Building Jalview from Source


`bin/`	used by eclipse for compiled classes -- no need to touch this	used by eclipse for compiled classes â no need to touch this
`build/`
`getdown/website/`	the assembled "download" folder used by getdown for downloads/upgrades	the assembled âdownloadâ folder used by getdown for downloads/upgrades
`getdown/files/`	`gradle.properties`	configurable properties for the build process
`RELEASE`	propertyfile configuring JALVIEW_VERSION (from jalview.version) and the release branch (from jalview.release). An alternative file can be specified via JALVIEW_RELEASE_FILE property

/*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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 @@
   
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (http://www.jalview.org/about/documentation).
+      href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation).
   
   
     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 http://www.jalview.org/community
+      href="https://www.jalview.org/community">https://www.jalview.org/community
   
   
     Logging, troubleshooting and reporting bugs
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 jvl file first, e.g. 
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. -       /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 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

You can use command line arguments to control memory settings in Windows and macOS too:
In Windows you must use, e.g.

       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa

In macOS you can use the macOS open command like this:

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index eea9de7..4bef1f6 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,8 +57,48 @@ li:before {
     
     
       2.11.1.3

+          27/10/2020
+      
+        
+        
+        
+      
+      
+        
+          
+            Find doesn't always highlight all matching
+            positions in a sequence
+          
+          
+            Space character in Jalview install path on
+            Windows prevents install4j launching getdown
+          
+        
+      
+    
+    
+      2.11.1.2

+          25/09/2020
+      
+        
+        
+      
+      
+        
+          
+            Fresh install of Jalview 2.11.1.1 reports
+            "Encountered problems opening
+            https://www.jalview.org/examples/exampleFile_2_7.jvp"
+          
+        
+      
+    
+    
+      2.11.1.1

-          15/09/2020
+          17/09/2020
       
         
           
@@ -185,6 +225,14 @@ li:before {
             file again, and if that fails, delete the original file and
             save in place.)
           
+          
+            Cannot process alignments from HTTPS urls
+            via command line
+          
+          
+            References to http://www.jalview.org in
+            program and documentation
+          
         
 Launching Jalview
         
           
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 @@
   
     The Jalview Desktop RSS News Reader
 The
     Jalview Desktop includes a built in news reader for the Jalview
+      href="https://www.jalview.org/feeds/desktop/rss">Jalview
       Desktop News Channel.
   
 
@@ -48,9 +48,9 @@
   

   
     The Jalview news reader was introduced in Jalview
+      href="https://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
       version 2.7. Its implementation is based on JSwingReader.
+      href="https://jswingreader.sourceforge.net/">JSwingReader.
   
   

   If you need to prevent the news-reader opening, then add the
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 2e18bae..a448aaa 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,12 +24,13 @@
 
 
   
-    Jalview 2.11.1.1
+    Jalview 2.11.1.3
   
-  Jalview 2.11.1.1 is the first patch release for Jalview version
-    2.11.1. In addition to fixes for some critical bugs, it also
-    contains a handful of new features suggested by the Jalview
-    community.
+  Jalview 2.11.1.3 is the third patch release, fixing a bug
+    introduced in last weeks Jalview 2.11.1.1 release affecting display
+    of Jalview's example project for some users. Together, these
+    releases include fixes for a number of critical bugs, and also contains a
+    handful of new features suggested by the Jalview community.
   
     Shift+arrow keys navigate to next gap or residue in cursor
       mode (enable with F2)
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c545c7f..d52e42a 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -417,7 +417,7 @@ public class Finder implements FinderI
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex += offset + 1;
+    residueIndex = searchPattern.matchedFrom()+1;
 
     /*
      * return false if the match is entirely in a hidden region
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
  * ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation
- * www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org
+ * www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org
  * FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.
@@ -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 341bcba..3a238bb 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,28 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -79,6 +57,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -86,6 +65,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -383,7 +363,7 @@ 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);
@@ -451,7 +431,9 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      protocol = AppletFormatAdapter.checkProtocol(file);
+
+      if (protocol == DataSourceType.FILE)
       {
         if (!(new File(file)).exists())
         {
@@ -463,8 +445,6 @@ public class Jalview
         }
       }
 
