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| 4 | <head> |
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| 5 | <title>What's New in Gmaj</title> |
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| 10 | <body> |
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| 11 | <p class=vvlarge> |
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| 12 | <h2>What's New in Gmaj</h2> |
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| 13 | <p class=vvlarge> |
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| 14 | <dl> |
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| 15 | <dt><b>2008-Jun-30</b><br> |
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| 16 | <dd> <ul> |
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| 17 | <li> Gmaj can display several MAF files simultaneously on the same plots, |
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| 18 | e.g. for comparing output from different alignment programs. |
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| 19 | <li> A new Tags menu allows the user to tag particular blocks for special |
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| 20 | treatment. Tagged blocks are conceptually separated from their MAFs |
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| 21 | and can be displayed, hidden, or exported as a group. |
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| 22 | <li> There are many new Export options, including MAF format and exporting |
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| 23 | only the tagged blocks. Export is now possible in applet mode, by |
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| 24 | posting the blocks to an administrator-designated URL (MAF format only). |
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| 25 | The Export dialog remembers previous selections if you use it repeatedly. |
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| 26 | <li> The parameters file has a new option <code>skipotherseq</code>, which |
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| 27 | causes MAF sequences that aren't mentioned to be ignored (handy for |
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| 28 | reducing the number of pips and saving memory). |
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| 29 | <li> Aliases can be given for each <code>seqname</code> in the parameters |
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| 30 | file, e.g. if two MAF files use different names for the same sequence. |
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| 31 | <li> A new menu item Help - Sequence Summary reports the aligning extents |
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| 32 | for all sequences (useful when fetching/trimming annotation files). |
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| 33 | <li> The long-standing <i>Scrollbar obscures block buttons</i> bug has been |
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| 34 | fixed, with additional usability enhancements such as remembering |
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| 35 | manual divider placement (click divider to release). |
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| 36 | <li> Minor fixes and improvements: |
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| 37 | <ul> |
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| 38 | <li> The <code>reconseq</code> field in the parameters file has been |
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| 39 | renamed to <code>reconorg</code> (because it specifies an organism |
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| 40 | rather than a single sequence); the old <code>reconseq</code> |
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| 41 | keyword is deprecated but still supported for the time being. |
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| 42 | The <code>seqfile</code> keyword from pre-MAF days is no longer |
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| 43 | supported. |
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| 44 | <li> Tiny mouse drags in plots are assumed to be accidental and treated |
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| 45 | as clicks, to avoid the annoying message "Zoom region can't be |
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| 46 | smaller than ... pixels". |
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| 47 | <li> Options - Mark Always Red is now the default, due to the |
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| 48 | <a href="gmaj_bugs.html#xor">rendering issue with XOR</a>. |
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| 49 | <li> The text alignment omits rows below the % identity threshold. |
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| 50 | <li> The row of block buttons and the position indicator's block list |
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| 51 | only include blocks that are in visible categories (according to |
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| 52 | the new MAF/Tagged checkboxes) and meet the % identity threshold. |
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| 53 | <li> When self-alignments include the trivial block, it is typically |
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| 54 | very slow to load and manipulate in the text panel due to its |
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| 55 | huge size. Gmaj requests confirmation before moving the mark to |
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| 56 | any block that covers the entire aligning extent of the reference |
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| 57 | sequence, but then remembers if you say OK and only shows the |
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| 58 | busy cursor thereafter. |
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| 59 | <li> The bundle file can contain pre-compressed files. |
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| 60 | <li> Several minor bug fixes and performance enhancements. |
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| 61 | <!-- |
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| 62 | <li> Bugfix: some settings and state values were inappropriately shared |
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| 63 | among applet invocations. |
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| 64 | <li> Bugfix: opening an applet for a pairwise dataset no longer distorts |
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| 65 | the initial multipip size for other applets. |
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| 66 | <li> Bugfix: the text view must not be scrolled if it's not displayed. |
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| 67 | <li> Bugfix: race condition when painting "Please wait" dialog is reduced. |
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| 68 | --> |
