| [2] | 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" |
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| 2 | "http://www.w3.org/TR/html4/loose.dtd"> |
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| 3 | <html> |
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| 4 | <head> |
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| 5 | <title>Starting and Running Gmaj</title> |
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| 6 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> |
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| 7 | <meta http-equiv="Content-Style-Type" content="text/css"> |
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| 8 | <link rel="stylesheet" type="text/css" href="gmaj.css"> |
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| 9 | </head> |
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| 10 | <body> |
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| 11 | <p class=vvlarge> |
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| 12 | <h2>Starting and Running Gmaj</h2> |
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| 13 | <p class=vvlarge> |
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| 14 | TABLE OF CONTENTS |
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| 15 | <p class=small> |
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| 16 | <ul class=notop> |
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| 17 | <li><a href="#intro">Introduction</a> |
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| 18 | <li><a href="#start">Starting Gmaj</a> |
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| 19 | <li><a href="#memory">Memory Allocation</a> |
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| 20 | <li><a href="#windows">Multi-Pip and Dotplot Windows</a> |
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| 21 | <li><a href="#state">The Zoom and the Mark</a> |
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| 22 | <li><a href="#layout">Window Layout</a> |
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| 23 | <li><a href="#mouse">Mouse Controls</a> |
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| 24 | <li><a href="#menu">Menus and Widgets</a> |
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| 25 | <li><a href="#copy">Copying and Printing</a> |
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| 26 | <li><a href="#notes">Footnotes</a> |
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| 27 | </ul> |
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| 28 | <p class=vlarge> |
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| 29 | |
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| 30 | <p class=hdr> |
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| 31 | <h3><a name="intro">Introduction</a></h3> |
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| 32 | <p> |
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| 33 | Gmaj can be run in two different modes: as an applet over the |
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| 34 | world-wide web (for viewing data delivered from a server), or as |
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| 35 | a stand-alone application (for viewing data stored on your own |
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| 36 | computer). These modes are mostly similar but have a few minor |
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| 37 | differences, as noted below. |
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| 38 | <p> |
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| 39 | |
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| 40 | <p class=hdr> |
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| 41 | <h3><a name="start">Starting Gmaj</a></h3> |
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| 42 | <p> |
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| 43 | If you are using Gmaj in applet mode, it will be started for you |
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| 44 | when you visit the applicable web page or submit a query to the |
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| 45 | server. If the Gmaj window does not appear automatically, just |
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| 46 | click on the labeled button to view the indicated data. Then |
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| 47 | skip the rest of this section. |
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| 48 | <p> |
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| 49 | If you are using Gmaj in stand-alone mode, you need to start it |
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| 50 | yourself. The Java runtime environment does not have its own |
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| 51 | GUI, so you generally need to run Gmaj from a command line (e.g., |
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| 52 | in the Command Prompt window on Windows XP). The basic command |
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| 53 | to type in looks like this: |
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| 54 | <pre> |
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| 55 | [path1]java -jar [path2]gmaj.jar |
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| 56 | </pre> |
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| 57 | where <code>[path1]</code> is the location of your |
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| 58 | <code>java</code> program file (perhaps |
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| 59 | <code>c:\windows\system32\</code> on WinXP, or |
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| 60 | <code>/usr/bin/java/</code> on a Unix system), and |
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| 61 | <code>[path2]</code> is the location where the |
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| 62 | <code>gmaj.jar</code> file was installed. Note that you can |
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| 63 | leave off <code>[path1]</code> if you have set up your system |
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| 64 | command path to include the location of the <code>java</code> |
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| 65 | program. Depending on how your system is set up, it may also be |
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| 66 | possible to run the jar file directly by just typing its name or |
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| 67 | double-clicking on it. |
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| 68 | <p> |
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| 69 | Since you haven't yet specified any data to display, Gmaj will |
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| 70 | begin by presenting a dialog box to prompt you for the name of |
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| 71 | your input file (see <a href="gmaj_input.html" |
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| 72 | >Input Files for Gmaj</a>). If the file is located in the |
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| 73 | current directory you can just type its name, otherwise you'll |
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| 74 | need to supply a complete path. When you click the OK button, |
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| 75 | a window will appear displaying the loaded data. |
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| 76 | <p> |
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| 77 | As an alternative to using the dialog box, you can specify the |
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| 78 | input file (plus additional parameters) on the command line. |
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| 79 | As of this writing, the command syntax is: |
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| 80 | <pre> |
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| 81 | [path1]java -jar [path2]gmaj.jar |
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| 82 | [-version] [-help] [-debug] [-urlpause <millisec>] |
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| 83 | [-initzoom <refseqname> <start> <end>] |
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| 84 | [-bundle <zipfile>] [<paramfile>|<alignfile>] |
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| 85 | </pre> |
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| 86 | <p> |
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| 87 | This has been wrapped here for easier readability, but should be |
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| 88 | typed all on one line. Arguments shown in square brackets |
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| 89 | <code>[]</code> are optional, while a vertical bar <code>|</code> |
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| 90 | indicates a choice between alternatives. Angle brackets |
