X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=53d5b4aaec081ad411fa5e7e31f3873b92a39175;hb=a69b975b0f7ba9d1004f9c7769ba6acc4140d074;hp=890551523db11da2f3769673a4eadb1ffcef6c4e;hpb=784398bbc60a0e6ae55c6cde1b4f5b1b6f4a5592;p=jalview.git

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 8905515..53d5b4a 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.ws;
 
@@ -11,6 +25,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.util.GroupUrlLink;
 
+import java.awt.Component;
 import java.awt.Cursor;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -36,89 +51,130 @@ import org.xml.sax.helpers.DefaultHandler;
 
 /**
  * Lightweight runnable to discover dynamic 'one way' group URL services
+ * 
  * @author JimP
- *
+ * 
  */
-public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSMenuEntryProviderI 
+public class EnfinEnvision2OneWay extends DefaultHandler implements
+        Runnable, WSMenuEntryProviderI
 {
-  private static EnfinEnvision2OneWay groupURLLinksGatherer=null;
-  public static EnfinEnvision2OneWay getInstance() {
-    if (groupURLLinksGatherer==null) {
+  private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
+
+  public static EnfinEnvision2OneWay getInstance()
+  {
+    if (groupURLLinksGatherer == null)
+    {
       groupURLLinksGatherer = new EnfinEnvision2OneWay();
     }
     return groupURLLinksGatherer;
   }
-  private void waitForCompletion() {
+
+  private void waitForCompletion()
+  {
     if (groupURLLinksGatherer.isRunning())
     {
-    // wait around and show a visual delay indicator  
-    Cursor oldCursor = Desktop.instance.getCursor();
-    Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
-    while (groupURLLinksGatherer.isRunning())
-    {
-      try {
-        Thread.sleep(100);
-      } catch (InterruptedException e ){};
+      // wait around and show a visual delay indicator
+      Cursor oldCursor = Desktop.instance.getCursor();
+      Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+      while (groupURLLinksGatherer.isRunning())
+      {
+        try
+        {
+          Thread.sleep(100);
+        } catch (InterruptedException e)
+        {
+        }
+        ;
+      }
+      Desktop.instance.setCursor(oldCursor);
     }
-    Desktop.instance.setCursor(oldCursor);
-    } 
   }
-  public Vector getEnvisionServiceGroupURLS() {
+
+  public Vector getEnvisionServiceGroupURLS()
+  {
     waitForCompletion();
     return groupURLLinks;
   }
+
   /**
-   * indicate if 
+   * indicate if
    */
-  private static String BACKGROUND="BACKGROUNDPARAM";
+  private static String BACKGROUND = "BACKGROUNDPARAM";
+
   /**
-   * contains null strings or one of the above constants - indicate if this URL is a special case.
+   * contains null strings or one of the above constants - indicate if this URL
+   * is a special case.
    */
   private Vector additionalPar = new Vector();
+
   /**
    * the enfin service URL
    */
-  private String enfinService=null;
-  private String description=null;
+  private String enfinService = null;
+
+  private String description = null;
+
   private String wfname;
-  /* (non-Javadoc)
-   * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
+   * java.lang.String, java.lang.String)
    */
   public void endElement(String uri, String localName, String qName)
           throws SAXException
   {
-    
-//  System.err.println("End element: : '"+uri+" "+localName+" "+qName);
-    if (qName.equalsIgnoreCase("workflow") && description!=null && description.length()>0)
+
+    // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
+    if (qName.equalsIgnoreCase("workflow") && description != null
+            && description.length() > 0)
     {
-      //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
-      //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-      System.err.println("Adding entry for "+wfname+" "+description);
-      if (wfname.toLowerCase().indexOf("funcnet")==-1)
+      // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+      // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+      System.err.println("Adding entry for " + wfname + " " + description);
+      if (wfname.toLowerCase().indexOf("funcnet") == -1)
       {
         groupURLdescr.addElement(description);
         groupURLdescr.addElement(description);
-        groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
-        groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
+        groupURLLinks
+                .addElement(wfname
+                        + "|"
+                        + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
+                        + wfname
+                        + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
+        groupURLLinks
+                .addElement(wfname
+                        + "|"
+                        + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
+                        + wfname
+                        + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
       }
     }
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
    */
   public void characters(char[] ch, int start, int length)
           throws SAXException
   {
-    if (description!=null) {
-      for (int i=start; i<start+length; i++) {
-      description+=ch[i];
+    if (description != null)
+    {
+      for (int i = start; i < start + length; i++)
+      {
+        description += ch[i];
       }
     }
   }
 
