Editing

From: jprocter Date: Mon, 27 Nov 2006 17:32:40 +0000 (+0000) Subject: 2.2 documentation X-Git-Tag: Release_2_2~22 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git 2.2 documentation --- diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 5252a30..c0c7f2c 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -21,7 +21,7 @@ - + diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 8cbf0ca..acf9665 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -50,7 +50,7 @@ sequence in the associated alignment window views. Rectangular region based selection is also possible, by holding the 'S' key whilst left-clicking and dragging the mouse over the display. By default, points are only associated with the alignment view from which the PCA -was calculated, but this may be changed via the Associate +was calculated, but this may be changed via the View→Associate Nodes sub-menu.

Initially, the display shows the first three components of the similarity space, but any eigenvector can be used by changing the diff --git a/help/html/colourSchemes/textcolour.gif b/help/html/colourSchemes/textcolour.gif new file mode 100644 index 0000000..a659156 Binary files /dev/null and b/help/html/colourSchemes/textcolour.gif differ diff --git a/help/html/colourSchemes/textcolour.html b/help/html/colourSchemes/textcolour.html index 586bb06..f40116a 100644 --- a/help/html/colourSchemes/textcolour.html +++ b/help/html/colourSchemes/textcolour.html @@ -5,12 +5,16 @@ Background Dependent Text Colour Background Dependent Text Colour
The Colour→Text Colour menu entry opens -the Text Colour dialog box. This contains a slider, and -two colour icons showing the text colour for dark backgrounds (left hand -end of slider), and light backgrounds (right hand end of slider). Drag -the slider to change the threshold for transitioning between dark and -light background colours, and select either of the colour boxes to open -a colour chooser to select a different text colour. +the "Adjust Foreground Text Colour Threshold" +dialog box, allowing the colour of symbols rendered on dark or light +backgrounds to be set for the current selection or the whole alignment.
+
+
The dialog box contains a slider, and two colour icons showing +the text colour for dark backgrounds (left hand end of slider), and +light backgrounds (right hand end of slider). Drag the slider to change +the threshold for transitioning between dark and light background +colours, and select either of the colour boxes to open a colour chooser +to select a different text colour.
diff --git a/help/html/editing/index.html b/help/html/editing/index.html index b0e8103..f71271a 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -1,56 +1,56 @@ - -Editing - -
Editing
-
There are two major ways to edit alignments - in 'Normal mode', -gaps are inserted and deleted at the mouse pointer in various ways by -clicking the left mouse button and pressing a combination of either -shift and control (or the apple key on Macs) and dragging the mouse. Pressing -F2 toggles the alternative 'Cursor -mode' keyboard editing facility, where the space bar and delete -keys add and remove gaps at the current editing position. The key -strokes for both these modes are summarised in the keystrokes table.
-
Tip: For large alignments, deselect "Calculate -> - Autocalculate Consensus" to prevent the alignment performing lengthy calculations - after every edit.
-
Inserting / removing gaps - hold down the - "Shift" key. Click on a residue with the mouse and drag it - to the left or right to insert gaps and remove gaps.
- If the current selection is a group over all sequences in the - alignment, or a group over some sequences or all columns in the - alignment, then hold down either "Control" - key and drag the residue left or right to edit all sequences in the defined - group at once.
-
Copy/paste/cut/delete - any sequences which are in the current selection - box (indicated in red) may be cut and / or copied to a new alignment or deleted. -
-
Undo / redo - editing of sequences (insertion/removal of gaps, removal - of sequences, trimming sequences etc) may be undone or redone at any time using - the appropriate menu items from the edit menu. The undo history list only allows - a maximum of 10 actions. -
Trimming alignment - First select a column by clicking the scale indicator - (above the sequences) The alignment may then be trimmed to the left or right - of this column. If multiple columns are selected, the alignment is trimmed to - the right of the rightmost selected column (or to the left of the leftmost selected - column)
-
Remove gapped columns - Removes columns within the alignment which - contain only space characters ("-" or "." or " ")
-
Removing gaps - Removes all gaps from the alignment. Gaps are "-" - or "." or " ".
-
Set gap character - Switches the gap character between "." - and "-". If the "Render Gaps" option from the "View" - menu is unticked all gaps will appear as blank spaces.
-

-
Editing In Selection Areas
-Editing can be restricted to the current selection area. -This allows the user to "Lock" the alignment either side of the selection -area. Any gap insertions or deletions will only affect the current selection area. -
-
In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, - the same number of gaps will be inserted at position 116, (between M and L). -
-
Locked selection area based editing was introduced in Jalview 2.08
-

