Menu controls
File Menu / Edit Menu / View Menu / Detail Menu / Legend / Help Menu

Chromoscape has a series of 6 buttons at the top of the display. Pressing these buttons will display a menu of choices, except for the Legend button, which displays a console of information. Clicking once on the button will cause the subject menu to appear, whereupon any choice in the menu can be selected by clicking on the menu item. Clicking again on the button or elsewhere in Chromoscape will close the menu display.

  File menu

The implementation of printing in Java (the language in which Chromoscape is written) is not suitable for the sort of multi-page outputs that Chromoscape can generate. Because of this, printing Chromoscape graphics is a 2-step process: generating printable output within Chromoscape, then printing it from your browser or from a file. This is discussed in full in the Printing Maps documentation.

Print using PDF: Chromoscape provides two options for printing graphics: generating a PDF file and generating a GIF snapshot. The Print using PDF option will generate a PDF file containing the graphic being viewed. The generated PDF will include the entire graphic, regardless of whether only a portion of the graphic is displayed in the graphic window at the time of PDF generation. Choosing this menu option will first open the Chromoscape PDF Generator console, which allows users to customize the PDF file being generated. The PDF file can then be used to print the map or for further manipulation using a PDF file editor. Details on generating, displaying, and printing Chromoscape PDF files can be found here.

Print GIF snapshot: This feature creates a snapshot GIF of whatever graphic or portion of a graphic is currently being displayed in the graphic display window of Chromoscape. Choosing this menu option will first open the GIF Snapshot Printing instructions console, which allows users to select the GIF orientation. The GIF file is automatically displayed in a new web browser window and can be printed or saved using the web browser. Details on generating, displaying, and printing Chromoscape GIF files can be found here.

Printing help: Printing help displays a console summarizing how to print graphics from Chromoscape. The text is as follows:

In order to print, this program allows two different options: generating a PDF file and generating a GIF snapshot. Generating the PDF file will open a PDF in your browser. This file will contain a complete printout of the map which you are viewing. You can then print from your PDF viewer. Generating the GIF snapshot will load a GIF image file in a new browser window. This GIF will be an exact reproduction of whatever you see in the Chromoscape window. This allows you to zoom in and print a more exact piece of the map. This GIF can then be printed from your internet browser when it opens. Why do we print this way? Because of security issues involved in internet applets, Chromoscape is not permitted to print directly using your computer's resources.

Exit: Exits the Chromoscape application. This is the recommended method for exiting Chromoscape.
  Edit menu

Find: Find allows you to search for an element or elements by name on the current display. The search is case-insensitive and supports a single wildcard (*) at either the start (as in *PCR1) or end (as in D1S4*). By default, all elements in the current display are searched, but you can limit the search to only the framework or intervaled markers. After you press Find to conduct the search, the name of each element meeting the search criteria is returned and displayed in a list, along with the view name and assigned tier. There is also a Find button and search text box located on the main Chromoscape display. This feature works identically to the Find feature in the Find console described here; entering a search term and pressing the Find button will open the Find console and display the results.

To locate one or more of the elements in the display, click on the element name(s) and press Select in Map (or simply double click on a single name. This selects the element(s) in the display and automatically scrolls the display if necessary to bring the element into view.
  View menu


Show Units: This is a checkbox option for whether chromosomal localization unit intervals (such as centiRays are shown in the display. The default setting has this feature activated. Click on the menu item to toggle the option from on to off, and vice-versa.

Highlight flanking framework markers:This is a checkbox option allowing the user to turn on and off a mode which, upon selection of an intervaled element (or elements), highlights the framework marker(s) which delimit its (their) localization boundaries. The region of the framework between the boundaries is also highlighted. In the example below, selection of the intervaled marker D7S10 shows that it is localized between the framework markers D7S2464 and D7S664. Note that all the flanking framework markers might not be highlighted if the zoom level is such that not all the framework marker labels are visible. However, zooming the map will bring them into view, and they will be highlighted.  The default setting has this feature inactivated. Click on the menu item to toggle the option from off to on, and vice-versa.

Highlight spanning intervaled elements: This is a checkbox option allowing the user to turn on and off a mode which, upon selection of a framework marker, highlights all the intervaled markers whose localization either intersects or spans that point. Additionally, if more than one framework marker is selected, all the intervaled markers within the interval defined by them are highlighted. This can help to better visualize an area of interest within the display. In the example below, selection of the 2 framework markers D7S513 and AFMa084wh5 shows that they are within the localization span of 12 intervaled markers.  The default setting has this feature inactivated. Click on the menu item to toggle the option from off to on, and vice-versa.
  Detail menu

Map Element: To retrieve detailed information for a specific map element, click on the label to select the map element, then choose this option. The detail will be displayed on a separate browser page. Double-clicking on an element name in the graphic itself is a shortcut for this menu item. 

Note: The interaction of the Java language and a Web browser requires that the page from which the applet started must be displayed in order for this option to work. Therefore, if you leave the Chromoscape launch page or iconify the window, no detail can be retrieved.

Select Map: Not applicable for eGenome.

  Legend button

Clicking the Legend button displays text describing what each text color represents.

Red element names denote that there are multiple elements with this marker name.

Blue element names denote that this element identifies one or more SNP's.

Green element names denote that there are multiple elements with this marker name AND the element also contains one or more SNP's.
  Help menu
About Chromoscape: Selecting About under the Help menu displays the version of Chromoscape you are using and the eGenome and GDB staff responsible for its creation and maintenance.

Help on Chromoscape: Selecting Help on Chromoscape under the Help menu opens the Chromoscape overview help page in a new browser window. Note: The interaction of the Java language and a Web browser requires that the page from which the applet started must be displayed in order for this option work. Therefore, if you leave that Chromoscape launch page or iconify the window, the help document cannot be displayed.

 Related Chromoscape help pages:

Except as otherwise indicated, Copyright 2005, The Children's Hospital of Philadelphia