-      protocol = AppletFormatAdapter.checkProtocol(file);
-
       try
       {
         format = new IdentifyFile().identify(file, protocol);
@@ -648,11 +628,14 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-          FileFormatI outFormat=null;
-          try {
+          FileFormatI outFormat = null;
+          try
+          {
             outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP) {
-            System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+          } catch (Exception formatP)
+          {
+            System.out.println("Couldn't parse " + outFormat
+                    + " as a valid Jalview format string.");
           }
           if (outFormat != null)
           {
@@ -694,23 +677,21 @@ 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");
-      if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+                      "https://www.jalview.org")
+                      + "/examples/exampleFile_2_7.jvp");
+      if (file.equals("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");
       }
 
-      protocol = DataSourceType.FILE;
-
-      if (file.indexOf("http:") > -1)
-      {
-        protocol = DataSourceType.URL;
-      }
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       if (file.endsWith(".jar"))
       {
@@ -996,7 +977,7 @@ 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/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4be7d0e..b1efed6 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -138,6 +138,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
@@ -1037,7 +1038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
@@ -1047,7 +1048,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
@@ -1094,7 +1095,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null || (currentFileFormat == null)
-            || fileName.startsWith("http"))
+            || HttpUtils.startsWithHttpOrHttps(fileName))
     {
       saveAs_actionPerformed(null);
     }
@@ -1749,7 +1750,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode 
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+   * or the sequence under cursor in keyboard mode
    * 
    * @param up
    *          or down (if !up)
@@ -1760,23 +1762,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      if (viewport.cursorMode) 
+      if (viewport.cursorMode)
       {
         sg = new SequenceGroup();
-        sg.addSequence(viewport.getAlignment()
-                .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
-      } else {
+        sg.addSequence(viewport.getAlignment().getSequenceAt(
+                alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+      }
+      else
+      {
         return;
       }
     }
-    
+
     if (sg.getSize() < 1)
     {
-        return;
+      return;
     }
-    
+
     // TODO: JAL-3733 - add an event to the undo buffer for this !
-    
+
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);
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)")
             + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
-            + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
+            + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
             + "

If  you use Jalview, please cite:"
             + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
             + "
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";
 
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ca0423b..0e062ac 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -24,6 +24,54 @@ import static jalview.math.RotatableMatrix.Axis.X;
 import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
 import jalview.analysis.Conservation;
 import jalview.analysis.PCA;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -85,6 +133,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.Format;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
@@ -150,54 +199,6 @@ import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties;
 import jalview.xml.binding.jalview.ThresholdType;
 import jalview.xml.binding.jalview.VAMSAS;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.SwingUtilities;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.Marshaller;
-import javax.xml.datatype.DatatypeConfigurationException;
-import javax.xml.datatype.DatatypeFactory;
-import javax.xml.datatype.XMLGregorianCalendar;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamReader;
-
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
  * 
@@ -946,7 +947,7 @@ public class Jalview2XML
         else
         {
           vamsasSeq = createVamsasSequence(id, jds);
-//          vamsasSet.addSequence(vamsasSeq);
+          // vamsasSet.addSequence(vamsasSeq);
           vamsasSet.getSequence().add(vamsasSeq);
           vamsasSetIds.put(id, vamsasSeq);
           seqRefIds.put(id, jds);
@@ -1339,9 +1340,8 @@ public class Jalview2XML
 
             if (colourScheme instanceof jalview.schemes.UserColourScheme)
             {
-              jGroup.setColour(
-                      setUserColourScheme(colourScheme, userColours,
-                              object));
+              jGroup.setColour(setUserColourScheme(colourScheme,
+                      userColours, object));
             }
             else
             {
@@ -1387,7 +1387,7 @@ public class Jalview2XML
         }
       }
 
-      //jms.setJGroup(groups);
+      // jms.setJGroup(groups);
       Object group;
       for (JGroup grp : groups)
       {
@@ -1524,11 +1524,13 @@ public class Jalview2XML
              * save any filter for the feature type
              */
             FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
-            if (filter != null)  {
-              Iterator filters = filter.getMatchers().iterator();
+            if (filter != null)
+            {
+              Iterator filters = filter.getMatchers()
+                      .iterator();
               FeatureMatcherI firstFilter = filters.next();
-              setting.setMatcherSet(Jalview2XML.marshalFilter(
-                      firstFilter, filters, filter.isAnded()));
+              setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+                      filters, filter.isAnded()));
             }
 
