Popup Menu

From a14da63fa1dabed03c67eadc39c6b4a61c5102f0 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 7 May 2007 15:21:39 +0000 Subject: [PATCH] 2.3 updates --- help/html/features/viewingpdbs.html | 5 +- help/html/menus/alwview.html | 58 ++++----- help/html/menus/popupMenu.html | 243 ++++++++++++++++++----------------- help/html/menus/wsmenu.html | 5 + help/html/whatsNew.html | 72 +++++------ 5 files changed, 197 insertions(+), 186 deletions(-) diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 353ca09..842ad3e 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -4,7 +4,7 @@

Viewing PDB Structures

Jalview has a simple 3D structure viewer which can visualize polypeptide backbone structures associated with a sequence in - a particular alignment view. It is accessed via the "Sequence→View + a particular alignment view. It is accessed via the "Strucutre→View PDB entry:" entry from the sequence's pop-up menu.

Since Jalview 2.3, Jmol has been integrated into the application and will also @@ -12,7 +12,8 @@ http://jmol.sourceforge.net/docs/JmolUserGuide/

To associate PDB files with a sequence, right click on a sequence ID and select - "Associate Structure with Sequence", and one of the submenus:
+ "Structure→ Associate Structure with Sequence", + and one of the submenus:

From File - You can load a PDB file from the local machine or network and associate it with the selected sequence. PDB files associated in this way diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index e58d4c2..85c9fdd 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -6,35 +6,35 @@
Alignment Window View Menu

-
New View (Control T)
- Creates a new view from the current alignment view.
-
Expand Views (X)
- Display each view associated with the alignment in its own alignment - window, allowing several views to be displayed simultaneously.
-
Gather Views (G)
- Each view associated with the alignment will be displayed within its - own tab on the current alignment window.
-
Show→(all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
-
Hide→(all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
-
Show Annotations
- If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the - conservation calculation, quality calculation and consensus values as - bar charts.
-
Show Sequence Features
- Show or hide sequence features on this alignment.
-
Seqence Feature Settings...
- Opens the Sequence - Feature Settings dialog box to control the colour and display of - sequence features on the alignment, and configure and retrieve features - from DAS annotation servers.
-
Overview - Window
- A scaled version of the alignment will be displayed in a small - window. A red box will indicate the currently visible area of the - alignment. Move the visible region using the mouse.
+
New View (Control T)
+ Creates a new view from the current alignment view.
+
Expand Views (X)
+ Display each view associated with the alignment in its own alignment window, + allowing several views to be displayed simultaneously.
+
Gather Views (G)
+ Each view associated with the alignment will be displayed within its own tab + on the current alignment window.
+
Show→(all Columns / Sequences)
+ All hidden Columns / Sequences will be revealed.
+
Hide→(all Columns / Sequences)
+ Hides the all the currently selected Columns / Sequences
+
Show Annotations
+ If this is selected the "Annotation Panel" will be + displayed below the alignment. The default setting is to display the conservation + calculation, quality calculation and consensus values as bar charts.
+
Show Sequence Features
+ Show or hide sequence features on this alignment.
+
Seqence Feature Settings...
+ Opens the Sequence Feature Settings dialog box to control the colour and display + of sequence features on the alignment, and configure and retrieve features + from DAS annotation servers.
+
Alignment Properties
+ Displays simple properties of current alignment view with additional + global alignment properties
+
Overview Window
+ A scaled version of the alignment will be displayed in a small + window. A red box will indicate the currently visible area of the alignment. + Move the visible region using the mouse.