-  /* (non-Javadoc)
-   * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
+   * java.lang.String, java.lang.String, org.xml.sax.Attributes)
    */
   public void startElement(String uri, String localName, String qName,
           Attributes attributes) throws SAXException
@@ -131,24 +187,30 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
     if (qName.equalsIgnoreCase("description"))
     {
       description = "";
-    } 
-    
-    
-    //System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
+    }
+
+    // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
     // super.startElement(uri,localName,qname,attributes);
   }
 
-  private boolean started=false;
-  private boolean running=false;
+  private boolean started = false;
+
+  private boolean running = false;
+
   private Vector groupURLLinks = null;
+
   private Vector groupURLdescr = null;
-  private static String[] allowedDb=new String[] {"UNIPROT","EMBL","PDB"} ;
-  
-  public EnfinEnvision2OneWay() {
+
+  private static String[] allowedDb = new String[]
+  { "UNIPROT", "EMBL", "PDB" };
+
+  public EnfinEnvision2OneWay()
+  {
     groupURLLinks = new Vector();
     groupURLdescr = new Vector();
-    
-    enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE", "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
+
+    enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
+            "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
     new Thread(this).start();
   }
 
@@ -156,17 +218,17 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
   {
     started = true;
     running = true;
-    try {
+    try
+    {
       SAXParserFactory spf = SAXParserFactory.newInstance();
       SAXParser sp = spf.newSAXParser();
-      sp.parse(new URL(enfinService).openStream(), this);      
+      sp.parse(new URL(enfinService).openStream(), this);
     } catch (Exception e)
     {
-      Cache.log.warn("Exception when discovering One Way services: ",e);      
-    }
-    catch (Error e)
+      Cache.log.warn("Exception when discovering One Way services: ", e);
+    } catch (Error e)
     {
-      Cache.log.warn("Error when discovering One Way services: ",e);
+      Cache.log.warn("Error when discovering One Way services: ", e);
     }
     running = false;
     Cache.log.debug("Finished running.");
@@ -174,42 +236,67 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
 
   /**
    * have we finished running yet ?
+   * 
    * @return false if we have been run.
    */
   public boolean isRunning()
   {
-    
+
     // TODO Auto-generated method stub
     return !started || running;
   }
-  public static void main(String[] args){
+
+  public static void main(String[] args)
+  {
     Cache.initLogger();
     EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
     while (ow.isRunning())
     {
-      try {
+      try
+      {
         Thread.sleep(50);
-      } catch (Exception e){};
-     
+      } catch (Exception e)
+      {
+      }
+      ;
+
     }
-    for (int i=0;i<ow.groupURLLinks.size();i++) {
-      System.err.println("Description"+ow.groupURLdescr.elementAt(i)+"Service URL: "+ow.groupURLLinks.elementAt(i));
+    for (int i = 0; i < ow.groupURLLinks.size(); i++)
+    {
+      System.err.println("Description" + ow.groupURLdescr.elementAt(i)
+              + "Service URL: " + ow.groupURLLinks.elementAt(i));
     }
   }
-  /// Copied from jalview.gui.PopupMenu
+
+  // / Copied from jalview.gui.PopupMenu
   /**
    * add a late bound URL service item to the given menu
    * 
    * @param linkMenu
-   * @param label -
-   *                menu label string
-   * @param urlgenerator GroupURLLink used to generate URL  
-   * @param urlstub Object array returned from the makeUrlStubs function.
+   * @param label
+   *          - menu label string
+   * @param urlgenerator
+   *          GroupURLLink used to generate URL
+   * @param urlstub
+   *          Object array returned from the makeUrlStubs function.
    */
-  private void addshowLink(JMenu linkMenu, String label, String descr, final GroupUrlLink urlgenerator, final Object[] urlstub)
+  private void addshowLink(JMenu linkMenu, String label, String descr,
+          final GroupUrlLink urlgenerator, final Object[] urlstub)
   {
+    Component[] jmi = linkMenu.getMenuComponents();
+    for (int i = 0; i < jmi.length; i++)
+    {
+      if (jmi[i] instanceof JMenuItem
+              && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
+      {
+        // don't add this - its a repeat of an existing URL.
+        return;
+      }
+    }
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText("Submit ("+urlgenerator.getNumberInvolved(urlstub)+" seqs) to workflow: "+descr);
+    item.setToolTipText("Submit ("
+            + urlgenerator.getNumberInvolved(urlstub)
+            + " seqs) to workflow: " + descr);
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -231,6 +318,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
 