             /*
@@ -1577,8 +1579,7 @@ public class Jalview2XML
 
             setting.setDisplay(
                     av.getFeaturesDisplayed().isVisible(featureType));
-            float rorder = fr
-                    .getOrder(featureType);
+            float rorder = fr.getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
@@ -1602,7 +1603,7 @@ public class Jalview2XML
           Group g = new Group();
           g.setName(grp);
           g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
-                          .booleanValue());
+                  .booleanValue());
           // fs.addGroup(g);
           fs.getGroup().add(g);
           groupsAdded.addElement(grp);
@@ -2368,7 +2369,8 @@ public class Jalview2XML
   {
     if (calcIdParam.getVersion().equals("1.0"))
     {
-      final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+      final String[] calcIds = calcIdParam.getServiceURL()
+              .toArray(new String[0]);
       Jws2Instance service = Jws2Discoverer.getDiscoverer()
               .getPreferredServiceFor(calcIds);
       if (service != null)
@@ -2654,12 +2656,12 @@ public class Jalview2XML
     return id;
   }
 
-  jalview.schemes.UserColourScheme getUserColourScheme(
-          JalviewModel jm, String id)
+  jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+          String id)
   {
     List uc = jm.getUserColours();
     UserColours colours = null;
-/*
+    /*
     for (int i = 0; i < uc.length; i++)
     {
       if (uc[i].getId().equals(id))
@@ -2668,7 +2670,7 @@ public class Jalview2XML
         break;
       }
     }
-*/
+    */
     for (UserColours c : uc)
     {
       if (c.getId().equals(id))
@@ -2696,10 +2698,9 @@ public class Jalview2XML
       newColours = new java.awt.Color[23];
       for (int i = 0; i < 23; i++)
       {
-        newColours[i] = new java.awt.Color(Integer.parseInt(
-                colours.getUserColourScheme().getColour().get(i + 24)
-                        .getRGB(),
-                16));
+        newColours[i] = new java.awt.Color(
+                Integer.parseInt(colours.getUserColourScheme().getColour()
+                        .get(i + 24).getRGB(), 16));
       }
       ucs.setLowerCaseColours(newColours);
     }
@@ -2778,7 +2779,7 @@ public class Jalview2XML
     viewportsAdded.clear();
     frefedSequence = null;
 
-    if (file.startsWith("http://"))
+    if (HttpUtils.startsWithHttpOrHttps(file))
     {
       url = new URL(file);
     }
@@ -2855,8 +2856,8 @@ public class Jalview2XML
           XMLStreamReader streamReader = XMLInputFactory.newInstance()
                   .createXMLStreamReader(jin);
           javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-          JAXBElement jbe = um
-                  .unmarshal(streamReader, JalviewModel.class);
+          JAXBElement jbe = um.unmarshal(streamReader,
+                  JalviewModel.class);
           JalviewModel object = jbe.getValue();
 
           /*
@@ -3276,7 +3277,8 @@ public class Jalview2XML
   AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
   {
-    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+            .get(0);
     List vamsasSeqs = vamsasSet.getSequence();
 
