Release History

From ae96518a241a9808dce180d926745aa7cdefc55f Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 15 Jan 2008 14:05:29 +0000 Subject: [PATCH] draft of 2.4 features in feature list --- help/html/releases.html | 822 ++++++++++++++++++++++++++++++----------------- 1 file changed, 529 insertions(+), 293 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index f70327e..a4c79c1 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,293 +1,529 @@ - -Release History - -

Release History

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Release	New Features	Issues Resolved
2.3 - 9/5/07	- Jmol 11.0.2 integration - PDB views stored in Jalview XML files - Slide sequences - Edit sequence in place - EMBL CDS features - DAS Feature mapping - Feature ordering - Alignment Properties - Annotation Scores - Sort by scores - Feature/annotation editing in applet -	- - Headless state operation in 2.2.1 - Incorrect and unstable DNA pairwise alignment - Cut and paste of sequences with annotation - Feature group display state in XML - Feature ordering in XML - blc file iteration selection using filename # suffix - Stockholm alignment properties - Stockhom alignment secondary structure annotation - 2.2.1 applet had no feature transparency - Number pad keys can be used in cursor mode - Structure Viewer mirror image resolved - -
2.2.1 - 12/2/07	- Non standard characters can be read and displayed - Annotations/Features can be imported/exported to the applet via textbox - Applet allows editing of sequence/annotation/group name & description - Preference setting to display sequence name in italics - Annotation file format extended to allow Sequence_groups - to be defined - Default opening of alignment overview panel can be specified in - preferences - PDB residue numbering annotation added to associated sequences -	- Applet crash under certain Linux OS with Java 1.6 installed - Annotation file export / import bugs fixed - PNG / EPS image output bugs fixed
2.2 - 27/11/06	- Multiple views on alignment - Sequence feature editing - "Reload" alignment - "Save" to current filename - Background dependent text colour - Right align sequence ids - User-defined lower case residue colours - Format Menu - Select Menu - Menu item accelerator keys - Control-V pastes to current alignment - Cancel button for DAS Feature Fetching - PCA and PDB Viewers zoom via mouse roller - User-defined sub-tree colours and sub-tree selection - 'New Window' button on the 'Output to Text box'	- New memory efficient Undo/Redo System - Optimised symbol lookups and conservation/consensus calculations - Region Conservation/Consensus recalculated after edits - Fixed Remove Empty Columns Bug (empty columns at end of alignment) - Slowed DAS Feature Fetching for increased robustness. - Made angle brackets in ASCII feature descriptions display correctly - Re-instated Zoom function for PCA - Sequence descriptions conserved in web service analysis results - Uniprot ID discoverer uses any word separated by ∣ - WsDbFetch query/result association resolved - Tree leaf to sequence mapping improved - Smooth fonts switch moved to FontChooser dialog box.
2.1.1 - 12/9/06	- Copy consensus sequence to clipboard -	- Image output - rightmost residues are rendered if sequence id panel - has been resized - Image output - all offscreen group boundaries are rendered - Annotation files with sequence references - all elements in file are - relative to sequence position - Mac Applet users can use Alt key for group editing -
