From 54fd45ab3a043979213400abdccf8c4ad768a83e Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 19 Feb 2008 11:17:35 +0000
Subject: [PATCH] add write
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7154 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
docs/act_file_menu.sgml | 78 +++++++++++++++++++++++++++++++++++++++++
docs/file_menu.sgml | 77 ++++++++++++++++++++++++++++++++++++++++
docs/menus.sgml | 75 ---------------------------------------
3 files changed, 155 insertions(+), 75 deletions(-)
diff --git a/docs/act_file_menu.sgml b/docs/act_file_menu.sgml
index f3a0ae56b..d7ad525a9 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 039550dc2..fa0b6236f 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 9431656af..55b4f055a 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>
--
GitLab