JAL-1201 tweak layout for applet page and allow monospace <pre> tags

diff --git a/examples/applets.html b/examples/applets.html
index b1d2f83..9437aed 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -139,183 +139,176 @@ document.onclick = mclose;
 </div>
 
 
-<div id="pageWrap">
+ <div id="pageWrap">
 
-<div id="sideNav">
-<ul>
-<li class="jvlite-nav-title"><a href="applets.html">JalviewLite Examples</a></li>
-<li><a href="appletParameters.html">Applet Parameters</a></li>
-<li><a href="jalviewLiteJs.html">Javascript API</a></li>
-<li><a href="formComplete.html">in-page API demo</a></li>
-<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
-</div>
+  <div id="sideNav">
+   <ul>
+    <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
+      Examples</a></li>
+    <li><a href="appletParameters.html">Applet Parameters</a></li>
+    <li><a href="jalviewLiteJs.html">Javascript API</a></li>
+    <li><a href="formComplete.html">in-page API demo</a></li>
+    <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+    <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+   </ul>
+  </div>
 
-<div id="content" class="content">
-        <p>JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page. It's one of the easiest ways of providing an interactive
-          display for precalculated alignments, features and annotations files.
-          It lacks some functionality available in the Jalview Desktop, however, such
-          as making images, saving files, and running web service jobs. This is mostly due to security
-          restrictions imposed on applets.</p>
-        <p align="left">For more information on how to use the applet in your
-          website, see <a href="appletParameters.html"><strong>full list of applet
-          parameters.</strong></a></p>
-        <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
-          of Jalview, which runs within your web browser. </p>
-        <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
-          cluster<br>
-          (15 sequences x 150 residues)</H4>
-        <div align="center"> </div>
-        <div align="center">
-          <table width="300" border="1" cellspacing="0" cellpadding="0">
-            <tr>
-              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
-                  <tr>
-                    <td width="100"> <applet code="jalview.bin.JalviewLite"
-                               width="140" height="35"
-                               archive="jalviewApplet.jar">
-                                               <param name="file" value="uniref50.fa">
-                        <param name="treeFile" value="ferredoxin.nw">
-                        <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
-                        <param name="showFullId" value="false">
-                        <param name="RGB"  value="F2F2FF">
-                        <param name="sortByTree" value="True">
-                        <param name="showSequenceLogo" value="true">
-                        <param name="showGroupConsensus" value="true">
-                        <param name="linkLabel_1" value="SRS">
-                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
-                        <param name="linkLabel_2" value="Uniprot">
-                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
-                      </applet></td>
-                    <td width="165">User Defined Colours, loads an associated Newick
-                      format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-          <p>&nbsp;</p>
-          <table width="300" border="1" cellspacing="0" cellpadding="0">
-            <tr>
-              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
-                  <tr>
-                    <td width="100"> <applet code="jalview.bin.JalviewLite"
-                               width="140" height="35"
-                               archive="jalviewApplet.jar">
-                        <param name="file" value="uniref50.fa">
-                        <param name="features" value="exampleFeatures.txt">
-                        <param name="showFeatureSettings" value="true">
-                        <param name="wrap" value="true">
-                        <param name="showAnnotation" value="false">
-                        <param name="windowHeight" value="500">
-                        <param name="windowWidth" value="650">
-                        <param name="showFullId" value="false">
-                        <param name="RGB"  value="F2F2FF">
-                        <param name="linkLabel_1" value="SRS">
-                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
-                        <param name="linkLabel_2" value="Uniprot">
-                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
-                      </applet> </td>
-                    <td width="165">Displays a features file on the alignment</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-            <p>&nbsp;</p>
-          <table width="300" border="1" cellspacing="0" cellpadding="0">
-            <tr>
-              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
-                  <tr>
-                    <td width="100"> <applet code="jalview.bin.JalviewLite"
-                               width="140" height="35"
-                               archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
-                        <param name="file" value="uniref50.fa">
-                        <!-- <param name="debug" value="true">
+  <div id="content" class="content">
+   <p>JalviewLite is a web based version of Jalview, which runs as a
+    Java applet in or on a web page. It's one of the easiest ways of
+    providing an interactive display for precalculated alignments,
+    features and annotations files. It lacks some functionality
+    available in the Jalview Desktop, however, such as making images,
+    saving files, and running web service jobs. This is mostly due to
+    security restrictions imposed on applets.</p>
+   <p align="left">
+    For more information on how to use the applet in your website, see <a
+     href="appletParameters.html"><strong>full list of
+      applet
+      <p>Pressing one of the buttons below will load up JalviewLite,
+       a cut down version parameters.
+    </strong></a>
+   </p>
+   of Jalview, which runs within your web browser.
+   </p>
+   <div align="center">
+    <p>
+     <h2>Ferredoxins, chloroplast precursor related UniRef50
+      cluster</h2>
+     <br /> (15 sequences x 150 residues)
+    </p>
+    <table width="90%">
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+       <param name="file" value="uniref50.fa">
+        <param name="treeFile" value="ferredoxin.nw">
+         <param name="userDefinedColour"
+          value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+          <param name="showFullId" value="false">
+       <param name="sortByTree" value="True">
+        <param name="showSequenceLogo" value="true">
+         <param name="showGroupConsensus" value="true">
+          <param name="linkLabel_1" value="Uniprot">
+           <param name="linkUrl_1"
+            value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+            <param name="linkLabel_2" value="Expasy">
+             <param name="linkUrl_2"
+              value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+       <param name="APPLICATION_URL"
+        value="http://www.jalview.org/services/launchApp">
+       </applet></td>
+      <td valign="center">User Defined Colours, loads an associated
+       Newick format tree file which is used to sort the alignment, and
+       group consensus and sequence logos are shown below the alignment.</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+       <param name="file" value="uniref50.fa">
+        <param name="features" value="exampleFeatures.txt">
+         <param name="showFeatureSettings" value="true">
+          <param name="wrap" value="true">
+           <param name="showAnnotation" value="false">
+            <param name="windowHeight" value="500">
+             <param name="windowWidth" value="650">
+              <param name="showFullId" value="false">
+       <param name="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <param name="linkUrl_2"
+           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+           <param name="APPLICATION_URL"
+            value="http://www.jalview.org/services/launchApp">
+       </applet></td>
+      <td valign="center">Displays a features file on the alignment</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+       <param name="file" value="uniref50.fa">
+        <!-- <param name="debug" value="true">
                         -->
-                        <param name="defaultColour" value="Strand Propensity">
-                        <param name="wrap" value="true">
-                        <param name="showAnnotation" value="false">
-                        <param name="windowHeight" value="500">
-                        <param name="windowWidth" value="650">
-                        <param name="showFullId" value="false">
-                        <param name="RGB"  value="F2F2FF">
-                        <param name="linkLabel_1" value="SRS">
