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Update GMAJ to latest version. Also have help link to the local

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copy of the supplied help documents.
This commit is contained in:
Daniel Blankenberg
2007-07-30 19:22:24 +00:00
parent 584999c5f0
commit 07a7dd60af
10 changed files with 1010 additions and 365 deletions
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static/gmaj/docs/gmaj.css
+4 -2
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@@ -1,17 +1,19 @@
body { color: black; background-color: white; background-repeat: no-repeat }
/* pre { font-family: monospace; } */ /* recommended at http://www.w3.org/MarkUp/Guide/Style, */
/* but confuses Mozilla */
body { color: black; background-color: white; background-repeat: no-repeat }
p.vvlarge { margin-top: 6ex; margin-bottom: 0 }
p.vlarge { margin-top: 4ex; margin-bottom: 0 }
p.large { margin-top: 3ex; margin-bottom: 0 }
p { margin-top: 2ex; margin-bottom: 0 }
p.small { margin-top: 1ex; margin-bottom: 0 }
p.tiny { margin-top: 0.5ex; margin-bottom: 0 }
p.hdr { margin-top: 3ex; margin-bottom: 0 }
p.subhdr { margin-top: 2.5ex; margin-bottom: 0 }
p.right { text-align: right; margin-right: 1ex }
p.scrollspace { margin-top: 100em; margin-bottom: 0 }
/* tbody { text-align: left; vertical-align: baseline } */
ul.lessindent { padding-left: 4ex }
img.lower { vertical-align: -4ex }
img.lower { vertical-align: -3ex }
code { padding-left: 0.5ex; padding-right: 0.5ex }
.baseline { vertical-align: baseline }
.notop { margin-top: 0 }
static/gmaj/docs/gmaj_bugs.html
+29 -2
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@@ -13,7 +13,8 @@
<p class=vvlarge>
The following anomalies in Gmaj's display and behavior have been
observed, but not yet resolved. Some of these are intermittent,
and some may depend on your platform and/or version of Java.
and some may depend on your computer platform and/or version of
Java.
<p>
If you experience any of these (or similar) problems, it may help
to switch to a different version of Java. For example, the first
@@ -60,6 +61,32 @@ around the problem in future releases of Gmaj.
pasting elsewhere. This is apparently due to a bug in Java;
hopefully Sun will fix it eventually.
<p>
<li> <i>Patchy rendering of mark circle and/or red segments.</i>&nbsp;
When using the Large Fonts option with Mark Color Varies,
the red circle and plot segments may not appear as solid
as they should. This is because Mark Color Varies is
implemented using Java's XOR drawing mode, and the thick
lines are built up from several thin ones, so whenever two
red pixels overlap they turn white again. Fixing this will
likely involve a custom implementation of Mark Color Varies
that doesn't use XOR. In the meantime, switching to Mark
Always Red when using Large Fonts should solve the problem
(except that it will be invisible against red underlays).
<p>
<!-- [fixed]
<li> <i>GUI rebuild breaks keyboard shortcuts.</i>&nbsp;
The items on the Options menu generally require all of the
open windows to be rebuilt, and although the window that was
active may still be in front, on some systems it might not
actually have the keyboard focus. So when you press a key,
say "<code>b</code>" for "Zoom - Back", one of the other
windows changes instead of the one you wanted. Even the
Escape key doesn't help, because it goes to the wrong
window too. Investigation of how best to prevent this is
underway; in the meantime you can fix it by clicking on a
different window and then returning to the one you want.
<p>
-->
<!--
<li> <i>Name.</i>&nbsp;
Description.
@@ -82,6 +109,6 @@ Thank you for using Gmaj, and helping us to make it better.
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
</body>
</html>
static/gmaj/docs/gmaj_help.html
+310 -154
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@@ -17,13 +17,16 @@ TABLE OF CONTENTS
<li><a href="#intro">Introduction</a>
<li><a href="#start">Starting Gmaj</a>
<li><a href="#memory">Memory Allocation</a>
<li><a href="#screen">Screen Layout</a>
<li><a href="#windows">Multi-Pip and Dotplot Windows</a>
<li><a href="#state">The Zoom and the Mark</a>
<li><a href="#layout">Window Layout</a>
<li><a href="#mouse">Mouse Controls</a>
<li><a href="#menu">Menus and Buttons</a>
<li><a href="#menu">Menus and Widgets</a>
<li><a href="#notes">Footnotes</a>
</ul>
<p class=vlarge>
<p class=hdr>
<h3><a name="intro">Introduction</a></h3>
<p>
Gmaj can be run in two different modes: as an applet over the
@@ -33,6 +36,7 @@ computer). These modes are mostly similar but have a few minor
differences, as noted below.
<p>
<p class=hdr>
<h3><a name="start">Starting Gmaj</a></h3>
<p>
If you are using Gmaj in applet mode, it will be started for you
@@ -44,14 +48,15 @@ skip the rest of this section.
If you are using Gmaj in stand-alone mode, you need to start it
yourself. The Java runtime environment does not have its own
GUI, so you generally need to run Gmaj from a command line (e.g.,
in the MS-DOS Prompt window on Windows 98). The basic command to
type in looks like this:
in the Command Prompt window on Windows XP). The basic command
to type in looks like this:
<pre>
[path1]java -jar [path2]gmaj.jar
</pre>
where <code>[path1]</code> is the location of your
<code>java</code> program file (perhaps <code>c:\windows\</code>
on Win98, or <code>/usr/bin/java/</code> on a Unix system), and
<code>java</code> program file (perhaps
<code>c:\windows\system32\</code> on WinXP, or
<code>/usr/bin/java/</code> on a Unix system), and
<code>[path2]</code> is the location where the
<code>gmaj.jar</code> file was installed. Note that you can
leave off <code>[path1]</code> if you have set up your system
@@ -70,7 +75,7 @@ a window will appear displaying the loaded data.
<p>
As an alternative to using the dialog box, you can specify the
input file (plus additional parameters) on the command line.
As of this writing, the full command syntax is:
As of this writing, the command syntax is:
<pre>
[path1]java -jar [path2]gmaj.jar
[-version] [-help] [-debug] [-urlpause &lt;millisec&gt;]
@@ -78,7 +83,7 @@ As of this writing, the full command syntax is:
[-bundle &lt;zipfile&gt;] [&lt;paramfile&gt;|&lt;alignfile&gt;]
</pre>
<p>
This has been wrapped for easier readability, but should be
This has been wrapped here for easier readability, but should be
typed all on one line. Arguments shown in square brackets
<code>[]</code> are optional, while a vertical bar <code>|</code>
indicates a choice between alternatives. Angle brackets
@@ -95,7 +100,7 @@ These parameters do the following:
<dd> Prints a brief help message with up-to-date syntax; then
exits.
<dt> <code>-debug</code>:
<dd> Instructs Gmaj to print a few extra warning messages in
<dd> Instructs Gmaj to print extra warning messages in
your terminal window if certain problems occur. Normally
you won't need this, as it is mainly for development
purposes.
@@ -131,12 +136,12 @@ These parameters do the following:
<dd> If you don't want to use any annotations or other
data-related options, you can simply specify the alignment
file directly, instead of creating a parameters file. This
must be in <code>.maf</code> format; see
<a href="gmaj_input.html">Input Files for Gmaj</a> for more
details.
must be in MAF format; see <a href="gmaj_input.html"
>Input Files for Gmaj</a> for more details.
</dl>
<p>
<p class=hdr>
<h3><a name="memory">Memory Allocation</a></h3>
<p>
If the dataset you want to view is large, you may need to give
@@ -155,17 +160,90 @@ will affect all applets you run via the Java Plug-in, not just
Gmaj).
<p>
<h3><a name="screen">Screen Layout</a></h3>
<p class=hdr>
<h3><a name="windows">Multi-Pip and Dotplot Windows</a></h3>
<p>
The Gmaj window is divided into several sections. Across the
top you will see a menu bar, and below that two lines containing
indicator boxes with information about the position of the mouse
pointer, the endpoints of the currently displayed zoom region,
and the location of the "mark" (<a href="#red">red</a> circle),
along with buttons for sliding the zoom region and selecting
alternative blocks at the marked position. (The menus and
buttons will be discussed individually in the <a href="#menu"
>Menus and Buttons</a> section of this document.)
Gmaj has two kinds of windows. The main one displays a number
of pips (percent identity plots) showing the pairwise alignments,
projected from the multiple alignment, of the reference sequence
against each of the other sequences. A pip is similar to a
dotplot, with the horizontal <code>x</code>-axis representing
positions in the reference sequence, but the vertical
<code>y</code>-axis represents the percentage of matching
nucleotides in each gap-free segment of the pairwise alignment,
instead of its position in the second sequence. The window you
see first when Gmaj opens is of this type, and if the alignment
is reference-independent, you can open more of these with other
sequences as the reference.
<p>
The second type of window focuses exclusively on a particular
pair of sequences, and displays one pip together with its
corresponding dotplot representation (similar to Gmaj's
predecessor, <a href="http://globin.bx.psu.edu/dist/laj/"
>Laj</a>). These windows are opened upon request, by clicking
on a button in the header for a particular pip in the multi-pip
window. Conceptually the dotplot windows are like children of
their parent multi-pip window: they have the same reference
sequence, and if you close a dotplot only that one window closes,
but if you close the parent all of its children close too.
<p>
<p class=hdr>
<h3><a name="state">The Zoom and the Mark</a></h3>
<p>
Gmaj has two main elements of user state that reflect the user's
interactive manipulation of the display. The first is the zoom
region, i.e. the portion of the reference and secondary sequences
that is currently displayed; this is one-dimensional for
multi-pip windows and two-dimensional for dotplots. As the zoom
is changed, the previous regions are remembered in a history
list, so you can go back and forward through it similar to a web
browser. Each Gmaj window has its own separate zoom and history;
when opening a new window the current zoom region is translated
initially, but then they are independent. As a convenience,
each new window begins with several zoom regions already in the
history: the fully unzoomed sequence length(s), as specified in
the MAF file; the aligning portion of the applicable sequence(s);
and an approximate translation of the previous window's current
zoom (or in the case of the very first window, the initial zoom
specified in the command-line or applet parameters, if any).