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| 69 | <li> Improved error checking and messages. |
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| 70 | <li> Tweaks in wording, punctuation, spacing, dialog title, etc. |
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| 71 | </ul> |
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| 72 | </ul> |
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| 73 | <p> |
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| 74 | <dt><b>2008-Jan-08</b><br> |
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| 75 | <dd> <ul> |
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| 76 | <li> Special treatment for pairwise alignments: |
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| 77 | <ul> |
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| 78 | <li> The dotplot is displayed immediately. |
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| 79 | <li> Self-alignments are allowed to use the same name for both sequences. |
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| 80 | </ul> |
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| 81 | <li> Filtering for underlays and highlights, based on score: |
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| 82 | <ul> |
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| 83 | <li> Scores are obtained from the annotation files. |
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| 84 | <li> A new text box widget (with keyboard shortcuts) allows you to set the |
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| 85 | display threshold. |
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| 86 | <li> Pointing at an underlay/highlight displays its score on the location |
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| 87 | status line. |
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| 88 | </ul> |
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| 89 | <li> The text alignment, headers, and status lines are now selectable for copying, |
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| 90 | and for the text alignment the selection is rectangular. |
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| 91 | <li> On a Mac, Gmaj uses standard key bindings (<code>Cmd-C</code>, |
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| 92 | <code>Cmd-V</code>, etc.). |
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| 93 | <li> Holding down the <code>Ctrl</code> key (on any platform) prevents the |
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| 94 | position indicator from changing; this is useful for copying it and for |
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| 95 | screenshots. |
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| 96 | <li> Bugfixes: |
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| 97 | <ul> |
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| 98 | <li> Empty fields in annotation files were not accepted due to improper |
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| 99 | handling. |
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| 100 | <li> When loading a new dataset with File - Open, the old windows were not |
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| 101 | closed properly. |
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| 102 | <li> Descenders of pip header characters were clipped off. |
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| 103 | </ul> |
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| 104 | <li> Minor adjustments to behavior, appearance, and messages, including: |
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| 105 | <ul> |
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| 106 | <li> Sequence names in the MAF cannot end with <code>~</code> (which is used |
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| 107 | internally for self-alignments). |
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| 108 | <li> The first click in an inactive window just activates it. |
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| 109 | </ul> |
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| 110 | <li> Updated and enhanced documentation. |
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| 111 | </ul> |
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| 112 | <p> |
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| 113 | <dt><b>2007-Jul-26</b><br> |
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| 114 | <dd> <ul> |
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| 115 | <li> Gmaj can now display dotplots in addition to the main multi-pip views, |
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| 116 | with color underlays for both sequences. |
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| 117 | <ul> |
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| 118 | <li> Dotplots are opened by clicking on buttons in the pip headers. |
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| 119 | <li> Each dotplot opens in a separate window, similar to the multi-pip |
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| 120 | view except it has pip, dotplot, and text panels for two sequences |
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| 121 | only. |
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| 122 | <li> Dotplot windows share the same reference sequence and mark with |
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| 123 | their parent multi-pip window but have independent zoom, and close |
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| 124 | automatically when the parent does. |
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| 125 | <li> There is only one mark for each reference sequence, so the circle |
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| 126 | will not appear in dotplots having a different secondary sequence |
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| 127 | than the mark. |
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| 128 | </ul> |
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| 129 | <li> Gmaj can now read annotation data in |
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| 130 | <a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml" |
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| 131 | >GFF</a> (v1 & v2), |
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| 132 | <a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF" |
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| 133 | >GTF</a>, and |
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| 134 | <a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED" |
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| 135 | >BED</a> formats in addition to its previous PipMaker-style formats. |
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| 136 | <ul> |
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| 137 | <li> UCSC |
