Starting and Running Gmaj



Gmaj can be run in two different modes: as an applet over the world-wide web (for viewing data delivered from a server), or as a stand-alone application (for viewing data stored on your own computer). These modes are mostly similar but have a few minor differences, as noted below.

Starting Gmaj

If you are using Gmaj in applet mode, it will be started for you when you visit the applicable web page or submit a query to the server. If the Gmaj window does not appear automatically, just click on the labeled button to view the indicated data. Then 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 Command Prompt window on Windows XP). The basic command to type in looks like this:

    [path1]java -jar [path2]gmaj.jar
where [path1] is the location of your java program file (perhaps c:\windows\system32\ on WinXP, or /usr/bin/java/ on a Unix system), and [path2] is the location where the gmaj.jar file was installed. Note that you can leave off [path1] if you have set up your system command path to include the location of the java program. Depending on how your system is set up, it may also be possible to run the jar file directly by just typing its name or double-clicking on it.

Since you haven't yet specified any data to display, Gmaj will begin by presenting a dialog box to prompt you for the name of your input file (see Input Files for Gmaj). If the file is located in the current directory you can just type its name, otherwise you'll need to supply a complete path. When you click the OK button, a window will appear displaying the loaded data.

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 command syntax is:

    [path1]java -jar [path2]gmaj.jar
        [-version] [-help] [-debug] [-urlpause <millisec>]
        [-initzoom <refseqname> <start> <end>]
        [-bundle <zipfile>] [<paramfile>|<alignfile>]

This has been wrapped here for easier readability, but should be typed all on one line. Arguments shown in square brackets [] are optional, while a vertical bar | indicates a choice between alternatives. Angle brackets <> signify meta-syntactic variables that should be replaced with your names or numbers. Don't type any of the brackets or the bar.

These parameters do the following:

Prints a message with information about Gmaj, including version, author, etc.; then exits.
Prints a brief help message with up-to-date syntax; then exits.
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.
Specifies how many milliseconds the program should pause before retrieving each file from a URL, in order to avoid overloading the server.
Specifies an initial zoom setting to be applied when the window opens. You will still be able to invoke the Unzoom or Set Zoom features interactively to see the entire sequence range. The <refseqname> must match one of the sequence names from the alignment file(s), and the endpoints must include the offset (if any) for that sequence from the parameters file. To specify the reference sequence without a zoom region, use -1 for both endpoints.
Specifies the name of a .zip or .jar file containing some or all of the data files. This option is mostly used with Gmaj's applet mode to streamline the data download, but it is also supported in stand-alone mode. It is described in Input Files for Gmaj.
This is the meta-data parameters file that lists the names of all the data files, plus a few related parameters such as display offsets and any intrinsic reference sequence. For more information about the contents and format of this file, please see Input Files for Gmaj and sample.gmaj.
If you don't want to use any annotations or other data-related options, you can specify a single alignment file directly, instead of creating a parameters file. This must be in MAF format; see Input Files for Gmaj for more details.

Memory Allocation

If the dataset you want to view is large, Gmaj may run out of memory, in which case Java will report an OutOfMemoryError. This message will appear in the command window where you started Gmaj (for stand-alone mode) or in the Java Console window of your web browser (for applet mode). If the Java Console window does not appear when you run the Gmaj applet, open the Java Plug-in Control Panel on your computer and click the setting for Show Console so you can see this and other Java messages.

The OutOfMemoryError is not uncommon, because the default amount of memory that Java allocates is rather small. You can give it more memory using the -Xmx switch (at least with Sun's Java; this option may not be supported by all vendors). For example, when using stand-alone mode the command line

    [path1]java -Xmx1024m -jar [path2]gmaj.jar
runs Gmaj with a heap memory allowance of ~1 gigabyte. For the applet, you can do this by opening the Java Plug-in Control Panel on your computer and entering -Xmx1024m in the Java Runtime Parameters box (this will affect all applets you run via the Java Plug-in, not just Gmaj).

Multi-Pip and Dotplot Windows

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 alignments, of a particular reference sequence against each of the other sequences. A pip is similar to a dotplot, with the horizontal x-axis representing positions in the reference sequence, but the vertical y-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 usually of this type, and if the alignments are reference-independent, you can open more of these with other sequences as the reference.

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, Laj). 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.

For the special case where the alignment files have only two sequences, the main window is redundant so Gmaj automatically hides it and shows the dotplot window directly.

