JAL-3416 Use JalviewInternalFrame instead of new JInternalFrame

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 5365dfa..6119db2 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -20,6 +20,17 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
 import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
@@ -36,18 +47,6 @@ import jalview.io.vamsas.Rangetype;
 import jalview.project.Jalview2XML;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
 import uk.ac.vamsas.client.IClientAppdata;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.Vobject;
@@ -506,8 +505,8 @@ public class VamsasAppDatastore
       }
       // ////////////////////////////////////////////
       // SAVE Alignment Sequence Features
-      for (int i = 0, iSize = alignment
-              .getAlignmentSequenceCount(); i < iSize; i++)
+      for (int i = 0,
+              iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
       {
         AlignmentSequence valseq;
         SequenceI alseq = (SequenceI) getvObj2jv(
@@ -1427,7 +1426,7 @@ public class VamsasAppDatastore
       String seqsetidobj = av.getSequenceSetId();
       views = Desktop.getViewports(seqsetidobj);
       Console.debug("Found " + (views == null ? " no " : "" + views.length)
-                      + " views for '" + av.getSequenceSetId() + "'");
+              + " views for '" + av.getSequenceSetId() + "'");
       if (views.length > 1)
       {
         // we need to close the original document view.
@@ -1687,7 +1686,7 @@ public class VamsasAppDatastore
                                 + ((Vobject) dataset
                                         .getDataSetAnnotations(dsa)
                                         .getSeqRef(0)).getVorbaId()
-                                                .getId());
+                                        .getId());
               }
               else
               {
@@ -1719,8 +1718,8 @@ public class VamsasAppDatastore
         {
           // LOAD ALIGNMENTS from DATASET
 
-          for (int al = 0, nal = dataset
-                  .getAlignmentCount(); al < nal; al++)
+          for (int al = 0,
+                  nal = dataset.getAlignmentCount(); al < nal; al++)
           {
             uk.ac.vamsas.objects.core.Alignment alignment = dataset
                     .getAlignment(al);
@@ -1837,8 +1836,8 @@ public class VamsasAppDatastore
             if (newasAnnots != null && newasAnnots.size() > 0)
             {
               // Add the new sequence annotations in to the alignment.
-              for (int an = 0, anSize = newasAnnots
-                      .size(); an < anSize; an++)
+              for (int an = 0,
+                      anSize = newasAnnots.size(); an < anSize; an++)
               {
                 jal.addAnnotation(
                         (AlignmentAnnotation) newasAnnots.elementAt(an));
@@ -1912,8 +1911,8 @@ public class VamsasAppDatastore
                       .getAction();
               if (alignment.getPropertyCount() > 0)
               {
-                for (int p = 0, pe = alignment
-                        .getPropertyCount(); p < pe; p++)
+                for (int p = 0,
+                        pe = alignment.getPropertyCount(); p < pe; p++)
                 {
                   if (alignment.getProperty(p).getName().equals("title"))
                   {