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| 138 | <a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks" |
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| 139 | >custom track</a> headers are supported, with multiple tracks and |
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| 140 | sequence names allowed in a single file. |
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| 141 | <li> There is currently no way to use just one particular track from a |
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| 142 | file, but lines in |
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| 143 | <a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html" |
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| 144 | >WIG</a> or other unrecognized formats are skipped. |
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| 145 | <li> Files in these generic formats can be reused in multiple panels |
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| 146 | (e.g. as both exons and underlays). |
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| 147 | <li> A new <code>tabext</code> field and file specification modifiers |
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| 148 | (seqname alias and type hint) in the parameters file facilitate |
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| 149 | interpretation of these formats. |
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| 150 | <li> Colors can be specified using UCSC-style RGB triplets (either |
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| 151 | per-line or per-track), or Gmaj provides defaults. |
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| 152 | <li> Currently there is no special support for multiple transcripts; |
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| 153 | when inferring UTRs, the largest bounding range of given CDS data |
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| 154 | is used. |
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| 155 | </ul> |
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| 156 | <li> A new control in the menu bar allows the user to limit the displayed |
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| 157 | alignments by their average % identity. |
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| 158 | <ul> |
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| 159 | <li> Keyboard shortcuts make it easy to move the threshold up and down. |
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| 160 | <li> The value for the current plot block is displayed with the mark |
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| 161 | information when applicable. |
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| 162 | </ul> |
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| 163 | <li> If the alignment file contains per-nucleotide reconstruction scores |
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| 164 | for an inferred ancestral sequence, they can be displayed as a pair of |
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| 165 | bar graphs, binned according to the current zoom region and panel size. |
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| 166 | <ul> |
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| 167 | <li> The scores are transformed via simple linear scaling, and should |
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| 168 | not be interpreted as probabilities. |
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| 169 | <li> A new <code>reconseq</code> field in the parameters file |
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| 170 | identifies the organism for the scores. |
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| 171 | </ul> |
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| 172 | <li> Miscellaneous: |
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| 173 | <ul> |
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| 174 | <li> "Unsupported MAF version" is now a warning instead of a fatal |
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| 175 | error. |
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| 176 | <li> A new <code>nowarn</code> field in the parameters file suppresses |
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| 177 | certain warnings/errors using a keyword shown in the message. |
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| 178 | <li> When opening a new window, the current zoom is translated to a |
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| 179 | roughly equivalent one in the new sequence(s). |
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| 180 | <li> Sequence choices in the Show dialog affect text rows and dotplots |
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| 181 | in addition to pips. |
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| 182 | <li> The default highlights built from exons now include the genes |
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| 183 | (light yellow). |
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| 184 | <li> The divider between the position indicator and the zoom indicator |
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| 185 | is draggable. |
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| 186 | <li> Plot segments are drawn thicker in Large Fonts mode. |
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| 187 | <li> Plots that are completely empty have a gray background. |
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| 188 | <li> The Set Zoom dialog accepts a blank box to mean "leave unchanged". |
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| 189 | <li> Tabbing is easier in input dialogs: labels are skipped unless the |
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| 190 | mouse is pointing at them. |
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| 191 | <li> Note that "<code>=</code>" is now required for settings in the |
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| 192 | parameters file (except <code>seq N:</code> lines), and |
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| 193 | lines with empty values (e.g. unused template items) are allowed |
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| 194 | and skipped. |
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| 195 | </ul> |
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| 196 | <!-- |
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| 197 | <li> Bug fixes: |
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| 198 | <ul> |
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| 199 | <li> Linkbar URLs are supposed to be optional; missing ones are now |
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| 200 | handled gracefully. |
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| 201 | <li> Entries in the parameters file for particular-pip underlays were |
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| 202 | not recognized properly if the underlay file was bundled. |