     // JalviewModelSequence jms = object.getJalviewModelSequence();
@@ -3335,11 +3337,10 @@ public class Jalview2XML
           if (tmpSeq.getStart() != jseq.getStart()
                   || tmpSeq.getEnd() != jseq.getEnd())
           {
-            System.err.println(
-                    String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
-                            tmpSeq.getName(), tmpSeq.getStart(),
-                            tmpSeq.getEnd(), jseq.getStart(),
-                            jseq.getEnd()));
+            System.err.println(String.format(
+                    "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+                    tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+                    jseq.getStart(), jseq.getEnd()));
           }
         }
         else
@@ -3622,8 +3623,8 @@ public class Jalview2XML
               else
               {
                 // defer to later
-                frefedSequence.add(
-                        newAlcodMapRef(map.getDnasq(), cf, mapping));
+                frefedSequence
+                        .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
               }
             }
           }
@@ -3831,8 +3832,7 @@ public class Jalview2XML
         jaa.setCalcId(annotation.getCalcId());
         if (annotation.getProperty().size() > 0)
         {
-          for (Annotation.Property prop : annotation
-                  .getProperty())
+          for (Annotation.Property prop : annotation.getProperty())
           {
             jaa.setProperty(prop.getName(), prop.getValue());
           }
@@ -3913,9 +3913,9 @@ public class Jalview2XML
         sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
         sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
         // attributes with a default in the schema are never null
-          sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
-          sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
-          sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+        sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+        sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+        sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
         sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
         if (jGroup.getConsThreshold() != null
                 && jGroup.getConsThreshold().intValue() != 0)
@@ -3959,8 +3959,9 @@ public class Jalview2XML
         if (addAnnotSchemeGroup)
         {
           // reconstruct the annotation colourscheme
-          sg.setColourScheme(constructAnnotationColour(
-                  jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+          sg.setColourScheme(
+                  constructAnnotationColour(jGroup.getAnnotationColours(),
+                          null, al, jalviewModel, false));
         }
       }
     }
@@ -4166,8 +4167,8 @@ public class Jalview2XML
    * @param av
    * @param ap
    */
-  protected void loadTrees(JalviewModel jm, Viewport view,
-          AlignFrame af, AlignViewport av, AlignmentPanel ap)
+  protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+          AlignViewport av, AlignmentPanel ap)
   {
     // TODO result of automated refactoring - are all these parameters needed?
     try
@@ -4275,8 +4276,8 @@ public class Jalview2XML
           for (int s = 0; s < structureStateCount; s++)
           {
             // check to see if we haven't already created this structure view
-            final StructureState structureState = pdbid
-                    .getStructureState().get(s);
+            final StructureState structureState = pdbid.getStructureState()
+                    .get(s);
             String sviewid = (structureState.getViewId() == null) ? null
                     : structureState.getViewId() + uniqueSetSuffix;
             jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
@@ -4339,8 +4340,8 @@ public class Jalview2XML
             colourByViewer &= structureState.isColourByJmol();
             jmoldat.setColourByViewer(colourByViewer);
 
-            if (jmoldat.getStateData().length() < structureState
-                    .getValue()/*Content()*/.length())
+            if (jmoldat.getStateData().length() < structureState.getValue()
+                    /*Content()*/.length())
             {
               jmoldat.setStateData(structureState.getValue());// Content());
             }
@@ -4535,7 +4536,8 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
+        newFileLoc
+                .append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -4848,9 +4850,9 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, List JSEQ,
-          List hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List autoAlan)
+          List hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List autoAlan)
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
@@ -4931,9 +4933,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -5009,9 +5010,8 @@ public class Jalview2XML
     af.changeColour(cs);
     viewport.setColourAppliesToAllGroups(true);
 
-    viewport
-            .setShowSequenceFeatures(
-                    safeBoolean(view.isShowSequenceFeatures()));
+    viewport.setShowSequenceFeatures(
+            safeBoolean(view.isShowSequenceFeatures()));
 
     viewport.setCentreColumnLabels(view.isCentreColumnLabels());
     viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
@@ -5035,13 +5035,13 @@ public class Jalview2XML
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
-      String[] renderOrder = new String[jm.getFeatureSettings()
-              .getSetting().size()];
+      String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+              .size()];
       Map featureColours = new Hashtable<>();
       Map featureOrder = new Hashtable<>();
 
-      for (int fs = 0; fs < jm.getFeatureSettings()
-              .getSetting().size(); fs++)
+      for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+              .size(); fs++)
       {
         Setting setting = jm.getFeatureSettings().getSetting().get(fs);
         String featureType = setting.getType();
@@ -5053,8 +5053,8 @@ public class Jalview2XML
                 .getMatcherSet();
         if (filters != null)
         {
-          FeatureMatcherSetI filter = Jalview2XML
-                  .parseFilter(featureType, filters);
+          FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+                  filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5086,8 +5086,7 @@ public class Jalview2XML
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
           FeatureColourI gc = new FeatureColour(maxColour, minColour,
-                  maxColour,
-                  noValueColour, min, max);
+                  maxColour, noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
             gc.setAttributeName(setting.getAttributeName().toArray(
@@ -5121,8 +5120,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5595,6 +5593,7 @@ public class Jalview2XML
       }
     }
   }
+
   /**
    * 
    * @param vamsasSeq
@@ -6341,8 +6340,8 @@ public class Jalview2XML
    * @param fcol
    * @return
    */
-  public static Colour marshalColour(
-          String featureType, FeatureColourI fcol)
+  public static Colour marshalColour(String featureType,
+          FeatureColourI fcol)
   {
     Colour col = new Colour();
     if (fcol.isSimpleColour())
@@ -6403,7 +6402,7 @@ public class Jalview2XML
           boolean and)
   {
     jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-  
+
     if (filters.hasNext())
     {
       /*
@@ -6453,7 +6452,7 @@ public class Jalview2XML
       }
       result.setMatchCondition(matcherModel);
     }
-  
+
     return result;
   }
 