The boundaries of the current region are displayed in a status
indicator in the upper right corner of the window, below the
menu bar.
<p>
The second state element is called the "mark", and it represents
a particular selected point in a particular pairwise pip+dotplot
and a particular MAF block. It is typically selected by clicking
in a pip, dotplot, or text alignment, and is drawn as a small
<a href="#red">red</a> circle in the plots, and also as a red
highlight in the text alignment. Unlike the zoom regions, the
mark is shared among several windows: there is at most one mark
for each reference sequence, and it appears in both the multi-pip
window for that sequence and the dotplot corresponding to
whichever pip the mark is currently in (the other dotplots, with
different secondary sequences, will show some indirect information
about the mark, but not the mark itself). Thus, moving the mark
in a dotplot window will also move it in the parent multi-pip and
vice-versa, but the mark for a different reference sequence is
independent. Information about the current mark and plot block
is displayed in one of the status indicators below the menu bar.
<p>
<p class=hdr>
<h3><a name="layout">Window Layout</a></h3>
<p>
Each Gmaj window is divided into several sections. Across the
top you will see a menu bar (including a text box for setting the
percent identity threshold), and below that two lines containing
status indicators with information about the position of the
mouse pointer, the boundaries of the currently displayed zoom
region, and the location of the mark (<a href="#red">red</a>
circle), along with buttons for sliding the zoom region and
selecting alternative blocks at the marked position. Several of
the dividers between these items are draggable, so you can adjust
the relative space they occupy. (The menus, threshold box, and
buttons are discussed individually in the <a href="#menu">Menus
and Widgets</a> section of this document.)
<p>
<i>Ruler:</i><br>
The first graphical panel is a horizontal ruler that displays
@@ -176,89 +254,119 @@ displayed. Precise locations can be determined via the position
indicator, which displays the exact coordinate of the mouse
pointer.
<p>
<i>Annotation links:</i><br>
Below the ruler is a panel that can display links to additional
information about various sequence regions. Each annotation is
represented by a color-coded bar spanning the region's position
in the reference sequence. (The bars' vertical positions are
not meaningful; they are only placed in rows for convenience, to
keep them from overlapping.) Pointing to a particular bar will
cause the position indicator to display the <code>x</code>
<i>Reconstruction scores:</i><br>
For ancestral reconstruction alignments, the MAF file may contain
scores indicating the confidence that 1) a particular inferred
ancestral nucleotide is correct, and that 2) it was present at
all. The next two panels display bar graphs of these scores when
the ancestral sequence is the reference. The scores are binned
according to the current zoom region and panel width, and the
mean score for each bin is graphed on a scale of 0 - 1 (note that
the scores are transformed via simple linear scaling, and should
not be interpreted as probabilities). For this to work, the
parameters file must specify which organism the scores apply to.
Otherwise, or if there are no scores in the file, or if a
different sequence is currently the reference, these panels will
not appear. The position indicator displays the horizontal
coordinate and vertical score position of the mouse pointer,
along with the score for the bar at that location (if any).
<p>
<i>Linkbars:</i><br>
Next is a panel that can display links to additional information
about various regions in the current reference sequence. Each
annotation is represented by a color-coded bar spanning the
region's position in the sequence. (The bars' vertical positions
are not meaningful; they are only placed in rows for convenience,
to keep them from overlapping.) Pointing to a particular bar
will cause the position indicator to display the <code>x</code>
coordinate of the pointer, and also the type and description of
that bar's annotation; otherwise only the <code>x</code>
coordinate will be shown. In applet mode, clicking on a bar
will open a separate browser window to visit the corresponding
web site. In stand-alone mode Gmaj is not working within a web
coordinate will be shown. In applet mode, clicking on a bar will
open a separate browser window to visit the corresponding web
site. In stand-alone mode Gmaj is not working within a web
browser, so instead it displays the URL for you to visit manually
via copy-and-paste. If you do not provide a links file, this
panel will not appear.
via copy-and-paste. If no links file is provided for the current
sequence, this panel will not appear.
<p>
<i>Sequence features:</i><br>
The next two panels contain schematic diagrams of the known
exons and repeats in the current reference sequence, respectively
(if these files were provided). Any additional features such as
CpG islands are included with the repeats. Again, the position
indicator displays the <code>x</code> coordinate of the mouse
pointer, and also identifies any features at that position.
exons and interspersed repeats in the current reference sequence,
respectively (if these files are provided). Any additional
features such as CpG islands are included with the repeats.
The diagram for repeats uses the same symbols as
<a href="http://pipmaker.bx.psu.edu/pipmaker/">PipMaker</a> to
indicate the various repeat categories (Alu, MIR, etc.), but only
if either the PipMaker category or the
<a href="http://www.repeatmasker.org/">RepeatMasker</a> name and
class/family are available. For example, BED and GTF repeat
files from the <a href="http://genome.ucsc.edu/cgi-bin/hgTables"
>UCSC Table Browser</a> include the RepeatMasker name but not the
class/family, so Gmaj cannot determine the PipMaker category and
draws all of them as "Other". As usual, the position indicator
displays the <code>x</code> coordinate of the mouse pointer, and
also identifies any features at that position.
<p>
<i>Pips:</i><br>
The following panels display a number of pips (percent identity
plots) showing the pairwise alignments, projected from the
multiple alignment, of the reference sequence against each of
the other sequences. A pip is similar to a dotplot, with the
horizontal <code>x</code>-axis representing the position in the
reference sequence, but the vertical <code>y</code>-axis
represents the percentage of matching nucleotides in each
gap-free segment of the pairwise alignment, instead of its
position in the second sequence. Only the top half of each plot
is shown, since segments matching less than 50% are usually not
very interesting. An additional feature of these panels is that
colored backgrounds, or "underlays", can be used to highlight
regions of interest (if you provide files with this information).
Vertical blue bars at the edges of the pips represent the
boundaries of the current zoom region, whose endpoints are
displayed in the zoom indicator. The position indicator displays
the horizontal coordinate and vertical percentage position of the
<i>Plots:</i><br>
The following panels display the alignment plots according to the
window type: either a scrollable stack of <a href="#windows"
>pips</a> (for the reference sequence against each of the others)
or a single pip and its corresponding dotplot. For pips, only
the top half of each plot is shown, since segments matching less
than 50% are usually not very interesting. Plots that are
completely empty (i.e. if that pair of sequences never occurs
together in any of the alignment blocks) will be painted gray.
An additional feature of these panels is that colored backgrounds,
or "underlays", can be used to highlight regions of interest (if
files with this information are provided); dotplots can display
these for both the reference and secondary sequences. Vertical
blue bars at the edges of the plots represent the boundaries of
the current zoom region, whose endpoints are displayed in the
zoom indicator. For a pip, the position indicator displays the
horizontal coordinate and vertical percentage position of the
mouse pointer, along with a list of <a href="#block">block
numbers</a> covering that location. It will also display labels
for the colored regions if these are included in the underlay
files.
numbers</a> covering that location. For a dotplot, it displays
the horizontal and vertical coordinates in the reference and
secondary sequences, respectively. It will also display labels
for the colored regions in both types of plots, if these are
included in the underlay files.
<p>
<i>Text view:</i><br>
The bottom panel displays a nucleotide-level view of a single
selected alignment block. (Initially it is empty, since you
haven't selected anything yet.) The top row of this display
shows the current reference sequence, while the rows for the
other sequences show a dot "<code>.</code>" wherever they match
the reference sequence, and only explicitly list the nucleotides
that don't match. (This matching is case-insensitive to deal
with soft masking, but non-nucleotide characters such as
selected alignment block: the one containing the mark
(<a href="#red">red</a> circle). Initially it is empty, since
you haven't set the mark yet. The top row of this display shows
the current reference sequence, while the rows for the other
sequences show a dot (<code>.</code>) wherever they match the
reference sequence, and only explicitly list the nucleotides that
don't match. (This matching is case-insensitive to deal with
soft masking, but non-nucleotide characters such as
<code>X</code> or <code>N</code> never match anything, even
themselves.) All of the sequences will likely have had gaps
"<code>-</code>" inserted by the alignment program. Note that
(<code>-</code>) inserted by the alignment program. Note that
most of the blocks will be much too long to fit across this
window, so a scrollbar is provided; the relative size of the
scrollbar's slider indicates what fraction of the alignment is
shown in the window. Shaded "highlights" (analogous to the pip
shown in the window. Colored "highlights" (analogous to the plot
underlays) can also be specified for each sequence; otherwise
Gmaj will provide default highlights based on the exons files
(if any). Whenever the mouse pointer is in this bottom panel,
the position indicator displays its location in the format
"<code>n:x</code>", where <code>n</code> is the column position
in the aligned block (starting with 0), and <code>x</code> is the
sequence position in the individual row (starting with 1). Note
that <code>x</code> does not include the gaps, but <code>n</code>
does. Labels for any highlights at that position are also
displayed.
<code>n:x</code>, where <code>n</code> is the column position
in this aligned block (starting with 0), and <code>x</code> is
the sequence position in the individual row (i.e., in that entire
chromosome or contig, starting with 1). Note that <code>x</code>
does not include the gaps, but <code>n</code> does. Labels for
any highlights at that position are also displayed.
<p>
With the exception of the text view, all of these panels use the
same horizontal coordinate scale (i.e., position in the current
reference sequence), and they are always kept vertically aligned
so they can be compared easily. Note that the partition between
the graphical panels and the text view is draggable, so you can
adjust the relative amount of space they occupy. Also,
individual panels can be hidden if desired, using the Options -
Show dialog (see <a href="#menu">Menus and Buttons</a>).
so they can be compared easily. Note that in the multi-pip
window the partition between the graphical panels and the text
view is draggable, so you can adjust the relative amount of space
they occupy. Also, individual panels can be hidden if desired,
using the Options - Show dialog (see <a href="#menu">Menus and
Widgets</a>).
<p>
<!--
<i>Dotplot:</i><br>
@@ -269,7 +377,7 @@ with the reference sequence along the horizontal
contigs, they will appear as separate horizontal bands across the
plot, each with its own <code>y</code>-axis coordinate system.