   /**
    * open the given link in a new browser window
+   * 
    * @param url
    */
   public void showLink(String url)
@@ -250,8 +338,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
       ex.printStackTrace();
     }
   }
+
   /**
    * called by a web service menu instance when it is opened.
+   * 
    * @param enfinServiceMenu
    * @param alignFrame
    */
@@ -260,27 +350,31 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
   {
     SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
     SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
-    if (sg==null) {
+    if (sg == null)
+    {
       // consider visible regions here/
     }
     enfinServiceMenu.removeAll();
-    JMenu entries = buildGroupURLMenu(seqs,sg);
-    if (entries!=null)
+    JMenu entries = buildGroupURLMenu(seqs, sg);
+    if (entries != null)
     {
-      for (int i=0,iSize=entries.getMenuComponentCount();i<iSize;i++)
+      for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
       {
         // transfer - menu component is removed from entries automatically
         enfinServiceMenu.add(entries.getMenuComponent(0));
       }
       // entries.removeAll();
       enfinServiceMenu.setEnabled(true);
-    } else {
+    }
+    else
+    {
       enfinServiceMenu.setEnabled(false);
     }
   }
 
   /**
    * construct a dynamic enfin services menu given a sequence selection
+   * 
    * @param seqs
    * @param sg
    * @param groupLinks
@@ -288,183 +382,218 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
    */
   private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
   {
-    
-    // TODO: usability: thread off the generation of group url content so root menu appears asap
+
+    // TODO: usability: thread off the generation of group url content so root
+    // menu appears asap
     // sequence only URLs
     // ID/regex match URLs
     JMenu groupLinksMenu = new JMenu("Group Link");
-    JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
+    JMenu[] linkMenus = new JMenu[]
+    { null, new JMenu("IDS"), new JMenu("Sequences"),
+        new JMenu("IDS and Sequences") }; // three types of url that might be
+                                          // created.
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
     Hashtable commonDbrefs = new Hashtable();
-    for (int sq = 0; sq<seqs.length;sq++) {
+    for (int sq = 0; sq < seqs.length; sq++)
+    {
 
