http to https

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index c8111d1..d70a61f 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -35,7 +35,7 @@
 
 % how the hell do we add another panel with text like : This tutorial introduces
 % the user to the features of Jalview, a multiple sequence alignment editor and
 
 % how the hell do we add another panel with text like : This tutorial introduces
 % the user to the features of Jalview, a multiple sequence alignment editor and

-% viewer available from http://www.jalview.org to the title page.
+% viewer available from https://www.jalview.org to the title page.

 
 % \renewcommand{menustyle}{\tt} %do something more advanced here.
 
 
 % \renewcommand{menustyle}{\tt} %do something more advanced here.
 

@@ -268,7 +268,7 @@ of publication quality graphics.
 
 The Jalview Desktop application can be downloaded from the download link on the
 Jalview website, which takes you to
 
 The Jalview Desktop application can be downloaded from the download link on the
 Jalview website, which takes you to

-\href{http://www.jalview.org/download}{(www.jalview.org/download)}. The page
+\href{https://www.jalview.org/download}{(www.jalview.org/download)}. The page

 automatically displays the options available for your computer (e.g. if you have
 Mac or PC), and a button to show all available downloads. These include special
 'executable Jar' distributions useful if you want to run a specific version of
 automatically displays the options available for your computer (e.g. if you have
 Mac or PC), and a button to show all available downloads. These include special
 'executable Jar' distributions useful if you want to run a specific version of

@@ -285,7 +285,7 @@ Jalview splash screen (Figure \ref{splash}).
 This gives information about the version and build date that you are running,
 information about later versions (if available), and the paper to cite in your
 publications. This information is also available on the Jalview web site at
 This gives information about the version and build date that you are running,
 information about later versions (if available), and the paper to cite in your
 publications. This information is also available on the Jalview web site at

-\url{http://www.jalview.org}.
+\url{https://www.jalview.org}.

 
 %[fig 2] 
 \begin{figure}[htbp]
 
 %[fig 2] 
 \begin{figure}[htbp]

@@ -315,7 +315,7 @@ from Jalview version 2.10.1).
 \exercise{Launching Jalview from the Jalview Website}{
 \label{start}
 \exstep{Open the Jalview web site
 \exercise{Launching Jalview from the Jalview Website}{
 \label{start}
 \exstep{Open the Jalview web site

-\href{http://www.jalview.org}{(www.jalview.org)}
+\href{https://www.jalview.org}{(www.jalview.org)}

 in your web browser. To instal Jalview, first click the 'Download' link in the top right hand corner of the Jalview homepage. This
 will open the download webpage, the options available will reflect if you have Mac or PC computer.}
 \exstep {Download the application by clicking the download link as appropriate for your computer operating system.}
 in your web browser. To instal Jalview, first click the 'Download' link in the top right hand corner of the Jalview homepage. This
 will open the download webpage, the options available will reflect if you have Mac or PC computer.}
 \exstep {Download the application by clicking the download link as appropriate for your computer operating system.}

@@ -347,7 +347,7 @@ preferences tab, type in the URL of the sequence you want to load.}
 \end{list}
 
 {\bf See the video at:
 \end{list}
 
 {\bf See the video at:

-\url{http://www.jalview.org/Help/Getting-Started}.}
+\url{https://www.jalview.org/Help/Getting-Started}.}

  }
 
 \subsubsection{Jalview News RSS Feed}
  }
 
 \subsubsection{Jalview News RSS Feed}

@@ -384,7 +384,7 @@ jalview-announce@jalview.org} list can also be subscribed to if you wish to be
 kept informed of new releases and developments. 
 
 Archives and mailing list
 kept informed of new releases and developments. 
 
 Archives and mailing list

-subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
+subscription details can be found in the Jalview web site's \href{https://www.jalview.org/community}{community section}.

 
 \begin{figure}[htbp]
 \begin{center}
 
 \begin{figure}[htbp]
 \begin{center}

@@ -432,7 +432,7 @@ combination {\bf Fn and F2} keys are needed, as the {\bf F2} button is
 often assigned to screen brightness. Jalview always starts up in normal mode.
 
 \exstep{Load an example alignment from its URL
 often assigned to screen brightness. Jalview always starts up in normal mode.
 