@@ -6464,8 +6463,7 @@ public class Jalview2XML
    * @param matcherSetModel
    * @return
    */
-  public static FeatureMatcherSetI parseFilter(
-          String featureType,
+  public static FeatureMatcherSetI parseFilter(String featureType,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
   {
     FeatureMatcherSetI result = new FeatureMatcherSet();
@@ -6480,7 +6478,7 @@ public class Jalview2XML
                       featureType, e.getMessage()));
       // return as much as was parsed up to the error
     }
-  
+
     return result;
   }
 
@@ -6495,8 +6493,7 @@ public class Jalview2XML
    * @throws IllegalStateException
    *           if AND and OR conditions are mixed
    */
-  protected static void parseFilterConditions(
-          FeatureMatcherSetI matcherSet,
+  protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
           boolean and)
   {
@@ -6518,7 +6515,7 @@ public class Jalview2XML
       else if (filterBy == FilterBy.BY_SCORE)
       {
         matchCondition = FeatureMatcher.byScore(cond, pattern);
-  
+
       }
       else if (filterBy == FilterBy.BY_ATTRIBUTE)
       {
@@ -6528,7 +6525,7 @@ public class Jalview2XML
         matchCondition = FeatureMatcher.byAttribute(cond, pattern,
                 attNames);
       }
-  
+
       /*
        * note this throws IllegalStateException if AND-ing to a 
        * previously OR-ed compound condition, or vice versa
@@ -6571,13 +6568,13 @@ public class Jalview2XML
   public static FeatureColourI parseColour(Colour colourModel)
   {
     FeatureColourI colour = null;
-  
+
     if (colourModel.getMax() != null)
     {
       Color mincol = null;
       Color maxcol = null;
       Color noValueColour = null;
-  
+
       try
       {
         mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
@@ -6586,7 +6583,7 @@ public class Jalview2XML
       {
         Cache.log.warn("Couldn't parse out graduated feature color.", e);
       }
-  
+
       NoValueColour noCol = colourModel.getNoValueColour();
       if (noCol == NoValueColour.MIN)
       {
@@ -6596,7 +6593,7 @@ public class Jalview2XML
       {
         noValueColour = maxcol;
       }
-  
+
       colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
@@ -6635,7 +6632,7 @@ public class Jalview2XML
       Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
       colour = new FeatureColour(color);
     }
-  
+
     return colour;
   }
 }
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d4fc233..286bfb2 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -268,7 +268,38 @@ public class Comparison
    */
   public static final boolean isNucleotide(SequenceI seq)
   {
-    return isNucleotide(new SequenceI[] { seq });
+    if (seq==null)
+    {
+      return false;
+    }
+    long ntCount = 0;
+    long aaCount = 0;
+
+    int len = seq.getLength();
+    for (int i = 0; i < len; i++)
+    {
+      char c = seq.getCharAt(i);
+      if (isNucleotide(c))
+      {
+        ntCount++;
+      }
+      else if (!isGap(c))
+      {
+        aaCount++;
+      }
+    }
+    /*
+     * Check for nucleotide count > 85% of total count (in a form that evades
+     * int / float conversion or divide by zero).
+     */
+    if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+    {
+      return true;
+    }
+    else
+    {
+      return false;
+    }
   }
 
   /**
@@ -285,45 +316,23 @@ public class Comparison
     {
       return false;
     }
-
-    int ntCount = 0;
-    int aaCount = 0;
+    // true if we have seen a nucleotide sequence
+    boolean na=false;
     for (SequenceI seq : seqs)
     {
       if (seq == null)
       {
         continue;
       }
+      na=true;
       // TODO could possibly make an informed guess just from the first sequence
       // to save a lengthy calculation
-      int len = seq.getLength();
-      for (int i = 0; i < len; i++)
-      {
-        char c = seq.getCharAt(i);
-        if (isNucleotide(c))
-        {
-          ntCount++;
-        }
-        else if (!isGap(c))
-        {
-          aaCount++;
-        }
+      if (seq.isProtein()) {
+        // if even one looks like protein, the alignment is protein
+        return false;
       }
     }
-
-    /*
-     * Check for nucleotide count > 85% of total count (in a form that evades
-     * int / float conversion or divide by zero).
-     */
-    if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
-
+    return na;
   }
 