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| 91 | <code><></code> signify meta-syntactic variables that |
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| 92 | should be replaced with your names or numbers. Don't type any |
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| 93 | of the brackets or the bar. |
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| 94 | <p> |
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| 95 | These parameters do the following: |
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| 96 | <dl> |
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| 97 | <dt> <code>-version</code>: |
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| 98 | <dd> Prints a message with information about Gmaj, including |
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| 99 | version, author, etc.; then exits. |
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| 100 | <dt> <code>-help</code>: |
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| 101 | <dd> Prints a brief help message with up-to-date syntax; then |
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| 102 | exits. |
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| 103 | <dt> <code>-debug</code>: |
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| 104 | <dd> Instructs Gmaj to print extra warning messages in |
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| 105 | your terminal window if certain problems occur. Normally |
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| 106 | you won't need this, as it is mainly for development |
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| 107 | purposes. |
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| 108 | <dt> <code>-urlpause</code>: |
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| 109 | <dd> Specifies how many milliseconds the program should pause |
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| 110 | before retrieving each file from a URL, in order to avoid |
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| 111 | overloading the server. |
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| 112 | <dt> <code>-initzoom</code>: |
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| 113 | <dd> Specifies an initial zoom setting to be applied when the |
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| 114 | window opens. You will still be able to invoke the Unzoom |
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| 115 | or Set Zoom features interactively to see the entire |
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| 116 | sequence range. The <code><refseqname></code> must |
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| 117 | match one of the sequence names from the alignment file(s), |
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| 118 | and the endpoints must include the offset (if any) for that |
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| 119 | sequence from the parameters file. To specify the reference |
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| 120 | sequence without a zoom region, use <code>-1</code> for both |
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| 121 | endpoints. |
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| 122 | <dt> <code>-bundle</code>: |
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| 123 | <dd> Specifies the name of a <code>.zip</code> or |
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| 124 | <code>.jar</code> file containing some or all of the data |
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| 125 | files. This option is mostly used with Gmaj's applet mode |
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| 126 | to streamline the data download, but it is also supported |
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| 127 | in stand-alone mode. It is described in |
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| 128 | <a href="gmaj_input.html">Input Files for Gmaj</a>. |
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| 129 | <dt> <code><paramfile></code>: |
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| 130 | <dd> This is the meta-data parameters file that lists the names |
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| 131 | of all the data files, plus a few related parameters such as |
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| 132 | display offsets and any intrinsic reference sequence. For |
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| 133 | more information about the contents and format of this file, |
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| 134 | please see <a href="gmaj_input.html">Input Files for Gmaj</a> |
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| 135 | and <code><a href="sample.gmaj">sample.gmaj</a></code>. |
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| 136 | <dt> <code><alignfile></code>: |
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| 137 | <dd> If you don't want to use any annotations or other |
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| 138 | data-related options, you can specify a single alignment |
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| 139 | file directly, instead of creating a parameters file. |
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| 140 | This must be in MAF format; see <a href="gmaj_input.html" |
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| 141 | >Input Files for Gmaj</a> for more details. |
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| 142 | </dl> |
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| 143 | <p> |
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| 144 | |
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| 145 | <p class=hdr> |
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| 146 | <h3><a name="memory">Memory Allocation</a></h3> |
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| 147 | <p> |
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| 148 | If the dataset you want to view is large, Gmaj may run out of |
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| 149 | memory, in which case Java will report an |
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| 150 | <code>OutOfMemoryError</code>. This message will appear in the |
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| 151 | command window where you started Gmaj (for stand-alone mode) or |
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| 152 | in the Java Console window of your web browser (for applet mode). |
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| 153 | If the Java Console window does not appear when you run the Gmaj |
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| 154 | applet, open the Java Plug-in Control Panel on your computer and |
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| 155 | click the setting for Show Console so you can see this and other |
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| 156 | Java messages. |
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| 157 | <p> |
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| 158 | The <code>OutOfMemoryError</code> is not uncommon, because the |
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| 159 | default amount of memory that Java allocates is rather small. |
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| 160 | You can give it more memory using the <code>-Xmx</code> switch |
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| 161 | (at least with Sun's Java; this option may not be supported by |
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| 162 | all vendors). For example, when using stand-alone mode the |
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| 163 | command line |
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| 164 | <pre> |
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| 165 | [path1]java -Xmx1024m -jar [path2]gmaj.jar |
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| 166 | </pre> |
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| 167 | runs Gmaj with a heap memory allowance of ~1 gigabyte. For the |
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| 168 | applet, you can do this by opening the Java Plug-in Control Panel |
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| 169 | on your computer and entering <code>-Xmx1024m</code> in the Java |
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| 170 | Runtime Parameters box (this will affect all applets you run via |
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| 171 | the Java Plug-in, not just Gmaj). |
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| 172 | <p> |
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| 173 | |
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| 174 | <p class=hdr> |
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| 175 | <h3><a name="windows">Multi-Pip and Dotplot Windows</a></h3> |