 \exstep{Load an example alignment from its URL

-(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
+(\url{https://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop

 using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ from URL} dialog
 box.
 (The URL should be stored in its history and clicking on the {\sl down arrow}
 using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ from URL} dialog
 box.
 (The URL should be stored in its history and clicking on the {\sl down arrow}

@@ -457,7 +457,7 @@ Documentation window. Select topics from the navigation panel on the left hand
 side or use the Search tab to locate specific key words.
 
 {\sl\bf See the video at: 
 side or use the Search tab to locate specific key words.
 
 {\sl\bf See the video at: 

-\url{http://www.jalview.org/Help/Getting-Started}.}
+\url{https://www.jalview.org/Help/Getting-Started}.}

 } 
 
 \subsection{Navigation in Normal Mode}
 } 
 
 \subsection{Navigation in Normal Mode}

@@ -537,7 +537,7 @@ expressions that can be used with it.
 \section{Loading Sequences and Alignments}
 \label{loadingseqs}
 %Jalview provides many ways to load your own sequences. %For this section of the
 \section{Loading Sequences and Alignments}
 \label{loadingseqs}
 %Jalview provides many ways to load your own sequences. %For this section of the

-% tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
+% tutorial you will need to download the file https://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.

 \subsection{Drag and Drop}
        In most operating systems you can drag a file icon from a file browser
        window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. 
 \subsection{Drag and Drop}
        In most operating systems you can drag a file icon from a file browser
        window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. 

@@ -588,13 +588,13 @@ close all windows.}
 %% TODO: omit or combine this exercise
 %% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
 \exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$
 %% TODO: omit or combine this exercise
 %% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
 \exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$

-Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{https://www.jalview.org/tutorial/alignment.fa} in the box.

 Click {\sl OK} to load the alignment.}
 
 %%TODO: omit or combine
 \exstep{{\bf Loading sequences from a file:} Close all windows using the
 {\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
 Click {\sl OK} to load the alignment.}
 
 %%TODO: omit or combine
 \exstep{{\bf Loading sequences from a file:} Close all windows using the
 {\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.

-Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
+Then type the same URL (\url{https://www.jalview.org/tutorial/alignment.fa}) into

 your web browser. Then from the browser, save the fasta file (.fa) file to your desktop using {\sl File
 $\Rightarrow$ Save Page as}.
 Open the file you have just saved on your computer in Jalview by selecting {\sl File
 your web browser. Then from the browser, save the fasta file (.fa) file to your desktop using {\sl File
 $\Rightarrow$ Save Page as}.
 Open the file you have just saved on your computer in Jalview by selecting {\sl File

@@ -607,7 +607,7 @@ Select the file and click {\sl OK} to load.}
 drop it onto the Jalview desktop window, the alignment should open.
 
 (ii) Open
 drop it onto the Jalview desktop window, the alignment should open.
 
 (ii) Open

-\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
+\url{https://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web

 browser. Test the differences
 between (a) dragging the URL directly from browser onto the Jalview
 desktop.
 browser. Test the differences
 between (a) dragging the URL directly from browser onto the Jalview
 desktop.

@@ -615,7 +615,7 @@ desktop.
 directory and drag it onto the desktop.) (b) dragging the URL from
 browser onto the existing alignment.fa alignment window in the Jalview desktop.
 
 directory and drag it onto the desktop.) (b) dragging the URL from
 browser onto the existing alignment.fa alignment window in the Jalview desktop.
 

-(iii) Open \url{http://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
+(iii) Open \url{https://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web

 browser. Note that this is a cDNA file. Drag the URL from
 browser onto the estrogenReceptorProtein.fa protein alignment window in
 the Jalview desktop. A dialogue box opens asking `Would you like to open as split
 browser. Note that this is a cDNA file. Drag the URL from
 browser onto the estrogenReceptorProtein.fa protein alignment window in
 the Jalview desktop. A dialogue box opens asking `Would you like to open as split

@@ -648,7 +648,7 @@ An alignment of about 174 sequences should load.}
 \exstep{These can be viewed using the Overview window accessible from {\sl View
 $\Rightarrow$ Overview Window.}}
 {\bf See the video at:
 \exstep{These can be viewed using the Overview window accessible from {\sl View
 $\Rightarrow$ Overview Window.}}
 {\bf See the video at:

-\url{http://www.jalview.org/Help/Getting-Started}} }
+\url{https://www.jalview.org/Help/Getting-Started}} }

 
 
 \subsection{From a URL}
 
 
 \subsection{From a URL}

@@ -734,7 +734,7 @@ the currently available memory at the bottom left hand side of the Desktop
 window's background. Should you need to increase the amount of memory available
 to Jalview, full instructions are given in the built in documentation (opened by
 selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
 window's background. Should you need to increase the amount of memory available
 to Jalview, full instructions are given in the built in documentation (opened by
 selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory

-parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
+parameters page (\url{https://www.jalview.org/jvmmemoryparams.html}).

 
 
 \section{Saving Sequences and Alignments}
 
 
 \section{Saving Sequences and Alignments}

@@ -803,7 +803,7 @@ suitable folder.}
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how many of the windows
 reopen. Are they the same as when they were saved ? } {\bf See the video at:
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how many of the windows
 reopen. Are they the same as when they were saved ? } {\bf See the video at:

-\url{http://www.jalview.org/Help/Getting-Started}.} }
+\url{https://www.jalview.org/Help/Getting-Started}.} }

 
 %% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
 \subsection{Jalview Projects}
 
 %% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
 \subsection{Jalview Projects}

@@ -1010,7 +1010,7 @@ Select appropriate menu option and pick an output format (eg BLC) from the
 \exstep{In the Alignment output window that opens, try manually editing the
 alignment before clicking the {\sl New Window} button. This opens the
 edited alignment in a new alignment window.} {\bf See the video at:
 \exstep{In the Alignment output window that opens, try manually editing the
 alignment before clicking the {\sl New Window} button. This opens the
 edited alignment in a new alignment window.} {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 % more? change colouring style. set border colour.
 }
 
 % more? change colouring style. set border colour.
 }
 

@@ -1043,7 +1043,7 @@ this will not work in cursor mode)}
 sequences, use hold [SHIFT], and select two sequences separated by
 one or more un-selected sequences, repeat using the [CTRL] key. Note how
 multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}
 sequences, use hold [SHIFT], and select two sequences separated by
 one or more un-selected sequences, repeat using the [CTRL] key. Note how
 multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}

-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -1150,7 +1150,7 @@ the mouse over this sequence. Bring up the Sequence ID context menu by right
 clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
 with (Sequence ID name )}. To reveal these hidden sequences, right click on the
 Sequence ID and in the context menu select {\sl Reveal All}.}
 clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
 with (Sequence ID name )}. To reveal these hidden sequences, right click on the
 Sequence ID and in the context menu select {\sl Reveal All}.}

-{\bf See the video at:  \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at:  \url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -1236,8 +1236,8 @@ right of the selected residue.
 \label{editingalignex}
 You are going to manually reconstruct part of the example Jalview
 alignment available at
 \label{editingalignex}
 You are going to manually reconstruct part of the example Jalview
 alignment available at

- \href{http://www.jalview.org/examples/exampleFile.jvp}
- {http://www.jalview.org/examples/exampleFile.jvp}.
+ \href{https://www.jalview.org/examples/exampleFile.jvp}
+ {https://www.jalview.org/examples/exampleFile.jvp}.

  
  {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
 
  
  {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
 

@@ -1249,7 +1249,7 @@ Remember to use [CTRL]-Z to undo an edit, or the {\sl File $\Rightarrow$
  want to start again.
 
 \exstep{ Load the URL
  want to start again.
 
 \exstep{ Load the URL

-\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
+\textsf{https://www.jalview.org/tutorial/unaligned.fa} which contains part of the

 ferredoxin alignment from PF03460.}
 
 \exstep{ Select the first 7 sequences, and press H key to hide them (or right click
 ferredoxin alignment from PF03460.}
 
 \exstep{ Select the first 7 sequences, and press H key to hide them (or right click

@@ -1325,7 +1325,7 @@ exercise.
 {\bf Mac users:} [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].
 
 \exstep{Load the sequence alignment at
 {\bf Mac users:} [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].
 
