Menus

From: jprocter Date: Thu, 16 Jun 2005 13:50:34 +0000 (+0000) Subject: more menu doco. X-Git-Tag: Release_2_0~14 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git more menu doco. --- diff --git a/help/help.jhm b/help/help.jhm index 3a4aac4..e387045 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -15,7 +15,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index c0b0adc..e441033 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -36,9 +36,9 @@ - - - + + + diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 5a014bb..c579677 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -42,7 +42,8 @@ phylogenetic tree construction, and may fail on very large alignments. href="../calculations/treeviewer.html">tree viewing window. In addition, a new entry with the same tree viewer window name will be added in the Sort menu so that the alignment can be reordered to reflect the ordering of -the leafs of the tree.

+the leafs of the tree. If the tree was calculated on a selected region +of the alignment, then the title of the tree view will reflect this.

External Sources for Phylogenetic Trees

A number of programs exist for the reliable construction of diff --git a/help/html/features/jalarchive.html b/help/html/features/jalarchive.html index 0a10cb2..b8d658d 100755 --- a/help/html/features/jalarchive.html +++ b/help/html/features/jalarchive.html @@ -7,10 +7,9 @@

Jalview Project Archives

These are XML files containing alignments, trees and Jalview -display information. A data exchange standard is currently being -developed, so there is no stable schema yet, but Jalview web services -will soon make use of the same interchange format. -

These are java archives of an XML file containing alignments, trees +and Jalview display information. A data exchange standard is currently +being developed, so there is no stable schema yet, but Jalview web +services will soon make use of the same interchange format.

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 943728f..e3dc703 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -6,22 +6,22 @@

Preferences

The "Visual" tab on the preferences window allows you to configure the default display for a new alignment window.

Maximise Window - If this is selected, a new alignment window will stretch +

Maximise Window - If this is selected, a new alignment window will stretch to fit the available space.

Show Annotations - If this is selected the new window will display an annotation +

Show Annotations - If this is selected the new window will display an annotation panel below the sequences. This annotation panel may have several rows describing - the whole alignment. The 3 standard annotations Conservation, Quality and Consensus + the whole alignment. The 3 standard annotations Conservation, Quality and Consensus may be shown or hidden by default.

Full Sequence ID - If selected the ID panel will display the name of a sequence +

Full Sequence ID - If selected the ID panel will display the name of a sequence plus the start and end residues in the format name/start-end. If not selected, the displayed ID will be the name of the sequence.

Font - The default font name, size and style can be set for a new alignment +

Font - The default font name, size and style can be set for a new alignment window.

Gap Symbol - The default gap symbol may be set to either "-" or "."

Colour - The default colour scheme for a new alignment window. If the chosen +

Gap Symbol - The default gap symbol may be set to either "-" or "."

Colour - The default colour scheme for a new alignment window. If the chosen option is "User Defined" then the last User Defined Colour loaded or saved via the User Defined Colours panel will be loaded.

Open file - If this is selected then the default alignment file will be opened +

Open file - If this is selected then the default alignment file will be opened when Jalview is started. You can change the default file by clicking on file name and either typing in the file path or selecting it from the file chooser window.

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index a15ad23..3538d0b 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,8 +1,8 @@ -Menus +Alignment Window Menus -

Alignment Menu

Alignment Window Menus

File

alignment format

Export
- Creates an alignment output maintaining the alignment background colours - and group colours. If the alignment is wrapped, the output will also be - wrapped and will have the same visible residue width as the open alignment. + Creates an alignment graphic with the current annotation, + alignment background colours and group colours. If the alignment is wrapped, the output will also + be wrapped and will have the same visible residue width as the + open alignment.
- HTML
  @@ -40,8 +42,7 @@
- CLUSTAL

Print
@@ -52,14 +53,16 @@ your alignment window width, whichever is the smaller.

Load Associated Tree
- Jalview can load in trees which are in the Newick file format - and associate them with a particular alignment. Note: the ids of the tree - file and your alignment MUST be the same.
+ Jalview can view trees stored in + the Newick file format, and associate them with the + alignment. Note: the ids of the tree file and your alignment + MUST be the same.

Close
- Close the alignment window. Be aware that changes to your alignment - will not be save unless specifically actioned from the "Save As" - menu.
+ Close the alignment window. Make sure you have + saved your alignment before you close - either as a Jalview + project or by using the Save As menu.

Edit
@@ -69,9 +72,9 @@
Undo
This will undo any edits you make to the alignment. This applies to insertion or deletion of gaps, cutting residues or sequences from the alignment or - pasting sequences to the current alignment or sorting the alignment. It - DOES NOT undo colour changes or adjustments to group sizes affect the annotation - panel.
+ pasting sequences to the current alignment or sorting the + alignment. NOTE: It DOES NOT undo colour + changes, adjustments to group sizes, or changes to the annotation panel.

Redo
Any actions which you undo can be redone using redo.
@@ -83,10 +86,14 @@ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.