-      int start,end;
-      if (sg!=null) {
+      int start, end;
+      if (sg != null)
+      {
         start = seqs[sq].findPosition(sg.getStartRes());
-        end=seqs[sq].findPosition(sg.getEndRes()); 
-      } else {
+        end = seqs[sq].findPosition(sg.getEndRes());
+      }
+      else
+      {
         // get total width of alignment.
         start = seqs[sq].getStart();
         end = seqs[sq].findPosition(seqs[sq].getLength());
       }
-      // we skip sequences which do not have any non-gaps in the region of interest
-      if (start>end)
+      // we skip sequences which do not have any non-gaps in the region of
+      // interest
+      if (start > end)
       {
         continue;
       }
       // just collect ids from dataset sequence
-      // TODO: check if IDs collected from selecton group intersects with the current selection, too
+      // TODO: check if IDs collected from selecton group intersects with the
+      // current selection, too
       SequenceI sqi = seqs[sq];
-      while (sqi.getDatasetSequence()!=null) {
-        sqi = sqi.getDatasetSequence(); }
+      while (sqi.getDatasetSequence() != null)
+      {
+        sqi = sqi.getDatasetSequence();
+      }
       DBRefEntry[] dbr = sqi.getDBRef();
-      if (dbr!=null && dbr.length>0)
+      if (dbr != null && dbr.length > 0)
       {
-        for (int d=0;d<dbr.length;d++)
+        for (int d = 0; d < dbr.length; d++)
         {
-          String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
           Object[] sarray = (Object[]) commonDbrefs.get(src);
-          if (sarray==null)
+          if (sarray == null)
           {
             sarray = new Object[2];
-            sarray[0] = new int[] { 0 };
+            sarray[0] = new int[]
+            { 0 };
             sarray[1] = new String[seqs.length];
-            
-            commonDbrefs.put(src,sarray);
+
+            commonDbrefs.put(src, sarray);
           }
-          
-          if (((String[])sarray[1])[sq]==null) {
-            if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
-              ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
-              ((int[])sarray[0])[0]++;
+
+          if (((String[]) sarray[1])[sq] == null)
+          {
+            if (!dbr[d].hasMap()
+                    || (dbr[d].getMap().locateMappedRange(start, end) != null))
+            {
+              ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+              ((int[]) sarray[0])[0]++;
             }
           }
         }
       }
     }
     // now create group links for all distinct ID/sequence sets.
-    boolean addMenu = false; // indicates if there are any group links to give to user  
-    for (int i = 0; i < groupURLLinks.size(); i++) {
-        String link = groupURLLinks.elementAt(i).toString();
-        String descr = groupURLdescr.elementAt(i).toString();
-//        boolean specialCase = additionalPar.elementAt(i).toString().equals(BACKGROUND);
-        GroupUrlLink urlLink = null;
-        try
-        {
-          urlLink = new GroupUrlLink(link);
-        } catch (Exception foo)
-        {
-          jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
-                  + "'", foo);
-          continue;
-        }
-        ;
-        if (!urlLink.isValid())
+    boolean addMenu = false; // indicates if there are any group links to give
+                             // to user
+    for (int i = 0; i < groupURLLinks.size(); i++)
+    {
+      String link = groupURLLinks.elementAt(i).toString();
+      String descr = groupURLdescr.elementAt(i).toString();
+      // boolean specialCase =
+      // additionalPar.elementAt(i).toString().equals(BACKGROUND);
+      GroupUrlLink urlLink = null;
+      try
+      {
+        urlLink = new GroupUrlLink(link);
+      } catch (Exception foo)
+      {
+        jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+                + "'", foo);
+        continue;
+      }
+      ;
+      if (!urlLink.isValid())
+      {
+        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        continue;
+      }
+      final String label = urlLink.getLabel();
+      boolean usingNames = false;
+      // Now see which parts of the group apply for this URL
+      String ltarget;
+      String[] seqstr, ids; // input to makeUrl
+      for (int t = 0; t < allowedDb.length; t++)
+      {
+        ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+        Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+        if (idset != null)
         {
-          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
-          continue;
-        }
-        final String label = urlLink.getLabel();
-        boolean usingNames = false;
-        // Now see which parts of the group apply for this URL
-        String ltarget;
-        String[] seqstr,ids; // input to makeUrl
-        for (int t=0;t<allowedDb.length; t++) {
-          ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-          Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
-          if (idset!=null)
+          int numinput = ((int[]) idset[0])[0];
+          String[] allids = ((String[]) idset[1]);
+          seqstr = new String[numinput];
+          ids = new String[numinput];
+          for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
           {
-            int numinput = ((int[])idset[0])[0];
-            String[] allids = ((String[])idset[1]);
-            seqstr = new String[numinput];
-            ids = new String[numinput];
-            for (int sq=0,idcount=0;sq<seqs.length;sq++)
+            if (allids[sq] != null)
             {
-              if (allids[sq]!=null) {
-                ids[idcount] = allids[sq];
-                seqstr[idcount++] = idandseqs[1][sq];
-              }
+              ids[idcount] = allids[sq];
+              seqstr[idcount++] = idandseqs[1][sq];
             }
-            addMenu = addMenu | createAndAddLinks(linkMenus,false,urlLink,label,ltarget,descr, ids,seqstr);
           }
+          addMenu = addMenu
+                  | createAndAddLinks(linkMenus, false, urlLink, label,
+                          ltarget, descr, ids, seqstr);
         }
-        // also do names only.
-        seqstr = idandseqs[1];
-        ids = idandseqs[0];
-        addMenu = addMenu | createAndAddLinks(linkMenus,true,urlLink,label,"Names",descr, ids,seqstr);
       }
+      // also do names only.
+      seqstr = idandseqs[1];
+      ids = idandseqs[0];
+      addMenu = addMenu
+              | createAndAddLinks(linkMenus, true, urlLink, label, "Names",
+                      descr, ids, seqstr);
+    }
     if (addMenu)
     {
       groupLinksMenu = new JMenu("Group Links");
-      for (int m=0;m<linkMenus.length; m++)
+      for (int m = 0; m < linkMenus.length; m++)
       {
-        if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+        if (linkMenus[m] != null
+                && linkMenus[m].getMenuComponentCount() > 0)
         {
           groupLinksMenu.add(linkMenus[m]);
         }
       }
-      
+
       return groupLinksMenu;
     }
     return null;
   }
 