 \exstep{Load the sequence alignment at

-\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
+\textsf{https://www.jalview.org/tutorial/unaligned.fa}, or continue using the

 edited alignment.  If you continue from the
 previous exercise, first right click on the sequence ID panel and select
 {\sl Reveal All}. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).}
 edited alignment.  If you continue from the
 previous exercise, first right click on the sequence ID panel and select
 {\sl Reveal All}. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).}

@@ -1617,7 +1617,7 @@ features are currently displayed (these are introduced later, in Section
 $\Rightarrow$ Show Sequence Features} option in the alignment window menu is
 ticked. If it is, select it to disable feature colouring.
 
 $\Rightarrow$ Show Sequence Features} option in the alignment window menu is
 ticked. If it is, select it to disable feature colouring.
 

-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -1633,11 +1633,11 @@ A dialog window will open.}
 \exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
 
 {\bf See the video at:
 \exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
 
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}} }
+\url{https://www.jalview.org/training/Training-Videos}.}} }

 
 \exercise{Alignment Layout}{
 \label{exscreen}
 
 \exercise{Alignment Layout}{
 \label{exscreen}

-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jvp}. 
+\exstep{Start Jalview and open the URL \textsf{https://www.jalview.org/examples/exampleFile.jvp}. 

 Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. 
 Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement, 
 sequence ID format and so on. }
 Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. 
 Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement, 
 sequence ID format and so on. }

@@ -1655,7 +1655,7 @@ The rows should now be reordered. Features and annotations are covered in more d
 a up/down arrow symbol should appear - click on the icon, the height of the {\sl Annotation Area} can be changed 
 by clicking and dragging this icon up or down.}
 \bf See the video at:
 a up/down arrow symbol should appear - click on the icon, the height of the {\sl Annotation Area} can be changed 
 by clicking and dragging this icon up or down.}
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 \section{Formatting and Graphics Output}
 \label{layoutandoutput}
 
 \section{Formatting and Graphics Output}
 \label{layoutandoutput}

@@ -1817,7 +1817,7 @@ resolution.}
 \exstep{Experiment with Jalview's other output options: try exporting an alignment view as 'BioJS', which employs the BioJS Multiple Sequence Alignment viewer. When would you use this type of export option ?}
 \exstep{Working with embedded BioJSON data. Drag and drop (or load via the file browser) the 'BioJS' HTML file in the previous step. Compare the original and imported alignment views - are there differences ?}
 \bf See the video at:
 \exstep{Experiment with Jalview's other output options: try exporting an alignment view as 'BioJS', which employs the BioJS Multiple Sequence Alignment viewer. When would you use this type of export option ?}
 \exstep{Working with embedded BioJSON data. Drag and drop (or load via the file browser) the 'BioJS' HTML file in the previous step. Compare the original and imported alignment views - are there differences ?}
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.
+\url{https://www.jalview.org/training/Training-Videos}.

 }
 
 % left out for Glasgow 2016
 }
 
 % left out for Glasgow 2016

@@ -1985,7 +1985,7 @@ calculations can be found in the on-line documentation.
 
 \exercise{Annotating Alignments}{
   \label{annotatingalignex}
 
 \exercise{Annotating Alignments}{
   \label{annotatingalignex}

-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. 
+\exstep{Load the alignment at \textsf{https://www.jalview.org/tutorial/alignment.fa}. 

 Right-click on the label name of the {\sl Conservation} annotation row to
 bring up the context menu and select {\sl Add New Row}. A dialog box will
 appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
 Right-click on the label name of the {\sl Conservation} annotation row to
 bring up the context menu and select {\sl Add New Row}. A dialog box will
 appear asking for {\sl Annotation Name} and {\sl Annotation Description}.

@@ -2046,7 +2046,7 @@ SEQUENCE\_REF statements surrounding the row specifying the sequence association
 annotation. 
 }
 \bf See the video at:
 annotation. 
 }
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 
 \section{Sequence Features}
 
 
 \section{Sequence Features}

@@ -2284,7 +2284,7 @@ features file.
 
 \exercise{Creating Features}{
 \label{featuresex}
 
 \exercise{Creating Features}{
 \label{featuresex}

-\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. 
+\exstep{Open the alignment at \textsf{https://www.jalview.org/tutorial/alignment.fa}. 

