Skip to content
Snippets Groups Projects
Commit 4f736659 authored by tjc's avatar tjc
Browse files

updates 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6919 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 4825465c
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 98 additions and 44 deletions
docs/menus.sgml
+ 98
− 44
View file @ 4f736659
...@@ -880,67 +880,96 @@ no errors in the formatting of the header. ...@@ -880,67 +880,96 @@ no errors in the formatting of the header.
</PARA> </PARA>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-CHANGE-QUALIFIERS"> <SECT2 ID="QUALIFIERS">
<TITLE>Change Qualifiers of Selected ...</TITLE> <TITLE>Qualifier(s) of Selected Feature</TITLE>
<SECT3 ID="EDITMENU-CHANGE-QUALIFIERS">
<TITLE>Change ...</TITLE>
<PARA> <PARA>
This function allows the user to add or change qualifiers on all the selected This function allows the user to add or change qualifiers on all the selected
features in one operation. The main part of the window acts like the features in one operation. The main part of the window acts like the
qualifier editing field of the feature edit window (see <XREF qualifier editing field of the feature edit window (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">). LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-REMOVE-QUALIFIERS"> <SECT3 ID="EDITMENU-REMOVE-QUALIFIERS">
<TITLE>Remove Qualifiers of Selected ...</TITLE> <TITLE>Remove ...</TITLE>
<PARA> <PARA>
This function allows the user to remove all qualifiers with a particular name This function allows the user to remove all qualifiers with a particular name
from all the selected features. from all the selected features.
</PARA> </PARA>
</SECT3>
<SECT3 ID="EDITMENU-CONVERT-QUALIFIERS">
<TITLE>Convert ...</TITLE>
<PARA>
This function allows the user to convert all qualifiers of a particular type
to another qualifier for all the selected features.
</PARA>
</SECT3>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-DUPLICATE-SELECTED-FEATURES"> <SECT2 ID="EDITMENU-SELECTED-FEATURES">
<TITLE>Duplicate Selected Features</TITLE> <TITLE>Selected Feature(s)</TITLE>
<SECT3 ID="EDITMENU-DUPLICATE-SELECTED-FEATURES">
<TITLE>Duplicate</TITLE>
<PARA> <PARA>
Make a copy of each selected feature. Each new feature will be added just Make a copy of each selected feature. Each new feature will be added just
after the original in the same entry as the original. [shortcut key: D] after the original in the same entry as the original. [shortcut key: D]
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-MERGE-SELECTED-FEATURES"> <SECT3 ID="EDITMENU-MERGE-SELECTED-FEATURES">
<TITLE>Merge Selected Features</TITLE> <TITLE>Merge</TITLE>
<PARA> <PARA>
Create a new feature that contains all the exons and qualifiers of the Create a new feature that contains all the exons and qualifiers of the
selected features. The selected features must all have the same key. selected features. The selected features must all have the same key.
[shortcut key: M] [shortcut key: M]
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-UNMERGE-SELECTED-FEATURE"> <SECT3 ID="EDITMENU-UNMERGE-SELECTED-FEATURE">
<TITLE>Unmerge Selected Feature</TITLE> <TITLE>Unmerge</TITLE>
<PARA> <PARA>
If the selection contains exactly two exons and those exons are adjacent in If the selection contains exactly two exons and those exons are adjacent in
the same feature, split the feature into two pieces between the exons. The the same feature, split the feature into two pieces between the exons. The
original feature is truncated and a new feature is created. The qualifiers of original feature is truncated and a new feature is created. The qualifiers of
the old feature are copied to new feature. the old feature are copied to new feature.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT3 ID="EDITMENU-UNMERGE-ALL-SEGMENTS">
<TITLE>Unmerge All Segments</TITLE>
<PARA>
All exons in a feature are unmerged.
</PARA>
</SECT3>
<SECT2 ID="EDITMENU-DELETE-SELECTED-FEATURES"> <SECT3 ID="EDITMENU-DELETE-SELECTED-FEATURES">
<TITLE>Delete Selected Features</TITLE> <TITLE>Delete</TITLE>
<PARA> <PARA>
Remove each selected feature from it's entry. Remove each selected feature from it's entry.
[shortcut key: control-delete] [shortcut key: control-delete]
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="DELETE-SELECTED-EXONS"> <SECT3 ID="DELETE-SELECTED-EXONS">
<TITLE>Delete Selected Exons</TITLE> <TITLE>Delete Exons</TITLE>
<PARA> <PARA>
Delete the selected exons. The last exon of a feature can't be deleted Delete the selected exons. The last exon of a feature can't be deleted
(delete the whole feature instead). (delete the whole feature instead).