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| 176 | <p> |
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| 177 | Gmaj has two kinds of windows. The main one displays a number |
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| 178 | of pips (percent identity plots) showing the pairwise alignments, |
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| 179 | projected from the multiple alignments, of a particular reference |
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| 180 | sequence against each of the other sequences. A pip is similar |
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| 181 | to a dotplot, with the horizontal <code>x</code>-axis |
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| 182 | representing positions in the reference sequence, but the |
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| 183 | vertical <code>y</code>-axis represents the percentage of |
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| 184 | matching nucleotides in each gap-free segment of the pairwise |
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| 185 | alignment, instead of its position in the second sequence. The |
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| 186 | window you see first when Gmaj opens is usually of this type, and |
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| 187 | if the alignments are reference-independent, you can open more of |
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| 188 | these with other sequences as the reference. |
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| 189 | <p> |
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| 190 | The second type of window focuses exclusively on a particular |
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| 191 | pair of sequences, and displays one pip together with its |
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| 192 | corresponding dotplot representation (similar to Gmaj's |
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| 193 | predecessor, <a href="http://globin.bx.psu.edu/dist/laj/" |
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| 194 | >Laj</a>). These windows are opened upon request, by clicking |
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| 195 | on a button in the header for a particular pip in the multi-pip |
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| 196 | window. Conceptually the dotplot windows are like children of |
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| 197 | their parent multi-pip window: they have the same reference |
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| 198 | sequence, and if you close a dotplot only that one window closes, |
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| 199 | but if you close the parent all of its children close too. |
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| 200 | <p> |
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| 201 | For the special case where the alignment files have only two |
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| 202 | sequences, the main window is redundant so Gmaj automatically |
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| 203 | hides it and shows the dotplot window directly. |
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| 204 | <p> |
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| 205 | |
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| 206 | <p class=hdr> |
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| 207 | <h3><a name="state">The Zoom and the Mark</a></h3> |
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| 208 | <p> |
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| 209 | Gmaj has two main elements of user state that reflect the user's |
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| 210 | interactive manipulation of the display. The first is the zoom |
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| 211 | region, i.e. the portion of the reference and secondary sequences |
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| 212 | that is currently displayed; this is one-dimensional for |
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| 213 | multi-pip windows and two-dimensional for dotplots. As the zoom |
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| 214 | is changed, the previous regions are remembered in a history |
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| 215 | list, so you can go back and forward through it similar to a web |
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| 216 | browser. Each Gmaj window has its own separate zoom and history; |
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| 217 | when opening a new window the current zoom region is translated |
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| 218 | initially, but then they are independent. As a convenience, |
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| 219 | each new window begins with several zoom regions already in the |
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| 220 | history: the fully unzoomed sequence length(s), as specified in |
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| 221 | the MAF files; the aligning portion of the applicable sequence(s); |
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| 222 | and an approximate translation of the previous window's current |
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| 223 | zoom (or in the case of the very first window, the initial zoom |
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| 224 | specified in the command-line or applet parameters, if any). |
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| 225 | The boundaries of the current region are displayed in a status |
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| 226 | indicator in the upper right corner of the window, below the |
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| 227 | menu bar. |
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| 228 | <p> |
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| 229 | The second state element is called the "mark", and it represents |
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| 230 | a particular selected point in a particular pairwise pip+dotplot |
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| 231 | and a particular MAF block. It is typically selected by clicking |
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| 232 | in a pip, dotplot, or text alignment, and is drawn as a small |
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| 233 | <a href="#red">red</a> circle in the plots, and also as a red |
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| 234 | highlight in the text alignment. Unlike the zoom regions, the |
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| 235 | mark is shared among several windows: there is at most one mark |
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| 236 | for each reference sequence, and it appears in both the multi-pip |
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| 237 | window for that sequence and the dotplot corresponding to |
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| 238 | whichever pip the mark is currently in (the other dotplots, with |
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| 239 | different secondary sequences, will show some indirect information |
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| 240 | about the mark, but not the mark itself). Thus, moving the mark |
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| 241 | in a dotplot window will also move it in the parent multi-pip and |
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| 242 | vice-versa, but the mark for a different reference sequence is |
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| 243 | independent. Information about the current mark and plot block |
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| 244 | is displayed in one of the status indicators below the menu bar. |
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| 245 | <p> |
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| 246 | |
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| 247 | <p class=hdr> |
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| 248 | <h3><a name="layout">Window Layout</a></h3> |
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| 249 | <p> |
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| 250 | Each Gmaj window is divided into several sections. Across the |
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| 251 | top you will see a menu bar (including text boxes for setting |
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| 252 | display thresholds), and below that two lines containing |
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| 253 | status indicators with information about the position of the |