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| 203 | <li> Attempting to display a reference sequence that had no alignments |
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| 204 | would cause a Java error. |
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| 205 | <li> On some platforms, rebuilding all of the Gmaj windows (e.g. when |
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| 206 | Options settings were changed) would leave the keyboard focus in |
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| 207 | the wrong window. |
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| 208 | </ul> |
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| 209 | --> |
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| 210 | <li> Various minor bug fixes, and improvements in appearance, behavior, |
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| 211 | messages, efficiency, and robustness. |
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| 212 | <li> Updated documentation. |
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| 213 | <ul> |
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| 214 | <li> Terminology: the optional colored clickable bars located above |
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| 215 | the exons panel were formerly called "annotations", "annotation |
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| 216 | links", or "hyperlink annotations", but are now referred to as |
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| 217 | "linkbars" so that "annotation" can be used in the general sense. |
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| 218 | </ul> |
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| 219 | </ul> |
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| 220 | <p> |
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| 221 | <dt><b>2006-Jun-17</b><br> |
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| 222 | <dd> <ul> |
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| 223 | <li> Gmaj can now be deployed as a web-based applet, as an alternative to |
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| 224 | the regular stand-alone mode. |
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| 225 | <a href="http://globin.bx.psu.edu/java/gmaj/demo.html">Demo</a> |
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| 226 | <ul> |
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| 227 | <li> New parameters <code>bundle</code>, <code>initzoom</code>, and |
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| 228 | <code>urlpause</code> facilitate applet use, but also work in |
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| 229 | stand-alone mode. |
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| 230 | <li> Clicking on hyperlinked annotations (colored bars) visits the |
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| 231 | referenced site (or in stand-alone mode, displays the url). |
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| 232 | <li> A new "Help - Manual" menu item visits a help page (or in |
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| 233 | stand-alone mode, displays the file location). |
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| 234 | <li> The "File - Export" feature does not work yet for applets. |
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| 235 | </ul> |
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| 236 | <li> Better conformance with the official UCSC specs for MAF format. |
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| 237 | <li> A new <code>refseq</code> field in the parameters file can be used |
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| 238 | to prevent selection of an inappropriate reference sequence when the |
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| 239 | alignments are not sequence-symmetric (e.g. from <i>multiz</i>). |
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| 240 | <li> Maximum zoom bounds are now the stated sequence length from the MAF |
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| 241 | file (not just the extent of the blocks), but the default initial |
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| 242 | view zooms to the aligned portion. |
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| 243 | <li> Search rules for relative filenames have been simplified, and Windows |
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| 244 | names starting with "<code>\</code>" are now handled better. |
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| 245 | <li> The panel for hyperlinked annotations is now labeled, and it displays |
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| 246 | the bars listed earliest in the file toward the top. |
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| 247 | <li> Colors for underlays and other annotations have been adjusted slightly. |
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| 248 | <li> The "Help - About" message now shows your current Java version and |
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| 249 | vendor. |
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| 250 | <li> Improved error reporting. |
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| 251 | <li> Message dialogs have better line wrapping, and their contents can |
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| 252 | be copied to the system clipboard (except in applets, due to a bug |
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| 253 | in Java). |
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| 254 | <li> Several minor bug fixes, tweaks, and internal improvements. |
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| 255 | <li> Documentation has been reorganized. |
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| 256 | </ul> |
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| 257 | <p> |
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| 258 | <dt><b>2006-Feb-08</b><br> |
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| 259 | <dd> <ul> |
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| 260 | <li> New arrow buttons slide the zoom region left or right by half a |
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| 261 | screenful. |
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| 262 | <li> The schematic diagrams for exons and repeats are now displayed in |
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| 263 | separate, labeled panels. |
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| 264 | <li> A new Show dialog on the Options menu allows individual panels |
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| 265 | to be displayed or hidden. |
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| 266 | <li> Users who have a one-button mouse can get crosshairs by using the |