-                        <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
-                        <param name="linkLabel_2" value="Uniprot">
-                        <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-                                               <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
-                        <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
-                      </applet> </td>
-                    <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-          <p>&nbsp;</p>
-                                               <table width="300" border="1" cellspacing="0" cellpadding="0">
-                                                       <tr>
-                                                               <td><table width="300" border="0" cellspacing="0"
-                                                                               cellpadding="0">
-                                                                               <tr>
-                                                                                       <td width="100"><applet code="jalview.bin.JalviewLite"
-                                                                                                       width="140" height="35" archive="jalviewApplet.jar">
-                                                                                                       <param name="file" value="jpred_msa.fasta">
-                                                                                                       <param name="jnetfile" value="jpred_msa.seq.concise">
-                                                                                                       <param name="defaultColour" value="Clustal">
-                                                                                                       <param name="showAnnotation" value="true">
-                                                                                                       <param name="windowHeight" value="515">
-                                                                                                       <param name="windowWidth" value="650">
-                                                                                                       <param name="showConservation" value="false">
-                                                                                                       <param name="showQuality" value="false">
-                                                                                                       <param name="showConsensus" value="false">
-                                                                                                       <param name="showFullId" value="false">
-                                                                                                       <param name="RGB" value="F2F2FF">
-                                                                                                       <param name="linkLabel_1" value="SRS">
-                                                                                                       <param name="linkUrl_1"
-                                                                                                               value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
-                                                                                                       <param name="linkLabel_2" value="Uniprot">
-                                                                                                       <param name="linkUrl_2"
-                                                                                                               value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-                                                                                                       <param name="APPLICATION_URL"
-                                                                                                               value="http://www.jalview.org/services/launchApp">
-                                                                                               </applet></td>
-                                                                                       <td width="165">Displays a Multiple Sequence Alignment
-                                                                                               Based JNet Prediction for a Sequence</td>
-                                                                               </tr>
-                                                                       </table></td>
-                                                       </tr>
-                                               </table>
-                                               <p>&nbsp;</p>
-                                               <table width="300" border="1" cellspacing="0" cellpadding="0">
-            <tr>
-              <td><table width="300" border="0" cellspacing="0" cellpadding="0">
-                  <tr>
-                    <td width="100"> <applet code="jalview.bin.JalviewLite"
-                               width="140" height="35"
-                               archive="jalviewApplet.jar">
-                        <param name="file" value="RF00031_folded.stk">
-                        <param name="defaultColour" value="Purine/Pyrimidine">
-                        <param name="showAnnotation" value="true">
-                        <param name="windowHeight" value="515">
-                        <param name="windowWidth" value="650">
-                        <param name="showConservation" value="false">
-                        <param name="showQuality" value="false">
-                        <param name="showConsensus" value="true">
-                        <param name="showFullId" value="false">
-                        <param name="RGB"  value="F2F2FF">
-                        <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
-                      </applet> </td>
-                    <td width="165">Displays an RFAM RNA fold family with secondary structure annotation</td>
-                  </tr>
-                </table></td>
-            </tr>
-          </table>
-        </div>
-</div>
+        <param name="defaultColour" value="Strand Propensity">
+         <param name="wrap" value="true">
+          <param name="showAnnotation" value="false">
+           <param name="windowHeight" value="500">
+            <param name="windowWidth" value="650">
+             <param name="showFullId" value="false">
+       <param name="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <param name="linkUrl_2"
+           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+       <param name="APPLICATION_URL"
+        value="http://www.jalview.org/services/launchApp">
+        <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+       </applet></td>
+      <td valign="center">Associates PDB file 1GAQ with sequence
+       FER1_MAIZE</td>
+     </tr>
+     <tr>
+      <td width="10%" valign="middle"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+       <param name="file" value="jpred_msa.fasta">
+        <param name="jnetfile" value="jpred_msa.seq.concise">
+         <param name="defaultColour" value="Clustal">
+          <param name="showAnnotation" value="true">
+           <param name="windowHeight" value="515">
+            <param name="windowWidth" value="650">
+             <param name="showConservation" value="false">
+              <param name="showQuality" value="false">
+               <param name="showConsensus" value="false">
+                <param name="showFullId" value="false">
+       <param name="linkLabel_1" value="Uniprot">
+        <param name="linkUrl_1"
+         value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+         <param name="linkLabel_2" value="Expasy">
+          <param name="linkUrl_2"
+           value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+       <param name="APPLICATION_URL"
+        value="http://www.jalview.org/services/launchApp">
+       </applet></td>
+      <td valign="center">Displays a Multiple Sequence Alignment
+       Based JNet Prediction for a Sequence</td>
+     </tr>
+    </table>
+    <p>
+    <h2>RF00031 RFAM Alignment with per seqeunce secondary
+     structure</h2>
+    </p>
+    <table width="90%">
+     <tr>
+      <td width="10%" valign="center"><applet
+        code="jalview.bin.JalviewLite" width="140" height="35"
+        archive="jalviewApplet.jar">
+       <param name="file" value="RF00031_folded.stk">
+        <param name="defaultColour" value="Purine/Pyrimidine">
+         <param name="showAnnotation" value="true">
+          <param name="windowHeight" value="515">
+           <param name="windowWidth" value="650">
+            <param name="showConservation" value="false">
+             <param name="showQuality" value="false">
+              <param name="showConsensus" value="true">
+               <param name="showFullId" value="false">
+       <param name="APPLICATION_URL"
+        value="http://www.jalview.org/services/launchApp">
+       </applet></td>
+      <td valign="center">Displays an RFAM RNA fold family with
+       secondary structure annotation</td>
+     </tr>
+    </table>
+   </div>
+  </div>
+ </div>
 