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| 254 | mouse pointer, the boundaries of the currently displayed zoom |
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| 255 | region, and the location of the mark (<a href="#red">red</a> |
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| 256 | circle), along with buttons for sliding the zoom region and |
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| 257 | selecting alternative blocks at the marked position. Several |
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| 258 | of the dividers between these items are <a href="#dividers" |
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| 259 | >draggable</a>, so you can adjust the relative space they |
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| 260 | occupy. Below these is a row of category checkboxes, which by |
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| 261 | default will only appear when there is more than one alignment |
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| 262 | file or if you have used the tagging feature. The menus, |
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| 263 | threshold boxes, buttons, and checkboxes are discussed |
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| 264 | individually in the <a href="#menu">Menus and Widgets</a> |
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| 265 | section of this document. |
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| 266 | <p> |
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| 267 | <i>Ruler:</i><br> |
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| 268 | The first graphical panel is a horizontal ruler that displays |
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| 269 | tick marks corresponding to positions in the currently selected |
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| 270 | reference sequence. These are intended to give you an immediate |
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| 271 | general feel for the location and scale of the region being |
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| 272 | displayed. Precise locations can be determined via the position |
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| 273 | indicator, which displays the exact coordinate of the mouse |
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| 274 | pointer. |
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| 275 | <p> |
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| 276 | <i>Reconstruction scores:</i><br> |
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| 277 | For ancestral reconstruction alignments, the MAF files may |
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| 278 | contain scores indicating the confidence that 1) a particular |
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| 279 | inferred ancestral nucleotide is correct, and that 2) it was |
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| 280 | present at all. The next two panels display bar graphs of these |
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| 281 | scores when the ancestral sequence is the reference. The scores |
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| 282 | are binned according to the current zoom region and panel width, |
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| 283 | and the mean score for each bin is graphed on a scale of 0 - 1 |
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| 284 | (note that the scores are transformed via simple linear scaling, |
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| 285 | and should not be interpreted as probabilities). For this to |
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| 286 | work, the parameters file must specify which organism the scores |
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| 287 | apply to. Otherwise, or if there are no scores in the file, or |
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| 288 | if a different sequence is currently the reference, these panels |
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| 289 | will not appear. The position indicator displays the horizontal |
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| 290 | coordinate and vertical score position of the mouse pointer, |
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| 291 | along with the score for the bar at that location (if any). |
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| 292 | <p> |
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| 293 | <i>Linkbars:</i><br> |
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| 294 | Next is a panel that can display links to additional information |
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| 295 | about various regions in the current reference sequence. Each |
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| 296 | annotation is represented by a color-coded bar spanning the |
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| 297 | region's position in the sequence. (The bars' vertical positions |
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| 298 | are not meaningful; they are only placed in rows for convenience, |
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| 299 | to keep them from overlapping.) Pointing to a particular bar |
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| 300 | will cause the position indicator to display the <code>x</code> |
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| 301 | coordinate of the pointer, and also the type and description of |
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| 302 | that bar's annotation; otherwise only the <code>x</code> |
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| 303 | coordinate will be shown. In applet mode, clicking on a bar will |
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| 304 | open a separate browser window to visit the corresponding web |
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| 305 | site. In stand-alone mode Gmaj is not working within a web |
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| 306 | browser, so instead it displays the URL for you to visit manually |
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| 307 | via copy-and-paste. If no links file is provided for the current |
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| 308 | sequence, this panel will not appear. |
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| 309 | <p> |
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| 310 | <i>Sequence features:</i><br> |
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| 311 | The next two panels contain schematic diagrams of the known |
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| 312 | exons and interspersed repeats in the current reference sequence, |
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| 313 | respectively (if these files are provided). Any additional |
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| 314 | features such as CpG islands are included with the repeats (which |
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| 315 | is why the label says "repeats+"). The diagram for repeats uses |
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| 316 | the same symbols as <a href="http://pipmaker.bx.psu.edu/pipmaker/" |
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| 317 | >PipMaker</a> to indicate the various repeat categories (Alu, MIR, |
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| 318 | etc.), but only if either the PipMaker category or the |
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| 319 | <a href="http://www.repeatmasker.org/">RepeatMasker</a> name and |
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| 320 | class/family are available. For example, BED and GTF repeat |
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| 321 | files from the <a href="http://genome.ucsc.edu/cgi-bin/hgTables" |
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| 322 | >UCSC Table Browser</a> include the RepeatMasker name but not the |
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| 323 | class/family, so Gmaj cannot determine the PipMaker category and |
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| 324 | draws all of them as "Other". As usual, the position indicator |
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| 325 | displays the <code>x</code> coordinate of the mouse pointer, and |
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| 326 | also identifies any features at that position. |
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| 327 | <p> |
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| 328 | <i>Plots:</i><br> |
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| 329 | The following panels display the alignment plots according to the |
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| 330 | window type: either a scrollable stack of <a href="#windows" |
