From 48040645e199f64d0bd396cc3a6137035a697737 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 17 Sep 2020 12:19:40 +0100
Subject: [PATCH] JAL-3741 http to https (and jar to jvp for exampleFile
 defaults!)

---
 help/help/html/features/commandline.html   |    2 +-
 help/help/html/features/groovy.html        |    8 ++++----
 help/help/html/features/jvlfiles.html      |    8 ++++----
 help/help/html/groovy/featuresCounter.html |    2 +-
 help/help/html/index.html                  |    4 ++--
 help/help/html/memory.html                 |    2 +-
 help/help/html/webServices/newsreader.html |    6 +++---
 src/jalview/bin/Cache.java                 |    6 +++---
 src/jalview/bin/Jalview.java               |   15 +++++++++------
 src/jalview/gui/BlogReader.java            |    2 +-
 src/jalview/gui/Desktop.java               |    8 ++++----
 src/jalview/gui/Preferences.java           |    4 ++--
 src/jalview/io/JSONFile.java               |    2 +-
 13 files changed, 36 insertions(+), 33 deletions(-)

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index f0e04d5..0ef78f9 100644
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -38,7 +38,7 @@
 
   <ul>
     <li>Standard installation on Linux/Unix:<pre>
-       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+       /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
     </li>
     <li>Standard installation on Windows:<pre>
       \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html
index ead4436..cc91154 100644
--- a/help/help/html/features/groovy.html
+++ b/help/help/html/features/groovy.html
@@ -39,7 +39,7 @@
     installation of Groovy. Just select <strong>Tools&#8594;Groovy
       Console...</strong> from the Jalview Desktop's drop-down menu. After a
     short pause, you should then see the <a
-      href="http://groovy-lang.org/groovyconsole.html">Groovy
+      href="https://groovy-lang.org/groovyconsole.html">Groovy
       Console</a> appear. This allows you to interactively execute Groovy
     scripts whilst Jalview is running. We've also provided a <strong>Calculations&#8594;Execute
       Groovy Script</strong> button so you can execute the currently loaded
@@ -101,7 +101,7 @@ print currentAlFrame.getTitle();</pre>
     InstallAnywhere version of Jalview, you can find additional groovy
     scripts in the examples/groovy subfolder of the installation
     directory. The examples are also available at <a
-      href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+      href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
   </p>
   <p>
     <em>Using Groovy to add new Alignment Calculations</em><br />We've
@@ -115,8 +115,8 @@ print currentAlFrame.getTitle();</pre>
     <em>Creating custom colourschemes</em><br/>
     You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
     <ul>
-    <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
-    <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
     
     </ul>
   </p>
diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html
index 27742b3..e23af30 100644
--- a/help/help/html/features/jvlfiles.html
+++ b/help/help/html/features/jvlfiles.html
@@ -46,12 +46,12 @@
   <pre>
 # Jalview Launch File
 # Please install the Jalview Desktop from 
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
 # and then try to open this file again
 jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
 jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
 jalview.apparg=-colour
 jalview.apparg=Clustal
 </pre>
@@ -62,7 +62,7 @@ jalview.apparg=Clustal
 # Please install the Jalview Desktop from 
 # http://www.jalview.org/getdown/release
 # and then try to open this file again
-appbase=http://www.jalview.org/getdown/archive/2_10_5/
+appbase=https://www.jalview.org/getdown/archive/2_10_5/
 </pre>
   For security, the Jalview application will only allow
   <em>appbase</em> URLs from www.jalview.org.
diff --git a/help/help/html/groovy/featuresCounter.html b/help/help/html/groovy/featuresCounter.html
index 3b6705b..bd7144e 100644
--- a/help/help/html/groovy/featuresCounter.html
+++ b/help/help/html/groovy/featuresCounter.html
@@ -43,7 +43,7 @@
   </ol>
   <strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
   <em><a
-    href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
+    href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
     - rendered with <a href="http://hilite.me">hilite.me</a></em>
   <!-- HTML generated using hilite.me --><div style="background: #f8f8f8; overflow:auto;width:auto;border:solid gray;border-width:.1em .1em .1em .8em;padding:.2em .6em;"><pre style="margin: 0; line-height: 125%"><span style="color: #408080; font-style: italic">/*</span>
 <span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
diff --git a/help/help/html/index.html b/help/help/html/index.html
index 8adbdb8..a6bb1b6 100755
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -45,7 +45,7 @@
   <p>
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (<a
-      href="http://www.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+      href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation</a>).
   </p>
   <p>
     If you are using the Jalview Desktop application and are looking for
@@ -54,7 +54,7 @@
     google the online version of these pages. If you don't find what you
     are looking for, or want to report a bug or make a feature request,
     then get in contact over at <a
-      href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+      href="https://www.jalview.org/community">https://www.jalview.org/community</a>
   </p>
   <p>
     <strong>Logging, troubleshooting and reporting bugs</strong><br />If
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 0374dcb..7d6fb85 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -80,7 +80,7 @@
       arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. <pre>
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
       settings in Windows and macOS too: <br /> In Windows you must
       use, e.g. <pre>
       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
diff --git a/help/help/html/webServices/newsreader.html b/help/help/html/webServices/newsreader.html
index c3c1d3f..2e8b69a 100644
--- a/help/help/html/webServices/newsreader.html
+++ b/help/help/html/webServices/newsreader.html
@@ -25,7 +25,7 @@
   <p>
     <strong>The Jalview Desktop RSS News Reader</strong><br /> The
     Jalview Desktop includes a built in news reader for the <a
-      href="http://www.jalview.org/feeds/desktop/rss">Jalview
+      href="https://www.jalview.org/feeds/desktop/rss">Jalview
       Desktop News Channel</a>.
   </p>
 