Copy
- Copies the currently selected residues to the system clipboard. The - format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE -
- Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.
+ Copies the currently selected residues to the system + clipboard - you can also do this by pressing <CTRL> and C + (<APPLE> and C on MacOSX).
+ If you try to paste the clipboard contents to a text editor, you will see + the format of the copied residues is a tab separated list:
+
+NAME START_RES END_RES SEQUENCE +

Paste
@@ -101,8 +108,9 @@

Delete
- This will delete the currently selected residues without making - a copy of them first.
+ This will delete the currently selected residues + without copying them to the clipboard. Like the other edit + operations, this can be undone with Undo.

Select All
Selects all the sequences and residues in the alignment.
@@ -119,7 +127,7 @@ selection.

Undefine Groups
- The alignment will be reset with no defined groups. WARNING: + The alignment will be reset with no defined groups.
WARNING: This cannot be undone.

Remove Left
@@ -135,29 +143,29 @@ or select "Deselect All" to deselect all columns.

Remove Empty Columns
- All columns which contain purely gap characters ("-", + All columns which only contain gap characters ("-", ".") will be deleted.
You may set the default gap character in preferences.

Remove All Gaps
- All gap characters ("-", ".") will be deleted from + All gap characters ("-", ".") will be deleted from the alignment.
You may set the default gap character in preferences.

Remove Redundancy
Selecting this option brings up a window asking you to select - a threshold. If the percentage identity between two sequences exceeds this - value one of the sequences (the shorter) is discarded. Press the "Apply" - button to remove redundant sequences.
+ a threshold. If the percentage identity between any two sequences + (under the current alignment) exceeds this + value then one of the sequences (the shorter) is discarded. Press the "Apply" + button to remove redundant sequences. The "Undo" button will undo the last + redundancy deletion.

Pad Gaps
- If the sequences in an alignment window are not all the same - length they can all be set to the length of the longest sequence by selecting - "Pad Gaps." Any sequences which are shorter than the longest sequence - in an alignment will have gap characters ("-" or ".") - appended to the beginning or end to make them equal length.
+ Adds gaps to the end of all the sequences so they + are all the same length. This is useful for making a tree using + unaligned sequences.
You may set the default gap character in preferences.

@@ -178,19 +186,20 @@

Font
- Change the font of the display. The default font can be set - from the "Choose Font" window, which is shown when the "Font - Menu" is selected.
+ Change the font of the display from the + "Choose Font" dialog box, which is shown when this + item is selected.

Wrap
- The default alignment display shows sequences in a single horizontal - row. If your alignment has only a few sequences you may wish to "Wrap" - the alignment so that the sequences are shown on multiple horizontal rows. + When ticked, the alignment display is + "wrapped" to the + width of the alignment window. This is useful if your alignment + has only a few sequences to view its full width at once.
Options are available to show the residue numbering at the start and/or end of an alignment as well as showing the alignment position above each sequence row.
- NOTE: In the current version the wrap alignment should be used for viewing, - not editing.
+ NOTE: When in wrapped alignment view, the + alignment cannot be edited or have regions selected on it.

Show Full Sequence ID
If this box is selected the sequence name will have the start @@ -208,11 +217,11 @@
Colour Text
If this is selected the residues will be coloured according to the background colour associated with that residue. The colour is slightly - darker than background to enable the residue to be read.
+ darker than background so the amino acid symbol remains visible.

Show Gaps
- If this is selected gap characters will be displayed as "." - or "-". If unselected gap characters will appear as blank spaces. + When this is selected, gap characters will be displayed as "." + or "-". If unselected, then gap characters will appear as blank spaces.
You may set the default gap character in preferences.

@@ -223,14 +232,14 @@
Sequence Features
If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features from the EBI. Features which are + the names to retrieve sequence features from the EBI. Features which are 1 residue in length are coloured red, sequences longer than 1 residue are coloured blue. Move the mouse over a coloured feature to display the details of the feature.
Note: The retrieved information will update the sequence start and end labels if they are incorrect.

-
Overview Window
+
Overview Window
A scaled version of the alignment will be displayed in a small window. A red box will indicate the currently visible area of the alignment. Move the visible region using the mouse.
@@ -245,7 +254,7 @@ If this is selected, any changes made to the background colour will be applied to all currently defined groups.
-
None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, +
Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, User Defined
See colours for @@ -257,7 +266,8 @@

Modify Conservation Threshold
Use this to display the conservation threshold slider window. - Useful if the window has been closed.
+ Useful if the window has been closed, or if the 'by + conservation' option appears to be doing nothing!
Above Identity Threshold
See Above Percentage Identity.
@@ -290,37 +300,68 @@ at the top.

+ The Sort menu will + have some additional options if you have just done a multiple + alignment calculation, or opened a tree viewer window.

Calculate Tree +
Functions for calculating trees on the alignment or the + currently selected region. See calculating trees.

Average Distance Using % Identity

Neighbour Joining Using % Identity

Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
- See calculating trees. -
-
+
Neighbour Joining Using Blosum62

Pairwise Alignments
- See pairwise alignments.
+ Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.

