From: jprocter <Jim Procter>
Date: Thu, 16 Jun 2005 17:39:14 +0000 (+0000)
Subject: lots of tidying in doco.
X-Git-Tag: Release_2_0~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=097286cf1aaa3767be06a2c99947265bc3417417;p=jalview.git

lots of tidying in doco.
---

diff --git a/help/help.jhm b/help/help.jhm
index e387045..91eba83 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -11,8 +11,11 @@
    
    <mapID target="webservice" url="html/webServices/index.html"/>
    <mapID target="clustal" url="html/webServices/clustal.html"/>
+   <mapID target="muscle" url="html/webServices/muscle.html"/>
+   <mapID target="jnet" url="html/webServices/jnet.html"/>
    
    <mapID target="io" url="html/io/index.html"/>
+   <mapID target="export" url="html/io/export.html"/>
    <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
@@ -42,6 +45,11 @@
    <mapID target="menus" url="html/menus/index.html"/>
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
    <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
+   <mapID target="alwFile" url="html/menus/alwfile.html"/>
+   <mapID target="alwEdit" url="html/menus/alwedit.html"/>
+   <mapID target="alwColour" url="html/menus/alwcolour.html"/>
+   <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
+
    <mapID target="popMenu" url="html/menus/popupMenu.html"/>
    
    
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index e441033..c2221ac 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -9,9 +9,12 @@
 		<tocitem text="Sequence Features" target ="seqfeatures"/>
 	</tocitem>
 	<tocitem text="Input /Output" target="io"/>
+  	<tocitem text="Making figures" target="export"/>
 	<tocitem text="Editing Alignment" target ="edit"/>
 	<tocitem text="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
+                <tocitem text="Muscle Alignment" target="muscle"/>
+          	<tocitem text="JNet Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
@@ -38,7 +41,12 @@
 	</tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
-		<tocitem text="Alignment Window" target="alMenu"/>
+		<tocitem text="Alignment Window" target="alMenu">
+                <tocitem text="File Menu" target="alwFile"/>
+                <tocitem text="Edit Menu" target="alwEdit"/>  
+                <tocitem text="Colour Menu" target="alwColour"/>
+                <tocitem text="Calculation Menu" target="alwCalc"/>
+                </tocitem>
 		<tocitem text="Popup Menu" target="popMenu"/>
 	</tocitem>
 </tocitem>
diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index adc44c9..47522ee 100755
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -6,7 +6,7 @@
 <p><strong>Sorting Sequences</strong></p>
 <p>Any group of selected sequences may be reordered by pressing the
 up or down arrow keys. The whole alignment may also be reordered by
-the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
+the use of the functions in the Sort menu (<strong>Calculate&#8594;Sort</strong>):
 </p>
 <ul>
 <li><p><strong>Sort by ID</strong></p>
@@ -26,7 +26,7 @@ fraction of conserved residues.
 order the sequences corresponding to those leaves in the
 alignment.<br>
 If a tree has been calculated from or associated with the current
-alignment, its name will appear in the submenu <em>Sort-&gt;By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort&#8594;By Tree Order</strong>.</p><p>
 </li>
 <li><p><strong>Sort by alignment ordering</strong></p>
 <p>Multiple alignment methods often order the sequences in their
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index c579677..c546497 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -3,9 +3,10 @@
 <body>
 <p><strong>Calculation of trees from alignments</strong></p>
 <p>Trees are calculated on either the complete alignment, or just the
-currently selected group of sequences. There are four different
-calculations, using one of two distance measures and constructing the
-tree from one of two algorithms :
+currently selected group of sequences, using the functions in the
+<strong>Calculate&#8594;Calculate tree</strong> submenu. There are
+four different calculations, using one of two distance measures and
+constructing the tree from one of two algorithms :
 </p>
 <p><strong>Distance Measures</strong></p>
 <p>Trees are calculated on the basis of a measure of similarity
diff --git a/help/html/io/export.html b/help/html/io/export.html
index f559c1a..771ccba 100755
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -3,7 +3,7 @@
 <title>Exporting alignments as artwork</title>
 </head>
 <body>
-<p><strong>Export<a name="export"></a></strong></p>
+<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>
 <p>The alignment view can be printed using
 <strong>File&#8594;Print</strong>, or exported in a number of ways via the
 <strong>File&#8594;Export</strong> menu:
diff --git a/help/html/io/index.html b/help/html/io/index.html
index c521747..332cdca 100755
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -7,8 +7,9 @@
 <p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of
   these file formats.</p>
 <p>Additionally, annotated whole sets of alignments and trees can be
-read from a Jalview
-(jar) format file using <strong>Desktop&#8594;Load Project</strong>. </p>
+read from a <a href="../features/jalarchive.html">Jalview (jar)
+format</a> file using <strong>Desktop&#8594;Load
+Project</strong>. </p>
 <p>Use the <strong>Desktop&#8594;Input Alignment</strong> menu to read in files from:</p>
 <ul>
   <li><strong>From File</strong>: the local file system</li>
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 3538d0b..c935bd2 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -341,7 +341,7 @@ NAME    START_RES    END_RES    SEQUENCE
         Submits all, or jut the currently selected sequences for
         alignment using Muscle. Do not use this if you are working with
         nucleic acid sequences.</em><br>
-        <li><strong>JPred</strong><br><em>
+        <li><strong>JNet</strong><br><em>
         Secondary structure prediction by network consensus. The
         behaviour of this calculation depends on the current selection:
         <ul>
diff --git a/help/html/webServices/clwqueued.gif b/help/html/webServices/clwqueued.gif
index 5bd4756..922806f 100755
Binary files a/help/html/webServices/clwqueued.gif and b/help/html/webServices/clwqueued.gif differ
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 5b507be..de04ec1 100755
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -3,7 +3,7 @@
         <body>
         <p><strong>Web services</strong></p>
         <p>A variety of web services are available from the Alignment window's
-          <strong>Calculations&#8594;Web Service&#8594;</strong> menu.
+          <strong>Calculations&#8594;Web Service</strong> menu.
             </p>
             <p>Jalview's distributed computations are SOAP based services exposing
               protein sequence alignment and secondary structure prediction programs. These services actually run
@@ -11,9 +11,14 @@
                   Dundee, and are maintained by the Barton group.
                   </p>
                   <p><strong>Web Service Dialog Box</strong></p>
-<img src="">                  
+<img src="clwqueued.gif">
 <p>
-                  This dialog box is displayed when a web service job is submitted.
+                  This dialog box is displayed when a web service job
+                  is submitted. It gives the name of the service and
+                  any method citation information, and monitors the
+                  progress of the calculation. The cancel button will
+                  permanently cancel the job, but this is only
+                  possible for some services.
                   </p>
                   <p>Current services:
                   <ul>