 We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in 
 iron binding so we will create them as features. Navigate to column 97, sequence 1. 
 Select the entire column by clicking in the ruler bar. Then right-click on the selection 
 We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in 
 iron binding so we will create them as features. Navigate to column 97, sequence 1. 
 Select the entire column by clicking in the ruler bar. Then right-click on the selection 

@@ -2321,7 +2321,7 @@ alignment window menu. The sequence features are now hidden. Repeat this step an
 displayed.}
 
 \bf See the video at:
 displayed.}
 
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 \chapter{Multiple Sequence Alignment}
 \label{msaservices}
 
 \chapter{Multiple Sequence Alignment}
 \label{msaservices}

@@ -2418,7 +2418,7 @@ number allowed by the server.
 \exercise{Multiple Sequence Alignment}{
 \label{msaex}
 \exstep{ Close all windows. Open the alignment at {\sf
 \exercise{Multiple Sequence Alignment}{
 \label{msaex}
 \exstep{ Close all windows. Open the alignment at {\sf

-http://www.jalview.org/tutorial/unaligned.fa}.  Select {\sl
+https://www.jalview.org/tutorial/unaligned.fa}.  Select {\sl

 Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. 
 A window will open giving the job status. After a short time, a second window will open
  with the results of the alignment.} 
 Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. 
 A window will open giving the job status. After a short time, a second window will open
  with the results of the alignment.} 

@@ -2446,7 +2446,7 @@ select and hide a few more columns in the N-terminal region, and submit the alig
 service again and explore the effect of local alignment on the non-homologous parts of the 
 N-terminal region.}
 {\bf See the video at:
 service again and explore the effect of local alignment on the non-homologous parts of the 
 N-terminal region.}
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 \section{Customising the Parameters used for Alignment}
 }
 
 \section{Customising the Parameters used for Alignment}

@@ -2555,7 +2555,7 @@ JABA service.
 % alignments (refer to section \ref{superposestructs} for instructions). Which
 % alignment gives the best RMSD ? }
 % \exstep{Apply the same alignment parameter settings to the example alignment
 % alignments (refer to section \ref{superposestructs} for instructions). Which
 % alignment gives the best RMSD ? }
 % \exstep{Apply the same alignment parameter settings to the example alignment

-% (available from \textsf{http://www.jalview.org/examples/uniref50.fa}). 
+% (available from \textsf{https://www.jalview.org/examples/uniref50.fa}). 

 % 
 % Are there differences ? If not, why not ?
 % }
 % 
 % Are there differences ? If not, why not ?
 % }

@@ -2630,7 +2630,7 @@ the matrix formed from the sum of pairwise substitution scores at each aligned
 position between each pair of sequences. The basic method is described in the
 1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl
 Nature Structural Biology} (1995) {\bf 2}, 171-8.
 position between each pair of sequences. The basic method is described in the
 1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl
 Nature Structural Biology} (1995) {\bf 2}, 171-8.

-PMID: 7749921} and implemented at the SeqSpace server at the EBI.\footnote{See \url{http://www.jalview.org/help/html/calculations/pca.html}.}
+PMID: 7749921} and implemented at the SeqSpace server at the EBI.\footnote{See \url{https://www.jalview.org/help/html/calculations/pca.html}.}

 % 
 % Jalview provides two different options for the PCA calculation: SeqSpace and
 % Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and
 % 
 % Jalview provides two different options for the PCA calculation: SeqSpace and
 % Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and

@@ -2663,7 +2663,7 @@ the {\sl File $\Rightarrow$ Save as $\Rightarrow$ \ldots } submenu.
 \exercise{Principal Component Analysis}
 {\label{pcaex}
 \exstep{Load the alignment at
 \exercise{Principal Component Analysis}
 {\label{pcaex}
 \exstep{Load the alignment at

-\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+\textsf{https://www.jalview.org/tutorial/alignment.fa}.}

 \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}.  in the alignment
 window and a dialogue box will open. Select the Principal Component Analysis option
 and then click the Calculate button.} 
 \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}.  in the alignment
 window and a dialogue box will open. Select the Principal Component Analysis option
 and then click the Calculate button.} 

