JAL-1632 similarity options on TreeChooser panel affect tree by PID

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cd4d138..954bb34 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 
+import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
@@ -36,9 +37,9 @@ 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.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -52,6 +53,7 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.security.AllPermission;
 import java.security.CodeSource;
@@ -291,6 +293,15 @@ public class Jalview
       }
     }
 
+    /*
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
+     */
+    if (Cache.getDefault("USE_FULL_SO", false))
+    {
+      SequenceOntologyFactory.setInstance(new SequenceOntology());
+    }
+
     if (!headless)
     {
       desktop = new Desktop();
@@ -331,7 +342,6 @@ public class Jalview
             Cache.log.debug("Starting questionnaire with default url: "
                     + defurl);
             desktop.checkForQuestionnaire(defurl);
-
           }
         }
       }
@@ -339,11 +349,12 @@ public class Jalview
       {
         System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
-      desktop.checkForNews();
-    }
 
-    if (!isHeadlessMode())
-    {
+      if (!aparser.contains("nonews"))
+      {
+        desktop.checkForNews();
+      }
+
       BioJsHTMLOutput.updateBioJS();
     }
 
@@ -499,16 +510,10 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(af
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
                   .getViewport().getAlignment(), data);
 
-          if (cs == null)
-          {
-            UserColourScheme ucs = new UserColourScheme("white");
-            ucs.parseAppletParameter(data);
-            cs = ucs;
-          }
-          else
+          if (cs != null)
           {
             System.out.println("CMD [-color " + data
                     + "] executed successfully!");
@@ -573,18 +578,14 @@ public class Jalview
         data = aparser.getValue("tree", true);
         if (data != null)
         {
-          jalview.io.NewickFile fin = null;
           try
           {
             System.out.println("CMD [-tree " + data
                     + "] executed successfully!");
-            fin = new NewickFile(data,
+            NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
-            if (fin != null)
-            {
-              af.getViewport().setCurrentTree(
-                      af.ShowNewickTree(fin, data).getTree());
-            }
+            af.getViewport().setCurrentTree(
+                    af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
             System.err.println("Couldn't add tree " + data);
@@ -650,10 +651,33 @@ public class Jalview
           {
             File imageFile = new File(file);
             imageName = imageFile.getName();
-            new HtmlSvgOutput(new File(file), af.alignPanel);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(file);
+
             System.out.println("Creating HTML image: " + file);
             continue;
           }
+          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+          {
+            if (file == null)
+            {
+              System.err.println("The output html file must not be null");
+              return;
+            }
+            try
+            {
+              BioJsHTMLOutput
+                      .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(file);
+            System.out.println("Creating BioJS MSA Viwer HTML file: "
+                    + file);
+            continue;
+          }
           else if (outputFormat.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new File(file), imageName);
@@ -795,10 +819,12 @@ public class Jalview
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
                     + "-html FILE\tCreate HTML file from alignment.\n"
+                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
                     + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                     + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                     + "-noquestionnaire\tTurn off questionnaire check.\n"
+                    + "-nonews\tTurn off check for Jalview news.\n"
                     + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                     + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                     // +