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| 331 | >pips</a> (for the reference sequence against each of the others) |
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| 332 | or a single pip and its corresponding dotplot. For pips, only |
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| 333 | the top half of each plot is shown, since segments matching less |
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| 334 | than 50% are usually not very interesting. Plot segments from |
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| 335 | the primary alignment file are drawn with thin black lines, while |
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| 336 | those from subsequent files are drawn with thicker brown lines. |
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| 337 | Tagged blocks are green, and the marked block is red (or orange |
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| 338 | if it is also tagged), though these may <a href="#red">vary</a> |
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| 339 | on colored backgrounds. When plot segments overlap, the marked |
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| 340 | and tagged ones are drawn "on top" so they won't be obscured, |
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| 341 | followed by other blocks from the primary alignment file and then |
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| 342 | the remaining files. Plots that are completely empty (i.e. if |
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| 343 | that pair of sequences never occurs together in any of the |
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| 344 | alignment blocks) will be painted gray. An additional feature of |
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| 345 | these panels is that colored backgrounds, or "underlays", can be |
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| 346 | used to highlight regions of interest (if files with this |
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| 347 | information are provided); dotplots can display these for both |
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| 348 | the reference and secondary sequences. Vertical blue bars at the |
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| 349 | edges of the plots represent the boundaries of the current zoom |
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| 350 | region, whose endpoints are displayed in the zoom indicator. For |
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| 351 | a pip, the position indicator displays the horizontal coordinate |
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| 352 | and vertical percentage position of the mouse pointer, along with |
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| 353 | a list of <a href="#numbering">block numbers</a> <a href="#cover" |
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| 354 | >covering</a> that location. For a dotplot, it displays the |
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| 355 | horizontal and vertical coordinates in the reference and secondary |
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| 356 | sequences, respectively. It will also display labels for the |
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| 357 | colored regions in both types of plots, if these are included in |
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| 358 | the underlay files. |
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| 359 | <p> |
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| 360 | <i>Text view:</i><br> |
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| 361 | The bottom panel displays a nucleotide-level view of a single |
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| 362 | selected alignment block: the one containing the mark |
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| 363 | (<a href="#red">red</a> circle). Initially it is empty, since |
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| 364 | you haven't set the mark yet. The top row of this display shows |
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| 365 | the current reference sequence, while the rows for the other |
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| 366 | sequences show a dot (<code>.</code>) wherever they match the |
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| 367 | reference sequence, and only explicitly list the nucleotides that |
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| 368 | don't match. (This matching is case-insensitive to deal with |
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| 369 | soft masking, but non-nucleotide characters such as |
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| 370 | <code>X</code> or <code>N</code> never match anything, even |
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| 371 | themselves.) All of the sequences will likely have had gaps |
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| 372 | (<code>-</code>) inserted by the alignment program. Note that |
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| 373 | most of the blocks will be much too long to fit across this |
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| 374 | window, so a scrollbar is provided; the relative size of the |
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| 375 | scrollbar's slider indicates what fraction of the alignment is |
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| 376 | shown in the window. Colored "highlights" (analogous to the plot |
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| 377 | underlays) can also be specified for each sequence; otherwise |
|---|
| 378 | Gmaj will provide default highlights based on the exons files |
|---|
| 379 | (if any). Whenever the mouse pointer is in this bottom panel, |
|---|
| 380 | the position indicator displays its location in the format |
|---|
| 381 | <code>n(x)</code>, where <code>n</code> is the column position |
|---|
| 382 | in this aligned block (starting with 0), and <code>x</code> is |
|---|
| 383 | the sequence position in the individual row (i.e., in that entire |
|---|
| 384 | chromosome or contig, starting with 1). Note that <code>x</code> |
|---|
| 385 | does not include the gaps, but <code>n</code> does. Labels for |
|---|
| 386 | any highlights at that position are also displayed. |
|---|
| 387 | <p> |
|---|
| 388 | With the exception of the text view, all of these data panels use |
|---|
| 389 | the same horizontal coordinate scale (i.e., position in the |
|---|
| 390 | current reference sequence), and they are always kept vertically |
|---|
| 391 | aligned so they can be compared easily. Note that in the |
|---|
| 392 | multi-pip window the partition between the graphical panels and |
|---|
| 393 | the text view is <a href="#dividers">draggable</a>, so you can |
|---|
| 394 | adjust the relative amount of space they occupy. Also, individual |
|---|
| 395 | panels can be hidden if desired, using the Options - Show dialog |
|---|
| 396 | (see <a href="#menu">Menus and Widgets</a>). |
|---|
| 397 | <p> |
|---|
| 398 | <!-- |
|---|
| 399 | <i>Dotplot:</i><br> |
|---|
| 400 | The large middle panel displays a dotplot view of the alignments, |
|---|
| 401 | with the reference sequence along the horizontal |
|---|
| 402 | <code>x</code>-axis and the secondary sequence along the vertical |
|---|
| 403 | <code>y</code>-axis. If the second sequence contains multiple |
|---|
| 404 | contigs, they will appear as separate horizontal bands across the |
|---|
| 405 | plot, each with its own <code>y</code>-axis coordinate system. |
|---|
| 406 | Whenever the mouse pointer is in this panel, the position |
|---|
| 407 | indicator displays its location in the format <code>x,y</code>, |
|---|
| 408 | where <code>x</code> is the position in the horizontal sequence |
|---|
| 409 | and <code>y</code> is the position in the vertical sequence. If |
|---|
| 410 | there are multiple contigs, then the contig name will be |
|---|
| 411 | displayed as well (actually only the first word is displayed, to |
|---|
| 412 | prevent long names from crowding out the other information). |
|---|
| 413 | <p> |
|---|
| 414 | --> |
|---|
| 415 | |
|---|
| 416 | <p class=hdr> |
|---|
| 417 | <h3><a name="mouse">Mouse Controls</a></h3> |
|---|
| 418 | <p> |
|---|
| 419 | As discussed in more detail <a href="#layout">above</a>, |
|---|
| 420 | pointing with the mouse in the plots or other panels causes the |
|---|
| 421 | position indicator below the menu bar to display information |
|---|
| 422 | about that location and/or data item. |
|---|
| 423 | <p> |
|---|
| 424 | You can select a particular alignment block by clicking on one |
|---|
| 425 | of its segments in any of the plots (pips or dotplots) with the |
|---|
| 426 | left mouse button. (You don't have to click exactly on it, |
|---|
| 427 | because Gmaj will automatically jump to the nearest point if you |
