From f902741a45fba3856958b893e37c74344d397a60 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 16 Jun 2005 17:44:01 +0000 Subject: [PATCH] separated alignment menu bits. --- help/html/menus/alwcalculate.html | 96 +++++++++++++++++++++++++++++++ help/html/menus/alwcolour.html | 39 +++++++++++++ help/html/menus/alwedit.html | 113 +++++++++++++++++++++++++++++++++++++ help/html/menus/alwfile.html | 70 +++++++++++++++++++++++ help/html/menus/alwview.html | 72 +++++++++++++++++++++++ 5 files changed, 390 insertions(+) create mode 100755 help/html/menus/alwcalculate.html create mode 100755 help/html/menus/alwcolour.html create mode 100755 help/html/menus/alwedit.html create mode 100755 help/html/menus/alwfile.html create mode 100755 help/html/menus/alwview.html diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html new file mode 100755 index 0000000..4d4264b --- /dev/null +++ b/help/html/menus/alwcalculate.html @@ -0,0 +1,96 @@ + +Alignment Window Menus + + +

Alignment Window Calculate Menu

+ +
+
+ + + diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html new file mode 100755 index 0000000..4d281634 --- /dev/null +++ b/help/html/menus/alwcolour.html @@ -0,0 +1,39 @@ + +Alignment Window Menus + + +

Alignment Window Colour Menu

+ +
+
    +
  • Apply Colour To All Groups
    +     If this is selected, any changes made to the background colour + will be applied to all currently defined groups.
    +
    • +
  • Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried + Index, Nucleotide, User Defined
    +     See colours for + a description of all colour schemes.
    +
    • +
  • By Conservation
    +     See Colouring + by Conservation.
    +
    • +
  • Modify Conservation Threshold
    +     Use this to display the conservation threshold slider window. + Useful if the window has been closed, or if the 'by + conservation' option appears to be doing nothing!
    • +
  • Above Identity Threshold
    +     See Above Percentage + Identity.
    +
    • +
  • Modify Identity Threshold
    +     Use this to set the threshold value for colouring above Identity. + Useful if the window has been closed.
    • +
+
+ + diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html new file mode 100755 index 0000000..dcd7d68 --- /dev/null +++ b/help/html/menus/alwedit.html @@ -0,0 +1,113 @@ + +Alignment Window Menus + + +

Alignment Window Edit Menu

+ +
+
    +
  • Undo
    + This will undo any edits you make to the alignment. This applies to insertion + or deletion of gaps, cutting residues or sequences from the alignment or + pasting sequences to the current alignment or sorting the + alignment. NOTE: It DOES NOT undo colour + changes, adjustments to group sizes, or changes to the annotation panel.
    +
    • +
  • Redo
    +     Any actions which you undo can be redone using redo.
    +
    • +
  • Cut
    +     This will make a copy of the currently selected residues before + removing them from your alignment. Click on a sequence name if you wish + to select a whole sequence.
    + Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
    +
    • +
  • Copy
    + Copies the currently selected residues to the system + clipboard - you can also do this by pressing <CTRL> and C + (<APPLE> and C on MacOSX).
    + If you try to paste the clipboard contents to a text editor, you will see + the format of the copied residues is a tab separated list:
    +
    +NAME    START_RES    END_RES    SEQUENCE
+

    +
    • +
  • Paste +
      +
    • To New Alignment
      +       A new alignment window will be created from sequences previously + copied or cut to the system clipboard.
      + Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
      • +
    • Add To This Alignment
      +       Copied sequences from another alignment window can be added + to the current Jalview alignment.
      +
      • +
    +
    • +
  • Delete
    +     This will delete the currently selected residues + without copying them to the clipboard. Like the other edit + operations, this can be undone with Undo.
    +
    • +
  • Select All
    +     Selects all the sequences and residues in the alignment.
    + Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
    +
    • +
  • Deselect All
    +     Removes the current selection box (red dashed box) from the + alignment window. All selected sequences, residues and marked columns will + be deselected.
    + Use <ESCAPE> to deselect all.
    +
    • +
  • Invert Selection
    +     Any sequence ids currently not selected will replace the current + selection.
    +
    • +
  • Undefine Groups
    +     The alignment will be reset with no defined groups.
    WARNING: + This cannot be undone.
    +
    • +
  • Remove Left
    +     If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, mouse + click the scale bar above the alignment. Click again to unmark a column, + or select "Deselect All" to deselect all columns.
    +
    • +
  • Remove Right
    +     If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, mouse + click the scale bar above the alignment. Click again to unmark a column, + or select "Deselect All" to deselect all columns.
    +
    • +
  • Remove Empty Columns
    +     All columns which only contain gap characters ("-", + ".") will be deleted.
    + You may set the default gap character in preferences. +
    +
    • +
  • Remove All Gaps
    + All gap characters ("-", ".") will be deleted from + the alignment.
    + You may set the default gap character in preferences. +
    +
    • +
  • Remove Redundancy
    +     Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between any two sequences + (under the current alignment) exceeds this + value then one of the sequences (the shorter) is discarded. Press the "Apply" + button to remove redundant sequences. The "Undo" button will undo the last + redundancy deletion.
    +
    • +
  • Pad Gaps
    +     Adds gaps to the end of all the sequences so they + are all the same length. This is useful for making a tree using + unaligned sequences.
    + You may set the default gap character in preferences. +
    • +
+
+ + diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html new file mode 100755 index 0000000..4aca47e --- /dev/null +++ b/help/html/menus/alwfile.html @@ -0,0 +1,70 @@ + +Alignment Window Menus + + +

Alignment Window File Menu

+ + + + diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html new file mode 100755 index 0000000..66f4284 --- /dev/null +++ b/help/html/menus/alwview.html @@ -0,0 +1,72 @@ + +Alignment Window Menus + + +

Alignment Window View Menu

+ +
+
    +
  • Font
    +     Change the font of the display from the + "Choose Font" dialog box, which is shown when this + item is selected.
    +
    • +
  • Wrap
    +     When ticked, the alignment display is + "wrapped" to the + width of the alignment window. This is useful if your alignment + has only a few sequences to view its full width at once.
    + Options are available to show the residue numbering at the start and/or + end of an alignment as well as showing the alignment position above each + sequence row.
    + NOTE: When in wrapped alignment view, the + alignment cannot be edited or have regions selected on it.
    +
    • +
  • Show Full Sequence ID
    +     If this box is selected the sequence name will have the start + and end position of the sequence appended to the name, in the format NAME/START-END
    +
    • +
  • Boxes
    + If this is selected the background of a residue will be coloured using the + selected background colour. Useful if used in conjunction with "Colour + Text."
    +
    • +
  • Text
    +     If this is selected the residues will be displayed using the + standard 1 character amino acid alphabet.
    +
    • +
  • Colour Text
    +     If this is selected the residues will be coloured according + to the background colour associated with that residue. The colour is slightly + darker than background so the amino acid symbol remains visible.
    +
    • +
  • Show Gaps
    +     When this is selected, gap characters will be displayed as "." + or "-". If unselected, then gap characters will appear as blank spaces. +
    + You may set the default gap character in preferences.
    +
    • +
  • 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.
    +
    • +
  • Sequence Features
    +     If the sequence names are Swissprot entries Jalview will use + the names to retrieve sequence features from the EBI. Features which are + 1 residue in length are coloured red, sequences longer than 1 residue are + coloured blue. Move the mouse over a coloured feature to display the details + of the feature.
    + Note: The retrieved information will update the sequence start and end labels + if they are incorrect.
    +
    • +
  • Overview Window
    +     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.
    • +
+
+ + -- 1.7.10.2