The Zoom and the Mark

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 files; 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.

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 red 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.

Window Layout

Each Gmaj window is divided into several sections. Across the top you will see a menu bar (including text boxes for setting display thresholds), 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 (red 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. Below these is a row of category checkboxes, which by default will only appear when there is more than one alignment file or if you have used the tagging feature. The menus, threshold boxes, buttons, and checkboxes are discussed individually in the Menus and Widgets section of this document.

The first graphical panel is a horizontal ruler that displays tick marks corresponding to positions in the currently selected reference sequence. These are intended to give you an immediate general feel for the location and scale of the region being displayed. Precise locations can be determined via the position indicator, which displays the exact coordinate of the mouse pointer.

Reconstruction scores:
For ancestral reconstruction alignments, the MAF files 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).

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 x coordinate of the pointer, and also the type and description of that bar's annotation; otherwise only the x 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 no links file is provided for the current sequence, this panel will not appear.

Sequence features:
The next two panels contain schematic diagrams of the known 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 (which is why the label says "repeats+"). The diagram for repeats uses the same symbols as PipMaker to indicate the various repeat categories (Alu, MIR, etc.), but only if either the PipMaker category or the RepeatMasker name and class/family are available. For example, BED and GTF repeat files from the UCSC Table Browser 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 x coordinate of the mouse pointer, and also identifies any features at that position.

The following panels display the alignment plots according to the window type: either a scrollable stack of pips (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. Plot segments from the primary alignment file are drawn with thin black lines, while those from subsequent files are drawn with thicker brown lines. Tagged blocks are green, and the marked block is red (or orange if it is also tagged), though these may vary on colored backgrounds. When plot segments overlap, the marked and tagged ones are drawn "on top" so they won't be obscured, followed by other blocks from the primary alignment file and then the remaining files. 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 block numbers 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.

Text view:
The bottom panel displays a nucleotide-level view of a single selected alignment block: the one containing the mark (red 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 (.) 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 X or N never match anything, even themselves.) All of the sequences will likely have had gaps (-) 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. 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 n(x), where n is the column position in this aligned block (starting with 0), and x is the sequence position in the individual row (i.e., in that entire chromosome or contig, starting with 1). Note that x does not include the gaps, but n does. Labels for any highlights at that position are also displayed.

With the exception of the text view, all of these data 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 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 Menus and Widgets).

Mouse Controls

As discussed in more detail above, pointing with the mouse in the plots or other panels causes the position indicator below the menu bar to display information about that location and/or data item.

You can select a particular alignment block by clicking on one of its segments in any of the plots (pips or dotplots) with the left mouse button. (You don't have to click exactly on it, because Gmaj will automatically jump to the nearest point if you miss; however proximity is measured in bases, not pixels, which can lead to non-intuitive results if the dotplot's zoom scale is highly skewed.) The spot will be marked with a small red circle, and the entire alignment block containing the mark will change color from black to red 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 block numbers covering the marked location. These buttons allow convenient selection of a different block at the same position in the reference sequence, from the same or a different alignment file (see Menus and Widgets). Note that there is only one mark at a time for each reference sequence, so the previous one, if any, will be unmarked.

In a similar fashion, clicking the left mouse button in the text view will move the mark (both the highlight and the red circle) to that position. However, gap positions cannot be selected in this manner because they do not 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 the same pip as before.

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, 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 Menus and Widgets). 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. If your rectangle is very tiny it will be treated as a click instead, to avoid unintended zooming.

Holding down the right mouse button over any of the white panels adds crosshairs at the mouse pointer's location, which is convenient for determining whether two regions really line up. If you have a one-button mouse, you can achieve the same effect by applying the Shift key when initially pressing the mouse button.

Note that these controls only work in the active window (usually indicated in the operating system by a differently colored title bar). If a window is not the active one, then your first click in it just activates the window; you will need to click again to set the mark, select a region, open a menu, etc.

Menus and Widgets

File - Open:
Loads a new set of data files into Gmaj, replacing the currently displayed data. A dialog box is presented for you to specify the new input file. (See discussion under Starting Gmaj, above.) This menu item does not appear in applet mode, because the user is unlikely to know the locations of other data files on the server; instead the webmaster should set up separate access for each dataset.