- - + +Editing + +
Editing
+
There are two major ways to edit alignments - in 'Normal mode', +gaps are inserted and deleted at the mouse pointer in various ways by +clicking the left mouse button and pressing a combination of either +shift and control (or the apple key on Macs) and dragging the mouse. Pressing +F2 toggles the alternative 'Cursor +mode' keyboard editing facility, where the space bar and delete +keys add and remove gaps at the current editing position. The key +strokes for both these modes are summarised in the keystrokes table.
+
Tip: For large alignments, deselect "Calculate -> + Autocalculate Consensus" to prevent the alignment performing lengthy calculations + after every edit.
+
Inserting / removing gaps - hold down the + "Shift" key. Click on a residue with the mouse and drag it + to the left or right to insert gaps and remove gaps.
+ If the current selection is a group over all sequences in the + alignment, or a group over some sequences or all columns in the + alignment, then hold down either "Control" + key and drag the residue left or right to edit all sequences in the defined + group at once.
+
Copy/paste/cut/delete - any sequences which are in the current selection + box (indicated in red) may be cut and / or copied to a new alignment or deleted. +
+
Undo / redo - editing of sequences (insertion/removal of gaps, removal + of sequences, trimming sequences etc) may be undone or redone at any time using + the appropriate menu items from the edit menu. The undo history list only allows + a maximum of 10 actions. +
Trimming alignment - First select a column by clicking the scale indicator + (above the sequences) The alignment may then be trimmed to the left or right + of this column. If multiple columns are selected, the alignment is trimmed to + the right of the rightmost selected column (or to the left of the leftmost selected + column)
+
Remove gapped columns - Removes columns within the alignment which + contain only space characters ("-" or "." or " ")
+
Removing gaps - Removes all gaps from the alignment. Gaps are "-" + or "." or " ".
+
Set gap character - Switches the gap character between "." + and "-". If the "Render Gaps" option from the "View" + menu is unticked all gaps will appear as blank spaces.
+

+
Editing In Selection Areas
+Editing can be restricted to the current selection area. +This allows the user to "Lock" the alignment either side of the selection +area. Any gap insertions or deletions will only affect the current selection area. +
+
In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, + the same number of gaps will be inserted at position 116, (between M and L). +
+
Locked selection area based editing was introduced in Jalview 2.08
+

+ + diff --git a/help/html/features/creatinFeatures.html b/help/html/features/creatinFeatures.html index 486b75b..0ebb52f 100644 --- a/help/html/features/creatinFeatures.html +++ b/help/html/features/creatinFeatures.html @@ -7,10 +7,10 @@

Jalview can create sequence features from the matches of a regular expression search, or from the currently selected area via the "selection→Create -sequence feature" entry in the selection area popup menu. In both +sequence feature" entry in the selection area popup menu. In both cases, the Create Features dialog box will then be opened:

Select or enter the attributes for the features being created, and then press OK to create the new features.

Each attribute is described below: diff --git a/help/html/features/das.gif b/help/html/features/das.gif new file mode 100644 index 0000000..1f884cb Binary files /dev/null and b/help/html/features/das.gif differ diff --git a/help/html/features/das.jpg b/help/html/features/das.jpg deleted file mode 100644 index 78e061b..0000000 Binary files a/help/html/features/das.jpg and /dev/null differ diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html index 5dc334e..c2b4d49 100644 --- a/help/html/features/dasfeatures.html +++ b/help/html/features/dasfeatures.html @@ -1,51 +1,65 @@ - - -DAS Features - - -

DAS Sequence Feature Retrieval

Jalview 2.1 can be set up to retrieve sequence features using the Distributed - Annotation System

Open the Feature Settings panel by selecting "View -> Feature Settings..."
Click on the "DAS Settings" tabbed - pane.
Select the sources to use for DAS feature retireval, then click the "Fetch - DAS Features" button.

If your DAS source selection contains sources which use Uniprot accession ids, - you will be asked whether Jalview should find Uniprot Accession ids for the - given sequence names. It is important to realise that many DAS sources only - use Uniprot accession ids, not names of sequences.
- The method of Uniprot accession id discovery is the same method which earlier - Jalview versions used for sequence feature retrieval, ie WSDbFetch provided - by the EBI.

The process is as described:

The Sequence Identification Process

Jalview will attempt to retrieve sequence features from Uniprot files using - the EBI dbFetch web service using the given sequence names (or Uniprot ID, if - available). A 100% match with the Uniprot record is required for Uniprot features - to be view on a sequence.

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!

- - + + + +DAS Features + + + +

DAS Sequence Feature Retrieval

Jalview includes a client for retrieving sequence features via +the Distributed Annotation System.

