JAL-1503 whats new and release history for 2.8.1 (still not complete)

diff --git a/help/help.jhm b/help/help.jhm
index 08d3ca9..cc272e8 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -47,6 +47,7 @@
    <mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
    <mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
+   <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
@@ -127,6 +128,7 @@
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />
    <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
+   <mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
    
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 4ff36ba..a65cafe 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -21,10 +21,9 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
  <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Protein Disorder Prediction" target="disorder"/>
-   <tocitem text="Alignment Conservation Analysis" target="aacon"/>
-  <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
- <tocitem text="Select columns containing sequence features" target="seqfeatures.settings"/>
+    <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+    <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+    <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
   </tocitem>
   <tocitem text="Editing Alignments" target ="edit"/>  
   <tocitem text="Cursor Mode" target="cursor"/>

diff --git a/help/html/releases.html b/help/html/releases.html
index b6fb83c..a240a49 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -35,51 +35,100 @@
                </td>
        </tr>
   <tr>
-  <td><div align="center">
-  <strong><a name="Jalview.2.8.1">2.8.1</a><br/><em>20/5/2014</em></strong>
-  </div>
-  </td>
-      <td> <!--  New features -->
-      <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
-      <ul>
-      <li>i18n Internationalisation of user interface and translation for Spanish locale</li>
-      </ul>
-      <em>Application</em><ul>
-        <li>Define/Undefine group on current selection with Ctrl-G</li>
- <li>Select columns containing particular features from Feature Settings dialog</li>
-<li>View all 'representative' PDB structures for selected sequences</li>
-<li>Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service</li>
-<li></li>
-      <li>Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows) </li>
-        </ul>
-      <em>Applet</em><ul>
-      
-        </ul> <em>Other improvements</em>
-        <ul>
-        </ul>
-      </td>
-      <td><!--  issues resolved -->
-        <em>Application</em><ul>
+                       <td><div align="center">
+                                       <strong><a name="Jalview.2.8.1">2.8.1</a><br />
+                                       <em>20/5/2014</em></strong>
+                               </div></td>
+                       <td>
+                               <!--  New features --> <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+                               <ul>
+                                       <li>Internationalisation of user interface (usually called i18n support) and
+                                               translation for Spanish locale</li>
+                                       <li>Define/Undefine group on current selection with
+                                               Ctrl-G/Shift Ctrl-G</li>
+                                               <li>Improved group creation/removal options in alignment/sequence Popup menu</li>
+                                       
+                               </ul> <em>Application</em>
+                       <ul>
+                                       <li>Interactive consensus RNA secondary structure prediction
+                                               VIENNA RNAAliFold JABA 2.1 service</li>
+                                       <li>Select columns containing particular features from Feature
+                                               Settings dialog</li>
+                                       <li>View all 'representative' PDB structures for selected
+                                               sequences</li>
+                                               <li>Update Jalview project format:<ul><li>
+                                                Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
+                                                </li><li>Per group and alignment annotation and RNA helix colouring</li></ul></li>
+        <li>New similarity measures for PCA and Tree calculation (PAM250) </li>
+        <li>Experimental support for retrieval and viewing of flanking
+            regions for an alignment</li>
+                               </ul> <em>Applet</em>
+                       <ul>
+
+                               </ul> <em>Other improvements</em>
+                               <li>Sensible precision for symbol distribution percentages shown in logo tooltip.</li>
+                               <li>Annotation panel height set according to amount of annotation when alignment first opened</li>
+                               </ul>
+                       </td>
+                       <td>
+                               <!--  issues resolved --> <em>Application</em>
+                       <ul>
+                                       <li>logo keeps spinning and status remains at queued or
+                                               running after job is cancelled</li>
+          <li>cannot export features from alignments imported from Jalview/VAMSAS projects</li>
+                                       <li>buggy slider for web service parameters that take float
+                                               values</li>
                                        <li>Newly created RNA secondary structure line doesn't have
                                                'display all symbols' flag set</li>
-                                 <li>T-COFFEE alignment score shading scheme not saved in
+                                       <li>T-COFFEE alignment score shading scheme and other annotation shading not saved in
                                                jalview project</li>
                                        <li>Local file cannot be loaded in freshly downloaded Jalview</li>
                                        <li>??? unresolved ??? Jalview icon not shown on dock in
                                                Mountain Lion/Webstart</li>
                                        <li>Load file from desktop file browser fails</li>
                                        <li>Occasional NPE thrown when calculating large trees</li>
-                               </ul>
-        <em>Applet</em>
-                       <ul>
+                                       <li>cannot reorder or slide sequences after dragging an
+                                               alignment onto desktop</li>
+                                       <li>Colour by annotation dialog throws NPE after using
+                                               'extract scores' function</li>
+                                       <li>Loading/cut'n'pasting an empty file leads to a grey
+                                               alignment window</li>
+                                       <li>Disorder thresholds rendered incorrectly after performing
+                                               iupred disorder prediction</li>
+                                       <li>Multiple group annotated consensus rows shown when
+                                               changing 'normalise logo' display setting</li>
+                                       <li>Annotation/RNA Helix colourschemes cannot be applied to alignment
+                                               with groups (2.8.0b1)</li>
+                                               <li>find shows blank dialog after 'finished searching' if nothing matches query</li>
+          <li>Null Pointer Exceptions raised when sorting by feature with lots of groups<!--  possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --></li>
+          <li>Errors in Jmol console when structures in alignment don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol --></li>
+          <li>Not all working JABAWS services are shown in Jalview's menu</li>
+          <li>JAVAWS version of jalview fails to launch with 'invalid literal/length code'</li>
+                               </ul> <em>Applet</em>
+                               <ul>
+  <li>
+                               <li>Remove group option shown in applet when selection is not a group</li>
                                        <li>Apply to all groups ticked but colourscheme changes don't
                                                affect groups</li>
-                               </ul> 
-                               <em>Other</em><ul>
-        <li></li>
-        </ul>
-      </td>
-    </tr>
+                               </ul> <em>Other</em>
+                       <ul>                    
+                        <li>Consensus sequence for alignments/groups with a single sequence were not calculated</li>
+                                       <li>annotation files that contain only groups imported as
+                                               annotation and junk sequences</li>
+                                       <li>Fasta files with sequences containing '*' incorrectly
+                                               recognised as PFAM or BLC</li>
+                                       <li>conservation/PID slider apply all groups option doesn't
+                                               affect background (2.8.0b1)
+                                       <li></li>
+                                       <li>redundancy highlighting is erratic at 0% and 100%</li>
+                                       <li>remove gapped columns fails for sequences with ragged
+                                               trailing gaps</li>
+                                               <li>AMSA annotation row with leading spaces is not registered correctly on import</li>
+          <li>Jalview crashes when selecting PCA analysis for certain alignments</li>
+          <li>Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting</li>
+                               </ul>
+                       </td>
+               </tr>
        <tr>
        <td><div align="center">
        <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
@@ -172,10 +221,12 @@
           <li>ClassCastException when generating EPS in headless
             mode</li>
           <li>Adjusting sequence-associated shading threshold only
-            changes one row&#39;s threshold</li>
+            changes one row&#39;s threshold</li>            
           <li>Preferences and Feature settings panel panel
             doesn&#39;t open</li>
-        </ul>
+                                       <li>hide consensus histogram also hides conservation and
+                                               quality histograms</li>
+                               </ul>
       </td>
     </tr>
   <tr>