From: amwaterhouse Date: Wed, 8 Jun 2005 14:09:02 +0000 (+0000) Subject: Spelling X-Git-Tag: Release_2_0~97 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git Spelling --- diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index e824d7d..47d1739 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -11,12 +11,12 @@ sequences tend to lie near each other in the space.

usually because the JVM has run out of memory. The next release of Jalview release will execute this calculation through a web service.

Principal components analysis is a technique for examining the -structure of complex datasets. The components are a set of dimensions -formed from the measured values in the dataset, and the principle +structure of complex data sets. The components are a set of dimensions +formed from the measured values in the data set, and the principle component is the one with the greatest magnitude, or length. The sets of measurements that differ the most should lie at either end of this principle axis, and the other axes correspond to less extreme -patterns of variation in the dataset. +patterns of variation in the data set.

In this case, the components are generated by an eigenvector @@ -29,21 +29,21 @@ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt= href="http://industry.ebi.ac.uk/SeqSpace/">http://industry.ebi.ac.uk/SeqSpace) at the EBI.

-

The PCA Viewer

+

The PCA Viewer

This is an interactive display of the sequences positioned within the similarity space. The colour of each sequence point is the same - as the sequence group coloring, white if no colour has been + as the sequence group colours, white if no colour has been defined for the sequence, and green if the sequence is part of a the currently selected group.

The 3d view can be rotated by dragging the mouse with the left mouse button pressed. The view can also be zoomed in and out with the up and down arrow - keys.

+ keys.

A tool tip gives the sequence ID corresponding to a point in the space, and clicking a point toggles the selection of the - corresponding sequence in the alignment window. Rectanglar region - based selection is also possible, by holding the 's' key whilst + corresponding sequence in the alignment window. Rectangular region + based selection is also possible, by holding the 'S' key whilst left-clicking and dragging the mouse over the display.

Initially, the display shows the first three components of the diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index e97e3b0..1f3d464 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -3,13 +3,9 @@

Removing redundancy

Selecting this option brings up a window asking you to select a threshold. - If the percentage identity between two sequences (based on the - current alignment) exceeds this value one of the + If the percentage identity between two sequences exceeds this value one of the sequences (the shorter) is discarded. The redundancy calculation is done when - the Apply button is pressed, and the undo button recovers the - original set or any previously calculated subset. The detection of - redundant sequences involves a pairwise comparison of all the - sequences, so you may have to wait a few moments when applying this to - large sequence sets.

+ the Apply button is pressed. For large numbers of sequences this can take a + long time as all pairs have to be compared.

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index a432824..adc44c9 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -14,11 +14,11 @@ the use of the functions in the Sort menu (Calculate->Sort): precedence of their names.

  • Sort by Group

    -

    Places sequences in the same group adjacent to eachother.

    +

    Places sequences in the same group adjacent to each other.

  • Sort by Pairwise Identity

    -

    Sequences are ordered by decreasing fraction of conserved residues -with respect to the first sequence in the alignment. +

    Places pairs of sequences together that align with the greatest +fraction of conserved residues.

  • Sort by Tree Order

    @@ -33,12 +33,15 @@ alignment, its name will appear in the submenu Sort->By Tree Order.< alignments by some measure of sequence identity.
    If the current alignment has been generated by one of Jalview's alignment web services, the alignment ordering can be recovered by -its corresponding entry in the Sort menu: +its corresponding entry in the Sort menu. +

  • -Reversing the Order -

    If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse -order for that property. In the case of trees and alignment orderings, Jalview will +

    Reversing the Order

    +

    Selecting any item from the Sort menu will sort sequences in an +ascending order according to the property defining the sort. If the +same sort is re-applied, the sequences will be sorted in the inverse +order. In the case of trees and alignment orderings, Jalview will remember your last choice for sorting the alignment and only apply the inverse ordering if you select the same tree or alignment ordering item again.

    diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index c767bf2..5a014bb 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -40,7 +40,7 @@ phylogenetic tree construction, and may fail on very large alignments.

    A newly calculated tree will be displayed in a new tree viewing window. In -addition, a new entry with the same treeviewer window name will be added in the Sort +addition, a new entry with the same tree viewer window name will be added in the Sort menu so that the alignment can be reordered to reflect the ordering of the leafs of the tree.

    diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index 3f855ac..77ed5eb 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -8,7 +8,7 @@ When a tree has been calculated from an alignment, or imported via a file or web service it is displayed by Jalview's tree viewing window. Trees can be rearranged, used to select sequences and groups - in the associated alignment, saved in newick format or exported as an + in the associated alignment, saved in Newick format or exported as an image or postscript file.

