From 9fb8dbc0e26d57a235a48b6f6054905e149dd169 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 14 Jun 2005 16:29:21 +0000 Subject: [PATCH] help file bits. --- help/help.jhm | 1 + help/html/features/seqfeatures.html | 51 +++++++++++++++++---------- help/html/io/file.png | Bin 0 -> 590 bytes help/html/io/fileformats.html | 55 +++++++++++++++++++++++++++++ help/html/io/index.html | 65 +++++++++++++++++++++++------------ 5 files changed, 131 insertions(+), 41 deletions(-) create mode 100755 help/html/io/file.png create mode 100755 help/html/io/fileformats.html diff --git a/help/help.jhm b/help/help.jhm index 36a54e4..3a4aac4 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -13,6 +13,7 @@ + diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 88a4d5d..6264724 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -13,33 +13,46 @@ e.g. a region of sequence with known structure

-

More information about the feature is given in a tooltip, which are +

More information about the feature is given in a tooltip, which is viewed by moving the mouse pointer over a sequence feature. The - associated text for the feature will then be displayed in a small - label will appear near the pointer.

+ description associated with the feature will then be displayed in a small + label near the pointer.

After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview must first determine if a - sequence is contained in uniprot and then retrieve its sequence - record. This delay should only happen once for a particular - alignment, as jalview caches uniprot records in a file in your home + the features are actually rendered, as jalview first determines if + the sequences are contained in Uniprot and then retrieves any sequence + records. This delay will normally only happen once for a particular + set of sequences, as jalview caches uniprot records in a file in your home directory called '.jalview.uniprot.xml'. -

The first step in this process is to try to use the ID (name) of - each sequence as an ID search in Uniprot. If there is no match, The - EBI Blast search is used in an attempt to obtain the Uniprot Id for - each sequence. You will be notified of any 100% matches with - Uniprot, but you must then manually change the name of the sequence, - by right clicking on the sequence ID and selecting - Sequence→Edit Name, before Jalview will show its sequence +

The Sequence Identification Process + +

+

The first step in the procedure for matching uniprot IDs to + sequences is to use the ID (name) of + each sequence to retrieve Uniprot records directly.

+

+ If a uniprot record (or set of records) is found for a sequence, + then the sequence is aligned to the one in the Uniprot record + to determine the correct start and end residue positions (which are + displayed when the 'Show Full Sequence ID' option is set). +

+ +

If the alignment reveals differences between the sequence in the + alignment and the one in the record, then Jalview will assume that + the aligned sequence is not the one in the uniprot record. + +

+ +

+ In some cases, the ID used to retrieve Uniprot records may be out of + date and you will be notified of that a 100% match between the + sequence and a Uniprot record was identified, but the sequence name + must be manually changed (by right clicking on the sequence ID and selecting + Sequence→Edit Name), before Jalview will show its sequence features.

  • remember to save your alignment if you have updated any of the sequence IDs!

-

- If a uniprot record (or set of records) is found for a sequence, - then the sequence in aligned to the one in the Uniprot record - to determine the correct start and end residue positions that will be - displayed when the 'Show Full Sequence ID' option is set.

diff --git a/help/html/io/file.png b/help/html/io/file.png new file mode 100755 index 0000000000000000000000000000000000000000..0978a62ae67925ca1e983343862c94b5cc2bc18b GIT binary patch literal 590 zcmV-U0WdKcYZXhu<6UgrJ4UKTxBFLSw+tSWrlze?W}YSr~g`VuOvpz{E=9 ztFtjNArTuwLZza?C=x{tFZFT*8yx5j zRIRcWGT8bb%rPPetd32`BG3y+mRSq#?cK-YK3!M)`fwmn7`-^6>Ww)5Z>RXVh1TJL zwx~aUN`uF{cnxEY;{dML<#4#9X`MzxB?Jn#I-OP~yrSq*6nTn!E1;0S@fg(42qekt ze!Cq+qZzCyu6!P88X`oXUjT@wu}Z}Tp;#`r39-~_ZHvVYR1VnCa^!ZP{w*uR^pTlF zVgy3eY7w3XmXB8&oAqWpfP}_!vDDIJP);U2KX=7`q0$EIgWtd1|G zlkNe(^(niv-mcX+jJ0MHA*4GTVE&=#K(5VIRaGHE(AeaQBvG21tZZ+yy0H@8YVBEx cuBxo{3%CL=QJ8CErvLx|07*qoM6N<$f|X|XCIA2c literal 0 HcmV?d00001 diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html new file mode 100755 index 0000000..5c888ff --- /dev/null +++ b/help/html/io/fileformats.html @@ -0,0 +1,55 @@ + + +Alignment Fileformats + + + + +

