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[jalview.git] / src / jalview / ws / EnfinEnvision2OneWay.java
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index f40831c..6a9371b 100644 (file)
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -284,7 +284,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
    *          Object array returned from the makeUrlStubs function.
    */
   private void addshowLink(JMenu linkMenu, String label, String descr,
-          String dbname, final GroupUrlLink urlgenerator, final Object[] urlstub)
+          String dbname, final GroupUrlLink urlgenerator,
+          final Object[] urlstub)
   {
     Component[] jmi = linkMenu.getMenuComponents();
     for (int i = 0; i < jmi.length; i++)
@@ -299,17 +300,17 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
     boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
     int i = urlgenerator.getNumberInvolved(urlstub);
     JMenuItem item = new JMenuItem(label);
-    // 
-    if (dbname==null || dbname.trim().length()==0)
+    //
+    if (dbname == null || dbname.trim().length() == 0)
     {
       dbname = "";
     }
     item.setToolTipText("<html>"
-            + JvSwingUtils.wrapTooltip("Submit " + i + " " +
-                    dbname +" "
-                    + (seqsorids ? "sequence" : "sequence id") + (i > 1 ? "s" : "")
-                    
-            + " to<br/>" + descr) + "</html>");
+            + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
+                    + (seqsorids ? "sequence" : "sequence id")
+                    + (i > 1 ? "s" : "")
+
+                    + " to<br/>" + descr) + "</html>");
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -319,7 +320,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
 
           public void run()
           {
-            try {
+            try
+            {
               showLink(urlgenerator.constructFrom(urlstub));
             } catch (UrlStringTooLongException ex)
             {
@@ -404,7 +406,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
    */
   private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
   {
-    if (groupURLdescr==null || groupURLLinks==null)
+    if (groupURLdescr == null || groupURLLinks == null)
       return null;
     // TODO: usability: thread off the generation of group url content so root
     // menu appears asap
@@ -476,7 +478,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
     /**
      * last number of sequences where URL generation failed
      */
-    int[] nsqtype = new int[] { 0,0,0,0,0,0,0,0,0,0};
+    int[] nsqtype = new int[]
+    { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
     for (int i = 0; i < groupURLLinks.size(); i++)
     {
       String link = (String) groupURLLinks.elementAt(i);
@@ -527,7 +530,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
           String[] allids = ((String[]) idset[1]);
           seqstr = new String[numinput];
           ids = new String[numinput];
-          if (nsqtype[urlLink.getGroupURLType()]>0 && numinput>=nsqtype[urlLink.getGroupURLType()])
+          if (nsqtype[urlLink.getGroupURLType()] > 0
+                  && numinput >= nsqtype[urlLink.getGroupURLType()])
           {
             continue;
           }
@@ -539,8 +543,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
               seqstr[idcount++] = idandseqs[1][sq];
             }
           }
-          try {createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
-                  descr, ids, seqstr);
+          try
+          {
+            createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
+                    descr, ids, seqstr);
           } catch (UrlStringTooLongException ex)
           {
             nsqtype[urlLink.getGroupURLType()] = numinput;
@@ -550,14 +556,17 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
       // also do names only.
       seqstr = idandseqs[1];
       ids = idandseqs[0];
-      if (nsqtype[urlLink.getGroupURLType()]>0 && idandseqs[0].length>=nsqtype[urlLink.getGroupURLType()])
+      if (nsqtype[urlLink.getGroupURLType()] > 0
+              && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
       {
         continue;
       }
-      
-      try {createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
-              ids, seqstr);
-      }catch (UrlStringTooLongException ex)
+
+      try
+      {
+        createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+                ids, seqstr);
+      } catch (UrlStringTooLongException ex)
       {
         nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
       }
@@ -590,7 +599,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
           GroupUrlLink urlLink, String label, String ltarget, String descr,
           String[] ids, String[] seqstr) throws UrlStringTooLongException
   {
-    Object[] urlset= urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+    Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
             + System.currentTimeMillis(), false);
 
     if (urlset != null)
@@ -615,6 +624,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
     }
     return false;
   }
+
   // / end of stuff copied from popupmenu
   public void attachWSMenuEntry(final JMenu wsmenu,
           final AlignFrame alignFrame)
@@ -643,19 +653,22 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
       {
         if (refresh && !isRunning())
         {
-          new Thread(new Runnable() {
-            public void run() {
-          try
-          {
-            buildGroupLinkMenu(enfinServiceMenu, alignFrame);
-          } catch (OutOfMemoryError ex)
+          new Thread(new Runnable()
           {
-            Cache.log.error(
-                    "Out of memory when calculating the Envision2 links.",
-                    ex);
-            enfinServiceMenu.setEnabled(false);
-          }
-            }}).start();
+            public void run()
+            {
+              try
+              {
+                buildGroupLinkMenu(enfinServiceMenu, alignFrame);
+              } catch (OutOfMemoryError ex)
+              {
+                Cache.log
+                        .error("Out of memory when calculating the Envision2 links.",
+                                ex);
+                enfinServiceMenu.setEnabled(false);
+              }
+            }
+          }).start();
           refresh = false;
         }
       }