3 <head><title>Preferences</title></head>
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6 <p><strong>Preferences</strong></p>
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7 <p>There are four tabs in the Preferences dialog box:
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9 <li>The <a href="#visual"><strong>"Visual"</strong> Preferences</a>
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10 tab allows you to configure the default display for a new alignment window.
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13 href="#connections"><strong>"Connections"</strong> Preferences</a>
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14 tab allows you to change the links made from Jalview to your default web browser.
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16 <li>The <a href="#output"><strong>"Output"</strong> Preferences</a>
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17 tab contains settings affecting the export of sequence alignments and EPS
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19 <li>The <a href="#editing"><strong>"Editing"</strong> Preferences</a>
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20 tab contains settings affecting the export of sequence alignments and EPS
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24 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
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25 <p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch
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26 to fit the available space.</p>
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27 <p><em>Show Annotations</em> - If this is selected the new window will display an annotation
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28 panel below the sequences. This annotation panel may have several rows describing
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29 the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
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30 may be shown or hidden by default.</p>
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31 <p><em>Full Sequence ID</em> - If selected the ID panel will display the name of a sequence
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32 plus the start and end residues in the format name/start-end. If not selected,
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33 the displayed ID will be the name of the sequence.</p>
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34 <p><em>Font</em> - The default font name, size and style can be set for a new
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35 alignment window. </p>
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36 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering
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37 of the alignment.</p>
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38 <p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>
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39 <p><em>Colour</em> - The default colour scheme for a new alignment window. If
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40 the chosen option is "User Defined" then the last User Defined Colour
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41 loaded or saved via the User Defined Colours panel will be loaded. </p>
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42 <p><em>Sort by</em> - When the alignment is loaded in, it will can be sorted by
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43 Id or pairwise identity.</p>
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44 <p><em>Open file</em> - If this is selected then the default alignment file will
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45 be opened when Jalview is started. You can change the default file by clicking
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46 on file name and either typing in the file path or selecting it from the file
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47 chooser window. </p>
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48 <p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>
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49 <p><em>URL Link From Sequence ID</em><br>
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50 Right click a sequence id to see a popup menu with "Link" as one of
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51 the items. By default the item "SRS" is added to this link menu. This
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52 link will show a web page in your default browser with the selected sequence
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53 id as part of the URL.<br>
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54 Jalview allows you to add your own custom links to other web pages. Click new
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55 to add a new link. You can name the link, this will be displayed on a new menu
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56 item under the "Link" menu when you right click on a sequence id.
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58 You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen
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59 sequence id when you click on it. </p>
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60 <p><em>Default Browser (Unix)</em><br>
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61 Its difficult in Java to detect the default web browser for Unix users. If Jalview
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62 can't find your default web browser, enter the name or full path to your web
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63 browser application. </p>
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64 <p><em>Proxy Server</em><br>
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65 If you normally use a proxy server for using the internet, you must tick the
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66 box "Use a Proxy Server" and enter the address and port details as
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67 necessary. Web Services will not work if you are using a proxy server and do
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68 not enter the settings here.</p>
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69 <p><a name="output"><strong>Output Preferences tab</strong></a></p>
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70 <p><em>EPS Rendering Style</em><br>
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71 This is a selection box which allows the
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72 user to set a default rendering style for EPS export:
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73 <ul><li>"Lineart"<br>EPS files will accurately
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74 reproduce the alignment view in Jalview and all characters will be
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75 converted into line art. Files generated in this way are large and are
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76 not easily editable, but have no font table dependencies.</li>
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77 <li>"Text"<br>EPS files will be a mixture of text and
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78 lineart. This produces compact files that can be edited easily in
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79 programs like Microsoft Word and Adobe Illustrator, but can be
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80 problematic if the fonts available to jalview are not accessible by
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81 the program reading the EPS file.
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82 <li>"Prompt each time"<br>Choose this to be asked select between Lineart and Text each time you make an EPS file.</li>
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85 <p><em>Sequence//Start-End Numbering</em><br>
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86 The output tab also has a group of checkboxes for each file format. If these
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87 are ticked, then Jalview will write files with the start and end sequence positions
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88 appended to each sequence id:
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93 <p>If the boxes are left unchecked for a particular format, the sequence limits
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94 will not be appended to the sequence id. </p>
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96 <p><em>Use Modeller Output</em></p>
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97 <p>This option only applies to PIR format output. Jalview can now read and write
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98 PIR files with sequence descriptions compatible with the program <a href="http://salilab.org/modeller/">Modeller</a>.
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99 If this option is selected Jalview will write the sequence description in the
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100 following format:</p>
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101 <pre>>P1;O80429_MAIZE
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102 sequence:O80429_MAIZE:1:.:140:.:.</pre>
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103 If a sequence description existed before the file was saved, it will be appended
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104 to the new Modeller style desciption. The Jalview id/start-end option is ignored
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105 if Modeller output is selected.
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106 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
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107 <p>There are currently 2 options available which can be selected / deselected.
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109 <p><em>AutoCalculate Consensus</em> - For large alignments it can be useful to
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110 deselect "Autocalculate Consensus" when editing. This prevents lengthy
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111 calculations which are performed after each sequence edit. New alignment windows
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112 will have their "Autocalculate Consensus" option set according to
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114 <p><em>Pad gaps when editing</em> - New alignment windows will "Pad Gaps"
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115 according to this setting.</p>
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git://source.jalview.org / jalview.git / blob