Open the Feature Settings panel by selecting "View -> + Feature Settings..."
Click on the "DAS Settings" + tabbed pane.
Select the sources to use for DAS feature retireval, then + click the "Fetch DAS Features" button. +
- Cancelling Feature Retrieval
  + Press the Cancel Fetch button to immediately stop + feature retrieval. This will not remove any features already added to + the alignment, but will halt any outstanding DAS requests.The + cancel fetch button is of particular use when one or more DAS + annotation servers are not responding! +
+

If your DAS source selection contains sources which use Uniprot +accession ids, you will be asked whether Jalview should find Uniprot +Accession ids for the given sequence names. It is important to realise +that many DAS sources only use Uniprot accession ids, rather than +Swissprot/Uniprot sequence names.
+

The Sequence Identification Process

+The method of Uniprot accession id discovery is the same method which +earlier Jalview versions used for sequence feature retrieval, and is now +also used for +PDB ID discovery +. Essentially, Jalview will try to retrieve Uniprot records via the +EBI's WSDbFetch interface using each sequence's ID string (or each +string in the ID separated by the '∣' symbol). +

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 a dialog box will be opened indicating that a 100% match +between the sequence and a Uniprot record was identified, but the +sequence name is different. In this case, the ID must be manually +changed (by right clicking on the sequence ID and selecting Sequence→Edit +Name), before Jalview will show its sequence features. +

Note
+ Please remember to save your alignment if either the start/end + numbering, or the sequence IDs were updated during the Uniprot ID + retrieval process.

DAS support was introduced in Jalview Version 2.1.

+ + diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html index f3e325d..30b36b1 100644 --- a/help/html/features/dassettings.html +++ b/help/html/features/dassettings.html @@ -1,32 +1,32 @@ - - -DAS Settings - - -

DAS Settings

Jalview can retrieve and visualize features from many DAS - sources at once. The DAS sources are discovered and selected via the DAS settings panel.

The available sources are listed in the table using each source's -Nickname as its identifier. Clicking on a source's entry in the table -reveals more information about that service in the panel to the -right. Select the tickbox in the "Use Source" column for a -source to add it to the set Jalview queries for alignment and sequence -features. -

You can filter the visible DAS sources by authority, type and "label". - You should read the DAS documentation to understand more about these values. -

Updating the list of sources

When the DAS Settings panel is first opened, and when the 'Refresh - source' buton is pressed, a list of DAS sources - is retrieved from the DAS registry URL (set by default to the DAS - registration server at - http://das.sanger.ac.uk/registry/das1/sources/).

Adding your own DAS Sources

You can add your own DAS source to the list by clicking the "Add Local - Source" button. Enter the URL and nickname of your additional service. - It should be noted that Jalview 2.1 will not query additional sources for more - information, but this will be implemented in future editions. -

- - + + +DAS Settings + + +

DAS Settings

Jalview can retrieve and visualize features from many DAS + sources at once. The DAS sources are discovered and selected via the DAS settings panel.

The available sources are listed in the table using each source's +Nickname as its identifier. Clicking on a source's entry in the table +reveals more information about that service in the panel to the +right. Select the tickbox in the "Use Source" column for a +source to add it to the set Jalview queries for alignment and sequence +features. +

You can filter the visible DAS sources by authority, type and "label". + You should read the DAS documentation to understand more about these values. +

Updating the list of sources

When the DAS Settings panel is first opened, and when the 'Refresh + source' buton is pressed, a list of DAS sources + is retrieved from the DAS registry URL (set by default to the DAS + registration server at + http://das.sanger.ac.uk/registry/das1/sources/).

Adding your own DAS Sources

You can add your own DAS source to the list by clicking the "Add Local + Source" button. Enter the URL and nickname of your additional service. + It should be noted that Jalview 2.1 will not query additional sources for more + information, but this will be implemented in future editions. +

+ + diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 77d62a7..b11e96b 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -1,77 +1,85 @@ - - -Sequence Features File - - -

Sequence Features File

The Sequence features file (which used to be known as the "Groups -file" prior to version 2.08) is a simple way of getting -your own sequence annotations into Jalview. It was introduced to allow -sequence features to be rendered in the Jalview applet, and so is -intentionally lightweight and minimal because the applet is often used -in situations where data file size must be kept to a minimum, and no -XML parser is available.

Features files are imported into Jalview in the following ways:
-

from the command line
- -features <Features filename>
Dragging a features file onto an alignment window
Via the "Load Features / Annotations" entry in the -File menu of an alignment window.

Sequence Features File Format

A features file is a simple ASCII text file, where each line -contains tab separated text fields. No comments are -allowed.

The first set of lines contain type definitions: -

Feature label	Feature Colour

-A feature type has a text label, and a colour (specified as a -red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma -separated numbers (ranging from 0 to 255)). -

The remaining lines in the file are the sequence annotation -definitions, where the now defined features are attached to regions on -particular sequences, optionally with some descriptive text (displayed -in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a -sequence, either by its text ID, or its index in an associated -alignment.

-description	sequenceId	sequenceIndex	start	end	featureType

Normally, -sequence features are associated with sequences rather than -alignments, and the sequenceIndex field is given as "-1". In -order to specify a sequence by its index in a particular alignment, the -sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the -sequenceId field will be used in preference to the sequenceIndex field.

-Feature annotations can be collected into named groups by prefixing -definitions with lines of the -form:

startgroup	groupname

.. and -subsequently post-fixing the group -with:endgroup groupname
Feature grouping -was introduced in version 2.08, and used to control whether a set of features -are either hidden or shown together in the sequence Feature settings -dialog box.

