Contig editor data viewers

The Contig editor's Viewer window displays a tabbed view of the current data.


Sequences
The Sequences tab contains a list of all opened sequences, including those not contained in a contig.  Check boxes next to the sequence names are used to select sequences that will be included when you assemble contigs.

Toolbar buttons:

  • Information: displays the sequence properties dialog box for the selected sequence.
  • Delete: removes the selected sequence from the list.

Contig list
The Contig list contains a tree view of contigs in the current project, and the sequences in each contig.  To view the sequences in a contig, click on the + sign beside the contig name.  Clicking on a contig name will activate the contig in the Editor window.  Clicking on a sequence name will scroll the sequence into view.

Toolbar buttons:

  • Information: displays the properties dialog box for the highlighted contig or sequence.
  • Delete: removes the highlighted contig or sequence from the project.

Right-click menu on a contig displays the following choices:

  • Go to this contig
  • Delete this contig
  • Contig properties - this item opens a dialog that you may use to change the name of the contig.  This new name will be displayed in the drop-down contig list in the main window and will be used as the sequence name when you export the consensus sequence
  • BLAST search consensus - this item will open the Online BLAST search dialog

Map view
The Contig map displays a graphical view of the current contig.  Each sequence is represented by a line.  Arrows indicate the sequence orientation.  Reversed sequences are dashed.  A bar at the top of the window represents the contig.  Coverage is indicated by the colors: Red (thin line) - sequenced once on one strand only; Blue - sequenced more than once on one strand; Green - sequenced at least once on both strands; Black - sequenced more than once on both strands.  Moving the mouse over a sequence displays lines showing the sequence end points on the contig.

Toolbar buttons:

  • Print: print the contig map.
  • Print preview: preview the printed map.
  • Name width: set the number of sequence name characters that are displayed.

Trace view
The Trace viewer allows you to view and print the unedited trace for each sequence.  The trace viewer scroll bar is customized to show colored bars representing all of the trace peaks.  The scroll bar thumb can be dragged to pan the trace to the left or right.  The edges of the scroll bar thumb can be dragged to set the horizontal scale of the trace. A slider control on the left-hand side of the window is used to set the vertical scale of the trace.

Toolbar buttons:

  • Print: Send the trace to the printer.
  • Print preview: View the trace in the print preview window.
  • Trace information: View the trace file header information.

Pretty view
The Pretty viewer provides a printable, formatted view of sequences.  It can also be used to copy or save the display in RTF format for use in a word processor.  The Pretty viewer presents a display of the sequences in the Sequence Selection List, optionally displaying sequence numbering and base coloring.  Parameters affecting how the alignment is displayed can be accessed through the Viewers toolbar.

Toolbar buttons:

  • Copy: place the contents of the Pretty view window onto the clip board in RTF format.
  • Save: save the window contents in RTF format.
  • Print: send the display to the printer.
  • Print preview: view the display in the print preview window.
  • Font: button allows you to set the display font.
  • Settings: set formatting options using the Pretty options dialog box, including the line and numbering parameters, character case, and color options.
  • Line length: sets the line length.
  • Case: choose the character case.
  • Color bases: toggle base coloring.