Selecting "Search" brings up a window which can remain present during normal editor operation. The window allows the user to select the direction of search, the type of search, and a value to search on. The value is entered into a value text box, then pressing the "search" button performs the search. If successful, the cursor is positioned accordingly. An audible tone indicates failure. Pressing the "Quit" button removes the search window. The search window is automatically removed when the contig editor is exited.
![[picture]](contig_editor.search.gif)
Searches are performed by scanning forwards or backwards, as appropriate, examining the visible data. Hence the "Reveal Cutoffs" button can be used to select whether or not searching should find matches within the cutoff data.
There are eight different search modes.
This positions the cursor at the numeric position specified in the value text window. Eg a value of "1234" causes the cursor to be placed at base number 1234 in the contig. Positioning withing a gel reading is achieved by prefixing the number with the "@" character, eg "@123" positions the cursor at base 123 of the sequence in which the cursor lies. Relative positions can be specified by prefixing the number with a plus or minus character. Eg "+1234" will advance the cursor 1234 bases. If possible, the cursor is positioned within the same sequence. The direction buttons have no effect on this operation.
This positions the cursor at the next place in the consensus sequence which is not an "A", "C", "G" or "T". The search can be performed either forwards or backwards from the current cursor position. The "Next Problem" button on the contig editor is identical to this search in a forwards direction.
This positions the cursor at the start of the next tag which has a comment containing the string specified in the value text window. The search performed is a regular expression search, and certain characters have special meaning. Be careful when your value string contains ".", "*", "[", "]", "\", "^" or "$". The search can be performed either forwards or backwards from the current cursor position. Searching with an empty value will find all tags.
This positions the cursor at the start of the next piece of sequence that matches the value specified in the text value window. The search is case insensitive. The search is performed on the gel readings themselves, rather than the consensus sequence. The search can be performed either forwards or backwards from the current cursor position.
This positions the cursor at the next place in the consensus sequence where the consensus calculation for each strand disagrees. When only sequences on one strand is present, the search will stop at every base. The search can be performed either forwards or backwards from the current cursor position.
This positions the cursor at the left end of the gel reading specified in the value text window. If the value is prefixed with a hash sign it is assumed to be a gel reading number. Otherwise it is assumed to be a gel reading name. Eg "#123" positions the cursor at the left end of gel reading number 123. "a16a12.s1" positions at the start of reading a16a12.s1. If the value was "a16" the cursor is positioned at the first reading which starts with "a16".
This positions the cursor at the next place in the contig where an edit has been made. An edit is determined by the quality value or the positioning of a base within a reading. The search can be performed either forwards or backwards from the current cursor position.
The Verify AND option is listed as 'Verify &' on the dialogue. The purpose of this search is to find bases in the consensus for which there is no evidence in the original readings. This option finds such bases where there is no evidence for the forward strand AND there is no evidence for the reverse strand. Hence it will possibly find less problems than Verify OR. Currently this searches only in the forward direction.
The Verify OR option is listed as 'Verify |' on the dialogue. The purpose of this search is to find bases in the consensus for which there is no evidence in the original readings. This option finds such bases where there is no evidence for the forward strand OR there is no evidence for the reverse strand. Hence it will possibly find more problems than Verify AND. Currently this searches only in the forward direction.
This positions the cursor at the start of the next tag which has the the same type as specified by the type value menu. To change the type, select off the menu that pops up when the mouse is clicked on the button labeled "Type:". The search can be performed either forwards or backwards of the current cursor position. To find all tags, use "search by annotation", with an empty text value string.