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| 267 | <code>Shift</code> key. |
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| 268 | <li> Minor aesthetic tweaks. |
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| 269 | </ul> |
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| 270 | <p> |
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| 271 | <dt><b>2005-Nov-20</b><br> |
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| 272 | <dd> <ul> |
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| 273 | <li> New export feature: Gmaj can now save the selected block (or all |
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| 274 | blocks in the current zoom region) to files in FastA sequence format |
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| 275 | for further processing by other programs. Options include clipping |
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| 276 | the sequences to the current zoom region, and restoring those that |
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| 277 | align in reverse complement to their original orientation. |
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| 278 | <li> The zoom resolution limit has been reduced to 4 bp (or pixels), |
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| 279 | instead of 10. |
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| 280 | <li> When setting the zoom by dragging out a rectangle, Gmaj will display |
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| 281 | an error message if the rectangle is too small (instead of beeping). |
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| 282 | </ul> |
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| 283 | <p> |
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| 284 | <dt><b>2005-Sep-30</b><br> |
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| 285 | <dd> <ul> |
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| 286 | <li> Improved handling of <code>X</code>, <code>N</code>, and |
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| 287 | unrecognized characters: |
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| 288 | <ul> |
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| 289 | <li> Bug fix: the percent identity computation now ignores these |
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| 290 | characters (in both numerator and denominator). |
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| 291 | <li> Bug fix: the text panel never shows dots for these characters. |
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| 292 | <li> One warning is issued for each unrecognized character. |
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| 293 | </ul> |
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| 294 | <li> New zoom features: |
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| 295 | <ul> |
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| 296 | <li> Gmaj keeps track of your zoom history for each window, so you can |
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| 297 | move back and forward through your previous zoom regions. A fresh |
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| 298 | selection discards the history from the current point forward, |
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| 299 | similar to a web browser. |
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| 300 | <li> The Unzoom facility does not go back, it just puts the maximum |
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| 301 | range into the history as a fresh selection. |
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| 302 | <li> A new indicator box below the menu bar shows the current zoom |
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| 303 | endpoints. |
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| 304 | <li> A Set Zoom dialog allows you to enter zoom endpoints explicitly. |
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| 305 | <li> When setting the zoom by dragging out a rectangle, a rectangle that |
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| 306 | is too small will no longer be treated as a click; instead Gmaj |
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| 307 | will beep (if possible). |
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| 308 | </ul> |
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| 309 | <li> Improved display of pip and text panels: |
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| 310 | <ul> |
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| 311 | <li> The divider between the pips and the text panel is now moveable, so |
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| 312 | you can drag it to adjust the relative space they occupy. |
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| 313 | <li> The text panel starts with an initial message to explain why it is |
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| 314 | empty. |
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| 315 | <li> After loading a file with many sequences, the pips will be scrolled |
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| 316 | to start at the top. |
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| 317 | <li> If the current mark can be transferred when selecting a new |
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| 318 | reference sequence, the pip panel will scroll to it (though the red |
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| 319 | circle may not be visible if the percent identity at that point is |
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| 320 | below 50%). |
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| 321 | <li> Vertical blue bars at the edges of the pips represent the |
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| 322 | boundaries of the current zoom region. |
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| 323 | </ul> |
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| 324 | <li> Improved display of block buttons: |
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| 325 | <ul> |
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| 326 | <li> If there are too many block buttons to fit in their panel, a |
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| 327 | scrollbar will appear so all of them can be accessed. |
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| 328 | <li> The divider between the mark indicator and the block buttons is now |
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| 329 | moveable, so you can drag it to adjust the relative space they |
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| 330 | occupy (this will reset when a new block is selected, since the |
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| 331 | number of block buttons will likely be different). |
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| 332 | </ul> |