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 2c50c02..b117218 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,118 +1,125 @@ - - -Popup Menu - - - -
Popup Menu
-This menu is visible when right clicking either within a -selected region on the alignment or on a selected sequence name. It may -not be accessible when in 'Cursor Mode' (toggled with the F2 key).
-
-
Selection -
-
Edit -
-
Copy
- Copys the selected region. In the applet version, the copied - sequences are not available to the system clipboard.
-
Cut
- Cuts the selected region from the alignment. In the applet - version, the copied sequences are not available to the system - clipboard.
-
To Upper Case
- Changes the case of selected region to lower case.
-
To Lower Case
- Changes the case of selected region to upper case. -
-
Toggle Case
- Switches the case of all residues within the selected - region.
-
-
-
Output to Textbox
- The selection area will be output to a a text window in the - selected alignment format.
-
Create - Sequence Feature...
- Opens the dialog box for creating sequence features over the - currently selected region on each selected sequence.
-
Group
- Group Operations -
-
GroupThis will display a window - asking for the name of the currently selected group. Click OK to set - the name, cancel to use the default group name.
-
Remove Group
- This will undefine the selected group.
-
Group Colour
- Sets the colour of - the group.
-
Boxes
- If selected the background of a residue within the selected - group will be coloured according to the assigned colour scheme. -
-
Text
- If selected the selected group will display text.
-
Colour Text
- If selected the selected group will display text in a colour - slightly darker than the background colour of that residue.
-
Border Colour
- Selecting this will display a "Colour Chooser" - window. Select a colour than press OK to set the border colour of a - group.
-
-
-
-
-
Sequence Id
- This menu is only visible if you right-click on a sequence - name. -
-
Edit Name/Description
- You may edit the name and description of each sequence. A - window will be displayed asking for a new sequence name and sequence - description to be entered. Press OK to accept your edit. To save - sequence descriptions, you must save in Fasta, PIR or Jalview File - format.
-
Associate Structure with Sequence -
-
From File
- Load a PDB file from local disk which will be associated - with this sequence. This file will be used if the user subsequently - clicks on "View PDB Structure" menu item.
-
Enter PDB id
- Enter the PDB id from an input window. This PDB id will be - used by the service WSDBFetch, provided by the EBI, to fetch the PDB - file if the user subsequently clicks on "View PDB - Structure" menu item.
-
Discover PDB ids
- This will use the service WSDBFetch, provided by the EBI, to - retrieve all PDB ids associated with the sequences in the alignment - if the sequences have valid Uniprot names or accession ids.
-
-
-
View PDB Structure
- If the sequence has an associated PDB file added by one of - the methods described above, Jalview will display a 3D interactive - viewer of the file.
- This entry is only present if the sequence has an associated PDB structure.
-
Represent Group With (Sequence Id)
- All sequences in the current selection group will be hidden, - apart from (Sequence Id). Any edits performed on the visible - representative sequence will be propagated to the hidden sequences.
-
Link
- This menu item lists all links which have been set up in the - Preferences Connections - tab.
-
-
-
-
Hide Sequences
- Hides the currently selected seuqences in this alignment view.
-
-
-
- - + + +Popup Menu + + + +
Popup Menu
+This menu is visible when right clicking either within a +selected region on the alignment or on a selected sequence name. It may +not be accessible when in 'Cursor Mode' (toggled with the F2 key).
+
+
Selection +
+
Edit +
+
Copy
+ Copys the selected region. In the applet version, the copied sequences + are not available to the system clipboard.
+
Cut
+ Cuts the selected region from the alignment. In the applet + version, the copied sequences are not available to the system clipboard.
+
Edit Sequence
+ Edit the selected sequence(s) directly. Spaces will be converted + to current gap character.
+
To Upper Case
+ Changes the case of selected region to lower case. +
+
To Lower Case
+ Changes the case of selected region to upper case. +
+
Toggle Case
+ Switches the case of all residues within the selected region.
+
+
+
Output to Textbox
+ The selection area will be output to a a text window in the + selected alignment format.
+
Create Sequence Feature...
+ Opens the dialog box for creating sequence features over the currently + selected region on each selected sequence.
+
Group
+ Group Operations +
+
GroupThis will display a window asking for + the name of the currently selected group. Click OK to set the name, + cancel to use the default group name.
+
Remove Group
+ This will undefine the selected group. +
+
Group Colour
+ Sets the colour + of the group.
+
Boxes
+ If selected the background of a residue within the selected + group will be coloured according to the assigned colour scheme. +
+
Text
+ If selected the selected group will display text.
+
Colour Text
+ If selected the selected group will display text in a + colour slightly darker than the background colour of that residue.
+
Border Colour
+ Selecting this will display a "Colour Chooser" + window. Select a colour than press OK to set the border colour of + a group.
+
+
+
+
+
Sequence Id
+ This menu is only visible if you right-click on a sequence name. + +
+
Edit Name/Description
+ You may edit the name and description of each sequence. A + window will be displayed asking for a new sequence name and sequence description + to be entered. Press OK to accept your edit. To save sequence descriptions, + you must save in Fasta, PIR or Jalview File format.
+