|---|
| 428 | miss; however proximity is measured in bases, not pixels, which |
|---|
| 429 | can lead to non-intuitive results if the dotplot's zoom scale is |
|---|
| 430 | highly skewed.) The spot will be marked with a small |
|---|
| 431 | <a href="#red">red</a> circle, and the entire alignment block |
|---|
| 432 | containing the mark will change color from black to |
|---|
| 433 | <a href="#red">red</a> in all of the plots for that reference |
|---|
| 434 | sequence (each block typically spans several gap-free segments). |
|---|
| 435 | Also, the corresponding text view for that block will appear in |
|---|
| 436 | the bottom panel with the marked position highlighted. Lastly, |
|---|
| 437 | the mark indicator will be filled in with information about the |
|---|
| 438 | marked block and position, and a row of buttons will appear next |
|---|
| 439 | to it showing the <a href="#numbering">block numbers</a> |
|---|
| 440 | <a href="#cover">covering</a> the marked location. These buttons |
|---|
| 441 | allow convenient selection of a different block at the same |
|---|
| 442 | position in the reference sequence, from the same or a different |
|---|
| 443 | alignment file (see <a href="#menu">Menus and Widgets</a>). |
|---|
| 444 | Note that there is only one mark at a time for each reference |
|---|
| 445 | sequence, so the previous one, if any, will be unmarked. |
|---|
| 446 | <p> |
|---|
| 447 | In a similar fashion, clicking the left mouse button in the |
|---|
| 448 | text view will move the mark (both the highlight and the |
|---|
| 449 | <a href="#red">red</a> circle) to that position. However, gap |
|---|
| 450 | positions cannot be selected in this manner because they do not |
|---|
| 451 | correspond to plot segments; if you click in a gap, the nearest |
|---|
| 452 | gap-free position is selected instead. Also, if you click on a |
|---|
| 453 | position in the reference sequence (which has no corresponding |
|---|
| 454 | pip), the mark will move to the new column but will remain in |
|---|
| 455 | the same pip as before. |
|---|
| 456 | <p> |
|---|
| 457 | You can "zoom in" on a particular region by dragging out a |
|---|
| 458 | rectangle with the left mouse button in any of the white panels |
|---|
| 459 | (ruler, annotations, pip, or dotplot). All of these panels |
|---|
| 460 | will always zoom together, to keep them lined up. This can be |
|---|
| 461 | repeated until the maximum resolution is reached; after that |
|---|
| 462 | Gmaj will display an error message. Additional zoom features |
|---|
| 463 | are available via the Zoom menu and arrow buttons (see |
|---|
| 464 | <a href="#menu">Menus and Widgets</a>). Note that selecting |
|---|
| 465 | a new region will cause any entries in your zoom history that |
|---|
| 466 | are forward of the current point to be discarded, similar to |
|---|
| 467 | a web browser. If your rectangle is very tiny it will be |
|---|
| 468 | treated as a click instead, to avoid unintended zooming. |
|---|
| 469 | <p> |
|---|
| 470 | Holding down the right mouse button over any of the white |
|---|
| 471 | panels adds crosshairs at the mouse pointer's location, which |
|---|
| 472 | is convenient for determining whether two regions really line |
|---|
| 473 | up. If you have a one-button mouse, you can achieve the same |
|---|
| 474 | effect by applying the <code>Shift</code> key when initially |
|---|
| 475 | pressing the mouse button. |
|---|
| 476 | <p> |
|---|
| 477 | Note that these controls only work in the active window (usually |
|---|
| 478 | indicated in the operating system by a differently colored title |
|---|
| 479 | bar). If a window is not the active one, then your first click |
|---|
| 480 | in it just activates the window; you will need to click again |
|---|
| 481 | to set the mark, select a region, open a menu, etc. |
|---|
| 482 | <p> |
|---|
| 483 | |
|---|
| 484 | <p class=hdr> |
|---|
| 485 | <h3><a name="menu">Menus and Widgets</a></h3> |
|---|
| 486 | <p> |
|---|
| 487 | <dl> |
|---|
| 488 | <dt>File - Open: |
|---|
| 489 | <dd> |
|---|
| 490 | Loads a new set of data files into Gmaj, replacing the currently |
|---|
| 491 | displayed data. A dialog box is presented for you to specify the |
|---|
| 492 | new input file. (See discussion under <a href="#start" |
|---|
| 493 | >Starting Gmaj</a>, above.) This menu item does not appear in |
|---|
| 494 | applet mode, because the user is unlikely to know the locations |
|---|
| 495 | of other data files on the server; instead the webmaster should |
|---|
| 496 | set up separate access for each dataset. |
|---|
| 497 | <p> |
|---|
| 498 | <dt>File - Export: |
|---|
| 499 | <dd> |
|---|
| 500 | Opens a dialog box that allows you to save alignment blocks in |
|---|
| 501 | MAF format or as FastA sequence files. A variety of options are |
|---|
| 502 | available re: which blocks to export, whether they should be |
|---|
| 503 | clipped and/or cleaned up, whether to omit certain sequences, |
|---|
| 504 | etc. Note that all-gap rows are always skipped, and so are |
|---|
| 505 | blocks that have no rows left. When exporting in MAF format, |
|---|
| 506 | if the alignment has a fixed, intrinsic reference sequence and |
|---|
| 507 | that row is all gaps, the entire block will be skipped. When |
|---|
| 508 | exporting FastA sequences, a separate file is created for each |
|---|
| 509 | sequence name (i.e. species or contig), and there is an option |
|---|
| 510 | to restore sequences that align in reverse complement to their |
|---|
| 511 | original orientation (which will also swap the order of the |
|---|
| 512 | endpoint coordinates in the FastA header). By default export is |
|---|
| 513 | not available in applet mode, because security restrictions make |
|---|
| 514 | it very awkward to save files on the client computer. However, |
|---|
| 515 | the applet administrator can <a href="gmaj_install.html#page" |
|---|
| 516 | >specify a URL</a> where the output can be sent instead (in this |
|---|
| 517 | case only MAF format is supported). |
|---|
| 518 | <p> |
|---|
| 519 | <dt>File - Close: |
|---|
| 520 | <dd> |
|---|
| 521 | Closes the current window, and if it is a multi-pip window, all |
|---|
| 522 | of its dotplot children are closed as well. When no windows are |
|---|
| 523 | left, Gmaj will exit. |
|---|
| 524 | <p> |
|---|
| 525 | <dt>File - Exit: |
|---|
| 526 | <dd> |
|---|
| 527 | Exits from Gmaj. In stand-alone mode, also exits from Java. |
|---|
| 528 | <p> |
|---|
| 529 | <dt>Options: |
|---|
| 530 | <dd> |
|---|
| 531 | This menu controls some of the aesthetic aspects of Gmaj. You |
|---|
| 532 | can choose between two sizes of fonts, which will also affect |
|---|
| 533 | some other viewability settings, such as the thickness of the |
|---|
| 534 | plot segments, the radius and thickness of the mark circle, the |
|---|
| 535 | blackness of the ruler numbers, and the height of the pips. You |
|---|
| 536 | can also choose to make the mark circle and the selected block's |
|---|
| 537 | plot segments change color with the background instead of always |
|---|
| 538 | being red (this makes them visible against red underlays, but is |
|---|
| 539 | more complicated to explain in a figure legend and causes |
|---|
| 540 | <a href="gmaj_bugs.html#xor">patchy rendering</a> when used with |
|---|
| 541 | Large Fonts). Lastly, the Show item opens a dialog where you can |
|---|
| 542 | choose which panels to display or hide, and whether the underlays |
|---|
| 543 | should be painted on dotplots. The sequence selections here |
|---|
| 544 | control which pips, dotplot windows, and text rows are displayed |
|---|
| 545 | (except where that sequence is the reference). They can also |
|---|
| 546 | serve to omit sequences from exports if desired; in this case |
|---|
| 547 | they apply even to the reference sequence, but if the alignments |
|---|
| 548 | have a fixed, intrinsic reference it will be grayed out to avoid |
|---|
| 549 | exporting "orphaned" blocks. The choices on this menu affect all |
|---|
| 550 | of the windows, not just the current one. |
|---|
| 551 | <p> |
|---|
| 552 | <dt>Reference: |
|---|
| 553 | <dd> |
|---|
| 554 | This menu allows you to select a different reference sequence |
|---|
| 555 | (unless the parameters file indicates that the alignments have a |
|---|
| 556 | fixed, intrinsic reference sequence). A new multi-pip window |
|---|
| 557 | will open, showing the same data from the perspective of the |
|---|
| 558 | sequence you chose. The mark (if any) will be copied to the new |
|---|
| 559 | window as closely as possible, and the current zoom region will |
|---|
| 560 | be translated to a roughly equivalent one showing the same blocks. |
|---|
| 561 | Thereafter, the windows will operate independently. The text |
|---|
| 562 | alignments will be rearranged to put the reference row at the top, |
|---|
| 563 | but the rows are always shown in their MAF orientation. Thus if |