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| 333 | <li> Miscellaneous: |
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| 334 | <ul> |
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| 335 | <li> The menus have been rearranged slightly, and Settings has been |
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| 336 | renamed to Options. |
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| 337 | <li> The keyboard shortcut for "Next Block" has been changed to |
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| 338 | "<code>n</code>", so "<code>b</code>" can invoke "Zoom - Back". |
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| 339 | <li> The cascade of RefSequence window positions wraps around the screen |
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| 340 | (in both width and height) so they are never placed completely |
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| 341 | offscreen. |
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| 342 | <li> When opening a new RefSequence window, Gmaj will use the size of |
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| 343 | the current window in case you have changed it. |
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| 344 | <li> Window sizing no longer requires Java 1.4 (accidentally introduced |
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| 345 | in the 2005-May-16 release). |
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| 346 | <li> Bug fix: radio buttons for mark color now take effect immediately |
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| 347 | in all windows. |
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| 348 | <li> Improved behavior of dialog boxes: pressing Enter invokes "Ok", |
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| 349 | Escape invokes "Cancel", and the cursor begins in the first text |
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| 350 | box. |
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| 351 | </ul> |
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| 352 | </ul> |
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| 353 | <p> |
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| 354 | <dt><b>2005-Sep-13</b><br> |
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| 355 | <dd> <ul> |
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| 356 | <li> <i>IMPORTANT BUG FIX:</i> Percent identities for the pip plots |
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| 357 | were being computed in a case-sensitive fashion, which lowered the |
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| 358 | scores when comparing soft-masked vs. unmasked sequences. (This bug |
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| 359 | did not affect the text view, just the pips. Nor did it affect |
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| 360 | <a href="http://globin.bx.psu.edu/dist/laj/">Laj</a>, which uses |
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| 361 | pre-computed percent identity scores from the <code>lav</code> file.) |
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| 362 | Note that hard masking and ambiguous nucleotides (<code>X</code>, |
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| 363 | <code>N</code>, <code>W</code>, <code>R</code>, etc.) are still treated |
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| 364 | literally. |
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| 365 | </ul> |
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| 366 | <p> |
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| 367 | <dt><b>2005-Aug-26</b><br> |
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| 368 | <dd> <ul> |
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| 369 | <li> Improved support for working with overlapping blocks (e.g. those due to |
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| 370 | genomic duplications): |
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| 371 | <ul> |
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| 372 | <li> A list of block numbers in the position indicator line shows the |
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| 373 | blocks covering the mouse pointer's location. |
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| 374 | <li> A row of buttons next to the mark indicator line shows the blocks |
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| 375 | covering the marked location, and allows convenient selection of |
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| 376 | a different block at the same position. |
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| 377 | <li> The pip segments for the currently selected block are painted last, |
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| 378 | so the red segments are not hidden by other blocks. |
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| 379 | </ul> |
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| 380 | <li> It is no longer required to list every sequence in the parameters file. |
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| 381 | Any sequences that appear in the alignment but are not mentioned in the |
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| 382 | parameters file will be displayed in the order they are encountered |
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| 383 | (filling in around any sequence numbers explicitly assigned in the |
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| 384 | parameters file). |
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| 385 | <li> A new parameter <code>underlays</code> (plain, without a number) can be |
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| 386 | used to specify a default underlay file for each reference sequence, so |
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| 387 | it is no longer necessary to list underlays for each pip separately when |
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| 388 | they are the same. The old <code>underlays.N</code> parameters are |
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| 389 | still supported as well, and override these new ones. |
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| 390 | <li> The <code>seqfile</code> parameter has been renamed to |
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| 391 | <code>seqname</code>, in order to reflect MAF semantics (but |
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| 392 | <code>seqfile</code> is still supported for backward compatibility). |
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| 393 | <li> Sequence label widths are now computed dynamically, based on the longest |
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| 394 | name and the current font. |
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| 395 | <li> When the font size is changed, pip heights are also adjusted. |