</PARA> </PARA>
</SECT3>
<SECT3 ID="DELETE-SELECTED-INTRONS">
<TITLE>Remove Introns</TITLE>
<PARA>
Delete the selected introns.
</PARA>
</SECT3>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-MOVE-SELECTED-FEATURES"> <SECT2 ID="EDITMENU-MOVE-SELECTED-FEATURES">
<TITLE>Move Selected Features To</TITLE> <TITLE>Move Selected Features To</TITLE>
<PARA> <PARA>
...@@ -957,8 +986,10 @@ from the sub-menu. ...@@ -957,8 +986,10 @@ from the sub-menu.
</PARA> </PARA>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-MET"> <SECT2 ID="EDITMENU-TRIM">
<TITLE>Trim Selected Features To Met</TITLE> <TITLE>Trim Selected Features</TITLE>
<SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-MET">
<TITLE>To Met</TITLE>
<PARA> <PARA>
For each of the selected features this function will attempt to move the start For each of the selected features this function will attempt to move the start
position to the first ATG in the feature if the feature does not already start position to the first ATG in the feature if the feature does not already start
...@@ -966,10 +997,10 @@ on a ATG codon. If there is no ATG in the first thirty percent of the bases ...@@ -966,10 +997,10 @@ on a ATG codon. If there is no ATG in the first thirty percent of the bases
of the feature the start position will be unchanged. The search will stop at of the feature the start position will be unchanged. The search will stop at
the end of the first segment of a multi-segment feature. the end of the first segment of a multi-segment feature.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-ANY"> <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-ANY">
<TITLE>Trim Selected Features To Any</TITLE> <TITLE>To Any</TITLE>
<PARA> <PARA>
This works in the same way as "Trim Selected Features To Met", but will This works in the same way as "Trim Selected Features To Met", but will
attempt to move the start position of the feature to the first TTG, ATG or GTG attempt to move the start position of the feature to the first TTG, ATG or GTG
...@@ -977,10 +1008,10 @@ in the feature if it does not already start on one of those codons. As above ...@@ -977,10 +1008,10 @@ in the feature if it does not already start on one of those codons. As above
it will only search the first thirty percent of the feature bases and will it will only search the first thirty percent of the feature bases and will
only search the first segment of a multi-segment feature. only search the first segment of a multi-segment feature.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-MET"> <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-MET">
<TITLE>Trim Selected Features To Next Met</TITLE> <TITLE>To Next Met</TITLE>
<PARA> <PARA>
For each of the selected features this function will attempt to move the start For each of the selected features this function will attempt to move the start
position to the next ATG in the feature (the first codon is skipped). If position to the next ATG in the feature (the first codon is skipped). If
...@@ -989,10 +1020,10 @@ start position will be unchanged. The search will stop at the end of the ...@@ -989,10 +1020,10 @@ start position will be unchanged. The search will stop at the end of the
first segment of a multi-segment feature. first segment of a multi-segment feature.
[shortcut key: T] [shortcut key: T]
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-ANY"> <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-ANY">
<TITLE>Trim Selected Features To Next Any</TITLE> <TITLE>To Next Any</TITLE>
<PARA> <PARA>
This works in the same way as "Trim Selected Features To Next Met", but will This works in the same way as "Trim Selected Features To Next Met", but will
attempt to move the start position of the feature to the next TTG, ATG or GTG attempt to move the start position of the feature to the next TTG, ATG or GTG
...@@ -1001,24 +1032,36 @@ first thirty percent of the feature bases and will only search the first ...@@ -1001,24 +1032,36 @@ first thirty percent of the feature bases and will only search the first
segment of a multi-segment feature. segment of a multi-segment feature.
[shortcut key: Y] [shortcut key: Y]
</PARA> </PARA>
</SECT3>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-EXTEND-TO-PREVIOUS-STOP-CODON"> <SECT2 ID="EDITMENU-EXTEND">
<TITLE>Extend to Previous Stop Codon</TITLE> <TITLE>Extend Selected Features</TITLE>
<SECT3 ID="EDITMENU-EXTEND-TO-PREVIOUS-STOP-CODON">
<TITLE>To Previous Stop Codon</TITLE>
<PARA> <PARA>
Extend each of the selected features which do not start on a stop codon so Extend each of the selected features which do not start on a stop codon so
that each feature starts just after the previous stop codon in this reading that each feature starts just after the previous stop codon in this reading
frame. frame.