Principal Component Analysis
- See Principal Component Analysis. + Shows a spatial clustering of the sequences based on the + BLOSUM62 scores in the alignment. See Principal Component Analysis.

-
Web Service
+
Web Service
-
- Selecting one of the following menu items will start a remote service - on the high powered computing facility at the University of Dundee. You - will need a continuous network connection in order to use these services. + Selecting one of the following menu items starts a remote service + on compute facilities at the University of Dundee. You need a + continuous network connection in order to use these services + through Jalview. -
Clustal Alignment
-
Clustal Realign
-
JPred
-
Muscle Alignment
-
+
+
Clustal Alignment
+ Submits all, or just the currently selected sequences for alignment with clustal W.
+
Clustal Realign
+ Submits the alignment or currently selected region for + re-alignment with clustal W. Use this if you have added some + new sequences to an existing alignment.
+
Muscle Alignment
+ Submits all, or jut the currently selected sequences for + alignment using Muscle. Do not use this if you are working with + nucleic acid sequences.
+
JPred
+ Secondary structure prediction by network consensus. The + behaviour of this calculation depends on the current selection: +
+
If nothing is selected, and the displayed sequences appear to + be aligned, then a JNet prediction will be run for the first + sequence in the alignment, using the current + alignment. Otherwise the first sequence will be submitted for prediction. +
+
If + just one sequence (or a region on one sequence) has been selected, + it will be submitted to the automatic JNet prediction server + for homolog detection and prediction. +
+
If a set of sequences are selected, and they appear to be aligned, +then the alignment will be used for a Jnet prediction on the +first sequence selected in the set (that is, the one +that was first clicked on). +
+ +

diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index e1ef461..1fa861a 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -1,8 +1,8 @@ -Desktop Menu +Desktop Menus -
Desktop Menu
+
Desktop Menus

File
@@ -18,12 +18,10 @@

Save Project
- Saves all currently open alignment windows with their current visible - settings as a Jalview File, with the .jar extension. Each alignment will - also save the currently active tree associated with the window, if one - exists.
+ Saves all currently open alignment windows with their current view + settings and any associated trees, as a Jalview Archive (which has a .jar extension).
Load Project
- Loads Jalview file formatted alignments only.
+ Loads Jalview archives only.
Quit
Close Jalview. Warning - any annotations you have made on alignments will be lost unless you Save your work before quitting.
diff --git a/help/html/webServices/clustal.html b/help/html/webServices/clustal.html index 6c9c481..94f0bee 100755 --- a/help/html/webServices/clustal.html +++ b/help/html/webServices/clustal.html @@ -1,7 +1,7 @@ Clustal Alignment -
Clustal Alignment
+
Calculations→Web Service→Clustal Alignment..

When this option is selected a progress window will appear giving you a message about whether your process is running. The alignment is sent to the Barton Group cluster and remotely aligned using Clustalw program.
diff --git a/help/html/webServices/clwqueued.gif b/help/html/webServices/clwqueued.gif new file mode 100755 index 0000000..5bd4756 Binary files /dev/null and b/help/html/webServices/clwqueued.gif differ diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 19fcd8f..5b507be 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,20 +1,44 @@ - -Web Services - -
Web services
-
Originally Jalview used SRS server to retrieve sequence features for a given - alignment. In addition certain remote alignment programs could be called from - the Jalview interface and the results displayed in a new alignment panel.
-
Jalview's web based computations are now being developed further, - using SOAP based services to expose protein sequence alignment and - secondary structure prediction programs. These services actually run - on the cluster based in Dundee, and maintained by the Barton group. -
In the future, Jalview will be able to discover services - dynamically, and the repertoire will include methods for repeat - analysis, sequence identification and remote homology - detection. The web service methodology will also allow potentially - expensive Jalview analysis functions like PCA to be distributed, if - necessary, when the user is dealing with very large numbers of sequences.
+ + Web Services + +
Web services
+
A variety of web services are available from the Alignment window's + Calculations→Web Service→ menu. +
+
Jalview's distributed computations are SOAP based services exposing + protein sequence alignment and secondary structure prediction programs. These services actually run + on the cluster based in the School of Life Sciences, University of + Dundee, and are maintained by the Barton group. +
+
Web Service Dialog Box
+ +
+ This dialog box is displayed when a web service job is submitted. +
+
Current services: +
+
ClustalW Multiple Alignment
+ The clustal W service remains one of the more popular Jalview features. +
+
Muscle Multiple Alignment
+ High Quality and High Throughput multiple alignments of proteins. This + method can sometimes be more accurate than ClustalW when dealing with + diverse sets of sequences. +
+
JNet Secondary Structure Prediction
+ This is a front end to the existing JNet www server. +
+
+
+
Watch this space! These are some of the services + planned to be released soon:
+
Repeat analysis +
+
Remote Homology Detection
+
+
+ In the future, Jalview will also be able to new discover services + dynamically, and distribute expensive analysis functions like PCA to the Dundee machines.