2.1 - 22/8/06	- MAFFT Multiple Alignment in default Web Service list - DAS Feature fetching - Hide sequences and columns - Export Annotations and Features - GFF file reading / writing - Associate structures with sequences from local PDB files - Add sequences to exisiting alignment - Recently opened files / URL lists - Applet can launch the full application - Applet has transparency for features (Java 1.2 required) - Applet has user defined colours parameter - Applet can load sequences from parameter "sequencex" -	- Redundancy Panel reinstalled in the Applet - Monospaced font - EPS / rescaling bug fixed - Annotation files with sequence references bug fixed -
2.08.1 - 2/5/06	- Change case of selected region from Popup menu - Choose to match case when searching - Middle mouse button and mouse movement can compress / expand the visible - width and height of the alignment -	- Annotation Panel displays complete JNet results -
2.08b - 18/4/06		- Java 1.5 bug - InternalMessageDialog fix for threads - Righthand label on wrapped alignments shows correct value -
2.08 - 10/4/06	- Editing can be locked to the selection area - Keyboard editing - Create sequence features from searches - Precalculated annotations can be loaded onto alignments - Features file allows grouping of features - Annotation Colouring scheme added - Smooth fonts off by default - Faster rendering - Choose to toggle Autocalculate Consensus On/Off -	- Drag & Drop fixed on Linux - Jalview Archive file faster to load/save, sequence descriptions saved. - -
2.07 - 12/12/05	- PDB Structure Viewer enhanced - Sequence Feature retrieval and display enhanced - Choose to output sequence start-end after sequence name for file output - Sequence Fetcher WSDBFetch@EBI - Applet can read feature files, PDB files and can be used for HTML - form input -	- HTML output writes groups and features - Group editing is Control and mouse click - File IO bugs -
2.06 - 28/9/05	- View annotations in wrapped mode - More options for PCA viewer -	- GUI bugs resolved - Runs with -nodisplay from command line -
2.05b - 15/9/05	- Choose EPS export as lineart or text - Jar files are executable - Can read in Uracil - maps to unknown residue -	- Known OutOfMemory errors give warning message - Overview window calculated more efficiently - Several GUI bugs resolved -
2.05 - 30/8/05	- Edit and annotate in "Wrapped" view -	- Several GUI bugs resolved -
2.04 - 24/8/05	- Hold down mouse wheel & scroll to change font size -	- Improved JPred client reliability - Improved loading of Jalview files -
2.03 - 18/8/05	- Set Proxy server name and port in preferences - Multiple URL links from sequence ids - User Defined Colours can have a scheme name and added to Colour Menu - Choose to ignore gaps in consensus calculation - Unix users can set default web browser - Runs without GUI for batch processing - Dynamically generated Web Service Menus -	- InstallAnywhere download for Sparc Solaris -
2.02 - 18/7/05		- Copy & Paste order of sequences maintains alignment order. -
2.01 - 12/7/05	- Use delete key for deleting selection. - Use Mouse wheel to scroll sequences. - Help file updated to describe how to add alignment annotations. - Version and build date written to build properties file. - InstallAnywhere installation will check for updates at launch of Jalview. -	- Delete gaps bug fixed. - FileChooser sorts columns. - Can remove groups one by one. - Filechooser icons installed. - Finder ignores return character when searching. Return key will initiate - a search. - -
2.0 - 20/6/05	- New codebase -