    Selecting sequence ids at the leaves of the tree selects the @@ -23,14 +23,14 @@

    Clicking anywhere along the extent of the tree (but not on a leaf or internal node) defines a tree 'partition', by cutting every branch - of the tree spanning the depth where the mouse-click occured. Groups + of the tree spanning the depth where the mouse-click occurred. Groups are created containing sequences at the leaves of each connected - subtree. These groups are each given a different colour, which are + sub tree. These groups are each given a different colour, which are reflected in other windows in the same way as if the sequence ids were selected, and can be edited in the same way as user defined sequence groups.

    -

    Tree partitions are useful for comparing clusterings produced by +

    Tree partitions are useful for comparing clusters produced by different methods and measures. They are also an effective way of identifying specific patterns of conservation and mutation corresponding to the overall phylogenetic structure, when combined @@ -47,7 +47,7 @@ associated with a tree. Trees calculated by Jalview have branch lengths, which correspond to the distance measure used to construct the tree. Tree imported from outside may also contain bootstrap information, or additional leaves from sequences not present in the associated -alignment. +alignment.

    The view menu contains options controlling the way a tree is rendered and labelled:

    diff --git a/help/html/colourSchemes/blosum.html b/help/html/colourSchemes/blosum.html index 83cc27e..7af6f14 100755 --- a/help/html/colourSchemes/blosum.html +++ b/help/html/colourSchemes/blosum.html @@ -12,9 +12,9 @@ td {

    Blosum62

    -

    Gaps are coloured white. If a residue matchs the consensus sequence residue - at that position it is colored dark blue. If it does not match the consensus - residue but the 2 residues have a positive Blosum62 score, it is colored light +

    Gaps are coloured white. If a residue matches the consensus sequence residue + at that position it is coloured dark blue. If it does not match the consensus + residue but the 2 residues have a positive Blosum62 score, it is coloured light blue.

    diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 7c5f7a8..3531330 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -15,7 +15,7 @@ td { program. Sequences can be coloured either by assigning a colour to specific residues, or on the basis of an alignment consensus. The residues in each column are coloured according to the consensus character assigned to that column. - In this way, you can choose to highlight, for example, conserved hydrophylic + In this way, you can choose to highlight, for example, conserved hydrophilic or hydrophobic positions in the alignment.

    diff --git a/help/html/colourSchemes/zappo.html b/help/html/colourSchemes/zappo.html index f796ec5..7770c43 100755 --- a/help/html/colourSchemes/zappo.html +++ b/help/html/colourSchemes/zappo.html @@ -12,7 +12,7 @@ td {

    Zappo Colours

    - The residues are coloured according to their physico-chemical properties as + The residues are coloured according to their physicochemical properties as follows:

    diff --git a/help/html/io/index.html b/help/html/io/index.html index b067512..bd2a790 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,13 +1,13 @@ -Input/Ouput +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, Pfam/Stockholm

    -

    The EBI has examples of +

    The EBI has examples of these file formats.

    Additionally annotated alignments can be read in from the Jalview format.

    -

    Use the "Input Alignment" menu at the top of the main application +

    Use the "Input Alignment" menu at the top of the main application window to read in files from

    -
    +
    • 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. It - DOES NOT undo colour changes or adjustments to group sizes affect the annotation + 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. It + DOES NOT undo colour changes or adjustments to group sizes affect 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 + 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. The - format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE + Copies the currently selected residues to the system clipboard. The + format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE
      Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.
    • -
    • Paste +
    • Paste
      • To New Alignment
        -
        A new alignment window will be created from sequences previously + 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 + Copied sequences from another alignment window can be added to the current Jalview alignment.
    • Delete
      -
      This will delete the currently selected residues without making + This will delete the currently selected residues without making a copy of them first.
    • Select All
      @@ -109,213 +109,213 @@ 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 +
      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 + Any sequence ids currently not selected will replace the current selection.
    • Undefine Groups
      -
      The alignment will be reset with no defined groups. WARNING: + 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, + 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, + 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 contain purely gap characters ("-", + All columns which contain purely gap characters ("-", ".") will be deleted.
      - You may set the default gap character in preferences. + You may set the default gap character in preferences.