File - Export:
Opens a dialog box that allows you to save alignment blocks in MAF format or as FastA sequence files. A variety of options are available re: which blocks to export, whether they should be clipped and/or cleaned up, whether to omit certain sequences, etc. Note that all-gap rows are always skipped, and so are blocks that have no rows left. When exporting in MAF format, if the alignment has a fixed, intrinsic reference sequence and that row is all gaps, the entire block will be skipped. When exporting FastA sequences, a separate file is created for each sequence name (i.e. species or contig), and there is an option to restore sequences that align in reverse complement to their original orientation (which will also swap the order of the endpoint coordinates in the FastA header). By default export is not available in applet mode, because security restrictions make it very awkward to save files on the client computer. However, the applet administrator can specify a URL where the output can be sent instead (in this case only MAF format is supported).

File - Close:
Closes the current window, and if it is a multi-pip window, all of its dotplot children are closed as well. When no windows are left, Gmaj will exit.

File - Exit:
Exits from Gmaj. In stand-alone mode, also exits from Java.

This menu controls some of the aesthetic aspects of Gmaj. You can choose between two sizes of fonts, which will also affect some other viewability 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 change color with the background instead of always being red (this makes them visible against red underlays, but is more complicated to explain in a figure legend and causes patchy rendering when used with Large Fonts). Lastly, the Show item opens a dialog where you can choose which panels to display or hide, and whether the underlays should be painted on dotplots. The sequence selections here control which pips, dotplot windows, and text rows are displayed (except where that sequence is the reference). They can also serve to omit sequences from exports if desired; in this case they apply even to the reference sequence, but if the alignments have a fixed, intrinsic reference it will be grayed out to avoid exporting "orphaned" blocks. The choices on this menu affect all of the windows, not just the current one.

This menu allows you to select a different reference sequence (unless the parameters file indicates that the alignments have a 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. The text alignments will be rearranged to put the reference row at the top, but the rows are always shown in their MAF orientation. Thus if the reference row is on the '-' strand, its coordinates will decrease from left to right in the text panel. 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.

Zoom - Back:
Moves backward in your zoom history for this window, returning to previous regions. Does not affect the mark.

Zoom - Forward:
Moves forward in your zoom history for this window. Does not affect the mark.

Zoom - Unzoom:
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 files. Has the same effect as entering the "valid range" endpoints in Set Zoom. Does not affect the mark.

Zoom - Set Zoom:
Presents a dialog box that allows you to enter arbitrary zoom 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 browser). Does not affect the mark.

Tags - Tag/Untag Block:
The tagging feature allows you to build an arbitrary subset of the alignment blocks for differential viewing or export (see Category Checkboxes). There is only one tagged subset in each invocation of Gmaj, and it pertains to all windows. This menu item toggles the status of the currently marked block (the one containing the red circle), tagging it if it's not already in the set, and removing the tag if it is.

Tags - Clear All Tags:
Empties the tagged subset by removing the tags from all blocks. Also hides the category checkboxes if they are no longer useful.

Help - About:
Displays a message window with information about Gmaj, including version, author, etc. Also reports the version of Java you are currently using.

Help - Manual:
In applet mode, opens a new browser window to view this help page. 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.

Help - Keys:
Displays a message window listing Gmaj's keyboard shortcuts. No Alt key is needed. The shortcuts will not work if the keyboard focus is in a text area (threshold boxes, status indicators, text alignment, panel headers, etc., as indicated by a purple border or highlight); in this case press Esc first to cancel any text operation and restore the focus to the active window's menu bar. Esc will also cancel dialog and message boxes.

Help - Sequence Summary:
Displays the aligning extents for all sequences (i.e., the smallest range in each sequence that includes all of its aligning regions). This is useful when fetching annotations from the UCSC Table Browser or other databases, or for identifying the relevant parts of already-in-hand annotation files so they can be trimmed down to size.

% Identity Box:
Allows you to set a threshold for filtering 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, with no penalty for gaps. A plot block below the threshold is not drawn or clickable in the plots, and the row for its secondary sequence is omitted in the text alignment panel; additionally it is excluded from the position indicator's block list and from the row of block buttons for the mark. However, these plot blocks are only hidden and still exist otherwise (e.g., for export). Setting the threshold will not move the mark, even if the marked position becomes hidden. 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 (the current plot block is either the marked one, or if a dotplot has a different secondary sequence, the corresponding projection from the same MAF block).