A complete example is shown below :

-domain	red
-metal ion-binding site	00ff00
-transit peptide	0,105,215
-chain	225,105,0
-modified residue	105,225,35
-signal peptide	0,155,165
-helix	ff0000
-strand	00ff00
-coil	cccccc
-Your Own description here	FER_CAPAA	-1	3	93	domain
-Your Own description here	FER_CAPAN	-1	48	144	chain
-Your Own description here	FER_CAPAN	-1	50	140	domain
-Your Own description here	FER_CAPAN	-1	136	136	modified residue
-Your Own description here	FER1_LYCES	-1	1	47	transit peptide
-Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
-Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
-startgroup	secondarystucture
-PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
-PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
-endgroup	secondarystructure
-

- -

- - + + + +Sequence Features File + + + +

Sequence Features File

The Sequence features file (which used to be known as the +"Groups file" prior to version 2.08) is a simple way of +getting your own sequence annotations into Jalview. It was introduced to +allow sequence features to be rendered in the Jalview applet, and so is +intentionally lightweight and minimal because the applet is often used +in situations where data file size must be kept to a minimum, and no XML +parser is available.

Features files are imported into Jalview in the following ways:
+

from the command line
+ -features <Features filename>
Dragging a features file onto an alignment window
Via the "Load Features / Annotations" entry in the File + menu of an alignment window.

Sequence Features File Format

A features file is a simple ASCII text file, where each line +contains tab separated text fields. No comments are +allowed.

The first set of lines contain type definitions: +

Feature label	Feature Colour

A feature +type has a text label, and a colour (specified as a red,green,blue 24 +bit triplet either in hexadecimal (eg. 00ff00) or as comma separated +numbers (ranging from 0 to 255)). The text label may contain simple HTML +document body tags if enclosed by "<html></html>" +and will be rendered as formatted tooltips in the Jalview Application +(the Jalview applet is not capable of rendering HTML tooltips, so all +formatting tags will be removed.

The remaining lines in the file are the sequence annotation +definitions, where the now defined features are attached to regions on +particular sequences, optionally with some descriptive text (displayed +in a tooltip when the mouse is near the feature on that sequence). There +are two alternate ways of referring to a sequence, either by its text +ID, or its index in an associated alignment. +

+description	sequenceId	sequenceIndex	start	end	featureType

+Normally, sequence features are associated with sequences rather than +alignments, and the sequenceIndex field is given as "-1". In +order to specify a sequence by its index in a particular alignment, the +sequenceId should be given as "ID_NOT_SPECIFIED", otherwise +the sequenceId field will be used in preference to the sequenceIndex +field. +

Feature annotations can be collected into named groups by +prefixing definitions with lines of the form:

startgroup	groupname

.. +and subsequently post-fixing the group with:endgroup groupname
Feature +grouping was introduced in version 2.08, and used to control whether a +set of features are either hidden or shown together in the sequence Feature settings dialog box.

A complete example is shown below : +

+domain	red
+metal ion-binding site	00ff00
+transit peptide	0,105,215
+chain	225,105,0
+modified residue	105,225,35
+signal peptide	0,155,165
+helix	ff0000
+strand	00ff00
+coil	cccccc
+Your Own description here	FER_CAPAA	-1	3	93	domain
+Your Own description here	FER_CAPAN	-1	48	144	chain
+Your Own description here	FER_CAPAN	-1	50	140	domain
+Your Own description here	FER_CAPAN	-1	136	136	modified residue
+Your Own description here	FER1_LYCES	-1	1	47	transit peptide
+Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
+Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
+startgroup	secondarystucture
+PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
+PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
+endgroup	secondarystructure
+

+ +

+ + diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index c5266d7..66413d9 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -1,51 +1,64 @@ -Hidden Regions + +Hidden Regions + -

Hidden Regions

Use the keyboard key "H" to hide / reveal selected columns and sequences. - To hide / reveal only selected sequences, use "Shift H", to hide / - reveal only selected columns, use "Control H".

Hidden Regions

Use the keyboard key "H" to hide / reveal selected +columns and sequences. To hide / reveal only selected sequences, use +"Shift H", to hide / reveal only selected columns, use +"Control H".

Hiding Sequences
-To hide selected sequences in an alignment, use the "View - -> Hide -> Selected Sequences" menu item or simply select "Hide - Sequences" from the Popup menu after a right click on the sequence Ids. -

Hidden sequences will not be used in any calculations, editing or web service - alignments performed on visible sequences.

+To hide selected sequences in an alignment, use the "View +-> Hide -> Selected Sequences" menu item or simply select "Hide +Sequences" from the Popup menu after a right click on the sequence +Ids.

Hidden sequences will not be used in any calculations, editing or +web service alignments performed on visible sequences.