+
Represent Group With (Sequence Id)
+ All sequences in the current selection group will be hidden, apart + from (Sequence Id). Any edits performed on the visible representative + sequence will be propagated to the hidden sequences.
+
Link
+ This menu item lists all links which have been set up in the Preferences + Connections tab.
+
+
+
+
Structure +
+
Associate Structure with Sequence +
+
From File
+ Load a PDB file from local disk which will be associated + with this sequence. This file will be used if the user subsequently + clicks on "View PDB Structure" menu item.
+
Enter PDB id
+ Enter the PDB id from an input window. This PDB id will + be used by the service WSDBFetch, provided by the EBI, to fetch the + PDB file if the user subsequently clicks on "View PDB Structure" + menu item.
+
Discover PDB ids
+ This will use the service WSDBFetch, provided by the + EBI, to retrieve all PDB ids associated with the sequences in the + alignment if the sequences have valid Uniprot names or accession ids. +
+
+
+
View Structure
+ If the sequence has an associated PDB file added by one + of the methods described above, Jalview will display a 3D interactive + viewer of the file.
+ This entry is only present if the sequence has an associated PDB structure.
+
+
+
+
Hide Sequences
+ Hides the currently selected seuqences in this alignment view.
+
+
+
+ + diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 9dbfe81..7584ca1 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -8,6 +8,11 @@ on compute facilities at the University of Dundee. You need a continuous network connection in order to use these services through Jalview.

+
Fetch DB References
+ This will use the service WSDBFetch, provided by the EBI, to retrieve all + database references and PDB ids associated with the selected sequences in + the alignment if the sequences have valid Uniprot names or accession ids. +

Alignment

ClustalW Multiple Sequence Alignment
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 8484a26..ede2a54 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,37 +1,35 @@ - - -What's new ? - - -
What's new ?
- -
Jalview Version 2.3
-
Jmol 11 integration
-PDB views in Jalview XML
-Slide sequences
-Edit sequence in place
-EMBL CDS features
-DAS Feature mapping
-Feature ordering
-Alignment Properties
-Annotation Scores
-Sort by scores
-Feature/annotation editing in applet
-
-

-
Issues Resolved
-

-Headless state operation in 2.2.1 -
Incorrect and unstable DNA pairwise alignment -
-Cut and paste of sequences with annotation -
-Feature group display state in XML
-Feature ordering in XML
-2.2.1 applet had no feature transparency
-
-

-
See the Release History page for -details of all new features and resolved issues.
- - + + +What's new ? + + +
What's new ?
+ +
Jalview Version 2.3
+
Jmol 11 integration
+ PDB views stored in Jalview XML files
+Slide sequences
+Edit sequence in place
+EMBL CDS features
+DAS Feature mapping
+Feature ordering
+Alignment Properties
+Annotation Scores
+Sort by scores
+Feature/annotation editing in applet
+
+

+
Issues Resolved
+

+ Headless state operation in 2.2.1
+ Incorrect and unstable DNA pairwise alignment
+ Cut and paste of sequences with annotation
+ Feature group display state in XML
+ Feature ordering in XML
+ 2.2.1 applet had no feature transparency
+ Number pad keys can be used in cursor mode
+

+
See the Release History page for +details of all new features and resolved issues.
+ + -- 1.7.10.2