The Editor Information Line

The very bottom line of the editor display is text line used by the editor to display pieces of useful information. Currently this gives information on individual bases, readings, the contig, and tags, as the mouse is moved over the appropriate object. For bases (in both readings and the consensus) this information is only displayed when a mouse button is pressed. The left mouse button displays with format BASE_BRIEF_FORMAT1 and format BASE_BRIEF_FORMAT2 is displayed when pressing 'Enter'. By default the only difference between the two is that 'Enter' will display the "unpadded position" of a base in the consensus - ie its position in the consensus after pads have been removed. The contents and format of the information displayed is completely configurable by adding the relevant definitions to your `.gaprc' file. The defaults are as follows.

set_def READ_BRIEF_FORMAT  \
        {Reading:%n(#%Rn)   Length:%l(%L)   Vector:%Tv   Clone:%Cn   \
         Chemistry:%a   Primer:%P   %c}

set_def CONTIG_BRIEF_FORMAT  \
        {Contig:%n(#%Rn)   Length:%l   %c}

set_def TAG_BRIEF_FORMAT  \
        {Tag type:%t   Direction:%d   Comment:"%.100c"}

set_def BASE_BRIEF_FORMAT1  \
	{Base confidence:%c  (Probability %p)   Position %P}

set_def BASE_BRIEF_FORMAT2  \
	{Base confidence:%c  (Probability %p)   Position %P   \
          Unpadded position %U}

Tag information is shown when the mouse is moved over an annotation. Read information is shown when the mouse is moved over the reading name in the names section of the display. Contig information is displayed when the mouse is moved over the "Consensus" line in the names display. If you wish to leave the contig editor window without changing the information line contents as the mouse moves over other information press and hold the Shift key whilst moving the mouse. This disables the automatic highlighting. The same mechanism also works for other windows (such as the template display).

The general style of the formats is the string to display with particular strings substituting % characters. For instance in the reading format %n is substituted by the reading name. The general format of a % expansion is:

• A percent sign.
• An optional minus sign to request left alignment of the information. When displaying information in a specific field with where that data does not fill the entire space allowed the information will, by default, be right justified. Adding a minus character here requests left justification.
• An optional minimum field width. This is a decimal number indicating how much space to leave for this information.
• An optional precision for numbers or maximum field width for strings. This is given as a fullstop followed by a decimal number.
• An optional 'R' to specify Raw mode. This changes the meaning of many (but not all) of the expansion requests to give a numercial representation of the data. For example %n is a reading name and %Rn is a reading number.
• Th expansion type itself. This is either one or two letters. See below for full details of their meanings.

To programmers this syntax may seem very similar to printf. This is intentional, but do not assume it is the same. Specifically the print syntax of %#, %+ and %0 will not work.

Reading Information

Example output is Reading:xc04a1.s1(#74) Length:295(474) Vector:m13mp18 Clone:test Chemistry:primer Primer:forward universal.

%%

A single % sign

%n

Reading name. Raw mode: number

%#

Reading number

%t

Trace name

%p

Position

%l

Clipped length

%L

Total length

%s

Start of clip

%e

End of clip

%S

Sense (whether complemented) - "+" or "-". Raw mode: 0/1

%a

Chemistry - "primer" or "terminator". Raw mode: 0/1

%d

Strand - "+" or "-". Raw mode: 0/1

%P

Primer - "unknown", "forward universal", "reverse universal", "forward custom" or "reverse custom". Raw mode: 0/1/2/3/4

%Tn

Template name. Raw mode: template number

%T#

Template number

%Tv

Template vector. Raw mode: template vector number

%Ti

Template insert size

%Cn

Clone name. Raw mode: clone number

%C#

Clone number

%Cv

Clone vector. Raw mode: clone vector number

%c

User defined text, taken from the the first note of type INFO.

Contig Information

Example output is Contig:xc04a1.s1(#74) Length:1316.

%%

Single % sign

%n

Left most reading name. Raw mode: reading number

%s

(As %n)

%e

Right most reading name. Raw mode: reading number

%#

Contig number

%l

Contig length

%E

Expected number of errors (can be slow on large contigs)

%c

User defined text, taken from the the first note of type INFO.

Tag Information

Example output is Tag type:OLIG Direction:- Comment:"template=xc04a1 sequence=

CGATTGCAGAATAAGACG".

%%

Single % sign

%p

Tag position

%d

Tag direction - "+", "-" or "=". Raw mode: 0/1/2

%t

Tag type (always 4 characters)

%l

Tag length

%n

Tag number (0 if unknown)

%c

Tag comment

Base Information

Example output is Base confidence:13 (Probability 0.954020) Position 3805 Unpadded position 3678.

%%

Single % sign

%c

Confidence value (phred style)

%p

Confidence value (as probability)

%P

Padded consensus base position

%U

Unpadded consensus base position