- - + + +Release History + + +

Release History

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+ Release +	+ New Features +	+ Issues Resolved +
+ 2.4 + Feb/2008 +	+ + New VAMSAS capabilities in Jalview + + treenode binding for VAMSAS tree exchange + local editing and update of sequences in VAMSAS alignments + (experimental) + Create new or select existing session to join + load and save of vamsas documents + + + Retrieval of cross-referenced sequences from other databases + + export annotation rows as CSV for spreadsheet import + Jalview projects record alignment dataset associations, EMBL + products, and cDNA sequence mappings + Linked highlighting of codon and amino acid from translation + and protein products + JPred3 web service + Generalised database reference retrieval and validation to + all fetchable databases + Application command line + + -tree parameter to open trees (introduced for passing from + applet) + -fetchfrom command line argument to specify nicknames of + DAS servers to query for alignment features + -dasserver command line argument to add new servers that + are also automatically queried for features + -groovy command line argument executes a given groovy + script after all input data has been loaded and parsed + + + Trees passed as applet parameters can be passed to + application (when using "View in full application") + MemoryMonitor added as an option under Desktop's Tools menu + + allow reading of JPred concise files as a normal filetype + sort sequences by named annotation scores + Re-instated Full AMSA support and .amsa file association + Stockholm annotation parsing and alignment properties import + + Applet Parameters + + feature group display control parameter + debug parameter + + + Applet API methods + + newView public method + Window (current view) specific get/set public methods + Feature display control methods + + + + New Jalview distribution features + + RELEASE file gives build properties for the latest Jalview + release. + Java 1.1 Applet build made easier and donotobfuscate + property controls execution of obfuscator + Build target for generating source distribution + Debug flag for javacc + .jalview_properties file is documented (slightly) in + jalview.bin.Cache + +	+ + selected region output includes visible annotations (for + certain formats) + edit label/displaychar contains existing label/char for + editing + update PDBEntries when DBRefEntries change (vamsas) + shorter peptide product names from EMBL records + Newick string generator makes compact representations + bootstrap values parsed correctly for tree files with + comments + pathological filechooser bug avoided by not allowing + filenames containing a ':' + Fixed exception when parsing GFF files containing global + sequence features + Alignment datasets are finalized only when number of + references from alignment sequences goes to zero + Close of tree branch colour box without colour selection + causes cascading exceptions + occasional negative imgwidth exceptions + better reporting of non-fatal warnings to user when file + parsing fails. + Save works when Jalview project is default format + Uniprot canonical names introduced for both das and vamsas + Histidine should be midblue (not pink!) in Zappo + error messages passed up and output when data read fails + edit undo recovers previous dataset sequence when sequence + is edited + allow PDB files without pdb ID HEADER lines (like those + generated by MODELLER) to be read in properly + annotation consisting of sequence associated scores can be + read and written correctly to annotation file + Aligned cDNA translation to aligned peptide works correctly + + Fixed display of hidden sequence markers and non-italic font + for representatives in Applet + Applet Menus are always embedded in applet window on Macs. + Newly shown features appear at top of stack (in Applet) + Annotations added via parameter not drawn properly due to + null pointer exceptions + Secondary structure lines are drawn starting from first + column of alignment + +
+ 2.3 + 9/5/07 +	+ + Jmol 11.0.2 integration + PDB views stored in Jalview XML files + Slide sequences + Edit sequence in place + EMBL CDS features + DAS Feature mapping + Feature ordering + Alignment Properties + Annotation Scores + Sort by scores + Feature/annotation editing in applet + +	+ + Headless state operation in 2.2.1 + Incorrect and unstable DNA pairwise alignment + Cut and paste of sequences with annotation + Feature group display state in XML + Feature ordering in XML + blc file iteration selection using filename # suffix + Stockholm alignment properties + Stockhom alignment secondary structure annotation + 2.2.1 applet had no feature transparency + Number pad keys can be used in cursor mode + Structure Viewer mirror image resolved + +
+ 2.2.1 + 12/2/07 +	+ + Non standard characters can be read and displayed + Annotations/Features can be imported/exported to the applet + via textbox + Applet allows editing of sequence/annotation/group name + & description + Preference setting to display sequence name in italics + Annotation file format extended to allow Sequence_groups to + be defined + Default opening of alignment overview panel can be specified + in preferences + PDB residue numbering annotation added to associated + sequences + +	+ + Applet crash under certain Linux OS with Java 1.6 installed + Annotation file export / import bugs fixed + PNG / EPS image output bugs fixed + +