Whenever the mouse pointer is in this panel, the position
indicator displays its location in the format "<code>x,y</code>",
indicator displays its location in the format <code>x,y</code>,
where <code>x</code> is the position in the horizontal sequence
and <code>y</code> is the position in the vertical sequence. If
there are multiple contigs, then the contig name will be
@@ -278,32 +386,34 @@ prevent long names from crowding out the other information).
<p>
-->
<p class=hdr>
<h3><a name="mouse">Mouse Controls</a></h3>
<p>
You can select a particular alignment block by clicking on one
of its segments in any of the pips with the left mouse button.
(Actually you don't have to click exactly on it, because
Gmaj will automatically jump to the nearest point if you miss.)
The spot will be marked with a small <a href="#red">red</a>
circle, and the entire alignment block containing the mark will
change color from black to <a href="#red">red</a> in all of the
pips (each block typically spans several gap-free segments).
Also, the corresponding text view for that block will appear in
the bottom panel with the selected position highlighted. Lastly,
the mark indicator will be filled in with information about the
marked block and position, and a row of buttons will appear next
to it showing the <a href="#block">block numbers</a> covering
the marked location. These buttons allow convenient selection
of a different block at the same position (see <a href="#menu"
>Menus and Buttons</a>). Note that there is only one mark at a
time in each window, so the previous one, if any, will be
unmarked.
of its segments in any of the plots (pips or dotplots) with the
left mouse button. (Actually you don't have to click exactly on
it, because Gmaj will automatically jump to the nearest point if
you miss.) The spot will be marked with a small <a href="#red"
>red</a> circle, and the entire alignment block containing the
mark will change color from black to <a href="#red">red</a> in
all of the plots for that reference sequence (each block typically
spans several gap-free segments). Also, the corresponding text
view for that block will appear in the bottom panel with the
marked position highlighted. Lastly, the mark indicator will be
filled in with information about the marked block and position,
and a row of buttons will appear next to it showing the
<a href="#block">block numbers</a> covering the marked location.
These buttons allow convenient selection of a different block at
the same position in the reference sequence (see <a href="#menu"
>Menus and Widgets</a>). Note that there is only one mark at
a time for each reference sequence, so the previous one, if any,
will be unmarked.
<p>
In a similar fashion, clicking the left mouse button in the
text view will move the mark (both the highlight and the
<a href="#red">red</a> circle) to that position. However, gap
positions cannot be selected in this manner because they do not
correspond to pip segments; if you click in a gap, the nearest
correspond to plot segments; if you click in a gap, the nearest
gap-free position is selected instead. Also, if you click on a
position in the reference sequence (which has no corresponding
pip), the mark will move to the new column but will remain in
@@ -311,12 +421,12 @@ the same pip as before.
<p>
You can "zoom in" on a particular region by dragging out a
rectangle with the left mouse button in any of the white panels
(ruler, links, exons, repeats, or pip). All of these panels
(ruler, annotations, pip, or dotplot). All of these panels
will always zoom together, to keep them lined up. This can be
repeated until the maximum resolution is reached; after that
Gmaj will display an error message. Additional zoom features
are available via the Zoom menu and arrow buttons (see
<a href="#menu">Menus and Buttons</a>). Note that selecting
<a href="#menu">Menus and Widgets</a>). Note that selecting
a new region will cause any entries in your zoom history that
are forward of the current point to be discarded (similar to
a web browser).
@@ -329,7 +439,8 @@ effect by applying the <code>Shift</code> key when initially
pressing the mouse button.
<p>
<h3><a name="menu">Menus and Buttons</a></h3>
<p class=hdr>
<h3><a name="menu">Menus and Widgets</a></h3>
<p>
<dl>
<dt>File - Open:
@@ -367,27 +478,32 @@ Exits from Gmaj. In stand-alone mode, also exits from Java.
<dd>
This menu controls some of the aesthetic aspects of Gmaj. You
can choose between two sizes of fonts, which will also affect
some other visibility settings, such as the radius and thickness
of the mark circle, the blackness of the ruler numbers, and the
height of the pips. You can also choose to make the mark circle
and the selected block's pip segments always red, instead of
changing with the background color (this is easier to explain in
a figure legend, but makes them invisible against red underlays).
Lastly, the Show item opens a dialog where you can choose which
individual panels to display or hide (currently it does not
affect which text rows are displayed, however). The choices on
this menu affect all of the windows, not just the current one.
some other visibility settings, such as the thickness of the plot
segments, the radius and thickness of the mark circle, the
blackness of the ruler numbers, and the height of the pips. You
can also choose to make the mark circle and the selected block's
plot segments always red, instead of changing with the background
color (this is easier to explain in a figure legend, but makes
them invisible against red underlays). Lastly, the Show item
opens a dialog where you can choose which individual panels to
display or hide (the sequence selections here also affect which
text rows and dotplot windows are shown), and whether the
underlays should be painted on dotplots. The choices on this
menu affect all of the windows, not just the current one.
<p>
<dt>RefSequence:
<dt>Reference:
<dd>
This menu allows you to select a different reference sequence
(unless the parameters file indicates that the alignment has a
fixed, intrinsic reference sequence). A new window will open,
showing the same data from the perspective of the sequence you
chose. The mark (if any) will be copied to the new window as
closely as possible, but the zoom will not. Thereafter, the
windows will operate independently. You can have one window
open for each sequence in the data.
fixed, intrinsic reference sequence). A new multi-pip window
will open, showing the same data from the perspective of the
sequence you chose. The mark (if any) will be copied to the new
window as closely as possible, and the current zoom region will
be translated to a roughly equivalent one showing the same blocks.
Thereafter, the windows will operate independently. You can have
one multi-pip window for each sequence in the data; if you
already have one for the newly-chosen reference sequence, it will
just be brought to the front unchanged.
<p>
<dt>Zoom - Back:
<dd>
@@ -401,15 +517,17 @@ affect the mark.
<p>
<dt>Zoom - Unzoom:
<dd>
Sets the zoom region to the widest, unzoomed view, i.e., the
full range for this reference sequence as specified in the
<code>.maf</code> file. Has the same effect as entering the
"valid range" endpoints in Set Zoom. Does not affect the mark.
Sets the zoom region for this window to the widest, unzoomed
view, i.e., the full length of this entire reference sequence
(and also this secondary sequence, for a dotplot) as specified in
the MAF file. Has the same effect as entering the "valid range"
endpoints in Set Zoom. Does not affect the mark.
<p>
<dt>Zoom - Set Zoom:
<dd>
Presents a dialog box that allows you to enter arbitrary zoom
endpoints (within the valid range for this reference sequence).
endpoints (within the valid ranges for the applicable sequences).
Any left empty will be interpreted to mean "leave unchanged".
The new region, if different from the current one, is added to
your zoom history for this window. Any regions forward of the
current point in your history are discarded (similar to a web
@@ -430,60 +548,98 @@ via copy-and-paste.
<p>
<dt>Help - Keys:
<dd>
Displays a message window listing Gmaj's keyboard shortcuts. No
<code>Alt</code> key is needed, since Gmaj doesn't use the
keyboard for much else.
Displays a message window listing Gmaj's keyboard shortcuts.
No <code>Alt</code> key is needed, since Gmaj doesn't use the
keyboard for much else. The shortcuts will not work if the
keyboard focus is in a text box (e.g. the one for % Identity);
in this case press <code>Esc</code> first to cancel the text
entry and restore the focus to the active window's menu bar.
<code>Esc</code> will also cancel dialog and message boxes.
<p>
<dt>% Identity Box:
<dd>
Allows you to set a threshold for limiting the displayed
alignments by the percent identity of the plot blocks (which are
pairwise projections of the MAF blocks). The percent identity
of each plot block is computed as the length-weighted average
percent identity of its gap-free segments. Blocks below the
threshold are not drawn or clickable in the plots, but still
exist otherwise (e.g. in the position indicator's block list for
pips; also a block already displayed in the text panel will not
disappear). The same threshold applies across all windows, and
keyboard shortcuts make it easy to adjust it up and down. Also,
the percent identity of the current plot block is shown in the
mark indicator when applicable (this is either the marked one,
or if a dotplot has a different secondary sequence, the
corresponding projection from the same MAF block).
<p>
<dt>Arrow Buttons:
<dd>
These two buttons are located to the right of the zoom indicator.
Clicking on one of them will slide the zoom region to the left or
right, respectively, by half of its width. The new region is
These buttons are located to the right of the zoom indicator.
Clicking on one of them will move the zoom region in the
indicated direction by half of its width. The new region is
added to your zoom history like any other zoom selection, so the
Zoom - Back command will return to where you were as usual.
<p>
<dt>Block Buttons:
<dd>
When a block is selected by clicking on a pip, a row of buttons
will appear to the right of the mark indicator showing all of the
<a href="#block">block numbers</a> covering the marked position.
(If there is not enough room for all of the buttons, a scrollbar
will appear; also the partition between this panel and the mark
indicator is draggable.) Clicking on one of the buttons causes
the mark to move to that block (in the same pip), and the pip
segment colors, text alignment, and mark indicator will be
updated accordingly. The new marked position (red circle) will
be as close as possible to the same coordinate in the reference
sequence, but it may have to move slightly to avoid gaps. This
makes it theoretically possible, though rare, that the resulting
block list (and therefore the row of buttons) may change.
When a mark is set (e.g. by clicking in a pip or dotplot), a row
of buttons will appear to the right of the mark indicator showing
all of the <a href="#block">block numbers</a> covering the marked
position in the pip. (If there is not enough room for
all of the buttons, a scrollbar will appear; also the partition
between this panel and the mark indicator is draggable.)
Clicking on one of the buttons causes the mark to move to that
block (in the same pip), and the segment colors, text alignment,
and mark indicator will be updated accordingly in all applicable
windows. The new marked position (<a href="#red">red</a> circle)
will be as close as possible to the same coordinate in the
reference sequence, but it may have to move slightly to avoid
gaps. This makes it theoretically possible, though rare, that
the resulting block list (and therefore the row of buttons) may
change.
<p>
<dt>Dotplot Buttons:
<dd>
These buttons are located to the right of each pip's sequence
label in the multi-pip window. Clicking on one of them will
open a dotplot window for that pair of reference and secondary
sequences. The zoom region will initially be translated from the
current one to show the same blocks, and will thereafter operate
independently. The mark, however, is shared between the
multi-pip window and all of its dotplots (see <a href="#state"
>The Zoom and the Mark</a>). If you already have a window for
that dotplot, it will just be brought to the front unchanged.