Hidden Sequences Representatives
-A more advanced hide involves a right-mouse click on a sequence, then selecting - "SequenceID -> Represent Group with SequenceId". Using this method - of hiding sequences, any edits performed on the visible group representative - will be propogated to all the sequences in that group.
- The hidden representative sequences will not be used in any - calculations or web service alignments (nb. this may change in - the future) -

+A more advanced hide involves a right-mouse click on a sequence, then +selecting "SequenceID -> Represent Group with +SequenceId". Using this method of hiding sequences, any edits +performed on the visible group representative will be propogated to all +the sequences in that group.
+The hidden representative sequences will not be used in any calculations +or web service alignments (nb. this may change in the future). +
+Warning:The representative sequence groups feature is +not fully implemented in the jalview 2.2 release, following the +introduction of Multiple views.

Hiding Columns
-To hide selected columns in an alignment, use the "View - -> Hide -> Selected Columns" menu item, or right click within a region - of selected columns in the scale above the alignment (only available in non - wrapped mode) and select "Hide Columns".

When an alignment view contains hidden columns, certain constraints -apply:

Editing the alignment is bound by the hidden columns, i.e. you cannot move residues - across a hidden column boundary.
Tree, pairwise alignment and PCA calculations will only be -performed using the visible parts of the alignment. -
Multiple Sequence - Alignments are performed locally on on each visible chunk of - the input, and concatenated with the hidden regions to form the - final result.
-

"View +-> Hide -> Selected Columns"

"Hide +Columns"

When an alignment view contains hidden columns, certain +constraints apply: +

Editing the alignment is bound by the hidden columns, i.e. + you cannot move residues across a hidden column boundary.
Tree, + pairwise + alignment and PCA + calculations will only be performed using the visible parts of + the alignment.
Multiple Sequence + Alignments are performed locally on on each visible chunk of the input, + and concatenated with the hidden regions to form the final result. +
+

Column Separability
Calculations where hidden columns are - excluded, and a single analysis performed on the result, are termed column-separable. - The simple Tree and PCA calculations are column separable because essentially the same results - would be obtained if the excluded hidden columns were replaced by gaps as the input to the calculation.

Multiple Sequence alignment and secondary structure prediction are both non-column-separable, and - so the exclusion of hidden regions leads to only 'locally optimal' results - sometimes - different to that obtained when using the full alignment.

Column Separability
+Calculations where hidden columns are excluded, and a single analysis +performed on the result, are termed column-separable. The +simple Tree and PCA calculations are column separable because +essentially the same results would be obtained if the excluded hidden +columns were replaced by gaps as the input to the calculation.

Multiple Sequence alignment and secondary structure prediction +are both non-column-separable, and so the exclusion of hidden regions +leads to only 'locally optimal' results - sometimes different to that +obtained when using the full alignment.

Multiple Alignment Views

-
Multiple alignment views allow's the same alignment to be viewed -in many different ways, either as multiple alignment tabs, or -simultaneously in linked alignment windows. A view is an independent -visualization of the same alignment, so each may have a different -ordering, colouring, row and column hiding and seuqence feature and -annotation display setting, but alignment, feature and annotation edits -are common to all, since this affects the underlying data.
-
A new view is created using the "View→New +
Multiple alignment views allows the same alignment to be viewed +independently in many different ways simultaneously. Each view is an +independent visualization of the same alignment, so each may have a +different ordering, colouring, row and column hiding and seuqence +feature and annotation display setting, but alignment, feature and +annotation edits are common to all, since this affects the underlying +data.
+
Create a new view using the "View→New View" menu item, or by pressing Control+T. A newly created view will be identical to the view it was created from, but any changes to the way the alignment is coloured or displayed will only @@ -29,15 +29,22 @@ to expand each view into its own linked alignment window. Expanded views are gathered back into into a single tabbed alignment window by pressing G, or by selecting "View→Gather").
-
Tree Viewers, PCA Viewers, and Multiple Views
+
Structure and Analysis Viewers and Multiple +Views

A tree calculated on a particular view, or loaded onto it, is by default associated with just that view. However, the Tree Viewer's "View→Associate leaves" submenu allows a tree's view association to be changed to to any or all other views.
-
The results of a PCA calculation on a particular view -may also be associated with other views, using the "Associate +
The results of a PCA +calculation on a particular view may also be associated with other +views, using the PCA Viewer's "View→Associate Nodes" submenu.
+
A PDB Structure Viewer opened on a +structure associated with a sequence in a particular view will also, by +default, only be associated with the sequence as it is displayed in that +view. The "View→Associate View" submenu allows the +association of alternative views.