-<div id ="footer">
+ <div id ="footer">
 <div id="innerFooter">
 <div id="copyright"><p>Copyright all rights reserved 2012</p></div>
 <div id="cite">

diff --git a/examples/css/style.css b/examples/css/style.css
index 7550b31..67d57a0 100644 (file)
--- a/examples/css/style.css
+++ b/examples/css/style.css
@@ -247,11 +247,32 @@ CONTENT
   height: auto;
   width: 710px;
   padding-top:23px;
-  padding-bottom:23px;
+  padding-bottom:12px;
   overflow-x:auto; 
   overflow-y:hidden; 
 }
-
+#content h1
+{
+       padding-top:29px;
+       font-size: 15pt;
+       font-style: bold;
+}
+#content h2
+{
+       padding-top:27px;
+       font-size: 13pt;
+       font-style: bold;
+}
+#content h3
+{
+       padding-top:25px;
+       font-size: 12pt;
+       font-style: bold italic;
+}
+#content pre
+{
+       font-family: monospace;
+}
 #sideNav
 {
 width:200px;
@@ -355,6 +376,11 @@ background: url("../images/train-arrow-3-normal.png") no-repeat scroll 0 0 trans
     padding-left: 5px;
 }
 
+td
+{
+    vertical-align: middle;
+}
+
 /********************************
 FOOTER
 ***********************************/