   private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
-          GroupUrlLink urlLink, String label, String ltarget, String descr, String[] ids,
-          String[] seqstr)
+          GroupUrlLink urlLink, String label, String ltarget, String descr,
+          String[] ids, String[] seqstr)
   {
-    Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
-    if (urlset!=null)
+    Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+            + System.currentTimeMillis(), false);
+    if (urlset != null)
     {
       int type = urlLink.getGroupURLType() & 3;
-      //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
+      // System.out.println(urlLink.getGroupURLType()
+      // +" "+((String[])urlset[3])[0]);
       // first two bits ofurlLink type bitfield are sequenceids and sequences
       // TODO: FUTURE: ensure the groupURL menu structure can be generalised
-      addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
+      addshowLink(linkMenus[type], label
+              + " "
+              + (usingNames ? (((type & 1) == 1) ? "(Names)" : "") : ("("
+                      + ltarget + ")")), descr, urlLink, urlset);
       return true;
     }
     return false;
   }
-  /// end of stuff copied from popupmenu
-  public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
+
+  // / end of stuff copied from popupmenu
+  public void attachWSMenuEntry(final JMenu wsmenu,
+          final AlignFrame alignFrame)
   {
     final JMenu enfinServiceMenu = new JMenu("Envision 2");
     wsmenu.add(enfinServiceMenu);
     enfinServiceMenu.setEnabled(false);
     wsmenu.addMenuListener(new MenuListener()
-      {
-        // this listener remembers when the menu was first selected, and
-        // doesn't rebuild the session list until it has been cleared and
-        // reselected again.
-        boolean refresh = true;
+    {
+      // this listener remembers when the menu was first selected, and
+      // doesn't rebuild the session list until it has been cleared and
+      // reselected again.
+      boolean refresh = true;
 
-        public void menuCanceled(MenuEvent e)
-        {
-          refresh = true;
-        }
+      public void menuCanceled(MenuEvent e)
+      {
+        refresh = true;
+      }
 
-        public void menuDeselected(MenuEvent e)
-        {
-          refresh = true;
-        }
+      public void menuDeselected(MenuEvent e)
+      {
+        refresh = true;
+      }
 
-        public void menuSelected(MenuEvent e)
+      public void menuSelected(MenuEvent e)
+      {
+        if (refresh)
         {
-          if (refresh)
+          try
           {
-            try {
-              buildGroupLinkMenu(enfinServiceMenu,alignFrame);
-            } catch (OutOfMemoryError ex)
-            {
-              Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
-              enfinServiceMenu.setEnabled(false);
-            }
-            refresh = false;
+            buildGroupLinkMenu(enfinServiceMenu, alignFrame);
+          } catch (OutOfMemoryError ex)
+          {
+            Cache.log.error(
+                    "Out of memory when calculating the Envision2 links.",
+                    ex);
+            enfinServiceMenu.setEnabled(false);
           }
+          refresh = false;
         }
-     });
-    
-    
+      }
+    });
+
   }
 
 }