<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
- <tr>
- <td>
- <div align="center"><strong><a name="Jalview2.6.1">2.6.1</a></strong><br>
- <em>15/11/2010</em></div>
- </td>
- <td><em>Application</em>
- <ul>
- <li>New warning dialog when the Jalview Desktop cannot contact web services</li>
- <li>JABA service parameters for a preset are shown in service job window</li>
- <li>JABA Service menu entries reworded</li>
-</ul>
- </td>
- <td>
- <ul>
- <li>Modeller PIR IO broken - cannot correctly import a pir file emitted by jalview</li>
-<li>Existing feature settings transferred to new alignment view created from cut'n'paste</li>
-<li>Improved test for mixed amino/nucleotide chains when parsing PDB files</li>
-<li>Consensus and conservation annotation rows occasionally become blank for all new windows</li>
-<li>Exception raised when right clicking above sequences in wrapped view mode</li>
- </ul>
- <em>Application</em>
- <ul>
- <li>multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang</li>
- <li>Web Service parameter layout breaks for long user parameter names</li>
- <li>Jaba service discovery hangs desktop if Jaba server is down</li>
- </ul>
- </td>
- </tr>
- <tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.7">2.7</a>
+ </strong><br> <em>20/09/2011</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>tweaked default layout of web services menu</li>
+ <li>view/alignment association menu to enable user to easily
+ specify which alignment a multi-structure view takes its
+ colours/correspondences from</li>
+ <li>allow properties file location to be specified as URL </li>
+ <li>extend jalview project to preserve associations between
+ many alignment views and a single Jmol display</li>
+ <li>Store annotation row height in jalview project file</li>
+ <li>annotation row column label formatting attributes stored
+ in project file</li>
+ <li>annotation row order for auto-calculated annotation rows
+ preserved in jalview project file</li>
+ <li>visual progress indication when Jalview state is saved
+ using Desktop window menu</li>
+ <li>visual indication that command line arguments are still
+ being processed</li>
+ <li>groovy script execution from URL</li>
+ <li>colour by annotation default min and max colours in
+ preferences</li>
+ <li>automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and matching
+ IDs</li>
+ <li>update JGoogleAnalytics to latest release (0.3)</li>
+ <li>'view structures' option to open many structures
+ in same window</li>
+ <li>Sort associated views menu option for tree panel</li>
+ <li>group all JABA and non-JABA services for a particular
+ analysis function in its own submenu</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>userdefined and autogenerated annotation rows for groups</li>
+ <li>adjustment of alignment annotation pane height</li>
+ <li>annotation scrollbar for annotation panel</li>
+ <li>drag to reorder annotation rows in annotation panel</li>
+ <li>'automaticScrolling' parameter</li>
+ <li>allow sequences with partial ID string matches to be
+ annotated from GFF/jalview features files</li>
+ <li>sequence logo annotation row in applet</li>
+ <li>Absolute paths relative to host server in applet
+ parameters are treated as such</li>
+ <li>New in the JalviewLite javascript API:
+ <ul>
+ <li>jalviewLite.js javascript library</li>
+ <li>Javascript callbacks for
+ <ul>
+ <li>applet initialisation</li>
+ <li>sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>scrollTo row and column alignment scrolling functions</li>
+ <li>select sequence/alignment regions from javascript</li>
+ <li>javascript structure viewer harness to pass messages
+ between Jmol and Jalview when running as distinct applets</li>
+ <li>sortBy method</li>
+ <li>set of applet and application examples shipped with
+ documentation</li>
+ <li>new example to demonstrate jalviewLite and Jmol
+ javascript message exchange</li>
+ </ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>enable Jmol displays to be associated with multiple
+ multiple alignments</li>
+ <li>Option to automatically sort alignment with new tree</li>
+ <li>user configurable link to enable redirects to a
+ www.jalview.org mirror</li>
+ <li>Jmol colours option for Jmol displays</li>
+ <li>configurable newline string when writing alignment and
+ other flat files</li>
+ <li>Allow alignment annotation description lines to contain
+ html tags</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>add groovy test harness for bulk load testing to examples
+ </li>
+ <li>groovy script to load and align a set of sequences using a
+ web service before displaying the result in the Jalview desktop</li>
+ <li>restructured javascript and applet api documentation</li>
+ <li>ant target to publish example html files with applet archive</li>
+ <li>netbeans project for building jalview from source</li>
+ <li>ant task to create online javadoc for jalview source</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>user defined colourscheme throws exception when current
+ built in colourscheme is saved as new scheme</li>
+ <li>AlignFrame->Save in application pops up save dialog for
+ valid filename/format</li>
+ <li>cannot view associated structure for uniprot sequence</li>