[shortcut key: Q] [shortcut key: Q]
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-EXTEND-TO-NEXT-STOP-CODON"> <SECT3 ID="EDITMENU-EXTEND-TO-NEXT-STOP-CODON">
<TITLE>Extend to Next Stop Codon</TITLE> <TITLE>To Next Stop Codon</TITLE>
<PARA> <PARA>
Extend each of the selected features which do not end on a stop codon so that Extend each of the selected features which do not end on a stop codon so that
each feature ends just before the next stop codon in this reading frame. each feature ends just before the next stop codon in this reading frame.
</PARA> </PARA>
</SECT3>
<SECT3 ID="EDITMENU-EXTEND-TO-NEXT-STOP-CODON-FIX">
<TITLE>To Next Stop Codon and Fix</TITLE>
<PARA>
Same as above but in addition this fixes the stop codons.
</PARA>
</SECT3>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-FIX-STOP-CODONS"> <SECT2 ID="EDITMENU-FIX-STOP-CODONS">
...@@ -1057,15 +1100,17 @@ Warn about inconsistencies such as overlapping CDSs. ...@@ -1057,15 +1100,17 @@ Warn about inconsistencies such as overlapping CDSs.
</PARA> </PARA>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-REVERSE-AND-COMPLEMENT"> <SECT2 ID="EDITMENU-BASES">
<TITLE>Bases</TITLE>
<SECT3 ID="EDITMENU-REVERSE-AND-COMPLEMENT">
<TITLE>Reverse And Complement</TITLE> <TITLE>Reverse And Complement</TITLE>
<PARA> <PARA>
Reverse and complement the sequence and all the features in all the entries Reverse and complement the sequence and all the features in all the entries
(active and inactive). (active and inactive).
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-REVERSE-AND-COMPLEMENT-CONTIG"> <SECT3 ID="EDITMENU-REVERSE-AND-COMPLEMENT-CONTIG">
<TITLE>Reverse And Complement Selected Contig</TITLE> <TITLE>Reverse And Complement Selected Contig</TITLE>
<PARA> <PARA>
Reverse and complement the sequence and all the features in a selected Reverse and complement the sequence and all the features in a selected
...@@ -1075,18 +1120,18 @@ deleted. The changes to the comparison file can be saved by right clicking ...@@ -1075,18 +1120,18 @@ deleted. The changes to the comparison file can be saved by right clicking
in the comparison window and selecting "Save Comparison File...". However, in the comparison window and selecting "Save Comparison File...". However,
ideally the comparison between the two sequences should be recalculated. ideally the comparison between the two sequences should be recalculated.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-DELETE-SELECTED-BASES"> <SECT3 ID="EDITMENU-DELETE-SELECTED-BASES">
<TITLE>Delete Selected Bases</TITLE> <TITLE>Delete Selected Bases</TITLE>
<PARA> <PARA>
Deletes the selected range of bases (if any) from both strands. The deletion Deletes the selected range of bases (if any) from both strands. The deletion
will not proceed if the selected range overlaps any features. will not proceed if the selected range overlaps any features.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-ADD-BASES-AT-SELECTION"> <SECT3 ID="EDITMENU-ADD-BASES-AT-SELECTION">
<TITLE>Add Bases At Selection</TITLE> <TITLE>Add Bases At Selection</TITLE>
<PARA> <PARA>
Prompt the user for some bases to insert just before the selected bases. The Prompt the user for some bases to insert just before the selected bases. The
...@@ -1095,14 +1140,23 @@ inserted anywhere in the sequence, including inside a feature. The same ...@@ -1095,14 +1140,23 @@ inserted anywhere in the sequence, including inside a feature. The same
bases, reversed and complemented, will be inserted at the corresponding place bases, reversed and complemented, will be inserted at the corresponding place
on the opposite strand. on the opposite strand.
</PARA> </PARA>
</SECT2> </SECT3>
<SECT2 ID="EDITMENU-ADD-FROM-FILE"> <SECT3 ID="EDITMENU-ADD-FROM-FILE">
<TITLE>Add Bases From File ...</TITLE> <TITLE>Add Bases From File ...</TITLE>
<PARA> <PARA>
Prompt the user for the name of a file containing the bases to insert just Prompt the user for the name of a file containing the bases to insert just
before the selected bases. before the selected bases.
</PARA> </PARA>
</SECT3>
<SECT3 ID="EDITMENU-REPLACE-BASES-AT-SELECTION">
<TITLE>Replace Bases At Selection</TITLE>
<PARA>
Prompt the user for some bases to replace the selected bases.
</PARA>
</SECT3>
</SECT2> </SECT2>
<SECT2 ID="EDITMENU-CONTIG-REORDERING"> <SECT2 ID="EDITMENU-CONTIG-REORDERING">
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment