3 <title>VAMSAS Interoperation</title>
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6 <p><strong>VAMSAS Interoperation</strong></p>
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7 <p>Jalview can interact with other applications using "the <strong>VAMSAS
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8 Interoperation framework</strong>" which is an experimental model for
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9 interoperation between bioinformatics applications (<strong>V</strong>isualization
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10 and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
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11 <strong>Alignements</strong> and <strong>S</strong>tructures).
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12 Currently, the only other VAMSAS enabled application is <a
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13 href="http://www.topali.org">TOPALi</a> - a user friendly program for
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14 phylogenetics and evolutionary analysis.
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15 <p>VAMSAS enabled applications access a shared bioinformatics
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16 dataset containing sequences, alignments, annotation and trees, which
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17 can be represented by an XML document analogous to a <a
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18 href="../features/jalarchive.html">Jalview Project Archive</a>.</p>
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20 <strong>Connecting to a VAMSAS session</strong><br>
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21 The VAMSAS functionality in Jalview is accessed through the Desktop's <strong>Vamsas</strong>
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22 menu. The options available in this menu depend on whether the
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23 application is currently interacting with a VAMSAS dataset in a <strong>VAMSAS
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24 session</strong>. When the application is not connected to a session is active,
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25 the menu options are as follows:<br>
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27 <li><em>Connect to an existing session</em><br>
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28 If visible, this submenu contains a list of existing sessions that the
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29 VAMSAS framework has discovered on your computer. <br>
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30 Choose one to connect to it.</li>
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31 <li><em>New VAMSAS Session</em><br>
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32 This option will create a new session on your computer.</li>
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33 <li><em>Load VAMSAS Session...</em><br>
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34 This option will open a file browser window allowing you to select a
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35 VAMSAS session archive from which a new session will be created.<br/>
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36 <em>New in 2.5:</em>Sessions created from an imported document inherit
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37 the file or URL for the document.</li>
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41 <strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
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42 communicate between different programs. This means that after starting a
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43 session, your firewall software may ask you whether to allow the java
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44 executable access to the internet (port 53782). If you do not allow
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45 this, messages will not be exchanged with other VAMSAS applications.</br>
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47 Once you have successfully connected to a VAMSAS session, any data made
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48 available by other VAMSAS applications will be automatically imported
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49 into Jalview. However, in order to share the data in Jalview with other
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50 VAMSAS applications, you must manually select the <strong>Vamsas→"Session
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51 Update"</strong> entry that is visible when a session is active. Selecting
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52 this option will update the VAMSAS session document, with the data
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53 loaded into Jalview. Any new alignments, trees and annotation will be
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54 written to the session, in addition to any edits you have made to data
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55 originally stored in the document. <br>
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56 <strong>Saving the current session</strong><br>
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57 You can save the current session as a VAMSAS Session archive using the <strong>Vamsas→"Session
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58 Update"</strong>. The file contains a snapshot of the current VAMSAS
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59 session, including data from any other applications connected to the
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60 session. <strong>Leaving a VAMSAS session</strong><br>
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61 A session can be disconnected from at any time using the <strong>Vamsas→"Stop
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62 Session"</strong> option. Selecting this option will only disconnect Jalview
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63 from the session - any other applications will remain connected to the
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64 session. If Jalview is the only application connected to the session and
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65 you have not yet saved the VAMSAS session then you will be prompted with
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66 an optional 'Save VAMSAS session...' dialog box, allowing the session to
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67 be saved and returned to at a later date. <br>
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68 <strong>VAMSAS Session Persistence</strong><br>
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69 VAMSAS sessions are persistent - this means that they exist
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70 independently of any VAMSAS applications that are connected to them.
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71 This means that if something goes wrong with a VAMSAS application and it
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72 crashes or otherwise fails, the VAMSAS session it is connected to will
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73 (hopefully) be unaffected. For instance, if Jalview is killed or crashes
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74 whilst it is still connected to a session, that session can be recovered
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75 in a new Jalview instance using the <strong>Vamsas→"Existing
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76 session"</strong> sub menu.</p>
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77 <strong>A quick Demo</strong>
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79 Jalview can talk to itself through VAMSAS. Simply start two copies of
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80 the application, create a new vamsas session in one, and connect to the
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81 new session in the other. Then load your data into one of the
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82 applications, and use the
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83 <strong>Vamsas→"Session Update"</strong>
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84 menu entry to try to propagate the data to the other application.
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88 <td>Data Sharing Capability</td>
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89 <td>Jalview Version</td>
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92 <td>Alignments, sequences and annotation, trees, database
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93 references, cDNA/protein mappings.</td>
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97 <td>Mouseover location across linked DNA, protein and structure
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102 <td>Jalview project settings (Multiple views, groups, tree
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103 partitions, colouring, window positions)</td>
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107 <td>Sequence region and column selections</td>
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112 <p>Version 0.2 of the VAMSAS client library is used in <em>Jalview
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113 2.5</em>. For further details about the VAMSAS framework, please check the
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114 <a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
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115 framework is implemented as a Java 1.4 Library and depends on a number
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116 of other open source projects. Its source is released under the
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117 LGPL license. </p>
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git://source.jalview.org / jalview.git / blob