</dl>
<p>
<!-- <hr align=left noshade size=1 width="20%" color=black> -->
<p class=hdr>
<h3><a name="notes">Footnotes</a></h3>
<p>
<a name="red"></a>
[1]&nbsp;
The circular mark and the selected block's pip segments are red
The circular mark and the selected block's plot segments are red
when the background is white, but by default are displayed in
different colors against other backgrounds to ensure good
contrast. A setting on the Options menu can make them always
red if desired. The selected pip segments are drawn last, so
different colors against other backgrounds for improved contrast.
A setting on the Options menu can make them always red if
desired. The selected block's plot segments are drawn last, so
they will not be obscured by other blocks.
<p>
<a name="block"></a>
[2]&nbsp;
An alignment block is considered to cover a pip position if it
contains rows for both of the pip's sequences and the position
falls within the endpoints of the reference sequence's row; there
are no "holes" due to gaps. Blocks in the <code>.maf</code> file
are numbered consecutively, starting with 0.
An alignment block is considered to cover a plot position if it
contains rows for both of the plot's sequences and the position
falls within the endpoints of the <b>reference</b> sequence's
row (not necessarily the row for the other sequence, as this is
a pip-oriented computation); there are no "holes" due to gaps.
Blocks in the MAF file are numbered consecutively, starting
with 0.
<p>
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
<p class=scrollspace>
</body>
static/gmaj/docs/gmaj_input.html
+403 -106
View File
@@ -21,13 +21,15 @@ TABLE OF CONTENTS
<li><a href="#align">Alignments</a>
<li><a href="#exon">Exons</a>
<li><a href="#repeat">Repeats</a>
<li><a href="#annot">Annotation Links</a>
<li><a href="#link">Linkbars</a>
<li><a href="#under">Underlays</a>
<li><a href="#high">Highlights</a>
<li><a href="#color">Color List</a>
<li><a href="#generic">Generic Annotation Formats</a>
</ul>
<p class=vlarge>
<p class=hdr>
<h3><a name="intro">Introduction</a></h3>
<p>
This page describes the input files supported by Gmaj, and their
@@ -36,14 +38,30 @@ required; the others are optional. Except where noted, all
information applies to both the stand-alone and applet modes of
Gmaj.
<p>
The annotation formats (exons, etc.) are essentially the same as
those used by <a href="http://globin.bx.psu.edu/dist/laj/">Laj</a>
and <a href="http://pipmaker.bx.psu.edu/pipmaker/">PipMaker</a>,
and you may find that PipMaker's associated utilities, such as
<a href="http://pipmaker.bx.psu.edu/piphelper/">PipHelper</a> and the
<a href="http://pipmaker.bx.psu.edu/pipmaker/tools.html">PipTools</a>,
can greatly facilitate the preparation of your files.
For annotations, Gmaj supports two broad categories of file
formats. The original set of formats is essentially the same as
those used by <a href="http://pipmaker.bx.psu.edu/pipmaker/"
>PipMaker</a> and <a href="http://globin.bx.psu.edu/dist/laj/"
>Laj</a>, where each destination for the data (exons panel, color
underlays, etc.) has its own file format tailored for the needs of
that display. These files can be cumbersome to prepare manually,
though PipMaker's associated utilities, such as
<a href="http://pipmaker.bx.psu.edu/piphelper/">PipHelper</a> and
the <a href="http://pipmaker.bx.psu.edu/pipmaker/tools.html"
>PipTools</a>, can significantly reduce the burden.
<p>
However, since sequence annotations are increasingly becoming
available in standardized formats from on-line resources such as
the <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Table
Browser</a>, Gmaj can now accept some of these formats as well.
These are referred to here as "generic" formats because they are
not restricted to a particular biological data type or Gmaj
display panel.
<p>
The PipMaker-style formats are described below in the sections for
each panel, while the generic ones are discussed in a separate
section, <a href="#generic">Generic Annotation Formats</a>.
<p class=large>
<center>
<table width=55%>
<tr>
@@ -52,10 +70,14 @@ can greatly facilitate the preparation of your files.
at http://www.clipart.co.uk/ -->
</td>
<td valign=top>
<ul class="notop lessindent">
<li><b>All files must consist solely of plain text ASCII characters.</b>
(For example, no Word documents.)
<li><b>All <a href="#coord">coordinates</a> for annotations are 1-based.</b>
<ul class="notop nobottom lessindent">
<li> <b>All files must consist solely of plain text ASCII
characters.</b>&nbsp; (For example, no Word documents.)
<p class=small>
<li> <b>All <a href="#coord">coordinates</a> for PipMaker-style
annotations are 1-based, closed interval.</b>&nbsp; Those
for generic annotations may be either 1-based or 0-based
and closed or half-open, depending on the format.
</ul>
</td>
</tr>
@@ -63,6 +85,7 @@ can greatly facilitate the preparation of your files.
</center>
<p>
<p class=hdr>
<h3><a name="param">Parameters File</a></h3>
<p>
The annotation files are optional, but because in some alignments
@@ -84,6 +107,7 @@ It contains detailed comments at the bottom explaining the syntax
and meaning of the parameters.
<p>
<p class=hdr>
<h3><a name="zip">Compression and Bundling</a></h3>
<p>
Gmaj supports a "bundle" option, which allows you to collect and
@@ -100,17 +124,20 @@ stand-alone mode. A few tips:
mention the parameters file on the command line or in the
applet tags; just specify the bundle. But if the parameters
file is not in the bundle, specify both.
<p class=small>
<li> Data files in the bundle should be referred to within the
parameters file using their plain filenames, without paths.
Any data files outside the bundle should be referred to
normally, using the rules described in
parameters file using their plain filenames, without paths,
and these must be unique. Any data files outside the bundle
should be referred to normally, using the rules described in
<code><a href="sample.gmaj">sample.gmaj</a></code>.
<li> Do not use filenames containing "<code>/</code>",
"<code>\</code>", or "<code>:</code>" in the bundle. Gmaj
<p class=small>
<li> Do not use filenames containing <code>/</code>,
<code>\</code>, or <code>:</code> in the bundle. Gmaj
needs to remove the path that may have been added to each
name by the zip or jar program, and since it doesn't know
what platform that program was run on, it treats all of
these characters as path separators.
<p class=small>
<li> If you are not using a parameters file (i.e., you want to
specify the <a href="#align">alignment file</a> directly,
without any annotations or other data-related options),
@@ -128,53 +155,62 @@ corresponding extension for the compression format to be
recognized.
<p>
<p class=hdr>
<h3><a name="coord">Coordinate Systems</a></h3>
<p>
If you supply any <a href="#exon">exons</a>,
<a href="#under">underlays</a>, or other annotations for Gmaj to
display, these files must all use position coordinates that refer
to the same original sequences identified in the <code>.maf</code>
<a href="#align">alignment file</a> (ignoring any display offsets
specified in the <a href="#param">parameters file</a>). However,
even though the <code>.maf</code> coordinates are 0-based, the
annotation files use a 1-based coordinate system (i.e., the first
nucleotide in the sequence is called "1"). This is for consistency
with PipMaker, which uses virtually the same annotation formats.
Gmaj adjusts the <code>.maf</code> coordinates to convert
everything to a 1-based system for display.
If you supply any annotations for Gmaj to display, these files
must all use position coordinates that refer to the same original
sequences identified in the MAF <a href="#align">alignment file</a>
(ignoring any display offsets specified in the <a href="#param"
>parameters file</a>). However, even though the MAF coordinates
are 0-based, the PipMaker-style annotation files all use a
1-based, closed-interval coordinate system (i.e., the first
nucleotide in the sequence is called "1", and specified ranges
include both endpoints). This is for consistency with PipMaker,
so the same files can be used with both programs, and the same
tools can be used to prepare them. Coordinates for generic
annotations may be either 1-based or 0-based and closed or
half-open, depending on the format, but Gmaj always adjusts
them as needed (including the ones in the MAF file) to convert
everything to a 1-based, closed-interval system for display.
<p>
<p class=hdr>
<h3><a name="align">Alignments</a></h3>
<p>
Gmaj is designed to display multiple alignments in
<code><a href="http://genome.ucsc.edu/FAQ/FAQformat">.maf</a></code>
format. It is especially suited for sequence-symmetric alignments
from programs such as <a href="http://www.bx.psu.edu/miller_lab/"
>TBA</a>, but can also display <code>.maf</code> files that have
a fixed reference sequence. (In the latter case it is a good idea
to set the <code>refseq</code> field in your <a href="#param"
>parameters file</a>, to avoid displaying the alignments with an
inappropriate reference sequence.) Gmaj displays only one
<a href="http://genome.ucsc.edu/FAQ/FAQformat">MAF</a> format.
It is especially suited for sequence-symmetric alignments from
programs such as <a href="http://www.bx.psu.edu/miller_lab/"
>TBA</a>, but can also display MAF files that have a fixed
reference sequence. (In the latter case it is a good idea to
set the <code>refseq</code> field in your <a href="#param"
>parameters file</a>, to prevent displaying the alignments with
an inappropriate reference sequence.) Gmaj displays only one
alignment file at a time.
<p>
<p class=hdr>
<h3><a name="exon">Exons</a></h3>
<p>
Each of these files lists the locations of genes, exons, and
coding regions in a particular reference sequence. The
directionality of a gene ("<code>&gt;</code>", "<code>&lt;</code>",
or "<code>|</code>"), its start and end positions, and name should
be on one line, followed by an optional line beginning with a
"<code>+</code>" character that indicates the first and last
nucleotides of the translated region (including the initiation
codon, <i>Met</i>, and the stop codon). These are followed by
lines specifying the start and end positions of each exon, which
must be listed in order of increasing address even if the gene
is on the reverse strand ("<code>&lt;</code>"). By default Gmaj
will supply exon numbers, but you can override this by specifying
your own name or number for individual exons. Blank lines are
ignored, and you can put an optional title line at the top.
Thus, the file might begin as follows:
coding regions in a particular reference sequence. The exons
and UTRs are displayed as black and gray boxes in a separate
panel above the alignment plots.