Multiple Views were introduced in Jalview 2.2
diff --git a/help/html/features/newkeystrokes.html b/help/html/features/newkeystrokes.html index 110e21c..8fd671e 100644 --- a/help/html/features/newkeystrokes.html +++ b/help/html/features/newkeystrokes.html @@ -4,10 +4,11 @@ New Key Strokes and Menus
Many new keyboard shortcuts have been added in Jalview 2.2 to make editing, selecting and navigating an -alignment even easier. Some of the commands in the Edit -and View menus present in earlier releases have also -been moved into their own Select and Format -menus. Some of the important new keystrokes are shown below : +alignment even easier. The selection commands in the Edit +menu, and the alignment formatting controls within the View +menu have also been moved into their own respective Select +and Format menus.
+
Some of the most important new keystrokes are shown below :

Page Up and Page Down scrolls through the alignment view.
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index bd240ea..97471a2 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,93 +1,136 @@ - -PDB Viewer - -
The PDB Viewer Window -
This interactive structure viewing window is opened by selecting the -"Sequence→View PDB -entry:" entry in the sequence id pop-up menu. This can only be -done for sequences which have an associated -PDB structure.
-
Controls
-
The structure is rendered as an alpha-carbon trace. -Moving the mouse over the structure brings up tooltips with a -residue name and PDB sequence position. If a mapping exists to a -residue in the associated sequence, then this will be highlighted in -the alignment window, and vice versa for viewing the coordinates -associated with a particular residue in the sequence.
-
Selecting a residue highlights its associated sequence residue and -alpha carbon location.
-
- - - - - - - -
Action Windows Unix Mac/OSX
Select/
Deselect
Residue Left Click Left -Click Click
Rotate View Left Click and Drag Left Click and -Drag Click and Drag
Roll View Right Click and drag Right Click and -Drag TODO
Move Origin Middle-Button and -Drag Middle-Button and Drag TODO
Zoom In Up Arrow Up Arrow Up -Arrow
Zoom Out Down Arrow Down Arrow Down Arrow
-
-
There are three menus: -
-
File
-
Save As
Saves the current view as an EPS or PNG file. -
-
View Mapping
-Opens a text window showing the alignment between the residues -corresponding to alpha-carbon atoms in the PDB structure and the -residues in the associated sequence. -
-
-
-
Colours
-
By Sequence
-Colours each residue in the structure with the colour of its -corresponding residue in the associated sequence as rendered in the -alignment window, including any Uniprot sequence features or region -colourings.
Residues which only exist in the PDB structure are -coloured white if they are insertions (relative to the associated -sequence in the alignment) and grey if they are N or C terminal -flanks outside the region mapped to the alignment window's sequence.
-
By Chain
-Assigns a random colour to each PDB chain. -
Charge & Cysteine
-Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and -cationic (Lysine or Arginine) residues in blue. -
-
Standard and User Defined Jalview colourschemes.
-The remaining entries apply the colourschemes available from the -standard and user defined amino acid colours. -
-
-
-
View
-These options can be turned off to improve performance when viewing -large structures, some at the expense of visual clarity.
-
Wireframe
-Draws thin lines rather than thick lines for the -alpha-carbon trace. -
Depthcue
Shades the structure so parts of the structure near -the front of the view are brighter than those further away. -
Z Buffering
-Applies depth sorting to correctly render occluded regions of the -backbone trace. -
-
Show All Chains
-When turned on, shows all chains in the PDB file, not just the one -associated with a sequence in the alignment window. -
-
-
-
-
-
Notes for PDB Viewing in the Jalview Applet -
The applet can only load PDB files by copying and pasting the text into - the popup window which appears when "Show PDB Structure" is selected - after right clicking on a sequence name.
- - + + +PDB Viewer + + +
The PDB Viewer Window +
This interactive structure viewing window is opened by selecting +the "Sequence→View PDB entry:" entry in +the sequence id pop-up menu. This +can only be done for sequences which have an associated +PDB structure.
+
Controls
+
The structure is rendered as an alpha-carbon trace. Moving the +mouse over the structure brings up tooltips with a residue name and PDB +sequence position. If a mapping exists to a residue in the associated +sequence, then this will be highlighted in the associated view in its +alignment window, and vice versa for viewing the coordinates associated +with a particular residue in the sequence in a particular view on the +alignment.
+
Selecting a residue highlights its associated sequence residue +and alpha carbon location.
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Action Windows Unix Mac/OSX
Select/
+ Deselect
+ Residue Left Click Left Click Click
Rotate View Left Click and Drag Left Click and Drag Click and Drag
Roll View Right Click and drag Right Click and Drag TODO
Move Origin Middle-Button and Drag Middle-Button and Drag TODO
Zoom In Up Arrow Up Arrow Up Arrow
Zoom Out Down Arrow Down Arrow Down Arrow
+
+
There are three menus: +
+
File
+ +
+
Save As
+ Saves the current view as an EPS or PNG file.
+
View Mapping
+ Opens a text window showing the alignment between the + residues corresponding to alpha-carbon atoms in the PDB structure and + the residues in the associated sequence.
+
+
+
Colours
+ +
+
By Sequence
+ Colours each residue in the structure with the colour of its + corresponding residue in the associated sequence as rendered in the + associated alignment view, including any Uniprot sequence features or + region colourings.
+ Residues which only exist in the PDB structure are coloured white if + they are insertions (relative to the associated sequence in the + alignment) and grey if they are N or C terminal flanks outside the + region mapped to the alignment window's sequence.
+
By Chain
+ Assigns a random colour to each PDB chain. +
Charge & Cysteine
+ Highlights cysteines in yellow, anionic (Aspartic Acid or + Glutamic Acid) residues in red, and cationic (Lysine or Arginine) + residues in blue.
+
Standard and User Defined Jalview + colourschemes.
+ The remaining entries apply the colourschemes available from the + standard and user defined amino + acid colours.
+
+
+
View
+ These options can be turned off to improve performance when + viewing large structures, some at the expense of visual clarity. +
+
Wireframe
+ Draws thin lines rather than thick lines for the + alpha-carbon trace.
+
Depthcue
+ Shades the structure so parts of the structure near the front + of the view are brighter than those further away.
+
Z Buffering
+ Applies depth sorting to correctly render occluded regions + of the backbone trace.
+
Show All Chains
+ When turned on, shows all chains in the PDB file, not just + the one associated with a sequence in the alignment window.
+
Associate View
+ Change which view on the associated sequence's alignment is to be + associated with the PDB viewer. +
+
+
+
+
Notes for PDB Viewing in the Jalview Applet +
The applet can only load PDB files by copying and pasting the +text into the popup window which appears when "Show PDB +Structure" is selected after right clicking on a sequence name.
+ + diff --git a/help/html/io/index.html b/help/html/io/index.html index d57de42..094fcbb 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,48 +1,57 @@ - -Input/Output - -
Input
-
Jalview can read alignment files in any of the following standard formats:
-
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, -NBRF/PIR (including MODELLER variant), Pfam/Stockholm
-
The EBI has examples of - these file formats.
-
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:
-
-
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
-
-
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. -
-
Jalview can also read jalview specific files for sequence features -and alignment annotation.
-
Output
-
Each alignment, whether it is the original or an edited version may be saved - in the standard formats using File→Save As
-
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
-Jalview will by default append the sequence start and end to each sequence name, -in the format /start-end. If you do not want this behaviour for a particular file -output, open the "Output" tab on the Preferences window where you can -select which file formats you want to append the start and end sequence positions -for. In the case of PIR format, the output tab also contains a switch -for turning on the output of Modeller style structured description -lines. -
Quantitative and symbolic alignment annotation can be exported as a -comma separated value file by right clicking on an annotation row -under the alignment.
-
You can also save the current set of alignments and their colours, annotations and -trees in a Jalview archive file using Desktop→Save project.
-

