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.
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.
Patchy rendering of mark circle and/or red segments.
+ 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).
+
+
+
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 red
-circle, and the entire alignment block containing the mark will
-change color from black to red 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 block numbers covering
-the marked location. These buttons allow convenient selection
-of a different block at the same position (see Menus and Buttons). 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 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 (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 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.
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
-Menus and Buttons). Note that selecting
+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).
@@ -329,7 +439,8 @@ effect by applying the Shift key when initially
pressing the mouse button.
-
+
+
- File - Open:
@@ -367,27 +478,32 @@ 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 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.
-
- RefSequence:
+
- Reference:
-
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.
- Zoom - Back:
-
@@ -401,15 +517,17 @@ affect the mark.
- Zoom - Unzoom:
-
-Sets the zoom region to the widest, unzoomed view, i.e., the
-full range for this reference sequence as specified in the
-
.maf 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.
- Zoom - Set Zoom:
-
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.
- Help - Keys:
-
-Displays a message window listing Gmaj's keyboard shortcuts. No
-
Alt key is needed, since Gmaj doesn't use the
-keyboard for much else.
+Displays a message window listing Gmaj's keyboard shortcuts.
+No Alt 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 Esc first to cancel the text
+entry and restore the focus to the active window's menu bar.
+Esc will also cancel dialog and message boxes.
+
+
- % Identity Box:
+
-
+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).
- Arrow Buttons:
-
-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.
- Block Buttons:
-
-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
-block numbers 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 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.
+
+
- 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.
+
[1]
-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.
[2]
-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 .maf 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 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.
+Blocks in the MAF file are numbered consecutively, starting
+with 0.
-Cathy Riemer, June 2006
+Cathy Riemer, July 2007