<p>
In the PipMaker-style exons format, the directionality of a gene
(<code>&gt;</code>, <code>&lt;</code>, or <code>|</code>), its
start and end positions, and name should be on one line, followed
by an optional line beginning with a <code>+</code> character that
indicates the first and last nucleotides of the translated region
(including the initiation codon, <i>Met</i>, and the stop codon).
These are followed by lines specifying the start and end positions
of each exon, which must be listed in order of increasing address
even if the gene is on the reverse strand (<code>&lt;</code>). By
default Gmaj will supply exon numbers, but you can override this
by specifying your own name or number for individual exons. Blank
lines are ignored, and you can put an optional title line at the
top. Thus, the file might begin as follows:
<pre>
My favorite genomic region
@@ -192,14 +228,19 @@ Thus, the file might begin as follows:
</pre>
<p>
<p class=hdr>
<h3><a name="repeat">Repeats</a></h3>
<p>
Each of these files lists interspersed repeats and other features
in a particular reference sequence. The first line identifies
this as a simplified repeats file (as opposed to RepeatMasker
output); it is ignored by Gmaj, which only accepts this simplified
format. Each subsequent line specifies the start, end, direction,
and type of an individual feature.
Each of these files lists interspersed repeats (and possibly other
features such as CpG islands) in a particular reference sequence.
These are displayed in a separate panel just below the exons,
using the same shapes and shading as PipMaker if possible.
<p>
In the PipMaker-style repeats format, the first line identifies
this as a simplified repeats file (as opposed to
<a href="http://www.repeatmasker.org/">RepeatMasker</a> output,
which Gmaj does not yet support). Each subsequent line specifies
the start, end, direction, and type of an individual feature.
<pre>
%:repeats
@@ -207,7 +248,7 @@ and type of an individual feature.
1365 1405 Simple
... etc.
</pre>
The allowed types are:
The allowed PipMaker types are:
<code>Alu</code>, <code>B1</code>, <code>B2</code>,
<code>SINE</code>, <code>LINE1</code>, <code>LINE2</code>,
<code>MIR</code>, <code>LTR</code>, <code>DNA</code>,
@@ -217,21 +258,24 @@ The allowed types are:
require a direction (<code>Right</code> or <code>Left</code>).
<p>
<h3><a name="annot">Annotation Links</a></h3>
<p class=hdr>
<h3><a name="link">Linkbars</a></h3>
<p>
Each of these files contains reference annotations, i.e., links
to web sites providing information about noteworthy regions in a
particular reference sequence, which are drawn as colored bars.
In applet mode Gmaj opens a new browser window to visit the
linked site when the user clicks on a bar. In stand-alone mode
Gmaj is not running within a web browser, so it just displays the
URL for the user to visit manually via cut-and-paste.
Each of these files contains reference annotations, i.e.,
noteworthy regions in a particular reference sequence, which are
drawn in a separate panel as colored bars. Typically each bar
has an associated URL pointing to a web site with more information
about the region, but this is not required. In applet mode Gmaj
opens a new browser window to visit the linked site when the user
clicks on a bar; in stand-alone mode Gmaj is not running within
a web browser, so it just displays the URL for the user to visit
manually via copy-and-paste.
<p>
The format first defines various types of hyperlinks and
associates a color with each of them, then specifies the type,
The PipMaker-style format first defines various types of links
and associates a color with each of them, then specifies the type,
position, description, and URL for each annotated region.
<pre>
# annotations for part of the mouse MHC class II region
# linkbars for part of the mouse MHC class II region
%define type
%name PubMed
@@ -259,10 +303,10 @@ The name must be a single word, perhaps containing underline
characters (e.g., <code>Entry_in_GenBank</code>), and the color
must come from Gmaj's <a href="#color">color list</a>.
<p>
The third stanza associates a PubMed annotation with positions
The third stanza associates a PubMed link with positions
1-2000 in this sequence. The label should be kept fairly
short, as it will be displayed on Gmaj's position indicator line
when the user points at this annotation. The summary is optional;
when the user points at this linkbar. The summary is optional;
it is used only by PipMaker and will be ignored by Gmaj. Also,
while PipMaker allows several summary/URL pairs within a single
annotation, Gmaj expects each field to occur at most once. If
@@ -277,18 +321,28 @@ to separate it from the last word of the previous line, while
a URL continuation does not.
<p>
Also note that stanzas should be separated by blank lines, and
lines beginning with a "<code>#</code>" character are comments
that will be ignored. The annotations can appear in the file in
lines beginning with a <code>#</code> character are comments
that will be ignored. The linkbars can appear in the file in
any order, and several can overlap at the same position with no
problem, since Gmaj will display them in multiple rows if
necessary.
necessary. In PipMaker this format is called "annotations with
hyperlinks".
<p>
<p class=hdr>
<h3><a name="under">Underlays</a></h3>
<p>
Each of these files specifies color underlays (i.e., colored
bands) to be painted on a particular pairwise pip. The format
supported by Gmaj looks like this:
Each of these files specifies underlays (colored bands) to be
painted on a particular pairwise pip and its corresponding
dotplot. The bands are specified as regions in the reference
sequence and are normally drawn vertically; however for a dotplot,
Gmaj will also look to see if you have specified an underlay file
for the transposed situation where the reference and secondary
sequences are swapped, and if so, will draw those underlays as
horizontal bands in the secondary sequence.
<p>
The PipMaker-style underlay format supported by Gmaj looks like
this:
<pre>
# partial underlays for the BTK region
@@ -312,50 +366,54 @@ displayed on Gmaj's position indicator line when the user points
the mouse at that band. The parentheses must be present if the
label is, and the label itself cannot contain any additional
parentheses. (The label is an extra feature not supported by
PipMaker.) A "<code>+</code>" or "<code>-</code>" character at
PipMaker.) A <code>+</code> or <code>-</code> character at
the end of a location line will paint just the upper or lower
half of the band, respectively. This allows you to differentiate
between the two strands, or to plot potentially overlapping
features like gene predictions and database matches.
half of the band on the pip (but is ignored for dotplots). This
allows you to differentiate between the two strands, or to plot
potentially overlapping features like gene predictions and
database matches.
<p>
Note that if two bands overlap, the one that was specified last
in the file appears "on top" and obscures the earlier one (except
for the special <code><a href="#hatch">Hatch</a></code> color).
Thus in this example, the green exons and red strongly conserved
regions cover up parts of the long yellow band representing the
gene. As in the links file, lines beginning with a
"<code>#</code>" character are comments that will be ignored.
gene. As in the links file, lines beginning with a <code>#</code>
character are comments that will be ignored.
<p>
<p class=hdr>
<h3><a name="high">Highlights</a></h3>
<p>
These files are analogous to the <a href="#under">underlay</a>
Highlight files are analogous to the <a href="#under">underlay</a>
files, but each of these specifies colored regions for a
particular sequence in the text view rather than for a pip.
They use the same format as the underlay files, except that any
"<code>+</code>" or "<code>-</code>" indicators will be ignored,
and the <code>Hatch</code> color is not supported for highlights.
Just as with underlays, labels can be included which will be
displayed when the user points at the highlight, and highlights
that are listed later in the file will cover up those that appear
earlier.
<p>
particular sequence in the text view, rather than for a plot.
If you do not specify a highlight file for a particular sequence,
Gmaj will automatically provide default highlights based on the
<a href="#exon">exons</a> file (if you provided one). These will
use different colors to indicate the forward vs. reverse strand.
If the exons file specifies a gene's translated region, then the
5&acute; and 3&acute; UTRs will be shaded using lighter colors.
These default highlights make it easy to examine the putative
start/stop codons and splice junctions, as well as providing a
visual connection between the graphical and text views. But if
for some reason you do not want any text highlights, you can
suppress them by specifying an empty highlight file.
use one color for whole genes, overlaid with different colors to
indicate exons on the forward vs. reverse strand. If the exons
file specifies a gene's translated region, then the 5&acute; and
3&acute; UTRs will be shaded using lighter colors. These default
highlights make it easy to examine the putative start/stop codons
and splice junctions, as well as providing a visual connection
between the graphical and text views. But if for some reason you
do not want any text highlights, you can suppress them by
specifying an empty highlight file.
<p>
The PipMaker-style format for highlights is the same as for
underlays, except that any <code>+</code> or <code>-</code>
indicators will be ignored, and the <code>Hatch</code> color is
not supported for highlights. Just as with underlays, labels can
be included which will be displayed when the user points at the
highlight, and highlights that are listed later in the file will
cover up those that appear earlier.
<p>
<p class=hdr>
<h3><a name="color">Color List</a></h3>
<p>
For Gmaj, the available colors are:
For Gmaj's PipMaker-style annotations, the available colors are:
<pre>
Black White Clear
Gray LightGray DarkGray
@@ -373,7 +431,7 @@ These names are case-sensitive (i.e., capitalization matters).
Not all of these are supported by PipMaker. Also, be aware that
the appearance of the colors may vary between PipMaker and Gmaj,
and from one printer or monitor to the next.
<p>
<p class=subhdr>
<a name="hatch"><b><code>Hatch</code></b></a>
<p>
In addition to the regular colors listed above, Gmaj supports a
@@ -385,13 +443,252 @@ appears "on top" and obscures the earlier one. However,
are always drawn after the other colors, and since the space
between the diagonal lines is transparent, they allow the other
colors to show through. Currently <code>Hatch</code> is only
supported for underlays, not for highlights or hyperlink
annotations.
supported for underlays, not for highlights or linkbars.
<p>
<p class=hdr>
<h3><a name="generic">Generic Annotation Formats</a></h3>
<p>
The standardized generic formats currently supported by Gmaj
include
<a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml"
>GFF</a> (v1 & v2),
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF"
>GTF</a>, and various flavors of
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED"
>BED</a> (including the full BED12 format, a.k.a. "gene BED").
For details on these formats, please see the specifications at
the above links; this document will mainly discuss their use
by Gmaj.
