diff --git a/docs/act_file_menu.sgml b/docs/act_file_menu.sgml index f3a0ae56ba6fbf46c951121b2e03093c482da8d3..d7ad525a90b9f205e0d91036e355b96803b99d62 100644 --- a/docs/act_file_menu.sgml +++ b/docs/act_file_menu.sgml @@ -66,6 +66,84 @@ Save all the entries that have been loaded on top of this sequence. </PARA> </SECT2> + + <SECT2 ID="WRITEMENU"> + <TITLE>Write</TITLE> + <PARA> + + </PARA> + + <SECT3 ID="WRITEMENU-AMINO-ACIDS-OF-SELECTED-FEATURES"> + <TITLE>Amino Acids Of Selected Features</TITLE> + <PARA> +Prompt for a file name and then write the translation of the bases of the +selected features to that file. The file is written in FASTA format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-PIR-DATABASE-OF-SELECTED-FEATURES"> + <TITLE>PIR Database Of Selected Features</TITLE> + <PARA> +Prompt for a file name and then write the translation of the bases of the +selected features to that file. The file is written in PIR format (similar to +FASTA, but with a * as the last line of each record). + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-BASES-OF-SELECTION"> + <TITLE>Bases Of Selection</TITLE> + <PARA> +Prompt for a file name and then write the bases of the selection to that +file in the selected format. If the selection consists of features (rather +than a base range) then the bases of each feature +will be written to the file as a separate record. If the selection is a range +of bases, then those bases will be written. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-UPSTREAM-BASES-OF-SELECTION"> + <TITLE>Upstream Bases Of Selection</TITLE> + <PARA> +Prompt for a number and a file name, then write that many bases upstream of +each selected feature to the file in the selected format. For example if the +selected feature has a +location of "<LITERAL>100..200</LITERAL>", then asking for 50 upstream will +write the bases in the range 50 to 99. Writing upstream bases of a feature on +the complementary strand will work in the expected way. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-DOWNSTREAM-BASES-OF-SELECTION"> + <TITLE>Downstream Bases Of Selection</TITLE> + <PARA> +Prompt for a number and a file name, then write that many bases downstream of +each selected feature to the file in the selected format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-ALL-BASES"> + <TITLE>All Bases</TITLE> + <PARA> +Prompt for a file name, then write the complete sequence to that file in the +selected format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-CODON-USAGE"> + <TITLE>Codon Usage of Selected Features</TITLE> + <PARA> +Prompt for a file name, then write a codon usage table for the selected +features. The file in written in the same format as the data at <ULINK +URL="http://www.kazusa.or.jp/codon/" TYPE="external">Kazusa codon usage +database site</ULINK>. In the output file each codon is followed by it's +occurrence count (per thousand) and it's percentage occurrence. (See <XREF +LINKEND="GRAPHMENU-USAGE-PLOTS"> to find out how to plot a usage graph). + </PARA> + </SECT3> + </SECT2> + + + <SECT2 ID="FILEMENU-EDIT-IN-ARTEMIS"> <TITLE>Edit In Artemis ...</TITLE> <PARA> diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml index 039550dc2f5364e1ac22dda4600d4dc7459b9ac8..fa0b6236f86ce3e33580592270d97017a0c97e86 100644 --- a/docs/file_menu.sgml +++ b/docs/file_menu.sgml @@ -151,6 +151,83 @@ This acts like "Save Default Entry", but save all the entries. </PARA> </SECT2> + + <SECT2 ID="WRITEMENU"> + <TITLE>Write</TITLE> + <PARA> + + </PARA> + + <SECT3 ID="WRITEMENU-AMINO-ACIDS-OF-SELECTED-FEATURES"> + <TITLE>Amino Acids Of Selected Features</TITLE> + <PARA> +Prompt for a file name and then write the translation of the bases of the +selected features to that file. The file is written in FASTA format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-PIR-DATABASE-OF-SELECTED-FEATURES"> + <TITLE>PIR Database Of Selected Features</TITLE> + <PARA> +Prompt for a file name and then write the translation of the bases of the +selected features to that file. The file is written in PIR format (similar to +FASTA, but with a * as the last line of each record). + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-BASES-OF-SELECTION"> + <TITLE>Bases Of Selection</TITLE> + <PARA> +Prompt for a file name and then write the bases of the selection to that +file in the selected format. If the selection consists of features (rather +than a base range) then the bases of each feature +will be written to the file as a separate record. If the selection is a range +of bases, then those bases will be written. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-UPSTREAM-BASES-OF-SELECTION"> + <TITLE>Upstream Bases Of Selection</TITLE> + <PARA> +Prompt for a number and a file name, then write that many bases upstream of +each selected feature to the file in the selected format. For example if the +selected feature has a +location of "<LITERAL>100..200</LITERAL>", then asking for 50 upstream will +write the bases in the range 50 to 99. Writing upstream bases of a feature on +the complementary strand will work in the expected way. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-DOWNSTREAM-BASES-OF-SELECTION"> + <TITLE>Downstream Bases Of Selection</TITLE> + <PARA> +Prompt for a number and a file name, then write that many bases downstream of +each selected feature to the file in the selected format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-ALL-BASES"> + <TITLE>All Bases</TITLE> + <PARA> +Prompt for a file name, then write the complete sequence to that file in the +selected format. + </PARA> + </SECT3> + + <SECT3 ID="WRITEMENU-CODON-USAGE"> + <TITLE>Codon Usage of Selected Features</TITLE> + <PARA> +Prompt for a file name, then write a codon usage table for the selected +features. The file in written in the same format as the data at <ULINK +URL="http://www.kazusa.or.jp/codon/" TYPE="external">Kazusa codon usage +database site</ULINK>. In the output file each codon is followed by it's +occurrence count (per thousand) and it's percentage occurrence. (See <XREF +LINKEND="GRAPHMENU-USAGE-PLOTS"> to find out how to plot a usage graph). + </PARA> + </SECT3> + </SECT2> + + <SECT2 ID="FILEMENU-CLONE-WINDOW"> <TITLE>Clone This Window</TITLE> <PARA> diff --git a/docs/menus.sgml b/docs/menus.sgml index 9431656af7d760f93c107df873ca1c0150ff1152..55b4f055a6236d3d854127571587b8c91d7768f6 100644 --- a/docs/menus.sgml +++ b/docs/menus.sgml @@ -1307,81 +1307,6 @@ called "ambiguous bases". </SECT2> </SECT1> -<SECT1 ID="WRITEMENU"> - <TITLE>The Write Menu</TITLE> - <PARA> - - </PARA> - - <SECT2 ID="WRITEMENU-AMINO-ACIDS-OF-SELECTED-FEATURES"> - <TITLE>Amino Acids Of Selected Features</TITLE> - <PARA> -Prompt for a file name and then write the translation of the bases of the -selected features to that file. The file is written in FASTA format. - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-PIR-DATABASE-OF-SELECTED-FEATURES"> - <TITLE>PIR Database Of Selected Features</TITLE> - <PARA> -Prompt for a file name and then write the translation of the bases of the -selected features to that file. The file is written in PIR format (similar to -FASTA, but with a * as the last line of each record). - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-BASES-OF-SELECTION"> - <TITLE>Bases Of Selection</TITLE> - <PARA> -Prompt for a file name and then write the bases of the selection to that -file in the selected format. If the selection consists of features (rather -than a base range) then the bases of each feature -will be written to the file as a separate record. If the selection is a range -of bases, then those bases will be written. - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-UPSTREAM-BASES-OF-SELECTION"> - <TITLE>Upstream Bases Of Selection</TITLE> - <PARA> -Prompt for a number and a file name, then write that many bases upstream of -each selected feature to the file in the selected format. For example if the -selected feature has a -location of "<LITERAL>100..200</LITERAL>", then asking for 50 upstream will -write the bases in the range 50 to 99. Writing upstream bases of a feature on -the complementary strand will work in the expected way. - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-DOWNSTREAM-BASES-OF-SELECTION"> - <TITLE>Downstream Bases Of Selection</TITLE> - <PARA> -Prompt for a number and a file name, then write that many bases downstream of -each selected feature to the file in the selected format. - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-ALL-BASES"> - <TITLE>All Bases</TITLE> - <PARA> -Prompt for a file name, then write the complete sequence to that file in the -selected format. - </PARA> - </SECT2> - - <SECT2 ID="WRITEMENU-CODON-USAGE"> - <TITLE>Codon Usage of Selected Features</TITLE> - <PARA> -Prompt for a file name, then write a codon usage table for the selected -features. The file in written in the same format as the data at <ULINK -URL="http://www.kazusa.or.jp/codon/" TYPE="external">Kazusa codon usage -database site</ULINK>. In the output file each codon is followed by it's -occurrence count (per thousand) and it's percentage occurrence. (See <XREF -LINKEND="GRAPHMENU-USAGE-PLOTS"> to find out how to plot a usage graph). - </PARA> - </SECT2> -</SECT1> - <SECT1 ID="RUNMENU"> <TITLE>The Run Menu</TITLE> <PARA>