|---|
| 564 | the reference row is on the '-' strand, its coordinates will |
|---|
| 565 | <i>decrease</i> from left to right in the text panel. You can |
|---|
| 566 | have one multi-pip window for each sequence in the data; if you |
|---|
| 567 | already have one for the newly-chosen reference sequence, it will |
|---|
| 568 | just be brought to the front unchanged. |
|---|
| 569 | <p> |
|---|
| 570 | <dt>Zoom - Back: |
|---|
| 571 | <dd> |
|---|
| 572 | Moves backward in your zoom history for this window, returning |
|---|
| 573 | to previous regions. Does not affect the mark. |
|---|
| 574 | <p> |
|---|
| 575 | <dt>Zoom - Forward: |
|---|
| 576 | <dd> |
|---|
| 577 | Moves forward in your zoom history for this window. Does not |
|---|
| 578 | affect the mark. |
|---|
| 579 | <p> |
|---|
| 580 | <dt>Zoom - Unzoom: |
|---|
| 581 | <dd> |
|---|
| 582 | Sets the zoom region for this window to the widest, unzoomed |
|---|
| 583 | view, i.e., the full length of this entire reference sequence |
|---|
| 584 | (and also this secondary sequence, for a dotplot) as specified in |
|---|
| 585 | the MAF files. Has the same effect as entering the "valid range" |
|---|
| 586 | endpoints in Set Zoom. Does not affect the mark. |
|---|
| 587 | <p> |
|---|
| 588 | <dt>Zoom - Set Zoom: |
|---|
| 589 | <dd> |
|---|
| 590 | Presents a dialog box that allows you to enter arbitrary zoom |
|---|
| 591 | endpoints (within the valid ranges for the applicable sequences). |
|---|
| 592 | Any left empty will be interpreted to mean "leave unchanged". |
|---|
| 593 | The new region, if different from the current one, is added to |
|---|
| 594 | your zoom history for this window. Any regions forward of the |
|---|
| 595 | current point in your history are discarded (similar to a web |
|---|
| 596 | browser). Does not affect the mark. |
|---|
| 597 | <p> |
|---|
| 598 | <dt>Tags - Tag/Untag Block: |
|---|
| 599 | <dd> |
|---|
| 600 | The tagging feature allows you to build an arbitrary subset of |
|---|
| 601 | the alignment blocks for differential viewing or export (see |
|---|
| 602 | <a href="#category">Category Checkboxes</a>). There is only one |
|---|
| 603 | tagged subset in each invocation of Gmaj, and it pertains to |
|---|
| 604 | all windows. This menu item toggles the status of the currently |
|---|
| 605 | marked block (the one containing the <a href="#red">red</a> |
|---|
| 606 | circle), tagging it if it's not already in the set, and removing |
|---|
| 607 | the tag if it is. |
|---|
| 608 | <p> |
|---|
| 609 | <dt>Tags - Clear All Tags: |
|---|
| 610 | <dd> |
|---|
| 611 | Empties the tagged subset by removing the tags from all blocks. |
|---|
| 612 | Also hides the category checkboxes if they are no longer useful. |
|---|
| 613 | <p> |
|---|
| 614 | <dt>Help - About: |
|---|
| 615 | <dd> |
|---|
| 616 | Displays a message window with information about Gmaj, including |
|---|
| 617 | version, author, etc. Also reports the version of Java you are |
|---|
| 618 | currently using. |
|---|
| 619 | <p> |
|---|
| 620 | <dt>Help - Manual: |
|---|
| 621 | <dd> |
|---|
| 622 | In applet mode, opens a new browser window to view this help |
|---|
| 623 | page. In stand-alone mode Gmaj is not working within a web |
|---|
| 624 | browser, so instead it displays the URL for you to visit manually |
|---|
| 625 | via copy-and-paste. |
|---|
| 626 | <p> |
|---|
| 627 | <dt>Help - Keys: |
|---|
| 628 | <dd> |
|---|
| 629 | Displays a message window listing Gmaj's keyboard shortcuts. No |
|---|
| 630 | <code>Alt</code> key is needed. The shortcuts will not work if |
|---|
| 631 | the keyboard focus is in a text area (threshold boxes, status |
|---|
| 632 | indicators, text alignment, panel headers, etc., as indicated by |
|---|
| 633 | a purple border or highlight); in this case press <code>Esc</code> |
|---|
| 634 | first to cancel any text operation and restore the focus to the |
|---|
| 635 | active window's menu bar. <code>Esc</code> will also cancel |
|---|
| 636 | dialog and message boxes. |
|---|
| 637 | <p> |
|---|
| 638 | <dt>Help - Sequence Summary: |
|---|
| 639 | <dd> |
|---|
| 640 | Displays the aligning extents for all sequences (i.e., the |
|---|
| 641 | smallest range in each sequence that includes all of its aligning |
|---|
| 642 | regions). This is useful when fetching annotations from the UCSC |
|---|
| 643 | Table Browser or other databases, or for identifying the relevant |
|---|
| 644 | parts of already-in-hand annotation files so they can be trimmed |
|---|
| 645 | down to size. |
|---|
| 646 | <p> |
|---|
| 647 | <dt>% Identity Box: |
|---|
| 648 | <dd> |
|---|
| 649 | Allows you to set a threshold for filtering the displayed |
|---|
| 650 | alignments by the percent identity of the plot blocks (which are |
|---|
| 651 | pairwise projections of the MAF blocks). The percent identity |
|---|
| 652 | of each plot block is computed as the length-weighted average |
|---|
| 653 | percent identity of its gap-free segments, with no penalty for |
|---|
| 654 | gaps. A plot block below the threshold is not drawn or clickable |
|---|
| 655 | in the plots, and the row for its secondary sequence is omitted |
|---|
| 656 | in the text alignment panel; additionally it is excluded from |
|---|
| 657 | the position indicator's block list and from the row of block |
|---|
| 658 | buttons for the mark. However, these plot blocks are only hidden |
|---|
| 659 | and still exist otherwise (e.g., for export). Setting the |
|---|
| 660 | threshold will not move the mark, even if the marked position |
|---|
| 661 | becomes hidden. The same threshold applies across all windows, |
|---|
| 662 | and keyboard shortcuts make it easy to adjust it up and down. |
|---|
| 663 | Also, the percent identity of the current plot block is shown in |
|---|
| 664 | the mark indicator when applicable (the current plot block is |
|---|
| 665 | either the marked one, or if a dotplot has a different secondary |
|---|
| 666 | sequence, the corresponding projection from the same MAF block). |
|---|
| 667 | <p> |
|---|
| 668 | <dt>Underlays Box: |
|---|
| 669 | <dd> |
|---|
| 670 | Allows you to set a threshold for filtering the displayed |
|---|
| 671 | underlays and highlights based on the optional score values you |
|---|
| 672 | have assigned in the annotation files. The GFF, GTF, and BED |
|---|
| 673 | formats already include a score field, and the PipMaker-style |
|---|
| 674 | underlay format has been extended to include one as well (see |
|---|
| 675 | <a href="gmaj_input.html">Input Files for Gmaj</a>). Some of |
|---|
| 676 | these formats allow floating-point score values, but they will |
|---|
| 677 | be rounded off to integers for comparison with the threshold. |
|---|
| 678 | Missing scores are treated as the maximum possible value, so |
|---|
| 679 | they will never be filtered out; however note that <code>0</code> |
|---|
| 680 | (which is sometimes used to mean "no score") will not be changed, |
|---|
| 681 | since Gmaj cannot distinguish this from a score that is really |
|---|
| 682 | zero. As with the % Identity box, the same threshold applies |
|---|
| 683 | across all windows, and keyboard shortcuts make it easy to adjust |
|---|
| 684 | it up and down. Also, pointing to a particular underlay or |
|---|
| 685 | highlight will show that annotation's score in the position |
|---|
| 686 | indicator. |
|---|
| 687 | <p> |
|---|
| 688 | <dt>Arrow Buttons: |
|---|
| 689 | <dd> |
|---|
| 690 | These buttons are located to the right of the zoom indicator. |
|---|
| 691 | Clicking on one of them will move the zoom region in the |
|---|
| 692 | indicated direction by half of its width or height. The new |
|---|
| 693 | region is added to your zoom history like any other zoom |
|---|
| 694 | selection, so the Zoom - Back command will return to where you |
|---|
| 695 | were as usual. |
|---|
| 696 | <p> |
|---|
| 697 | <dt>Block Buttons: |
|---|
| 698 | <dd> |
|---|
| 699 | When a mark is set (e.g. by clicking in a pip or dotplot), a row |
|---|
| 700 | of buttons will appear to the right of the mark indicator showing |
|---|
| 701 | the <a href="#numbering">block numbers</a> <a href="#cover" |
|---|
| 702 | >covering</a> the marked position in the pip. (If there is not |
|---|
| 703 | enough room for all of the buttons, a scrollbar will appear; |
|---|
| 704 | also the partition between this panel and the mark indicator is |
|---|
| 705 | <a href="#dividers">draggable</a>.) Clicking on one of the |
|---|
| 706 | buttons causes the mark to move to that block (in the same pip), |
|---|
| 707 | and the segment colors, text alignment, and mark indicator will |
|---|
| 708 | be updated accordingly in all applicable windows. The new marked |
|---|
| 709 | position (<a href="#red">red</a> circle) will be as close as |
|---|
| 710 | possible to the same coordinate in the reference sequence, but |
|---|
| 711 | it may have to move slightly to avoid gaps. This makes it |
|---|