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| 396 | <li> A new option on the Settings menu makes the mark circle and selected |
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| 397 | block's pip segments always red, instead of changing with the background. |
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| 398 | <li> A new color <code>Clear</code> is provided, which is colorless and |
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| 399 | transparent. It is intended for gene introns, so the same file can be |
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| 400 | used for pip underlays (white background) and text highlights (gray |
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| 401 | background). |
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| 402 | <li> New colors <code>Brown</code> and <code>LightBrown</code> have also been |
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| 403 | added, and <code>LightRed</code> and <code>Green</code> were tweaked. |
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| 404 | <li> When a gap in the text view is clicked, the nearest gap-free position |
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| 405 | is selected (up or down, instead of always down). |
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| 406 | <li> Work-arounds for a few display problems in JRE 1.5 have been added. |
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| 407 | <li> The RefSeq menu has been renamed to "RefSequence" in order to avoid |
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| 408 | confusion with the NCBI database. |
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| 409 | <li> The jar manifest and About information have been updated. |
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| 410 | <li> Support for alignment files in <code>.bb</code> format (from the old |
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| 411 | <i>blockbuilder</i> program) has been discontinued. The only alignment |
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| 412 | format currently supported is MAF. |
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| 413 | <li> Due to a new mechanism for registering keyboard shortcuts, Gmaj now |
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| 414 | requires <b>Java 1.3 or higher</b>. |
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| 415 | <li> This version should still be considered <b>beta quality</b>; please |
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| 416 | report any bugs to |
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| 417 | <img align=top alt="image of email address" src="cathy.gmaj.png">. |
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| 418 | </ul> |
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| 419 | <p> |
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| 420 | <dt><b>2005-May-16</b><br> |
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| 421 | <dd> <ul> |
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| 422 | <li> Gmaj can now handle a wider variety of MAF files, including those |
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| 423 | containing reverse-complement alignments. |
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| 424 | <li> The "proper threading" requirement has been eliminated. |
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| 425 | <li> Dynamic memory management for plot and underlay data allows larger files |
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| 426 | to be viewed. |
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| 427 | <li> The pip section is now scrollable when there are many sequences. |
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| 428 | <li> Rows in the text alignment are sorted to match the order of pips. |
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| 429 | <li> This release should be considered <b>beta quality</b>. In particular, |
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| 430 | the numbering for reverse-complement alignments has not been thoroughly |
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| 431 | tested. |
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| 432 | </ul> |
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| 433 | <p> |
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| 434 | <dt><b>2004-Mar-12</b><br> |
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| 435 | <dd> <ul> |
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| 436 | <li> A new Settings menu allows the user to choose between two sizes of fonts |
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| 437 | and associated settings. |
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| 438 | <li> Initial window positions are cascaded according to reference sequence. |
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| 439 | <li> The usage message has been adjusted to show the full command syntax, |
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| 440 | instead of our local wrapper script shortcut. |
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| 441 | <li> Empty alignment files are handled more gracefully. |
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| 442 | <li> Minor aesthetic tweaks. |
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| 443 | </ul> |
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| 444 | <p> |
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| 445 | <dt><b>2004-Jan-14</b><br> |
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| 446 | <dd> <ul> |
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| 447 | <li> Gmaj normally expects that the alignment data will be properly |
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| 448 | <i>chained</i>, i.e., that for each sequence it is possible to order |
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| 449 | the blocks so that every nucleotide from that sequence in the interval |
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| 450 | <code>[1,length]</code> appears exactly once, and in the same order as |
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| 451 | the original sequence. (Note that MAF files are 0-based, so |
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| 452 | <code>+1</code> is added to all MAF coordinates to convert them to |
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| 453 | Gmaj's 1-based system.) |
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| 454 | However, sometimes you may want to use Gmaj to display a subset of such |
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| 455 | data (e.g., output from the <i>slice_maf</i> program). Gmaj can now |
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| 456 | handle input data where the chain starts after position <code>1</code> |
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| 457 | and/or ends before position <code>length</code>, as long as it is still |
