Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 763b10b..966e952 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -29,15 +29,17 @@ 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.FileLoader;
-import jalview.io.FormatAdapter;
 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;
@@ -51,6 +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;
@@ -355,7 +358,9 @@ public class Jalview
       BioJsHTMLOutput.updateBioJS();
     }
 
-    String file = null, protocol = null, format = null, data = null;
+    String file = null, data = null;
+    FileFormatI format = null;
+    DataSourceType protocol = null;
     FileLoader fileLoader = new FileLoader(!headless);
     Vector<String> getFeatures = null; // vector of das source nicknames to
                                        // fetch
@@ -388,13 +393,13 @@ public class Jalview
       {
         try
         {
-          String viprotocol = AppletFormatAdapter
+          DataSourceType viprotocol = AppletFormatAdapter
                   .checkProtocol(vamsasImport);
-          if (viprotocol == jalview.io.FormatAdapter.FILE)
+          if (viprotocol == DataSourceType.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
           }
-          else if (viprotocol == FormatAdapter.URL)
+          else if (viprotocol == DataSourceType.URL)
           {
             inSession = desktop.vamsasImport(new URL(vamsasImport));
           }
@@ -483,7 +488,13 @@ public class Jalview
 
       protocol = AppletFormatAdapter.checkProtocol(file);
 
-      format = new IdentifyFile().identify(file, protocol);
+      try
+      {
+        format = new IdentifyFile().identify(file, protocol);
+      } catch (FileFormatException e1)
+      {
+        // TODO ?
+      }
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
@@ -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!");
@@ -628,17 +633,17 @@ public class Jalview
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
-          format = aparser.nextValue();
+          String outputFormat = aparser.nextValue();
           file = aparser.nextValue();
 
-          if (format.equalsIgnoreCase("png"))
+          if (outputFormat.equalsIgnoreCase("png"))
           {
             af.createPNG(new File(file));
             imageName = (new File(file)).getName();
             System.out.println("Creating PNG image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("svg"))
+          else if (outputFormat.equalsIgnoreCase("svg"))
           {
             File imageFile = new File(file);
             imageName = imageFile.getName();
@@ -646,21 +651,44 @@ public class Jalview
             System.out.println("Creating SVG image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("html"))
+          else if (outputFormat.equalsIgnoreCase("html"))
           {
             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 (format.equalsIgnoreCase("imgMap"))
+          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);
             System.out.println("Creating image map: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("eps"))
+          else if (outputFormat.equalsIgnoreCase("eps"))
           {
             File outputFile = new File(file);
             System.out.println("Creating EPS file: "
@@ -709,20 +737,26 @@ public class Jalview
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = "File";
+      protocol = DataSourceType.FILE;
 
       if (file.indexOf("http:") > -1)
       {
-        protocol = "URL";
+        protocol = DataSourceType.URL;
       }
 
       if (file.endsWith(".jar"))
       {
-        format = "Jalview";
+        format = FileFormat.Jalview;
       }
       else
       {
-        format = new IdentifyFile().identify(file, protocol);
+        try
+        {
+          format = new IdentifyFile().identify(file, protocol);
+        } catch (FileFormatException e)
+        {
+          // TODO what?
+        }
       }
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -789,6 +823,7 @@ 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"