X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=19ff3e7ab3b2a88dd12bbebe52462f9e863ea167;hb=ab7509436f09413b122dace2ecd6692f6f06d347;hp=92cc453223be92895a18ae464df40223b7620b56;hpb=ff4d98fbde57ca9dea2fc607d36d80a00963746d;p=jalview.git

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 		<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>&#39;view structures&#39; 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>&#39;automaticScrolling&#39; 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-&gt;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 &#39;show all
+						hidden annotation rows&#39; 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 &#39;reset
+						services&#39; 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>&lt;= 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&#39;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&#39;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>