
        </ul>
        </li>
        <li><strong>Export Features</strong><em><br>

diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index dc2b8a1..578a53e 100644 (file)
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -54,6 +54,7 @@
                <li><strong>Undefine Groups (Control U)<br>
   </strong><em>The alignment will be reset with no defined groups.<br>
   <strong>WARNING</strong>: This cannot be undone.</em></li>
+  <li><strong>Select/Hide Columns by Annotation...</strong> <br/><em>Select or hide columns of an alignment by filtering with properties of any annotation row added to that alignment</em></li>
   
 </ul>
 </body>

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index f84922e..9d6a0c6 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -158,14 +158,13 @@
                                                        based URL links that matched the description line.
                                        </em><strong><br> </strong></li>
                        </ul></li>
-               <li><strong>View Structure</strong> </strong><em>This menu is only
-                               visible if you right-click on a sequence name. If the
-                               sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser' 
-                               dialogue with options to select the structure which will eventually be opened in
+               <li><strong>3D Structure Data...</strong> </strong><em>This menu is 
+                               visible when you right-click on a sequence name. When this option is clicked, Jalview will open a <a href="../features/structurechooser.html">'Structure Chooser' </a>  
+                                dialogue with options to select the structure which will eventually be opened in
                                a 3D interactive view.<br> These entries will only be present if the sequence
-                               has <a href="../features/viewingpdbs.html">associated PDB
-                                       structures</a>.<br /> If the sequence or alignment has RNA structure,
-                               then <strong>2D RNA</strong> entries will also be present enabling
+                               has <a href="../features/viewingpdbs.html">associated PDB structures</a>.
+                               <br /> If the sequence or alignment has RNA structure,
+                               then <strong>VARNA 2D Structure</strong> entries will also be present enabling
                                you to open a linked view of the RNA structure in <a
                                href="../features/varna.html">VARNA</a>.
                </em>