+ 2.2 + 27/11/06 +	+ + Multiple views on alignment + Sequence feature editing + "Reload" alignment + "Save" to current filename + Background dependent text colour + Right align sequence ids + User-defined lower case residue colours + Format Menu + Select Menu + Menu item accelerator keys + Control-V pastes to current alignment + Cancel button for DAS Feature Fetching + PCA and PDB Viewers zoom via mouse roller + User-defined sub-tree colours and sub-tree selection + 'New Window' button on the 'Output to Text box' + +	+ + New memory efficient Undo/Redo System + Optimised symbol lookups and conservation/consensus + calculations + Region Conservation/Consensus recalculated after edits + Fixed Remove Empty Columns Bug (empty columns at end of + alignment) + Slowed DAS Feature Fetching for increased robustness. + Made angle brackets in ASCII feature descriptions display + correctly + Re-instated Zoom function for PCA + Sequence descriptions conserved in web service analysis + results + Uniprot ID discoverer uses any word separated by ∣ + WsDbFetch query/result association resolved + Tree leaf to sequence mapping improved + Smooth fonts switch moved to FontChooser dialog box. + +
+ 2.1.1 + 12/9/06 +	+ + Copy consensus sequence to clipboard + +	+ + Image output - rightmost residues are rendered if sequence + id panel has been resized + Image output - all offscreen group boundaries are rendered + Annotation files with sequence references - all elements in + file are relative to sequence position + Mac Applet users can use Alt key for group editing + +
+ 2.1 + 22/8/06 +	+ + MAFFT Multiple Alignment in default Web Service list + DAS Feature fetching + Hide sequences and columns + Export Annotations and Features + GFF file reading / writing + Associate structures with sequences from local PDB files + Add sequences to exisiting alignment + Recently opened files / URL lists + Applet can launch the full application + Applet has transparency for features (Java 1.2 required) + Applet has user defined colours parameter + Applet can load sequences from parameter "sequencex" + +	+ + Redundancy Panel reinstalled in the Applet + Monospaced font - EPS / rescaling bug fixed + Annotation files with sequence references bug fixed + +
+ 2.08.1 + 2/5/06 +	+ + Change case of selected region from Popup menu + Choose to match case when searching + Middle mouse button and mouse movement can compress / expand + the visible width and height of the alignment + +	+ + Annotation Panel displays complete JNet results + +
+ 2.08b + 18/4/06 +		+ + Java 1.5 bug - InternalMessageDialog fix for threads + Righthand label on wrapped alignments shows correct value + +
+ 2.08 + 10/4/06 +	+ + Editing can be locked to the selection area + Keyboard editing + Create sequence features from searches + Precalculated annotations can be loaded onto alignments + Features file allows grouping of features + Annotation Colouring scheme added + Smooth fonts off by default - Faster rendering + Choose to toggle Autocalculate Consensus On/Off + +	+ + Drag & Drop fixed on Linux + Jalview Archive file faster to load/save, sequence + descriptions saved. + +
+ 2.07 + 12/12/05 +	+ + PDB Structure Viewer enhanced + Sequence Feature retrieval and display enhanced + Choose to output sequence start-end after sequence name for + file output + Sequence Fetcher WSDBFetch@EBI + Applet can read feature files, PDB files and can be used for + HTML form input + +	+ + HTML output writes groups and features + Group editing is Control and mouse click + File IO bugs + +
+ 2.06 + 28/9/05 +	+ + View annotations in wrapped mode + More options for PCA viewer + +	+ + GUI bugs resolved + Runs with -nodisplay from command line + +
+ 2.05b + 15/9/05 +	+ + Choose EPS export as lineart or text + Jar files are executable + Can read in Uracil - maps to unknown residue + +	+ + Known OutOfMemory errors give warning message + Overview window calculated more efficiently + Several GUI bugs resolved + +
+ 2.05 + 30/8/05 +	+ + Edit and annotate in "Wrapped" view + +	+ + Several GUI bugs resolved + +
+ 2.04 + 24/8/05 +	+ + Hold down mouse wheel & scroll to change font size + +	+ + Improved JPred client reliability + Improved loading of Jalview files + +
+ 2.03 + 18/8/05 +	+ + Set Proxy server name and port in preferences + Multiple URL links from sequence ids + User Defined Colours can have a scheme name and added to + Colour Menu + Choose to ignore gaps in consensus calculation + Unix users can set default web browser + Runs without GUI for batch processing + Dynamically generated Web Service Menus + +	+ + InstallAnywhere download for Sparc Solaris + +
+ 2.02 + 18/7/05 +		+ + Copy & Paste order of sequences maintains alignment + order. + +
+ 2.01 + 12/7/05 +	+ + Use delete key for deleting selection. + Use Mouse wheel to scroll sequences. + Help file updated to describe how to add alignment + annotations. + Version and build date written to build properties file. + InstallAnywhere installation will check for updates at + launch of Jalview. + +	+ + Delete gaps bug fixed. + FileChooser sorts columns. + Can remove groups one by one. + Filechooser icons installed. + Finder ignores return character when searching. Return key + will initiate a search. + + +
+ 2.0 + 20/6/05 +	+ + New codebase + +

+ + -- 1.7.10.2