Alignment Fileformats +

Jalview understands a wide range of sequence alignment formats. In +order to determine which format has been used for an alignment, +jalview tries to detect some text or formatting unique to one of the formats: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
FormatUnique File FeatureFile Extension
FASTA>SequenceName
+THISISASEQENCE
.fa, .fasta
MSF!! AA_MULTIPLE_ALIGNMENT 1.0
+..
+//
.msf
CLUSTALWCLUSTAL.aln
PILEUPPileUp
PIR>P1;.pir
BLC>Seq1
+>Seq2
.blc
PFAMSequenceName THISISASEQENCE.pfam
+

The file extensions are used to associate jalview alignment icons +with alignment files: +

+ + diff --git a/help/html/io/index.html b/help/html/io/index.html index bd2a790..3db67ee 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -6,35 +6,56 @@

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

The EBI has examples of these file formats.

-

Additionally annotated alignments can be read in from the Jalview format.

-

Use the "Input Alignment" menu at the top of the main application - window to read in files from

+

Additionally, annotated whole sets of alignments and trees can be +read from a Jalview +(jar) format file using Desktop→Load Project.

+

Use the Desktop→Input Alignment menu to read in files from:

    -
  • the local file system
  • -
  • a website URL
  • -
  • or by copying and pasting into the "Cut & Paste" text window
  • +
  • From File: the local file system
  • +
  • From URL: the web (please use the full url)
  • +
  • from Textbox: a copy and paste into the + "Cut & Paste" text window
-

If a file is of an unknown format or there is any other error reading the alignment - file you will be given an error message, the alignment will not be read in. +

Jalview will try to recognise the file type automatically (using +some special features). If a +file is of an unknown format or there is any other error reading the +alignment file then you will be given an error message. If you think +Jalview really should be able to read your file, then send an email +containing the problem file to jalview@jalview.org.

Output

Each alignment, whether it is the original or an edited version may be saved - in the standard formats

+ in the standard formats using File→Save As

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

-

You may save annotated alignments in the Jalview file format.

+

You can also save the current set of alignments and their colours, annotations and +trees in a Jalview archive file using Desktop→Save project.

 

Export

-

The alignment may also be saved as a HTML web page.

-

You may save a Portable Networks Graphics (PNG) image of your alignment.

-

You may save the alignment as an Encapsulated Postscript file. This is a vector - graphics file which may be modified in various graphics applications, such as - Adobe Illustrator.
-
- Tip: When importing to a Microsoft document, a snapshot image is taken of your - file - this will be blurred. Right-click the image and choose "Edit image." - This will restore the high quality EPS file format output.
- NB. Mac OSX users will find that eps files are automatically converted into - PDF files.

-

The alignment can be printed from a local printer.

+

The alignment view can be printed using +File→Print, or exported in a number of ways via the +File→Export menu: +

    +
  • HTML
    for viewing in a web browser +
  • +
  • PNG - a Portable Networks Graphics image
    For low quality +diagrams and powerpoint presentations +
  • +
  • EPS - an Encapsulated Postscript Document
    For high quality +diagrams and publications. +
+ +

Tips for working with EPS Files

  • The EPS file generated by jalview contains vector + graphics which are directly editable in graphics applications such as + Adobe Illustrator.
  • +
  • When importing an EPS into to a Microsoft office document, a snapshot image of the + file will be displayed which often looks blurred. Right-click the + image and choose "Edit image." to convert it to word + drawing objects which give a truer WYSIWIG representation. +
  • +
  • + Mac OSX users will find that eps files are automatically converted into + PDF files. +
  • +

    -- 1.7.10.2