The Format Menu contains the tools needed to alter the display of information in the various Gene Construction Kit windows. Because of the large number of choices available, all of the items in the Format Menu are hierarchical in nature. Many of the items in the Format Menu are available in a number of windows.
The Fill Submenu provides the ability to define the pattern used to fill any selected object (construct segments or objects in the Illustration Window).
The Lines Submenu provides control over the attributes of lines and arrows, which are a special kind of line. This submenu is available when a line is selected in the Illustration Window or a segment or region is selected in the Construct Window. Clicking on the bottom part of the Lines Submenu will allow you to place arrowheads at one or both ends of the selected line. The size and shape of the arrowhead can be adjusted by choosing the Size Arrowhead… option.
Font, Style, and Size Submenus are standard Macintosh menus that allow you to define these text attributes. These submenus are available anytime that text is selected in the Illustration Window or the Construct Window and will function to alter the display of the selected text. In the Gel Window, setting these attributes will set the display of the legend text and of the text when viewing the digests as a table.
The Color Submenu allows you to define the color of any selected object. You can define an object’s color even if you are running on a Mac Plus or SE or other black and white system. Color can apply to text, construct segments, marked sites, regions, and symbols in the Construct Window; and to text, lines (arrows), rectangles, round rectangles, and ellipses in the Illustration Window. You can choose to add new colors to the menu by using the Add A Color… Submenu. New colors can be defined using the Color Picker or by choosing to add the currently selected color. The Remove A Color… Submenu allows you to remove any of your previously added colors from the color menu. Added colors can be useful to identify certain construct features (e.g. orange can signify a coding region).
Selecting the Symbol Submenu will display a graphical submenu containing all the available symbols that can be used for marked sites. Note that symbols may be chosen even if the site is being displayed by name.
The Site Markers Submenu provides the ability to define exactly what information will be displayed when a site marker is placed on the screen. In this submenu, one can choose to display the site marker either as a symbol or as text by using Show Site as Symbol and Show Site as Text. When showing the marker as text, both the site name and/or position can be displayed using the appropriate items in this menu. Set Position Delimiters… can be used to define the exact format in which the marker position is indicated. The other items in this submenu define the attachment point of the line connecting the site marker to the construct. By using Attach at Center, Attach at Left, Attach at Right, Attach at Top, Attach at Middle, Attach at Bottom, and Attach at Nearest Position, one can precisely define the placement of the markers. Attach at Nearest Position is the default alignment and will place the attachment to the site text at the closest attachment point to the construct.
The Grouping Submenu is only selectable when the sequence view of a Construct Window is active. Grouping refers to the number of nucleotides that are placed adjacent to each other without any intervening spaces. Insert Line Break will force the character immediately after the insertion point to begin a new line. Remove Line Breaks will remove line breaks only from the selected segment. If no segments are selected, then all line breaks will be removed. The Grouping Submenu should be used in conjunction with the Display Submenu of the Construct Menu to precisely define the layout of the sequence.
The Chronography Submenu provides access to the Gene Construction Kit’s archiving feature that can track all the steps in the synthesis of a construct and present alternative views of the information in the construct. The appearance of a construct can be defined as a new generation at any time. The information for defining a generation consists of the marked sites, the regions, and the thickness, fill pattern, color and direction for each segment of the construct (i.e. all aspects of the appearance of the construct). Using the Start New Generation option will define a new generation. You can keep (or not) features of the current display in the new generation that is being defined.
The middle section of the Chronography Submenu allows navigation through all the different generations. Show Previous Generation will display the previous generation for the selected segment(s). Note that this does not alter the DNA sequence in any way – it simply displays the current DNA sequence in different ways. Show Most Ancient Generation will display a generation corresponding to the oldest generation in existence for the selected region of the construct. As with Show Previous Generation, if a segment was not present at the target generation, it will be displayed as a thin gray line.
Show Next Generation will be selectable only when there is a more recent generation to be shown. Show Most Recent Generation will display the most recent generation defined for each segment selected. Pick a Generation… will allow you to choose a generation to display.
In order to use Discard Generations…, the selection in the construct must be from a single generation. The concept of discarding a generation is discussed at length in the manual. The most recent (current) generation is defined as generation 0. One generation in the past is generation 1, two generations in the past is generation 2, etc. Keep in mind that discarding generations just discards your formatted views of the DNA sequence – it does not change the DNA sequence stored with the construct!
The Preferences Submenu allows you to set the default values to be used when empty windows are created. A Construct, Illustration, or Gel Window can be opened from the Preferences Submenu. To set a default characteristic, just define the attribute using menu selections as you would in the normal window.