<p>
These formats are all <b>tab-separated</b>, and despite their
differences are similar enough that Gmaj can extract comparable
fields and treat them more or less the same. Note that Gmaj is
not intended as a format validator: parsing is more lenient in
some respects than the official format specifications, and Gmaj
will ignore fields it has no use for. Also, interpretation of
these open-ended formats depends partly on what type of annotation
is expected; e.g. if Gmaj is trying to read exons from a GFF v1
file, it will assume that the group field is the gene name. It
will generally show warning messages to keep the user apprised
of any such assumptions it is making (if these become too annoying
they can be individually suppressed in the <a href="#param"
>parameters file</a>; see <code><a href="sample.gmaj"
>sample.gmaj</a></code> for details). Because one of the main
reasons for supporting these formats is to enable the use of
annotation files obtained from public sources, Gmaj tries not to
balk at anomalies that are probably not the user's fault, and
when practical will simply skip questionable items with a warning
message. Each type of message will generally be displayed only
once, and not repeated for every item with the same problem.
<p>
<p class=subhdr>
<a name="fileext"><b>Filename Extensions</b></a>
<p>
In order to distinguish generic files from PipMaker-style ones
and handle them appropriately, Gmaj requires that files in
generic formats have names ending with any of certain extensions.
The default list is <code>.gff</code>, <code>.gtf</code>,
<code>.bed</code>, <code>.ct</code>, and <code>.trk</code>, but
this can be customized (see <code><a href="sample.gmaj"
>sample.gmaj</a></code>).
<p>
<p class=subhdr>
<a name="quote"><b>Quoting</b></a>
<p>
Some of the generic formats require text values to be enclosed
in double quotes (<code>" "</code>). Even when not strictly
required it is usually a good idea to do so, especially if the
value contains spaces. The official specifications generally
don't say what to do if a value contains embedded quote
characters, but Gmaj supports a rudimentary mechanism for
escaping them with a backslash (<code>\</code>). However it
does not provide for escaping the backslash: quoted values
should not end with <code>\</code> (insert a space before the
final quote if necessary).
<p>
<p class=subhdr>
<a name="gencoord"><b>Coordinates</b></a>
<p>
The GFF and GTF formats use 1-based, closed-interval coordinates
(i.e., sequence numbering starts with "1", and specified ranges
include both endpoints), while BED uses a 0-based, half-open
system (the first nucleotide of the sequence is numbered "0",
and the ending position is not included in the region). For all
of these formats, positions are given relative to the beginning
of the named sequence regardless of which strand the feature is
on (unlike MAF), and <code>start</code> must be less than or
equal to <code>end</code>.
<p>
<p class=subhdr>
<a name="gffconv"><b>GFF Conventions</b></a>
<p>
BED format is relatively fixed in how its fields are used, but
GFF and GTF are more variable and require additional conventions
for most effective use with Gmaj. In particular, the values of
the "feature" field and the optional "attributes" affect how Gmaj
will interpret and display an item.
<p>
Values of the feature field that are recognized for special
treatment include:
<p class=tiny>
<ul class="notop nobottom">
<li> <code>gene</code> or values starting with <code>gene_</code>
<li> <code>exon</code> or values starting with <code>exon_</code>
<li> <code>start_codon</code>, <code>str_codon</code>,
<code>stop_codon</code>, <code>stp_codon</code>, or
<code>cds</code>
<li> <code>repeatmasker</code> or any of the
<a href="#repeat">PipMaker repeat or CpG types</a>
</ul>
<p class=tiny>
Of these, only the PipMaker types are case-sensitive.
<p>
For GFF v2 and GTF, the currently recognized attribute tags are:
<p class=tiny>
<ul class="notop nobottom">
<li> <code>gene</code> or <code>gene_id</code>: the name of the
gene, e.g. for grouping exons (<code>transcript_id</code> is
ignored)
<li> <code>name</code>: an optional name for this individual item,
e.g. for an exon label
<li> <code>sequence</code> (when feature is
<code>repeatmasker</code>): the name/class/family of the
repeat, e.g. <code>AluJb/SINE/Alu</code>
<li> <code>color</code>: a <a href="#gencolor">color</a>
specification in UCSC format, e.g. <code>0,0,255</code>
<li> <code>url</code> or <code>ucsc_id</code>: the URL for
linkbars; <code>$$</code> will be replaced with the value of
<code>name</code>
</ul>
<p class=tiny>
These keywords are not case-sensitive, but they cannot have
multiple values.
<p>
<p class=subhdr>
<a name="custom"><b>Custom Tracks</b></a>
<p>
Along with the basic formats listed above, Gmaj also supports UCSC
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks"
>custom track</a> headers.
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK"
>Track lines</a> can specify certain settings for an entire
track; currently <code><a href="#gencolor">color</a></code>,
<code><a href="#gencolor">itemRgb</a></code>, <code>offset</code>,
and <code>url</code> are supported. They also allow several
tracks (even in mixed formats) to be combined in a single file.
Gmaj does not currently provide a way to use just one particular
track from such a file (it will be treated as one big bag of
annotations), but lines in unsupported formats such as
<a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html"
>WIG</a> are gracefully skipped.
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#lines"
>Browser lines</a> are also skipped; Gmaj's initial zoom position
is controlled by command-line or applet parameters rather than by
individual annotation files.
<p>
<p class=subhdr>
<a name="multiseq"><b>Multiple Sequences</b></a>
<p>
Generic files can also contain annotations for several sequences,
because unlike the PipMaker-style formats, they all have a
"seqname" or "chrom" field that Gmaj can use to select the
appropriate lines. Ideally Gmaj expects this field to match
the sequence name from the <a href="#align">alignment file</a>,
but has two ways to deal with exceptions. If there is only one
seqname in the annotation file, then Gmaj will go ahead and use
it, but will display a warning (unless the mismatch can be fixed
by prepending the organism name, or the organism name plus
<code>chr</code>, to the annotation seqname). But if the file
has annotations for several sequences and some don't match the
alignment file, you need to tell Gmaj which is which by adding
an alias in the <a href="#param">parameters file</a> (see
<code><a href="sample.gmaj">sample.gmaj</a></code>).
<p>
<p class=subhdr>
<a name="reuse"><b>Reusing Files</b></a>
<p>
One of the advantages of using generic formats is that files can
be reused in multiple panels without reformatting, e.g. as both
exons and underlays. Normally linkbars, underlays, and text
highlights are simply handled as arbitrary regions of a specified
color, since they could represent any type of biological feature.
However, you can ask Gmaj to interpret them as exons or repeats
by adding a type hint in the <a href="#param">parameters file</a>
(see <code><a href="sample.gmaj">sample.gmaj</a></code>). Note
that currently this will also cause any <a href="#gencolor"
>specified colors</a> in that file to be overridden with Gmaj's
defaults.
<p>
Combining several biological types of annotations (e.g. exons
and repeats) in one file is possible, but not recommended. Gmaj
will try to skip lines that are not appropriate for the type it
is seeking, but it may draw more than you want.
<p>
<p class=subhdr>
<a name="cds"><b>Coding Sequence</b></a>
<p>
Currently Gmaj has no special support for multiple transcripts.
When inferring UTRs, all of the CDS-related items for a single
gene name are combined, and the interval from the lowest
coordinate to the highest is used as the CDS. Also, some of the
formats' rules specify whether or not the initiation and stop
codons should be included in the CDS, but Gmaj does not make
adjustments to compensate for that; instead it simply includes
all of the given endpoints in the CDS.
<!-- and leaves it up to the user to interpret the display based
on the convention used in the files he/she provided. [the user
does not supply files for applets] -->
<p>
<p class=subhdr>
<a name="gencolor"><b>Colors</b></a>
<p>
Colors can be specified for individual annotation lines via the
<code>itemRgb</code> field (for BED) or a <code>color</code>
attribute (for GFF v2 or GTF). However, for <a href="#custom"
>custom tracks</a>, these are governed by the track line's
<code>itemRgb</code> attribute, which defaults to off per the
UCSC specification. Thus if you have track lines and want to
use the per-item colors, you need to include
<code>itemRgb=On</code> in the track attributes.
<p>
Track lines can also have a <code>color</code> attribute for
the entire track, which will be used if <code>itemRgb</code> is
off, or if an individual item does not have its own color.
However in a rare break from the UCSC specification, Gmaj does
not use black as the default if the track color is unspecified
(black underlays and highlights just don't work with black plots
and text). Instead it uses its own default colors, which for
genes/exons are the same as the colors for <a href="#high"
>default highlights</a>, or light gray for other annotations.
Note that these defaults will also override your colors when
<a href="#reuse">type hints</a> are used.
<p>
All of the above-mentioned color values are specified in UCSC
format, which consists of three comma-separated RGB values from
0-255 (e.g. <code>0,0,255</code>).
<p>
<p class=subhdr>
<a name="sort"><b>Sorting</b></a>
<p>
The order of the lines is not supposed to matter in these generic
formats, but for most of the Gmaj panels it does matter: exons
need to be grouped by gene and ordered by position so UTRs can be
inferred and exon numbers assigned, early underlays are covered
up by later ones, etc. Gmaj solves this problem by sorting the
data before it is displayed. Exons are sorted first by gene name
in ascending order, and then within each gene by start position
(ascending) and lastly in case of a tie, by end position
(descending). All other annotation types are sorted first by
length in descending order, and then in case of a tie by start
position (ascending). This usually produces a reasonable display,
but if you need direct control of the order, you can use the
PipMaker-style formats instead.
<p>
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
<p class=scrollspace>
</body>
static/gmaj/docs/gmaj_install.html
+7 -6
View File
@@ -71,11 +71,12 @@ page apply only to applet setup.
<h3><a name="data">Data Files</a></h3>
<p>
Gmaj can display several kinds of data, including alignments,
exons, repeats, annotation links, color underlays, and text
highlights, with a meta-data parameters file to tie them all
together. For detailed descriptions of these files and their
format requirements, please see <a href="gmaj_input.html"
In addition to the alignment data, Gmaj can display several
kinds of annotations, including genes/exons, repeats, linkbars,
color underlays, text highlights, and reconstruction scores for
ancestral sequences, with a meta-data parameters file to tie
them all together. For detailed descriptions of these files and
their format requirements, please see <a href="gmaj_input.html"
>Input Files for Gmaj</a>.