   /**
diff --git a/src/jalview/util/HttpUtils.java b/src/jalview/util/HttpUtils.java
index a5a9460..74f77a2 100644
--- a/src/jalview/util/HttpUtils.java
+++ b/src/jalview/util/HttpUtils.java
@@ -64,4 +64,9 @@ public class HttpUtils
     return false;
   }
 
+  public static boolean startsWithHttpOrHttps(String file)
+  {
+    return file.startsWith("http://") || file.startsWith("https://");
+  }
+
 }
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 95e6c0d..1f45f70 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -123,6 +123,19 @@ public class FinderTest
     assertEquals(matches.get(1).getEnd(), 6);
   }
 
+  @Test(groups = "Functional")
+  public void testFind_findAll()
+  {
+    /*
+     * simple JAL-3765 test
+     * single symbol should find *all* matching symbols 
+     */
+    Finder f = new Finder(av);
+    f.findAll("M", false,false,false);
+    SearchResultsI sr = f.getSearchResults();
+    assertEquals(sr.getCount(),5);
+    
+  }
   /**
    * Test for (undocumented) find residue by position
    */
diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 6f6841d..2e646f5 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -85,15 +85,15 @@ public class ComparisonTest
     seq = new Sequence("DNA", "ACTugGCCAG");
     SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
     /*
-     * 90% DNA:
+     * 90% DNA but one protein sequence - expect false
      */
-    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] {
         new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
         new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
     /*
-     * 80% DNA:
+     * 80% DNA but one protein sequence - Expect false
      */
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq2, seq2 }));
diff --git a/utils/install4j/install4j8_template.install4j b/utils/install4j/install4j8_template.install4j
index a02cd6d..d540935 100644
--- a/utils/install4j/install4j8_template.install4j
+++ b/utils/install4j/install4j8_template.install4j
@@ -127,7 +127,7 @@
           
         
       
-      
+

Building Jalview from Source

tl;dr

Java 11 compliant JDK

All platforms

Alternative/CLI install of AdoptOpenJDK 11

MacOS

Windows

Linux

For Debian based distributions (e.g. Mint, Ubuntu, Debian)

For Debian based distributions (e.g.Â Mint, Ubuntu, Debian)

for RPM-based distributions (e.g. Fedora, CentOS, RedHat)

for RPM-based distributions (e.g.Â Fedora, CentOS, RedHat)

Downloading the Jalview source tree

What's in the source tree?

Whatâs in the source tree?

Minimal Jalview Build

Jalview in a Jar File

Distributed Jar Files

Single shadow Jar File

Building the `getdown` launcher

Running tests

Excluding some tests

Installer packaging with install4j

Gradle properties

`CHANNEL`

JALVIEW_VERSION and the RELEASE file

`install4jMediaTypes`

Enabling Code Coverage with OpenClover

Troubleshooting report generation

Setting up in Eclipse IDE

Installing Eclipse IDE

Importing Jalview as an Eclipse project

Importing an already downloaded git repo

Using Eclipse IDE to download the git repo

Additional views

Building Jalview from Source

tl;dr

Java 11 compliant JDK

All platforms

Alternative/CLI install of AdoptOpenJDK 11

MacOS

Windows

Linux

For Debian based distributions (e.g. Mint, Ubuntu, Debian)

For Debian based distributions (e.g.Â Mint, Ubuntu, Debian)

for RPM-based distributions (e.g. Fedora, CentOS, RedHat)

for RPM-based distributions (e.g.Â Fedora, CentOS, RedHat)

Downloading the Jalview source tree

What's in the source tree?

Whatâs in the source tree?

Minimal Jalview Build

Jalview in a Jar File

Distributed Jar Files

Single shadow Jar File

Building the getdown launcher

Running tests

Excluding some tests

Installer packaging with install4j

Gradle properties

CHANNEL

JALVIEW_VERSION and the RELEASE file

install4jMediaTypes

Enabling Code Coverage with OpenClover

Troubleshooting report generation

Setting up in Eclipse IDE

Installing Eclipse IDE

Importing Jalview as an Eclipse project

Importing an already downloaded git repo

Using Eclipse IDE to download the git repo

Additional views

Whatâs in the source tree?

Building the `getdown` launcher

`CHANNEL`

`install4jMediaTypes`