@@ -48,9 +48,9 @@
   <br />
   <p>
     The <em>Jalview news reader</em> was introduced in <a
-      href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
+      href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
       version 2.7</a>. Its implementation is based on <a
-      href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
+      href="https://jswingreader.sourceforge.net/">JSwingReader</a>.
   </p>
   <br />
   <em>If you need to prevent the news-reader opening, then add the
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 2ea7196..600d19c 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -174,8 +174,8 @@ import jalview.ws.sifts.SiftsSettings;
  * when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
  * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.</li>
@@ -432,7 +432,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 613cc02..1e292ba 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -383,7 +383,7 @@ public class Jalview
             // String defurl =
             // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
             // //
-            String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+            String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
             Cache.log.debug(
                     "Starting questionnaire with default url: " + defurl);
             desktop.checkForQuestionnaire(defurl);
@@ -696,13 +696,16 @@ public class Jalview
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
               jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
-                      + "/examples/exampleFile_2_7.jar");
+                      "https://www.jalview.org")
+                      + "/examples/exampleFile_2_7.jvp");
       if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+                      "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
+        file.replace("http:", "https:");
         // hardwire upgrade of the startup file
-        file.replace("_2_3.jar", "_2_7.jar");
+        file.replace("_2_3", "_2_7");
+        file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
@@ -998,7 +1001,7 @@ public class Jalview
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                     + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
-                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                    + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
   private static void startUsageStats(final Desktop desktop)
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 65c8b5a..c43c699 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -256,7 +256,7 @@ public class BlogReader extends JPanel
     chan.setURL(
             jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
                     jalview.bin.Cache.getDefault("www.jalview.org",
-                            "http://www.jalview.org")
+                            "https://www.jalview.org")
                             + "/feeds/desktop/rss"));
     loadLastM();
     _channelModel.addChannel(chan);
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7564dda..0441e5e 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -927,7 +927,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (java.lang.ClassCastException cex)
     {
       Cache.log.warn(
-              "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
               cex);
     }
   }
@@ -1135,7 +1135,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     panel.add(history);
     history.setPreferredSize(new Dimension(400, 20));
     history.setEditable(true);
-    history.addItem("http://www.");
+    history.addItem("https://www.");
 
     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
 
@@ -1351,7 +1351,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                       "..Checking..")
               + " is available for download from "
               + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
+                      "https://www.jalview.org")
               + " !!");
       if (red)
       {
@@ -1362,7 +1362,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             "AUTHORFNAMES",
             "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
-            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
             + "<br><br>If  you use Jalview, please cite:"
             + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
             + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 1f61bae..f51bfbf 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -289,8 +289,8 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
-                    + "/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+                    + "/examples/exampleFile_2_7.jvp"));
 
     /*
      * Set Colours tab defaults
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index fda22dc..0e3cca7 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -71,7 +71,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private static String version = new BuildDetails().getVersion();
 
-  private String webstartUrl = "http://www.jalview.org/services/launchApp";
+  private String webstartUrl = "https://www.jalview.org/services/launchApp";
 
   private String application = "Jalview";
 
-- 
1.7.10.2