<p>
When setting up Gmaj as an applet, the data files must be
@@ -158,6 +159,6 @@ file URLs, button label, etc. A few things to note:
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
</body>
</html>
static/gmaj/docs/gmaj_news.html
+127 -20
View File
@@ -12,13 +12,121 @@
<h2>What's New in Gmaj</h2>
<p class=vvlarge>
<dl>
<dt><b>2007-Jul-26</b><br>
<dd> <ul>
<li> Gmaj can now display dotplots in addition to the main multi-pip views,
with color underlays for both sequences.
<ul>
<li> Dotplots are opened by clicking on buttons in the pip headers.
<li> Each dotplot opens in a separate window, similar to the multi-pip
view except it has pip, dotplot, and text panels for two sequences
only.
<li> Dotplot windows share the same reference sequence and mark with
their parent multi-pip window but have independent zoom, and close
automatically when the parent does.
<li> There is only one mark for each reference sequence, so the circle
will not appear in dotplots having a different secondary sequence
than the mark.
</ul>
<li> Gmaj can now read annotation data in
<a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml"
>GFF</a> (v1 & v2),
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF"
>GTF</a>, and
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED"
>BED</a> formats in addition to its previous PipMaker-style formats.
<ul>
<li> UCSC
<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks"
>custom track</a> headers are supported, with multiple tracks and
sequence names allowed in a single file.
<li> There is currently no way to use just one particular track from a
file, but lines in
<a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html"
>WIG</a> or other unrecognized formats are skipped.
<li> Files in these generic formats can be reused in multiple panels
(e.g. as both exons and underlays).
<li> A new <code>tabext</code> field and file specification modifiers
(seqname alias and type hint) in the parameters file facilitate
interpretation of these formats.
<li> Colors can be specified using UCSC-style RGB triplets (either
per-line or per-track), or Gmaj provides defaults.
<li> Currently there is no special support for multiple transcripts;
when inferring UTRs, the largest bounding range of given CDS data
is used.
</ul>
<li> A new control in the menu bar allows the user to limit the displayed
alignments by their average % identity.
<ul>
<li> Keyboard shortcuts make it easy to move the threshold up and down.
<li> The value for the current plot block is displayed with the mark
information when applicable.
</ul>
<li> If the alignment file contains per-nucleotide reconstruction scores
for an inferred ancestral sequence, they can be displayed as a pair of
bar graphs, binned according to the current zoom region and panel size.
<ul>
<li> The scores are transformed via simple linear scaling, and should
not be interpreted as probabilities.
<li> A new <code>reconseq</code> field in the parameters file
identifies the organism for the scores.
</ul>
<li> Miscellaneous:
<ul>
<li> "Unsupported MAF version" is now a warning instead of a fatal
error.
<li> A new <code>nowarn</code> field in the parameters file suppresses
certain warnings/errors using a keyword shown in the message.
<li> When opening a new window, the current zoom is translated to a
roughly equivalent one in the new sequence(s).
<li> Sequence choices in the Show dialog affect text rows and dotplots
in addition to pips.
<li> The default highlights built from exons now include the genes
(light yellow).
<li> The divider between the position indicator and the zoom indicator
is draggable.
<li> Plot segments are drawn thicker in Large Fonts mode.
<li> Plots that are completely empty have a gray background.
<li> The Set Zoom dialog accepts a blank box to mean "leave unchanged".
<li> Tabbing is easier in input dialogs: labels are skipped unless the
mouse is pointing at them.
<li> Note that "<code>=</code>" is now required for settings in the
parameters file (except <code>seq&nbsp;N:</code> lines), and
lines with empty values (e.g. unused template items) are allowed
and skipped.
</ul>
<!--
<li> Bug fixes:
<ul>
<li> Linkbar URLs are supposed to be optional; missing ones are now
handled gracefully.
<li> Entries in the parameters file for particular-pip underlays were
not recognized properly if the underlay file was bundled.
<li> Attempting to display a reference sequence that had no alignments
would cause a Java error.
<li> On some platforms, rebuilding all of the Gmaj windows (e.g. when
Options settings were changed) would leave the keyboard focus in
the wrong window.
</ul>
-->
<li> Various minor bug fixes, and improvements in appearance, behavior,
messages, efficiency, and robustness.
<li> Updated documentation.
<ul>
<li> Terminology: the optional colored clickable bars located above
the exons panel were formerly called "annotations", "annotation
links", or "hyperlink annotations", but are now referred to as
"linkbars" so that "annotation" can be used in the general sense.
</ul>
</ul>
<p>
<dt><b>2006-Jun-17</b><br>
<dd> <ul>
<li> Gmaj can now be deployed as a web-based applet, as an alternative to
the regular stand-alone mode.
&nbsp;<a href="http://globin.bx.psu.edu/java/gmaj/demo.html">Demo</a>
<ul>
<li> New parameters <code>bundle</code>, <code>initzoom</code>, and
<li> New parameters <code>bundle</code>, <code>initzoom</code>, and
<code>urlpause</code> facilitate applet use, but also work in
stand-alone mode.
<li> Clicking on hyperlinked annotations (colored bars) visits the
@@ -27,14 +135,13 @@
stand-alone mode, displays the file location).
<li> The "File - Export" feature does not work yet for applets.
</ul>
<li> Better conformance with the official UCSC specs for <code>.maf</code>
format.
<li> Better conformance with the official UCSC specs for MAF format.
<li> A new <code>refseq</code> field in the parameters file can be used
to prevent selection of an inappropriate reference sequence when the
alignments are not sequence-symmetric (e.g. from <i>multiz</i>).
<li> Maximum zoom bounds are now the stated sequence length from the
<code>.maf</code> file (not just the extent of the blocks), but the
default initial view zooms to the aligned portion.
<li> Maximum zoom bounds are now the stated sequence length from the MAF
file (not just the extent of the blocks), but the default initial
view zooms to the aligned portion.
<li> Search rules for relative filenames have been simplified, and Windows
names starting with "<code>\</code>" are now handled better.
<li> The panel for hyperlinked annotations is now labeled, and it displays
@@ -183,8 +290,8 @@
they are the same. The old <code>underlays.N</code> parameters are
still supported as well, and override these new ones.
<li> The <code>seqfile</code> parameter has been renamed to
<code>seqname</code>, in order to reflect <code>.maf</code> semantics
(but <code>seqfile</code> is still supported for backward compatibility).
<code>seqname</code>, in order to reflect MAF semantics (but
<code>seqfile</code> is still supported for backward compatibility).
<li> Sequence label widths are now computed dynamically, based on the longest
name and the current font.
<li> When the font size is changed, pip heights are also adjusted.
@@ -204,7 +311,7 @@
<li> The jar manifest and About information have been updated.
<li> Support for alignment files in <code>.bb</code> format (from the old
<i>blockbuilder</i> program) has been discontinued. The only alignment
format currently supported is <code>.maf</code>.
format currently supported is MAF.
<li> Due to a new mechanism for registering keyboard shortcuts, Gmaj now
requires <b>Java 1.3 or higher</b>.
<li> This version should still be considered <b>beta quality</b>; please
@@ -214,8 +321,8 @@
<p>
<dt><b>2005-May-16</b><br>
<dd> <ul>
<li> Gmaj can now handle a wider variety of <code>.maf</code> files, including
those containing reverse-complement alignments.
<li> Gmaj can now handle a wider variety of MAF files, including those
containing reverse-complement alignments.
<li> The "proper threading" requirement has been eliminated.
<li> Dynamic memory management for plot and underlay data allows larger files
to be viewed.
@@ -243,9 +350,9 @@
<i>chained</i>, i.e., that for each sequence it is possible to order
the blocks so that every nucleotide from that sequence in the interval
<code>[1,length]</code> appears exactly once, and in the same order as
the original sequence. (Note that <code>.maf</code> files are 0-based,
so <code>+1</code> is added to all <code>.maf</code> coordinates to
convert them to Gmaj's 1-based system.)
the original sequence. (Note that MAF files are 0-based, so
<code>+1</code> is added to all MAF coordinates to convert them to
Gmaj's 1-based system.)
However, sometimes you may want to use Gmaj to display a subset of such
data (e.g., output from the <i>slice_maf</i> program). Gmaj can now
handle input data where the chain starts after position <code>1</code>
@@ -257,11 +364,11 @@
<p>
<dt><b>2003-Sep-16</b><br>
<dd> <ul>
<li> Gmaj can now handle alignment files in the <code>.maf</code> format
produced by the <i>tba</i> program, in addition to the <code>.bb</code>
format produced by <i>blockbuilder</i>.
<li> When using a <code>.maf</code> alignment, the semantics of the parameters
file are a bit different, and its rules are stricter. (See
<li> Gmaj can now handle alignment files in the MAF format produced by
the <i>TBA</i> program, in addition to the <code>.bb</code> format
produced by <i>blockbuilder</i>.
<li> When using a MAF alignment, the semantics of the parameters file
are a bit different, and its rules are stricter. (See
<code><a href="sample.gmaj">sample.gmaj</a></code> for details.)
<li> Gmaj still doesn't support reverse complement alignments, or multiple
contigs per sequence.
@@ -315,6 +422,6 @@
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
</body>
</html>
static/gmaj/docs/gmaj_readme.html
+16 -16
View File
@@ -2,23 +2,23 @@
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title>Information About Gmaj</title>
<title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta http-equiv="Content-Style-Type" content="text/css">
<link rel="stylesheet" type="text/css" href="gmaj.css">
</head>
<body>
<p class=vvlarge>
<h2>Information About Gmaj</h2>
<h2>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</h2>
<p class=vvlarge>
Gmaj is a tool for viewing and manipulating Generalized Multiple
Alignments (GMAs) produced by programs such as
<a href="http://www.bx.psu.edu/miller_lab/">TBA</a> (though it
can also be used with <code>.maf</code> format alignments from
other sources). It can display interactive graphical and text
representations of the alignments, a diagram showing the
locations of exons and repeats, and other annotations -- all
with the user's choice of reference sequence.
Gmaj is a tool designed for viewing and manipulating Generalized
Multiple Alignments (GMAs) produced by sequence-symmetric alignment
programs such as <a href="http://www.bx.psu.edu/miller_lab/">TBA</a>
(though it can also be used with MAF format alignments from other
sources). It can display interactive graphical and text
representations of the alignments, diagrams showing the locations
of exons and repeats, and other annotations -- all with the user's
choice of reference sequence.