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| 458 | contiguous. In this case Gmaj will issue a warning message, but will |
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| 459 | proceed to use the actual interval it found in your file for threading |
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| 460 | the blocks, instead of the usual <code>[1,length]</code>. |
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| 461 | </ul> |
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| 462 | <p> |
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| 463 | <dt><b>2003-Sep-16</b><br> |
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| 464 | <dd> <ul> |
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| 465 | <li> Gmaj can now handle alignment files in the MAF format produced by |
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| 466 | the <i>TBA</i> program, in addition to the <code>.bb</code> format |
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| 467 | produced by <i>blockbuilder</i>. |
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| 468 | <li> When using a MAF alignment, the semantics of the parameters file |
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| 469 | are a bit different, and its rules are stricter. (See |
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| 470 | <code><a href="sample.gmaj">sample.gmaj</a></code> for details.) |
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| 471 | <li> Gmaj still doesn't support reverse complement alignments, or multiple |
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| 472 | contigs per sequence. |
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| 473 | </ul> |
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| 474 | <p> |
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| 475 | <dt><b>2003-Jul-14</b><br> |
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| 476 | <dd> <ul> |
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| 477 | <li> The "phantom repeats" phenomenon that was occurring with Java 1.4.x |
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| 478 | has been greatly reduced, but not completely eliminated. It appears |
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| 479 | to be due to a clipping problem involving integer overflow, so that |
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| 480 | items which should be off-screen are drawn anyway. This (or a related |
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| 481 | bug) may also manifest as the disappearance of items for certain zoom |
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| 482 | windows. These problems can also occur with items other than repeats, |
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| 483 | such as underlays and even pip segments, though this is less common. |
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| 484 | Manual clipping seems to solve the problem, and this release of Gmaj |
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| 485 | should always display pip segments, underlays, and annotation bars |
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| 486 | correctly. Items in the "features" panel (exons, repeats, CpG islands, |
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| 487 | etc.) are more difficult to clip manually, but a first approximation |
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| 488 | has helped quite a bit. It is still possible to experience these |
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| 489 | problems if you zoom in very closely on a long feature. |
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| 490 | <p> |
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| 491 | <li> If underlay labels are not provided but "kinds" (color meanings) are, |
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| 492 | then Gmaj will use the kind as a default label, but only for the |
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| 493 | underlay bands that are on top (i.e., not obscured by another band). |
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| 494 | </ul> |
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| 495 | <p> |
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| 496 | <dt><b>2003-Apr-10</b><br> |
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| 497 | <dd> <ul> |
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| 498 | <li> Fixed keyboard shortcuts, and failure to exit upon closing last |
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| 499 | window. |
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| 500 | <li> New Help - Keys menu item lists keyboard shortcuts. |
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| 501 | <li> Tweak appearance of the Unzoom button. |
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| 502 | <li> Minor clarifications in documentation. |
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| 503 | </ul> |
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| 504 | <p> |
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| 505 | <dt><b>2003-Apr-07</b><br> |
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| 506 | <dd> <ul> |
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| 507 | <li> Fixed several bugs in the text panel, including scrolling |
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| 508 | behavior and cursor display. |
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| 509 | <li> Added a comment in the <code>sample.gmaj</code> file regarding |
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| 510 | the <code>#:gmaj</code> tag. |
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| 511 | </ul> |
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| 512 | <p> |
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| 513 | <dt><b>2003-Mar-31</b><br> |
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| 514 | <dd> <ul> |
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| 515 | <li> Preliminary beta-quality release. Still has a few display |
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| 516 | and behavior anomalies, and possibly other minor bugs. |
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| 517 | </ul> |
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| 518 | </dl> |
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| 519 | <p> |
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| 520 | |
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| 521 | <p class=vvlarge> |
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| 522 | <hr> |
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| 523 | <i>Cathy Riemer, June 2008</i> |
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| 524 | </body> |
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| 525 | </html> |
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