    • Remove All Gaps
      - All gap characters ("-", ".") will be deleted from + All gap characters ("-", ".") will be deleted from the alignment.
      - You may set the default gap character in preferences. + 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 two sequences exceeds this - value one of the sequences (the shorter) is discarded. Press the "Apply" - button to reomove redundant sequences.
      + Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between two sequences exceeds this + value one of the sequences (the shorter) is discarded. Press the "Apply" + button to remove redundant sequences.
    • Pad Gaps
      -
      If the sequences in an alignment window are not all the same - length they can all be set to the length of the longest sequence by selecting - "Pad Gaps." Any sequences which are shorter than the longest sequence - in an alignment will have gap characters ("-" or ".") + If the sequences in an alignment window are not all the same + length they can all be set to the length of the longest sequence by selecting + "Pad Gaps." Any sequences which are shorter than the longest sequence + in an alignment will have gap characters ("-" or ".") appended to the beginning or end to make them equal length.
      - You may set the default gap character in preferences. + You may set the default gap character in preferences.
    • Search
    -
    +
    • Find
      -
      Select this to search + Select this to search for residues, sequence name or residue position within the alignment.
    • View
    -
    +
    • Font
      -
      Change the font of the display. The default font can be set - from the "Choose Font" window, which is shown when the "Font + Change the font of the display. The default font can be set + from the "Choose Font" window, which is shown when the "Font Menu" is selected.
    • Wrap
      -
      The default alignment display shows sequences in a single horizontal - row. If your alignment has only a few sequences you may wish to "Wrap" - the alignment so that the sequences are shown on multiple horizontal rows. - 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 + The default alignment display shows sequences in a single horizontal + row. If your alignment has only a few sequences you may wish to "Wrap" + the alignment so that the sequences are shown on multiple horizontal rows. + 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: In the current version the wrap alignment should be used for viewing, + NOTE: In the current version the wrap alignment should be used for viewing, not editing.
    • Show Full Sequence ID
      -
      If this box is selected the sequence name will have the start + 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 + 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 + 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 + 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 to enable the residue to be read.
    • Show Gaps
      -
      If this is selected gap characters will be displayed as "." - or "-". If unselected gap characters will appear as blank spaces. + If this is selected gap characters will be displayed as "." + or "-". If unselected 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 - calulation, quality calculation and consensus values as bar charts.
      + 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 + 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 + 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. + 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.
    • Colour
    -
    +
    • Apply Colour To All Groups
      -
      If this is selected, any changes made to the background colour + If this is selected, any changes made to the background colour will be applied to all currently defined groups.
    • -
    • None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, - Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried +
    • None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, User Defined
      -
      See colours for +
      See colours for a description of all colour schemes.
    • By Conservation
      -
      See Colouring + See Colouring by Conservation.
    • Modify Conservation Threshold
      -
      Use this to display the conservation threshold slider window. + Use this to display the conservation threshold slider window. Useful if the window has been closed.
    • Above Identity Threshold
      -
      See Above Percentage + See Above Percentage Identity.
    • Modify Identity Threshold
      -
      Use this to set the threshold value for colouring above Identity. + Use this to set the threshold value for colouring above Identity. Useful if the window has been closed.
    • Calculate
    -
    +
      -
    • Sort +
    • Sort
      • by ID
        -
        This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. + This will sort the sequences according to sequence name. + If the sort is repeated, the order of the sorted sequences will be inverted.
      • by Group
        -
        This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. + This will sort the sequences according to sequence name. + If the sort is repeated, the order of the sorted sequences will be inverted.
      • by Pairwise Identity
        -
        This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put + This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put at the top.
    • -
    • Calculate Tree +
    • Calculate Tree
      • Average Distance Using % Identity
      • Neighbour Joining Using % Identity
      • Average Distance Using Blosum62
      • Neighbour Joining Using Blosum62
        -
        See calculating trees. + See calculating trees.
    • -
    • Paiwise Alignments
      +
    • Pairwise Alignments
      See pairwise alignments.
    • Principal Component Analysis
      - See Principal Component Analysis. + See Principal Component Analysis.
    • Web Service
      -
      +
        - Selecting one of the following menu items will start a remote service - on the high powered computing faciltiy at the University of Dundee. You - will need a continuous network connection in order to use these services. - + Selecting one of the following menu items will start a remote service + on the high powered computing facility at the University of Dundee. You + will need a continuous network connection in order to use these services. +
      • Clustal Alignment
      • Clustal Realign
      • JPred