X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=40448d21f0ccf25a62bd05e62fd05d9323476168;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=72e9698ce0f3791ceec89e627f39b81aeb912ecf;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 72e9698..40448d2 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -48,11 +48,11 @@ import jalview.ws.params.WsParamSetI;
 
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
- *
+ * 
  * Note: the vamsas objects referred to here are primitive versions of the
  * VAMSAS project schema elements - they are not the same and most likely never
  * will be :)
- *
+ * 
  * @author $author$
  * @version $Revision: 1.134 $
  */
@@ -60,7 +60,7 @@ public class Jalview2XML
 {
   /**
    * create/return unique hash string for sq
-   *
+   * 
    * @param sq
    * @return new or existing unique string for sq
    */
@@ -266,7 +266,7 @@ public class Jalview2XML
 
   /**
    * Writes a jalview project archive to the given Jar output stream.
-   *
+   * 
    * @param jout
    */
   public void SaveState(JarOutputStream jout)
@@ -407,7 +407,7 @@ public class Jalview2XML
   /**
    * create a JalviewModel from an algnment view and marshall it to a
    * JarOutputStream
-   *
+   * 
    * @param ap
    *          panel to create jalview model for
    * @param fileName
@@ -464,7 +464,7 @@ public class Jalview2XML
     }
 
     JSeq jseq;
-    Set<String> calcIdSet=new HashSet<String>();
+    Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
     String id = "";
@@ -2269,7 +2269,7 @@ public class Jalview2XML
         // Construct new annotation from model.
         AnnotationElement[] ae = an[i].getAnnotationElement();
         jalview.datamodel.Annotation[] anot = null;
-        java.awt.Color firstColour=null;
+        java.awt.Color firstColour = null;
         int anpos;
         if (!an[i].getScoreOnly())
         {
@@ -2297,11 +2297,10 @@ public class Jalview2XML
             // {
             // anot[ae[aa].getPosition()].displayCharacter = "";
             // }
-            anot[anpos].colour = new java.awt.Color(
-                    ae[aa].getColour());
-            if (firstColour==null)
+            anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+            if (firstColour == null)
             {
-              firstColour=anot[anpos].colour;
+              firstColour = anot[anpos].colour;
             }
           }
         }
@@ -2318,7 +2317,7 @@ public class Jalview2XML
                   an[i].getGraphType());
 
           jaa.graphGroup = an[i].getGraphGroup();
-          jaa._linecolour=firstColour;
+          jaa._linecolour = firstColour;
           if (an[i].getThresholdLine() != null)
           {
             jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
@@ -2338,7 +2337,7 @@ public class Jalview2XML
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
-          jaa._linecolour=firstColour;
+          jaa._linecolour = firstColour;
         }
         // register new annotation
         if (an[i].getId() != null)
@@ -3306,7 +3305,7 @@ public class Jalview2XML
     if (view.hasNormaliseSequenceLogo())
     {
       af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
-    } 
+    }
     if (view.hasShowDbRefTooltip())
     {
       af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
@@ -3535,7 +3534,7 @@ public class Jalview2XML
 
   /**
    * TODO remove this method
-   *
+   * 
    * @param view
    * @return AlignFrame bound to sequenceSetId from view, if one exists. private
    *         AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
@@ -3546,7 +3545,7 @@ public class Jalview2XML
 
   /**
    * Check if the Jalview view contained in object should be skipped or not.
-   *
+   * 
    * @param object
    * @return true if view's sequenceSetId is a key in skipList
    */
@@ -3619,7 +3618,7 @@ public class Jalview2XML
   }
 
   /**
-   *
+   * 
    * @param vamsasSeq
    *          sequence definition to create/merge dataset sequence for
    * @param ds
@@ -3743,7 +3742,7 @@ public class Jalview2XML
 
   /**
    * make a new dataset ID for this jalview dataset alignment
-   *
+   * 
    * @param dataset
    * @return
    */
@@ -3930,7 +3929,7 @@ public class Jalview2XML
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see java.lang.Object#finalize()
    */
   @Override
@@ -4008,13 +4007,13 @@ public class Jalview2XML
    * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
    * object goes out of scope. - also populates the datasetIds hashtable with
    * alignment objects containing dataset sequences
-   *
+   * 
    * @param vobj2jv
    *          Map from ID strings to jalview datamodel
    * @param jv2vobj
    *          Map from jalview datamodel to ID strings
-   *
-   *
+   * 
+   * 
    */
   public void setObjectMappingTables(Hashtable vobj2jv,
           IdentityHashMap jv2vobj)
@@ -4086,7 +4085,7 @@ public class Jalview2XML
    * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
    * objects created from the project archive. If string is null (default for
    * construction) then suffix will be set automatically.
-   *
+   * 
    * @param string
    */
   public void setUniqueSetSuffix(String string)
@@ -4098,7 +4097,7 @@ public class Jalview2XML
   /**
    * uses skipList2 as the skipList for skipping views on sequence sets
    * associated with keys in the skipList
-   *
+   * 
    * @param skipList2
    */
   public void setSkipList(Hashtable skipList2)