From 40c1738cb93e566805232429d1217814b9ee6e5f Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 27 Nov 2006 09:34:59 +0000 Subject: [PATCH] 2.2 documentation --- help/html/features/creatinFeatures.html | 74 +++++++++++++------------- help/html/features/editingFeatures.html | 52 +++++++++---------- help/html/features/multipleViews.html | 86 +++++++++++++++---------------- help/html/features/reloadSave.html | 38 +++++++------- 4 files changed, 125 insertions(+), 125 deletions(-) diff --git a/help/html/features/creatinFeatures.html b/help/html/features/creatinFeatures.html index 04e5fdc..486b75b 100644 --- a/help/html/features/creatinFeatures.html +++ b/help/html/features/creatinFeatures.html @@ -1,38 +1,38 @@ - - -Creating Sequence Features - - -Creating Sequence Features -

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 -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: -

-

Sequence Feature Creation was introduced in Jalview Version 2.2

- + + +Creating Sequence Features + + +Creating Sequence Features +

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 +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: +

+

Sequence Feature Creation was introduced in Jalview Version 2.2

+ \ No newline at end of file diff --git a/help/html/features/editingFeatures.html b/help/html/features/editingFeatures.html index e8fd6f5..ff4d5ca 100644 --- a/help/html/features/editingFeatures.html +++ b/help/html/features/editingFeatures.html @@ -1,26 +1,26 @@ - - -Amending or Deleting Sequence Features - - -Amending or Deleting Sequence Features -

Double clicking a position in the alignment with one or more -displayed sequence features opens the "Amend/Delete -Features" dialog box.

-

-

The dialog box only allows one of the features at the -double-clicked position to be edited or deleted at a time, and it will -also be highlighted in black in the alignment window.

-

Choose which feature is to be modified by selecting it from the Sequence -Feature Name pull down -menu. In addition to the Name, group, colour and description attributes -described for the new feature dialog -box, a feature's start and end position can be changed either by -entering a new position directly or by using the adjacent up and down -buttons.

-

Select Amend to update the feature, Delete -to remove the selected feature, or Cancel to leave the -feature unchanged.

-

Sequence feature editing was implemented in Jalview 2.2

- - + + +Amending or Deleting Sequence Features + + +Amending or Deleting Sequence Features +

Double clicking a position in the alignment with one or more +displayed sequence features opens the "Amend/Delete +Features" dialog box.

+

+

The dialog box only allows one of the features at the +double-clicked position to be edited or deleted at a time, and it will +also be highlighted in black in the alignment window.

+

Choose which feature is to be modified by selecting it from the Sequence +Feature Name pull down +menu. In addition to the Name, group, colour and description attributes +described for the new feature dialog +box, a feature's start and end position can be changed either by +entering a new position directly or by using the adjacent up and down +buttons.

+

Select Amend to update the feature, Delete +to remove the selected feature, or Cancel to leave the +feature unchanged.

+

Sequence feature editing was implemented in Jalview 2.2

+ + diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html index 0df2ec1..e31a06b 100644 --- a/help/html/features/multipleViews.html +++ b/help/html/features/multipleViews.html @@ -1,44 +1,44 @@ - - -Multiple Alignment Views - - -

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 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 affect the new view. -

-

A particular view may focus on some specific aspect of an alignment - -for example, hiding all but the region of an alignment containing a -particular domain. Right-clicking a view's tab opens -the View Name dialog box, allowing it to be renamed to something more -meaningful. -

-

Viewing Multiple Views Simultaneously

-

Multiple views of an alignment are, by default, gathered together as tabs -within a single alignment window. They can be viewed simultanously by -pressing X (or via -"View→Expand") 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 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.

-

Multiple Views were introduced in Jalview 2.2

+ + +Multiple Alignment Views + + +

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 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 affect the new view. +

+

A particular view may focus on some specific aspect of an alignment - +for example, hiding all but the region of an alignment containing a +particular domain. Right-clicking a view's tab opens +the View Name dialog box, allowing it to be renamed to something more +meaningful. +

+

Viewing Multiple Views Simultaneously

+

Multiple views of an alignment are, by default, gathered together as tabs +within a single alignment window. They can be viewed simultanously by +pressing X (or via +"View→Expand") 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 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.

+

Multiple Views were introduced in Jalview 2.2

\ No newline at end of file diff --git a/help/html/features/reloadSave.html b/help/html/features/reloadSave.html index ae6b53e..709f792 100644 --- a/help/html/features/reloadSave.html +++ b/help/html/features/reloadSave.html @@ -1,20 +1,20 @@ - - -Reload and Save Alignment - - -

Reload and Save Alignment

-

Jalview remembers the original source of an alignment if it has -been loaded from a file or -URL.

    -
  • "File→Reload" will reload the -alignment from its original source, discarding any edits or applied -colouring and features since the last save.
    • -
  • "File→Save" will save the -alignment back to the same filename, with the same format, easing the -the process of editing and updating an alignment file in -place. -
    • -
- + + +Reload and Save Alignment + + +

Reload and Save Alignment

+

Jalview remembers the original source of an alignment if it has +been loaded from a file or +URL.

    +
  • "File→Reload" will reload the +alignment from its original source, discarding any edits or applied +colouring and features since the last save.
    • +
  • "File→Save" will save the +alignment back to the same filename, with the same format, easing the +the process of editing and updating an alignment file in +place. +
    • +
+ \ No newline at end of file -- 1.7.10.2