@@ -2682,7 +2682,7 @@ different (arbitrarily selected) colour.
 Note how the colour of the sequence ID label matches both the colour of
 the partitioned tree and the points in the PCA plot.} 
 {\bf See the video at:
 Note how the colour of the sequence ID label matches both the colour of
 the partitioned tree and the points in the PCA plot.} 
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 \begin{figure}[hbtp]
 }
 
 \begin{figure}[hbtp]

@@ -2764,7 +2764,7 @@ preserve these.
 {\label{treeex}
 
 \exstep{Open the alignment at
 {\label{treeex}
 
 \exstep{Open the alignment at

-\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+\textsf{https://www.jalview.org/tutorial/alignment.fa}.}

 
 \exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
 window menu and a dialogue box opens. In the tree section select Neighbour
 
 \exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
 window menu and a dialogue box opens. In the tree section select Neighbour

@@ -2803,7 +2803,7 @@ Comparing the location of individual sequences between the three trees illustrat
 alignment for the calculation of trees.
 
 {\bf See the video at:
 alignment for the calculation of trees.
 
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 }
 
 
 }
 

@@ -2844,7 +2844,7 @@ can help when working with larger alignments.
 
 %\exercise{Pad Gaps in an Alignment}{
 %\exstep{Open the alignment at
 
 %\exercise{Pad Gaps in an Alignment}{
 %\exstep{Open the alignment at

-% \textsf{http://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
+% \textsf{https://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the

 %alignment.}
 %\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
 %Neighbour Joining Using BLOSUM62}.
 %alignment.}
 %\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
 %Neighbour Joining Using BLOSUM62}.

@@ -2860,7 +2860,7 @@ can help when working with larger alignments.
 %{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
 
 %{\bf See the video at:
 %{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
 
 %{\bf See the video at:

-%\url{http://www.jalview.org/training/Training-Videos}.}
+%\url{https://www.jalview.org/training/Training-Videos}.}

 %}
 
  \exercise{Tree Based Conservation Analysis}{
 %}
 
  \exercise{Tree Based Conservation Analysis}{

@@ -2888,7 +2888,7 @@ BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
 it is used in the next set of exercises. }
 
 {\bf See the video at:
 it is used in the next set of exercises. }
 
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -3019,7 +3019,7 @@ both of the columns that you wish to use to subdivide the alignment.}}
 \exstep{Switch back to the original view, and experiment with subdividing
 the tree groups made in the previous exercise.}
 {\bf See the video at:
 \exstep{Switch back to the original view, and experiment with subdividing
 the tree groups made in the previous exercise.}
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 \begin{figure}[]
 }
 
 \begin{figure}[]

@@ -3271,7 +3271,7 @@ when associated alignment views are modified.
 \exercise{Viewing Structures with the integrated Jmol Viewer}{
 \label{viewingstructex}
 \exstep{Load the alignment at
 \exercise{Viewing Structures with the integrated Jmol Viewer}{
 \label{viewingstructex}
 \exstep{Load the alignment at

-\textsf{http://www.jalview.org/examples/exampleFile.jvp}.}
+\textsf{https://www.jalview.org/examples/exampleFile.jvp}.}

 \exstep{Right-click on the
 sequence ID label of {\sl FER1\_SPIOL} to open
 the ID popup menu and select {\sl 3D Structure Data}. After a short pause, a
 \exstep{Right-click on the
 sequence ID label of {\sl FER1\_SPIOL} to open
 the ID popup menu and select {\sl 3D Structure Data}. After a short pause, a

@@ -3320,7 +3320,7 @@ and then the {\sl Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} comma
 function to save the alignment as a Jalview Project (jvp). Now close the alignment and the structure view, and load the project file you just saved.
 Verify that the Jmol display is as it was when you just saved the file.}
 {\bf See the video at:
 function to save the alignment as a Jalview Project (jvp). Now close the alignment and the structure view, and load the project file you just saved.
 Verify that the Jmol display is as it was when you just saved the file.}
 {\bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 }
 
 \exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{
 }
 
 \exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{

@@ -3379,7 +3379,7 @@ If this does not work then you may need to set the {\sl Path to Chimera program}
 the Chimera structure viewer sits outside the Jalview desktop and a Chimera
 view window sits inside the Jalview desktop.
 
 the Chimera structure viewer sits outside the Jalview desktop and a Chimera
 view window sits inside the Jalview desktop.
 