<p>
The program is written in Java in order to provide a graphical
user interface that is portable across a variety of computer
@@ -53,8 +53,8 @@ The following additional documentation files are included:
<p>
<li> <a href="gmaj_bugs.html">Known Bugs in Gmaj</a><br>
A discussion of the known bugs and anomalies we have
observed, but not yet tracked down. Some of these may
depend on your version of Java.
observed, but not yet resolved. Some of these may depend
on your computer platform and/or version of Java.
<p>
<li> <a href="gmaj_install.html">Installing Gmaj</a><br>
Describes how to unpack and set up Gmaj, for both
@@ -72,14 +72,14 @@ The following additional documentation files are included:
<li> <code><a href="sample.gmaj">sample.gmaj</a></code><br>
A sample template for the parameters file that tells Gmaj
which data files to load, among other things. Includes
some explanatory comments at the bottom. This file is
optional if you don't want to display any annotations or
use the other features it provides.
explanatory comments at the bottom. This file is optional
if you don't want to display any annotations or use the
other features it provides.
</ul>
<p>
<p class=vvlarge>
<hr>
<i>Cathy Riemer, June 2006</i>
<i>Cathy Riemer, July 2007</i>
</body>
</html>
static/gmaj/docs/sample.gmaj
+113 -53
View File
@@ -9,38 +9,41 @@ title = "My favorite genomic region"
datapath = /home/cathy/mydata/favreg/
alignfile = tba.maf
refseq = any
reconseq = none
tabext = .gff .gtf .bed .ct .trk
nowarn = maf_version repeat_type_missing
seq 0:
seqname = human
exons = exons.human
repeats = repeats.human
links = links.human
underlays = underlays.human
underlays.1 = underlays.human-mouse
underlays.2 = underlays.human-rat
highlights = highlights.human
offset = 1300000
seqname = human.chr11
exons = human.exons.bed chr11
repeats = human.repeats
links = human.links
underlays = human.exons.bed chr11 exons
#underlays.1 = human-mouse.underlays
#underlays.2 = human-rat.underlays
highlights = human.highlights
offset = 4730995
seq 1:
seqname = mouse
exons = exons.mouse
repeats = repeats.mouse
links = links.mouse
underlays = underlays.mouse
underlays.0 = underlays.mouse-human
underlays.2 = underlays.mouse-rat
highlights = highlights.mouse
seqname = mouse.chr7
exons = mouse.exons
repeats = mouse.repeats
links = mouse.links
underlays = mouse.underlays
#underlays.0 = mouse-human.underlays
#underlays.2 = mouse-rat.underlays
highlights = mouse.highlights
offset = 0
seq 2:
seqname = rat
exons = exons.rat
repeats = repeats.rat
links = links.rat
underlays = underlays.rat
underlays.0 = underlays.rat-human
underlays.1 = underlays.rat-mouse
highlights = highlights.rat
seqname = rat.chr1
exons = rat.exons
repeats = rat.repeats
links = rat.links
underlays = rat.underlays
#underlays.0 = rat-human.underlays
#underlays.1 = rat-mouse.underlays
highlights = rat.highlights
offset = 0
#----------------------------------------------------------------
@@ -53,13 +56,18 @@ offset = 0
# Syntax:
#
# Each key=value pair must reside on its own single, separate
# line. Other than that, the format is fairly loose. Even the
# order of lines is arbitrary, except that "seq N:" defines the
# current sequence until it is superseded by a new "seq N:" line.
# Either the '=' sign or whitespace suffices to separate keywords
# from values. A '#' at the beginning of a line marks a comment
# that will be ignored, except for the identifier tag "#:gmaj" at
# the top, which is mandatory.
# line. (Note that although the '=' was formerly optional, it
# is now required.) Other than that, the format is fairly loose.
# Even the order of lines is arbitrary, except that "seq N:"
# defines the current sequence until it is superseded by a new
# "seq N:" line. Values containing spaces must be enclosed in
# double quotes. Embedded quotes in such strings can be escaped
# with '\', but there is no way to escape the backslash: quoted
# values should not end with '\' (insert a space before the
# final quote if necessary). Lines with missing values are
# skipped. A '#' at the beginning of a line marks a comment
# that will be ignored, except for the identifier tag "#:gmaj"
# at the top, which is mandatory.
#
# Required Fields:
#
@@ -78,16 +86,16 @@ offset = 0
# 2. the "datapath" specified here (if any)
# 3. the same directory as this parameters file
#
# If you are using Gmaj's "bundle" feature, refer to files
# located in the bundle by their plain filenames, without any
# path.
# If you are using Gmaj's "bundle" feature, you must refer to
# the files located in the bundle by their plain filenames,
# without any path.
#
# Title:
#
# This string will be used as the title for the Gmaj windows.
# It should briefly describe the alignment data, including the
# name of the locus. It does not control the applet button's
# label, however, because the applet has not read this file yet;
# Typically it describes the alignment data, including the name
# of the locus. It does not control the applet button's label,
# however, because the applet has not read this file yet;
# instead there is a separate applet parameter for that.
#
# Reference Sequence:
@@ -97,42 +105,93 @@ offset = 0
# was generated by a sequence-symmetric program such as TBA, so
# the user should be allowed to select the reference sequence
# interactively. Otherwise, the value must match the appropriate
# sequence name from the maf file (including the contig name, if
# sequence name from the MAF file (including the contig name, if
# applicable).
#
# Reconstructed Sequence:
#
# If the alignment file includes score rows for an ancestral
# reconstruction, the reconseq field identifies which organism
# these scores apply to. The default value "none" means Gmaj
# will ignore the scores; otherwise the value must match the
# species prefix of the appropriate sequence names from the MAF
# file. Contig name extensions (e.g. ".chrX") are omitted, as
# the scores can apply to any contig for that organism.
#
# Tabular File Extensions:
#
# The tabext field specifies which filename extensions should
# be treated as generic, tab-delimited formats (GFF/GTF/BED)
# instead of the old PipMaker-style formats. The default list
# is ".gff .gtf .bed .ct .trk". Note that it doesn't actually
# matter which of these is used for a particular file, just
# whether it is in the list.
#
# Warning Suppression:
#
# The nowarn field lists keywords for particular warning
# messages that should not be displayed. This is especially
# useful for applets, when the administrator has seen the
# warning, checked the data, and determined that everything
# is OK and the end user does not need to see the warning.
# The keyword for each suppressible message is displayed at
# the bottom of the message.
#
# Sequence Numbers and Sequence Names:
#
# The seqname field serves to match up the parameter entries with
# the sequence name in each row of the maf alignment (including
# the sequence name in each row of the MAF alignment (including
# the contig name, if applicable). The sequence number assigns
# the display order, and is also used to identify the secondary
# sequence for pip-specific underlays (see below).
# sequence for plot-specific underlays (see below).
#
# Sequence numbers start with 0 and must turn out to be
# consecutive, after Gmaj fills in any gaps you leave with the
# maf sequences you don't mention here. Thus if the alignment
# MAF sequences you don't mention here. Thus if the alignment
# file includes ten sequences, the valid sequence numbers would
# be 0-9, and Gmaj will assign any that you omit (in the order
# it encounters them).
#
# File Specification Modifiers:
#
# The generic, tabular annotation formats (GFF/GTF/BED) allow
# entries for several sequences to be combined in one file,
# since they can be distinguished by the "seqname" or "chrom"
# column. However in this case Gmaj will expect the column
# value to match the seqname from the MAF alignment. If it
# does not (e.g. if the MAF file includes a species prefix but
# the annotation file omits it), you can add a sequence alias
# after the filename to tell Gmaj what to look for in the
# annotation file.
#
# Gmaj has special support for annotation data that represents
# exons or repeats (namely adding exon numbers and inferring
# UTRs, or finding the PipMaker repeat category). For the exons
# and repeats panels this is automatic, but you can also invoke
# it explicitly for files used as linkbars, underlays, or text
# highlights by adding a type hint of "exons" or "repeats" after
# the filename. This only works if the file is in a generic
# (GFF/GTF/BED) format and contains the appropriate type of data
# (genes/exons or repeats).
#
# Underlays and Highlights:
#
# Gmaj allows you to specify color underlays independently for
# each pip, i.e., for each combination of reference and secondary
# sequences. Thus in the "seq 1:" section, the "underlays.0"
# entry specifies the underlay file to be used when sequence 1 is
# the reference and sequence 0 is the second sequence. Note that
# there is e.g. no "underlays.1" entry in the "seq 1:" section,
# since we do not currently have any pips aligning sequences with
# themselves.
# each plot, i.e. for each combination of reference and
# secondary sequences. Thus in the "seq 1:" section, the
# "underlays.0" entry specifies the underlay file to be used
# when sequence 1 is the reference and sequence 0 is the second
# sequence. Note that there is e.g. no "underlays.1" entry in
# the "seq 1:" section, since we do not currently have any plots
# aligning sequences with themselves.
#
# However, specifying a quadratic number of files quickly becomes
# burdensome as the number of sequences grows. For the common
# case where the same underlay file is used for most or all of a
# particular reference sequence's pips, the plain "underlays"
# particular reference sequence's plots, the plain "underlays"
# entry (without a number) provides a default for that reference
# sequence. This can still be overridden as needed by numbered
# entries for special pips.
# entries for special plots.
#
# The highlights file specifies colors for a particular row of
# the text display, so there is only one for each sequence. If
@@ -146,7 +205,8 @@ offset = 0
# displayed references for a particular sequence. For example,
# this allows positions to be labeled with respect to some larger
# region. However, note that all annotations must still be
# specified relative to the portion that was actually aligned.
# specified relative to the sequences referred to in the MAF
# file.
#
#----------------------------------------------------------------
# $Revision: 1.8 $$Date: 2006/06/17 02:35:44 $
# Cathy Riemer, July 2007
static/gmaj/gmaj.jar
BIN
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tools/visualization/GMAJ.xml
+1 -6
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@@ -17,14 +17,9 @@ You can use this tool to view a set of MAF alignments. You may also include opt
For detailed information on GMAJ, click here_.
.. _here: http://globin.cse.psu.edu/dist/gmaj/
.. _here: /static/gmaj/docs/gmaj_readme.html
Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.
.. class:: infomark
**Note:** This Applet version of GMAJ is still under beta development.
</help>
</tool>