- - + + +Input/Output + + +
Input
+
Jalview can read alignment files in any of the following standard +formats:
+
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, +NBRF/PIR (including MODELLER variant), Pfam/Stockholm
+
The EBI has examples +of these file formats.
+
Additionally, whole sets of coloured and annotated alignments and +trees can be read from a Jalview +(jar) format file using Desktop→Load Project.
+
Press "Control O" to open a file browser, or use +the Desktop→Input Alignment menu to read in +alignments from:
+
+
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
+
+
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.
+
Jalview can also read jalview specific files for sequence features and alignment annotation.
+
Output
+
Each alignment, whether it is the original or an edited version +may be saved in the standard formats using File→Save +As
+
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, +NBRF/PIR, Pfam/Stockholm
+Jalview will by default append the sequence start and end to each +sequence name, in the format /start-end. If you do not want this +behaviour for a particular file output, open the "Output" tab +on the +Preferences +window where you can select which file formats you want to append the +start and end sequence positions for. In the case of PIR format, the +output tab also contains a switch for turning on the output of Modeller +style structured description lines. +
Quantitative and symbolic alignment +annotation can be exported as a comma separated value file by right +clicking on an annotation row under the alignment.
+
You can also save the current set of alignments and their +colours, annotations and trees in a Jalview archive file using Desktop→Save +project.
+

+ + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 376792f..0795189 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -30,9 +30,11 @@ determine which alignment format to save as.
Output to Textbox
- The alignment will be displayed in plain text in a new window - which you can "Copy and Paste" using the pull down menu, or - your standard operating system copy and paste keys.
+ The alignment will be displayed in plain text in a new + window, which you can "Copy and Paste" using the pull down + menu, or your standard operating system copy and paste keys. The + output window also has a "New Window" + button to import the (possibly edited) text as a new alignment.
Select the format of the text by selecting one of the following menu items.
diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index eb45924..bf1fed5 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -15,9 +15,10 @@ Add sequences to the visible alignment from file, URL, or cut & paste window
Reload
- Reloads the alignment from the original file, if available.
Warning: - This will delete any edits, analyses and colourings applied since the - alignment was last saved, and cannot be undone.
+ Reloads the alignment from the original file, if available.
+ Warning: This will delete any edits, analyses and + colourings applied since the alignment was last saved, and cannot be + undone.
Save (Control S)
Saves the alignment to the file it was loaded from (if available), in the same format, updating the original in place.
@@ -26,9 +27,11 @@ open, use the "Files of type:" selection box to determine which alignment format to save as.
Output to Textbox
- The alignment will be displayed in plain text in a new window + The alignment will be displayed in plain text in a new window, which you can "Copy and Paste" using the pull down menu, or - your standard operating system copy and paste keys.
+ your standard operating system copy and paste keys. The output window + also has a "New Window" button to import the + (possibly edited) text as a new alignment.
Select the format of the text by selecting one of the following menu items.
@@ -47,8 +50,8 @@ the number of residues per line of your alignment will depend on the paper width or your alignment window width, whichever is the smaller.
Export Image
- Creates an alignment graphic with the current view's 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. diff --git a/help/html/menus/index.html b/help/html/menus/index.html index 03d764a..cd1fd78 100755 --- a/help/html/menus/index.html +++ b/help/html/menus/index.html @@ -1,18 +1,22 @@ -Menus + +Jalview's Menus + -
Menus
-
Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment - Menu" and the "Popup Menu".
-
The Desktop Menu is always visible and is the - starting point for loading new alignments.
-
The Alignment Menu is visible once and alignment - has been opened.
-
The Popup Menu is made visible by clicking with - the right mouse button on a sequence or the name of a sequence in an alignment - window.
-
The Annotations Menu is opened by right-clicking on an annotation row label.
+
Jalview's Menus
+
Menus are used in 3 places in Jalview - the "Desktop +Menu", the "Alignment Menu" and the "Popup +Menu".
+
The Desktop Menu is always visible +and is the starting point for loading new alignments.
+
The Alignment Window Menus are +accessible once an alignment has been opened.
+
The Popup Menus are opened by +clicking with the right mouse button in the alignment display area or on +a sequence label in the alignment window.
+
The Annotations Menu is opened +by right-clicking on an annotation row label or in an annotation row.
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index f885bd8..2c50c02 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -110,10 +110,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

Hide Sequences
- This menu item lists all links which have been set up in the Preferences Connections tab. - It is only displayed when you right click (Apple click) on a sequence - id.
+ Hides the currently selected seuqences in this alignment view.

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 344c322..651292e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,54 +1,50 @@ -What's new ? + +What's new ? + -
What's new ?
+
What's new ?

Jalview Version 2.2
-
Multiple views with different styles, colours, hidden regions for one alignment -
-
Easily add, amend and delete sequence features -
-
"Reload" alignment from File or URL to revert to original -
-
"Save" to current filename or "Save As" to new filename -
-
Set different text colour for dark or light background -
-
Right align sequence ids -
+
Multiple views with different styles, colours, hidden regions for +one alignment
+
Easily add, amend and delete sequence features
+
"Reload" alignment from File or URL to revert to +original
+
"Save" to current filename or "Save As" to +new filename
+
New "New Window" button on the +"Output To Textbox" opens output window for quick 'sequence +editing'.
+
Set different text colour for dark or light background
+
Right align sequence ids

Set colour of lower case residues in a user defined colour scheme
-
Menu Rearrangements: New Format for alignment layout and Select for region selection. -
-
Menu item accelerator keys added -
-
Control-V pastes sequences to active window, Control-Shift-V pastes to a new window. -
-
Raise/Minimise alignment and all associated windows from desktop window's window menu +
Menu Rearrangements: New Format for alignment +layout and Select for region selection.

+
Menu item accelerator keys added
+
Control-V pastes sequences to active window, Control-Shift-V +pastes to a new window.
+
Raise/Minimise alignment and all associated windows from desktop +window's window menu

Select and colour whole branches of a tree

'New Window' button on the 'Output to Text box' alignment output option to open a new alignment window after editing.

Issues Resolved

-
-Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system. -
+
Optimisations for large alignments: faster multithreaded +calculations and Undo/Redo system.

Remove empty columns - if empty columns exist at the end of the -alignment bug fixed. -
-
DAS feature fetching slowed down, doesn't overload DAS servers -
-
DAS feature fetching can be cancelled -
-
Correct display of > and < symbols for feature descriptions without explicit <html> tags. -
-
Zoom working in PCA viewer -
-
Sequence Descriptions retained after running a web service -
+alignment bug fixed.
+
DAS feature fetching slowed down, doesn't overload DAS servers
+
DAS feature fetching can be cancelled
+
Correct display of > and < symbols for feature descriptions +without explicit <html> tags.
+
Zoom working in PCA viewer
+
Sequence Descriptions retained after running a web service

-
See the Release History page for details of all - new features and resolved issues.
+
See the Release History page for +details of all new features and resolved issues.

Action	Windows	Unix	Mac/OSX
Select/ Deselect Residue	Left Click	Left -Click	Click
Rotate View	Left Click and Drag	Left Click and -Drag	Click and Drag
Roll View	Right Click and drag	Right Click and -Drag	TODO
Move Origin	Middle-Button and -Drag	Middle-Button and Drag	TODO
Zoom In	Up Arrow	Up Arrow	Up -Arrow
Zoom Out	Down Arrow	Down Arrow	Down Arrow