-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}}

 
 
 \subsection{Superimposing Structures}
 
 
 \subsection{Superimposing Structures}

@@ -3512,7 +3512,7 @@ in each component of this protein-DNA complex. Instructions for recreating this
 Interfaces}{\label{dnmtcomplexex}
 
 \exstep{Download the PDB file at
 Interfaces}{\label{dnmtcomplexex}
 
 \exstep{Download the PDB file at

-\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. 
+\textsf{\url{https://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. 

 This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
 server.}
 
 This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
 server.}
 

@@ -3624,7 +3624,7 @@ the mouse in the annotation label panel and select the ``Hide this row'' option.
 The Annotations dropdown menu on the alignment window also provides options for
 reordering and hiding autocalculated and sequence associated annotation. 
 
 The Annotations dropdown menu on the alignment window also provides options for
 reordering and hiding autocalculated and sequence associated annotation. 
 

-\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by 
+\exstep{ Open the alignment at \url{https://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by 

 clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
 Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure
 Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) 
 clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
 Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure
 Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) 

@@ -3667,7 +3667,7 @@ original alignment window.}
 follow the instructions to view the Jalview annotations file created from the annotations
 generated by the JPred server for your sequence.
 \bf See the video at:
 follow the instructions to view the Jalview annotations file created from the annotations
 generated by the JPred server for your sequence.
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 \begin{figure}[htbp]
 \begin{center}
 
 \begin{figure}[htbp]
 \begin{center}

@@ -3742,7 +3742,7 @@ select that sequence.
 \subsection{Disorder Predictors provided by JABAWS 2.0}
 For full details of each predictor and the results that Jalview can display,
 please consult
 \subsection{Disorder Predictors provided by JABAWS 2.0}
 For full details of each predictor and the results that Jalview can display,
 please consult

-\href{http://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
+\href{https://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's

 protein disorder service documentation}. Short descriptions of the methods provided in JABAWS 2.0 are given below:
 
 \subsubsection{DisEMBL}
 protein disorder service documentation}. Short descriptions of the methods provided in JABAWS 2.0 are given below:
 
 \subsubsection{DisEMBL}

@@ -3851,7 +3851,7 @@ Temperature Factor annotation to alignment}} option in your Structures preferenc
 ({\sl Tool  $\Rightarrow$ Preferences  $\Rightarrow$ Structure)}.
 
 \exstep{Open the alignment from
 ({\sl Tool  $\Rightarrow$ Preferences  $\Rightarrow$ Structure)}.
 
 \exstep{Open the alignment from

-\url{http://www.jalview.org/tutorial/interleukin7.fa}. } 
+\url{https://www.jalview.org/tutorial/interleukin7.fa}. } 

 
 \exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
 $\Rightarrow$ Disorder Prediction $\Rightarrow$ Disembl with defaults}.}
 
 \exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
 $\Rightarrow$ Disorder Prediction $\Rightarrow$ Disembl with defaults}.}

@@ -3874,7 +3874,7 @@ box. Then shade the sequences by the long and short disorder predictors. {\sl
 Note} how well the disordered regions predicted by each method agree
 with the structure.}
 \bf See the video at:
 Note} how well the disordered regions predicted by each method agree
 with the structure.}
 \bf See the video at:

-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}

 
 \chapter{DNA and RNA Sequences}
 \label{dnarna}
 
 \chapter{DNA and RNA Sequences}
 \label{dnarna}

@@ -4383,7 +4383,7 @@ happening?}
 \exstep{Hit OK to save your preferences -- you have now added a new JABA
 service to Jalview!}
 \exstep{Try out your new JABA services by loading the ferredoxin sequences from
 \exstep{Hit OK to save your preferences -- you have now added a new JABA
 service to Jalview!}
 \exstep{Try out your new JABA services by loading the ferredoxin sequences from

-http://www.jalview.org/tutorial/alignment.fa}
+https://www.jalview.org/tutorial/alignment.fa}

 \exstep{Launch an alignment using one
 of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the {\sl Web Service} menu on the alignment window.
 
 \exstep{Launch an alignment using one
 of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the {\sl Web Service} menu on the alignment window.