Introduction

The Gap Contig Selector is used to display, select and reorder contigs. In the Contig Selector all contigs are shown as colinear horizontal lines separated by short vertical lines. The length of the horizontal lines is proportional to the length of the contigs and their left to right order represents the current ordering of the contigs. This Contig Order is stored in the Gap database and users can change it by dragging the lines representing the contigs in the display. The Contig Selector can also be used to select contigs for processing and tags (see section Annotation readings and contigs) can be displayed in the Contig Selector window. As the mouse is moved over a contig, it is highlighted and the contig name (left most reading name) and length are displayed in the status line. The number in brackets is the contig number.

The figure shows a typical display from the Contig Selector. At the top is a View menu. Below that are buttons for undoing zoom requests and for displaying the crosshair. The four boxes to the right display the X and Y coordinates of the crosshair. The two on the right represent the Y coordinate and are not shown in this plot as the contig selector is in its one dimensional mode. The two leftmost boxes display the X coordinate: the leftmost is the position in the contig and the second leftmost is the position in the overall consensus. The crosshair is the vertical line spanning the panel below. This panel shows the lines that represent the contigs and the currently active tags. Those tags shown above the contig lines are on readings and those below are on the consensus. The information line is showing data for the contig that is currently under the crosshair.