From bb105fcca41253815982584f4c8f6fae1f8e10a3 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 27 Nov 2006 17:32:40 +0000 Subject: [PATCH] 2.2 documentation --- help/helpTOC.xml | 2 +- help/html/calculations/pca.html | 2 +- help/html/colourSchemes/textcolour.gif | Bin 0 -> 21788 bytes help/html/colourSchemes/textcolour.html | 16 ++- help/html/editing/index.html | 112 +++++++-------- help/html/features/creatinFeatures.html | 4 +- help/html/features/das.gif | Bin 0 -> 37535 bytes help/html/features/das.jpg | Bin 53308 -> 0 bytes help/html/features/dasfeatures.html | 116 +++++++++------- help/html/features/dassettings.html | 64 ++++----- help/html/features/featuresFormat.html | 162 +++++++++++----------- help/html/features/hiddenRegions.html | 97 +++++++------ help/html/features/multipleViews.html | 29 ++-- help/html/features/newkeystrokes.html | 9 +- help/html/features/pdbviewer.html | 229 ++++++++++++++++++------------- help/html/io/index.html | 105 +++++++------- help/html/menus/alignmentMenu.html | 8 +- help/html/menus/alwfile.html | 17 ++- help/html/menus/index.html | 28 ++-- help/html/menus/popupMenu.html | 5 +- help/html/whatsNew.html | 72 +++++----- 21 files changed, 589 insertions(+), 488 deletions(-) create mode 100644 help/html/colourSchemes/textcolour.gif create mode 100644 help/html/features/das.gif delete mode 100644 help/html/features/das.jpg 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.

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zjk*PD+NbAQsAbxvk(#diTCjUMsqI>@f0_k!+OU6`t*d$kj=BU!zyTJ30Vd!APJjX~ zV6!*-vM>7rKAW>edjd3Dv`rhdDS)&uyR=c8v^hJqU7NK{TeCkqwNKl%O`EiB8?{SY zwpAOnJ9`2`TeNB0vpGAqSsS-sn*v~4w^tjrFQB)9d$XB)w?TWjPy4uKo4JJ>xTX8L zyPLR6`?DP&x}Tdex?7vLZ~L>c`?ZxjyK_6cQ#-k5JGwiYx#1hSb6c}z`@Ykgy 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.

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zR+%vLtVsD9umqJH44eKfKy2z{Q2G5SWg@&hMw23`Wgs!KU>{}8|i{cX6G!F3xl z&a*-N5@+bRw<3MmB zDkh_Ptm<=lB4eze_ZpgNF|Cck@8u5c@Pv8mN>kVdOpWEwm_F5QH0}+DnFigNjU|8s z3x=HLQb^kHWGW>1BtNWC=iaQ(zlv5ZaW;0_?7b&{+wNC0HaHEFrN$|YUQPt#FBYfb z*Q@xLy-9owW&g{@L2I1z$%xf5neS|sQifqc2k28Fo?0lI6Dc{fdK~%ssGcw=>=!ke zKbsyW{zpxq(Gio*+Uh~h(N$#g{{p#|Qq+lnRZqW4>^Y=A*p!AWpaYINwz - -DAS Features - - -

DAS Sequence Feature Retrieval

-

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

-
    -
  1. Open the Feature Settings panel by selecting "View -> Feature Settings..."
  2. -
  3. Click on the "DAS Settings" tabbed - pane.
  4. -
  5. Select the sources to use for DAS feature retireval, then click the "Fetch - DAS Features" button.
  6. -
-

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.

+
    +
  1. Open the Feature Settings panel by selecting "View -> + Feature Settings..."
  2. +
  3. Click on the "DAS Settings" + tabbed pane.
  4. +
  5. 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! +
    +
  6. +
+

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.

    -
  • +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. +

      +
    -

    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.

     

     

     

    diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html index c4929e5..36bda32 100644 --- a/help/html/features/multipleViews.html +++ b/help/html/features/multipleViews.html @@ -4,14 +4,14 @@

    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.

      -

      - - - - - - - -
      ActionWindowsUnixMac/OSX
      Select/
      Deselect
      Residue
      Left ClickLeft -ClickClick
      Rotate ViewLeft Click and DragLeft Click and -DragClick and Drag
      Roll ViewRight Click and dragRight Click and -DragTODO
      Move OriginMiddle-Button and -DragMiddle-Button and DragTODO
      Zoom InUp ArrowUp ArrowUp -Arrow
      Zoom OutDown ArrowDown ArrowDown 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.

      +

      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      ActionWindowsUnixMac/OSX
      Select/
      + Deselect
      + Residue
      Left ClickLeft ClickClick
      Rotate ViewLeft Click and DragLeft Click and DragClick and Drag
      Roll ViewRight Click and dragRight Click and DragTODO
      Move OriginMiddle-Button and DragMiddle-Button and DragTODO
      Zoom InUp ArrowUp ArrowUp Arrow
      Zoom OutDown ArrowDown ArrowDown 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.

      -- 1.7.10.2