#### beta2 #### [05-19-2005] - added labels if mouse over Rna2DViewer and Rnalign buttons - behavior changed for the lower toolbar in Rna2DViewer - by clicking on the brush icon in Rna2DViewer, you switch between the simplified line representation, or the explicit display of all bases - added buttons in Rna2DViewer and Rnalign to capture the view in a PNG file - added one button in Rna2DViewer to save the current layout in a jython script (now, the "disk" button is only used to save the 2D structure in an SVG file) - within Rna2DViewer, saving the current layout mean now : the position for each helix, the labels for each single-strand and helix, the zoom level and the position of the view on the secondary structure - Rna2DViewer displays the origin of the view attached to each RNA secondary structure . When one saves the RNA secondary structure coordinates (in an RnaML or SVG file), these coordinates are recalculated relative to this origin and to the final zoom level of the current view - within Rna2DViewer, one can modify single-strand and helix names from the topological viewer and from the 2D view - Rna2DViewer provides a "select all" item in its "Edit" menu. This will select all the helices at once. - fixed bug #206 (Gaps not deleted from the 2D/3D bracket notation) - fixed bug #207 (Sequence order in the alignments not saved) - fixed bug #208 ("Nothing" 3D mode not available) #### beta3 #### [06-30-2005] -added new "org.fjossinet.s2s.utilities" package. It will contain unix command-line tools using the S2S APIs -added org.fjossinet.s2s.utilities.PDB2Brackets tool Rna2DViewer -the color chooser stores the precedent choices -added a colors toolbar. When a color is used on a secondary structure, the color is stored in this new bar. -reorganization of the toolbars' locations -added a spinner to select how many nearest neighbors will be showed for selected structures. With the '*' choice, all the neighbors will be showed, so the complete molecule -a single-strand between two helices can recalculate its coordinates automatically or let the user define each base position. A button allowing to switch between the two modes has been added -if a single-strand is surrounded with two selected helices and doesn't recalculate automatically its coordinates, this single-strand is automatically selected -added the 5' and 3' ends to the display -2D display optimized to be faster Rnalign -depending on the structural mask chosen, only the consensus or the 2D/3D bracket notation is displayed. The "Bases" and "Sequence" coloring modes display both. -added a '*' character before the name of the reference molecule -pseudo-knots annotated as in the Rfam database. The 5' half of a stem is represented with uppercase letters, e.g. "A" and the 3' with lowercase e.g. "a". Nested knots are dealt with by using other letters. -double-click on the Consensus Structure label allows to edit the bracket notation directly Bugs fixed -fixed bug #219 (Error for the alignment element in the RnaML output) -fixed bug #222 (No centring on a single-strand from Rnalign to Rna2DViewer) -fixed bug #223 (Bad orientation for some single-strands when helices flipped) -fixed bug #224 (Conflict generated by the '>' characters in a FASTA export) #### beta4 #### [07-18-2005] -added a new way to install S2S -the documentation is not anymore provided with the S2S package. It is now in a separate archive. S2SViewer -added an new menu names "S2S" containing a "Preferences" item to configure S2S #### beta5 #### [07-22-2005] -fixed bug #226 (S2S cannot open files with spaces in its absolute path) -the function to find pseudoknots has been modified and fixed. Now, it should find all the pknots in a 3D structure. To do that, S2S searches all helices with interlocked strands like : __________________ | _________|_________ | | | | ------ ---- ------ ---- and give to these helices a label like : __________________ | _________|_________ | | | | ------ ---- ------ ---- A B a b Within S2SViewer, these helices will be named A/a and B/b Within the Rnalign's bracket notations, the display will be like : AAAAAAXXXXBBBBXXXXXaaaaaaXXXXXbbbbXXXXXXXXXXXX A message is printed in the terminal for each couple of interlocked helices found. S2SViewer -for some 3D structures with more than one molecule, phosphodiester bonds linked to InterHelices have been defined as children of the Model element. They have been moved as children of their Molecule element (a phosphodiester node cannot be above a Molecule node in the tree representation). -added "Center" 3D mode -the helices are named "HX" with X value between 1 to n. The helix H1 is the first one encountered starting from the 5' end of the sequence. Using the same rule, the single strands are named "SSX". Rna2DViewer -added a button to hide/display the 5'->3' orientation on the phosphodiester bonds -added the "Display peers" choice in the "View" menu. This allows to show the sstrands and/or helices establishing base-base interactions with user-selected bases in the SecondaryCanvas -added a "Show" button attached to the spinner to apply the current spinner value to the display -added a "Number" button attached to the Number list to apply the current numbering value to the display. This button substitutes the yellow circle button in the upper toolbar.