Map viewer

You can see map information as well as reference map by use of the viewer once you click 'Map viewer' link of each virus.
There are two modes of the viewer, java mode (see 1.) and image mode (see 2.).

1. java mode

This is a default (and an initial) mode. In this mode, you can obtain a set of entries which cover a specific region on the genome.
Functions or properties of parts of the viewer are described below.

1.1. menu bar

It locates on the top of the viewer. Items of the menu bar, which extracts a data set or changes drawing style of the map, are changed by the most left menu. The followings are functions of the items.

1.1.1. data menu

You can extract data set of the specified locus or the region of the genome. There are three methods to choose a locus or a region.

By cliking the filled box of a locus.
The box darkens.
By dragging a region on the map.
The red line (linear genome) or the red fan-shape (circular genome) is shown at the region.
By typing start and end position in the fields in the menu.

Then you can obtain one of the following data sets by clicking a button in the menu.

entry : full annotated data (entries)
sequence : nucleic acids sequences
peptide : amini acids sequences

1.1.2. division menu

This menu is available on account mode only. You can make a private division from the obtained data. After choosing a region by the same way as 'data menu' and typing a division name in the field, the new private division is made by clicking 'make' button.

1.1.3. font menu

You can change a font (face, style, and size) which is used to draw loci names and scales in the map.

1.1.4. redraw menu

You can force to redraw the graphic by selecting this item.

1.2. map graphic

At the center of the viewer, map information as well as reference map are displayed. In this graphic, filled boxes that show the loci (reference map) are on the top, the ruler of the base position on the genome is next, and under the ruler are numerous horizontal lines, each of which shows the location of each entry (map information).

In the case of circular genome (eg. HBV), a circular-style map is displayed. In this graphic, the ruler of the base position is in the center, thick arcs which show the loci (reference map) are next, and on the outside are numerous arcs and circles, each of which shows the location of each entry (map information).

1.3. items to change the graphic size

You can change the size of graphic by typing width/height to fields and then clicking 'resize' button.

2. image mode

In this mode, map is displayed by a JPEG image file instead of JAVA. Although data extraction is not available in the mode, you can print or save the map. You can use the mode of the viewer by clicking '[image mode]' at the bottom of the java-mode viewer.
Functions or properties of parts of the viewer are described below.

2.1. map graphic

At the top of the viewer, a map is displayed by nearly the same style as java-mode map.

2.2. items to change the graphic style

You can change the size of graphic or font size which is used to draw loci names and scales. After filling width and height fields and/or choosing font size, you click 'redraw' button and you can get a map of a new style.