comand line support for svg generation

Release_2_8_2_Branch only for JAL-1469 -removed changes to BioJS importer
code

Conflicts:
	.classpath
	src/jalview/io/HtmlFile.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 046d132..184c267 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,8 +20,11 @@
  */
 package jalview.bin;
 
-import java.awt.FlowLayout;
-import java.awt.Frame;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.BufferedReader;
@@ -39,13 +42,11 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
 
-import javax.swing.*;
-
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
+import javax.swing.UIManager;
 
 /**
  * Main class for Jalview Application <br>
@@ -451,6 +452,7 @@ public class Jalview
         {
           FeatureFetcher ff = startFeatureFetching(getFeatures);
           if (ff != null)
+          {
             while (!ff.allFinished() || af.operationInProgress())
             {
               // wait around until fetching is finished.
@@ -462,6 +464,7 @@ public class Jalview
 
               }
             }
+          }
           getFeatures = null; // have retrieved features - forget them now.
         }
         if (groovyscript != null)
@@ -495,6 +498,14 @@ public class Jalview
             System.out.println("Creating PNG image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("svg"))
+          {
+            File imageFile = new java.io.File(file);
+            imageName = imageFile.getName();
+            af.createSVG(imageFile);
+            System.out.println("Creating SVG image: " + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new java.io.File(file), imageName);