Underlays Box:
Allows you to set a threshold for filtering the displayed underlays and highlights based on the optional score values you have assigned in the annotation files. The GFF, GTF, and BED formats already include a score field, and the PipMaker-style underlay format has been extended to include one as well (see Input Files for Gmaj). Some of these formats allow floating-point score values, but they will be rounded off to integers for comparison with the threshold. Missing scores are treated as the maximum possible value, so they will never be filtered out; however note that 0 (which is sometimes used to mean "no score") will not be changed, since Gmaj cannot distinguish this from a score that is really zero. As with the % Identity box, the same threshold applies across all windows, and keyboard shortcuts make it easy to adjust it up and down. Also, pointing to a particular underlay or highlight will show that annotation's score in the position indicator.

Arrow Buttons:
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 or height. 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.

Block Buttons:
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 the block numbers 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 (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.

Category Checkboxes:
These controls are located in a separate panel below the mark indicator, and allow you to show or hide several groups of alignment blocks en masse. There is one checkbox for each of the alignment files in the input, and an extra one for the tagged blocks (whose label shows how many blocks are tagged); the colors of the labels correspond to the plot segments they control. The tagged blocks are considered to be withdrawn from their files for this purpose, so all of the categories are disjoint. These settings apply across all windows, and as with the % identity threshold, hidden blocks are omitted from the plots and certain lists, but still exist otherwise. By default this panel only appears when it is relevant (i.e. if there is more than one alignment file, or you have used the tagging feature), but you can also show or hide it temporarily from the Options - Show dialog.

Dotplot Buttons:
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 The Zoom and the Mark). If you already have a window for that dotplot, it will just be brought to the front unchanged.

Draggable Dividers:
Several of the panel dividers can be moved by dragging them with the mouse to adjust the amount of space allocated to the items on each side. These include the vertical bars separating the left and right sides of the status indicator panels, and the horizontal bar separating the pips from the text alignment in a multi-pip window. On most platforms Java draws these dividers with a pattern of little bumps to suggest a grip. In Gmaj they also have a sticky feature that remembers if you moved them manually and keeps them at that position (until they are rebuilt due to a font change, etc.). In sticky mode the divider appears pushed in, like a button; if you want to return to the default floating mode (where the divider is repositioned automatically as the panel content changes), just click on the pushed-in divider to release it.

Copying and Printing

Gmaj supports copy/paste via the system clipboard from most of its text panels and dialog boxes, using mouse selection followed by the standard keystrokes (Ctrl-C/Ctrl-V on Windows and Linux, Cmd-C/Cmd-V on Mac). Some labels are not copyable, but their values generally are. (Exception: with some versions of Java, all dialog text may be uncopyable in applet mode due to a bug.)

In Gmaj's multi-pip and dotplot windows the text alignment, panel headers, and status indicators are copyable. Clicking in any of these components (e.g. to sweep out a selection with the mouse) will transfer the keyboard focus to that component, as indicated by purple lines around it. This is necessary for the Copy keystroke to work; however it means that Gmaj's other keyboard shortcuts will be disabled until the focus is restored, either by clicking somewhere else or by pressing the Esc key. Note that the mouse selection in the text alignment is rectangular (unlike the usual line-wrapped stream), and all of these components can be scrolled if necessary by dragging the mouse just outside their borders.

Gmaj does not currently have its own print capability. The recommended way to record a particular Gmaj view is to use your operating system's "screenshot", "print screen", or "grab" facility to save an image of the window to a file, then adjust it as needed using image-editing software. (Be careful with rescaling and format conversions, as these may degrade the image.)

To prevent the position indicator from changing when you move the mouse, hold down the Ctrl key. This is useful both for copying the position indicator's contents and for taking screenshots.


[1]  By default the circular mark and the selected block's plot segments are always red (or orange), regardless of the background color behind them, and similarly tagged blocks are always green. A setting on the Options menu can make these colors vary with the background (so they are not invisible against like-colored underlays), however this causes patchy rendering when used with Large Fonts. These special blocks are drawn last, so they will not be obscured by ordinary ones.

[2]  Blocks in the MAF files are numbered consecutively, starting with 0. MAF files are also numbered starting with 0, in the order they are listed in the parameters file. If there are several MAF files, they are catenated into one big list of blocks, and the block numbers for the second file continue where the first left off. However, Gmaj also records the relative block numbers within each file, and displays this information in the mark indicator and certain error messages in the form maf#.block#.

[3]  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 reference 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. In order to appear in the row of block buttons for the mark or in the position indicator's block list for pips, a block must also be in a visible category (according to the category checkboxes) and meet the % identity threshold (in the applicable plot).

Cathy Riemer, June 2008