Merge branch 'develop' into features/filetypeEnum

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3294c26..1ab837f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -28,8 +28,11 @@ 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;
@@ -344,7 +347,9 @@ 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
@@ -377,13 +382,13 @@ 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));
           }
@@ -472,7 +477,13 @@ 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);
@@ -617,17 +628,17 @@ 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();
@@ -635,7 +646,7 @@ 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();
@@ -643,13 +654,13 @@ public class Jalview
             System.out.println("Creating HTML image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("imgMap"))
+          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: "
@@ -698,20 +709,26 @@ 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,