+ <li>pdb file association breaks for Uniprot sequence P37173</li>
+ <li>associate PDB from file dialog does not tell you which
+ sequence is to be associated with the file</li>
+ <li>find All raises null pointer exception when query only
+ matches sequence IDs</li>
+ <li>pre 2.6 jalview project cannot be loaded into v2.6</li>
+ <li>Jalview project with Jmol views created with Jalview 2.4
+ cannot be loaded</li>
+ <li>filetype associations not installed for webstart launch</li>
+ <li>two or more chains in a single PDB file associated with
+ sequences in different alignments do not get coloured by their
+ associated sequence</li>
+ <li>visibility status of autocalculated annotation row not
+ preserved when project is loaded</li>
+ <li>tree bootstraps are not preserved when saved as a jalview
+ project</li>
+ <li>envision2 workflow tooltips are corrupted</li>
+ <li>enabling show group conservation also enables colour by
+ conservation</li>
+ <li>duplicate group associated conservation or consensus
+ created on new view</li>
+ <li>annotation scrollbar not displayed after 'show all
+ hidden annotation rows' option selected</li>
+ <li>alignment quality not updated after alignment annotation
+ row is hidden then shown</li>
+ <li>preserve colouring of structures coloured by sequences in pre
+ jalview 2.7 projects</li>
+ <li>Web service job parameter dialog is not laid out properly
+ </li>
+ <li>web services menu not refreshed after 'reset
+ services' button is pressed in preferences</li>
+ <li>annotation off by one in jalview v2_3 example project</li>
+ <li>structures imported from file and saved in project get
+ name like jalview_pdb1234.txt when reloaded</li>
+ <li>Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>alignment height set incorrectly when lots of annotation
+ rows are displayed</li>
+ <li>relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>view follows highlighting does not work for positions in
+ sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>export features raises exception when no features exist</li>
+ <li>separator string used for serialising lists of ids for
+ javascript api is modified when separator string provided as
+ parameter</li>
+ <li>null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>relative URLs for datasources assumed to be relative to
+ applet's codebase</li>
+ <li>status bar not updated after finished searching and search
+ wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between several
+ jalview applets causes race conditions and memory leaks</li>
+ <li>hover tooltip and mouseover of position on structure not
+ sent from Jmol in applet</li>
+ <li>certain sequences of javascript method calls to applet API
+ fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>view follows structure mouseover scrolls beyond position
+ with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue with/without
+ hidden columns</li>
+ <li>Sequence length given in alignment properties window is
+ off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>positional search results are only highlighted between
+ user-supplied sequence start/end bounds</li>
+ <li>end attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a given
+ sequence position</li>
+ <li>sequence numbering not preserved in MSF alignment output</li>
+ <li>Jalview PDB file reader does not extract sequence from
+ nucleotide chains correctly</li>
+ <li>annotation row height and visibility attributes not stored
+ in jalview project</li>
+ <li>structure colours not updated when tree partition changed
+ in alignment</li>
+ <li>sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>colour by annotation dialog does not restore current state
+ </li>
+ <li>Hiding (nearly) all sequences doesn't work properly</li>
+ <li>sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
+ tool</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6.1">2.6.1</a>
+ </strong><br> <em>15/11/2010</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>New warning dialog when the Jalview Desktop cannot contact
+ web services</li>
+ <li>JABA service parameters for a preset are shown in service
+ job window</li>
+ <li>JABA Service menu entries reworded</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>Modeller PIR IO broken - cannot correctly import a pir
+ file emitted by jalview</li>
+ <li>Existing feature settings transferred to new alignment
+ view created from cut'n'paste</li>
+ <li>Improved test for mixed amino/nucleotide chains when
+ parsing PDB files</li>
+ <li>Consensus and conservation annotation rows occasionally
+ become blank for all new windows</li>
+ <li>Exception raised when right clicking above sequences in
+ wrapped view mode</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>multiple multiply aligned structure views cause cpu usage
+ to hit 100% and computer to hang</li>
+ <li>Web Service parameter layout breaks for long user
+ parameter names</li>
+ <li>Jaba service discovery hangs desktop if Jaba server is
+ down</li>
+ </ul></td>
+ </tr>
+ <tr>
<td>
<div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
<em>26/9/2010</em></div>
git://source.jalview.org / jalview.git / blobdiff