comand line support for svg generation

diff --git a/.classpath b/.classpath
index 801980d..26cfdb0 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -55,5 +55,6 @@
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin17"/>
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

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);

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 77da038..3cb7c3f 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -70,10 +70,13 @@ public class HtmlFile extends AlignFile
         JSONObject sequence = sequenceIter.next();
         String sequcenceString = sequence.get("seq").toString();
         Sequence seq = new Sequence(sequence.get("name").toString(),
-                sequcenceString, 0, sequcenceString.length());
+                sequcenceString, Integer.valueOf(sequence.get("start")
+                        .toString()), Integer.valueOf(sequence.get("end")
+                        .toString()));
 
         JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
-        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
+        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
+                jsonSeqArray, seq);
         if (retrievedSeqFeatures != null)
         {
           seq.setSequenceFeatures(retrievedSeqFeatures);
@@ -88,7 +91,7 @@ public class HtmlFile extends AlignFile
   }
 
   public SequenceFeature[] getJalviewSequenceFeatures(
-          JSONArray jsonSeqFeatures)
+          JSONArray jsonSeqFeatures, Sequence seq)
   {
     SequenceFeature[] seqFeatures = null;
     int count = 0;
@@ -105,11 +108,10 @@ public class HtmlFile extends AlignFile
         Long begin = (Long) jsonFeature.get("xStart");
         Long end = (Long) jsonFeature.get("xEnd");
         String type = (String) jsonFeature.get("text");
-
         // String color = (String) jsonFeature.get("fillColor");
 
-        sequenceFeature.setBegin(begin.intValue());
-        sequenceFeature.setEnd(end.intValue());
+        sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
+        sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
         sequenceFeature.setType(type);
         seqFeatures[count++] = sequenceFeature;
       }