| 712 | theoretically possible, though rare, that the resulting block |
|---|
| 713 | list (and therefore the row of buttons) may change. |
|---|
| 714 | <p> |
|---|
| 715 | <a name="category"></a> |
|---|
| 716 | <dt>Category Checkboxes: |
|---|
| 717 | <dd> |
|---|
| 718 | These controls are located in a separate panel below the mark |
|---|
| 719 | indicator, and allow you to show or hide several groups of |
|---|
| 720 | alignment blocks en masse. There is one checkbox for each of |
|---|
| 721 | the alignment files in the input, and an extra one for the tagged |
|---|
| 722 | blocks (whose label shows how many blocks are tagged); the colors |
|---|
| 723 | of the labels correspond to the plot segments they control. The |
|---|
| 724 | tagged blocks are considered to be withdrawn from their files |
|---|
| 725 | for this purpose, so all of the categories are disjoint. |
|---|
| 726 | These settings apply across all windows, and as with the |
|---|
| 727 | % identity threshold, hidden blocks are omitted from the plots |
|---|
| 728 | and certain lists, but still exist otherwise. |
|---|
| 729 | <!-- |
|---|
| 730 | in Gmaj's parlance they define the term <i>visible block</i>: |
|---|
| 731 | a block is "visible" if it is not hidden by these checkboxes, |
|---|
| 732 | even if it is not actually showing on the screen for some other |
|---|
| 733 | reason (e.g. not in zoom region, below % identity threshold, |
|---|
| 734 | in bottom half of pip, etc.). |
|---|
| 735 | --> |
|---|
| 736 | By default this panel only appears when it is |
|---|
| 737 | relevant (i.e. if there is more than one alignment file, or you |
|---|
| 738 | have used the tagging feature), but you can also show or hide it |
|---|
| 739 | temporarily from the Options - Show dialog. |
|---|
| 740 | <p> |
|---|
| 741 | <dt>Dotplot Buttons: |
|---|
| 742 | <dd> |
|---|
| 743 | These buttons are located to the right of each pip's sequence |
|---|
| 744 | label in the multi-pip window. Clicking on one of them will |
|---|
| 745 | open a dotplot window for that pair of reference and secondary |
|---|
| 746 | sequences. The zoom region will initially be translated from the |
|---|
| 747 | current one to show the same blocks, and will thereafter operate |
|---|
| 748 | independently. The mark, however, is shared between the |
|---|
| 749 | multi-pip window and all of its dotplots (see <a href="#state" |
|---|
| 750 | >The Zoom and the Mark</a>). If you already have a window for |
|---|
| 751 | that dotplot, it will just be brought to the front unchanged. |
|---|
| 752 | <p> |
|---|
| 753 | <a name="dividers"></a> |
|---|
| 754 | <dt>Draggable Dividers: |
|---|
| 755 | <dd> |
|---|
| 756 | Several of the panel dividers can be moved by dragging them with |
|---|
| 757 | the mouse to adjust the amount of space allocated to the items |
|---|
| 758 | on each side. These include the vertical bars separating the |
|---|
| 759 | left and right sides of the status indicator panels, and the |
|---|
| 760 | horizontal bar separating the pips from the text alignment in a |
|---|
| 761 | multi-pip window. On most platforms Java draws these dividers |
|---|
| 762 | with a pattern of little bumps to suggest a grip. In Gmaj |
|---|
| 763 | they also have a sticky feature that remembers if you moved |
|---|
| 764 | them manually and keeps them at that position (until they are |
|---|
| 765 | rebuilt due to a font change, etc.). In sticky mode the divider |
|---|
| 766 | appears pushed in, like a button; if you want to return to the |
|---|
| 767 | default floating mode (where the divider is repositioned |
|---|
| 768 | automatically as the panel content changes), just click on the |
|---|
| 769 | pushed-in divider to release it. |
|---|
| 770 | </dl> |
|---|
| 771 | <p> |
|---|
| 772 | |
|---|
| 773 | <p class=hdr> |
|---|
| 774 | <h3><a name="copy">Copying and Printing</a></h3> |
|---|
| 775 | <p> |
|---|
| 776 | Gmaj supports copy/paste via the system clipboard from most of |
|---|
| 777 | its text panels and dialog boxes, using mouse selection followed |
|---|
| 778 | by the standard keystrokes |
|---|
| 779 | (<code>Ctrl-C</code>/<code>Ctrl-V</code> on Windows and Linux, |
|---|
| 780 | <code>Cmd-C</code>/<code>Cmd-V</code> on Mac). Some labels are |
|---|
| 781 | not copyable, but their values generally are. (Exception: with |
|---|
| 782 | some versions of Java, all dialog text may be uncopyable in |
|---|
| 783 | applet mode due to a <a href="gmaj_bugs.html#dialogcopy">bug</a>.) |
|---|
| 784 | <p> |
|---|
| 785 | In Gmaj's multi-pip and dotplot windows the text alignment, panel |
|---|
| 786 | headers, and status indicators are copyable. Clicking in any of |
|---|
| 787 | these components (e.g. to sweep out a selection with the mouse) |
|---|
| 788 | will transfer the keyboard focus to that component, as indicated |
|---|
| 789 | by purple lines around it. This is necessary for the Copy |
|---|
| 790 | keystroke to work; however it means that Gmaj's other keyboard |
|---|
| 791 | shortcuts will be disabled until the focus is restored, either by |
|---|
| 792 | clicking somewhere else or by pressing the <code>Esc</code> key. |
|---|
| 793 | Note that the mouse selection in the text alignment is |
|---|
| 794 | rectangular (unlike the usual line-wrapped stream), and all of |
|---|
| 795 | these components can be scrolled if necessary by dragging the |
|---|
| 796 | mouse just outside their borders. |
|---|
| 797 | <p> |
|---|
| 798 | Gmaj does not currently have its own print capability. The |
|---|
| 799 | recommended way to record a particular Gmaj view is to use your |
|---|
| 800 | operating system's "screenshot", "print screen", or "grab" |
|---|
| 801 | facility to save an image of the window to a file, then adjust |
|---|
| 802 | it as needed using image-editing software. (Be careful with |
|---|
| 803 | rescaling and format conversions, as these may degrade the |
|---|
| 804 | image.) |
|---|
| 805 | <p> |
|---|
| 806 | To prevent the position indicator from changing when you move the |
|---|
| 807 | mouse, hold down the <code>Ctrl</code> key. This is useful both |
|---|
| 808 | for copying the position indicator's contents and for taking |
|---|
| 809 | screenshots. |
|---|
| 810 | <p> |
|---|
| 811 | |
|---|
| 812 | <!-- <hr align=left noshade size=1 width="20%" color=black> --> |
|---|
| 813 | <p class=hdr> |
|---|
| 814 | <h3><a name="notes">Footnotes</a></h3> |
|---|
| 815 | <p> |
|---|
| 816 | <a name="red"></a> |
|---|
| 817 | [1] |
|---|
| 818 | By default the circular mark and the selected block's plot |
|---|
| 819 | segments are always red (or orange), regardless of the background |
|---|
| 820 | color behind them, and similarly tagged blocks are always green. |
|---|
| 821 | A setting on the Options menu can make these colors vary with |
|---|
| 822 | the background (so they are not invisible against like-colored |
|---|
| 823 | underlays), however this causes <a href="gmaj_bugs.html#xor" |
|---|
| 824 | >patchy rendering</a> when used with Large Fonts. These special |
|---|
| 825 | blocks are drawn last, so they will not be obscured by ordinary |
|---|
| 826 | ones. |
|---|
| 827 | <p> |
|---|
| 828 | <a name="numbering"></a> |
|---|
| 829 | [2] |
|---|
| 830 | Blocks in the MAF files are numbered consecutively, starting |
|---|
| 831 | with 0. MAF files are also numbered starting with 0, in the |
|---|
| 832 | order they are listed in the parameters file. If there are |
|---|
| 833 | several MAF files, they are catenated into one big list of |
|---|
| 834 | blocks, and the block numbers for the second file continue where |
|---|
| 835 | the first left off. However, Gmaj also records the relative |
|---|
| 836 | block numbers within each file, and displays this information |
|---|
| 837 | in the mark indicator and certain error messages in the form |
|---|
| 838 | <code>maf#.block#</code>. |
|---|
| 839 | <p> |
|---|
| 840 | <a name="cover"></a> |
|---|
| 841 | [3] |
|---|
| 842 | An alignment block is considered to cover a plot position if it |
|---|
| 843 | contains rows for both of the plot's sequences and the position |
|---|
| 844 | falls within the endpoints of the <b>reference</b> sequence's |
|---|
| 845 | row (not necessarily the row for the other sequence, as this is |
|---|
| 846 | a pip-oriented computation); there are no "holes" due to gaps. |
|---|
| 847 | In order to appear in the row of block buttons for the mark or in |
|---|
| 848 | the position indicator's block list for pips, a block must also |
|---|
| 849 | be in a visible category (according to the <a href="#category" |
|---|
| 850 | >category checkboxes</a>) and meet the % identity threshold (in |
|---|
| 851 | the applicable plot). |
|---|
| 852 | <p> |
|---|
| 853 | |
|---|
| 854 | <p class=vvlarge> |
|---|
| 855 | <hr> |
|---|
| 856 | <i>Cathy Riemer, June 2008</i> |
|---|
| 857 | |
|---|
| 858 | <p class=scrollspace> |
|---|
| 859 | </body> |
|---|
| 860 | </html> |
|---|
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