Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950

merging refactored wsui with mchmmer to get latest service parameters goodness.

diff --cc help/help.jhm
Simple merge

diff --cc help/helpTOC.xml
Simple merge

diff --cc help/html/features/preferences.html
index 52e88db,5bca358..cbbca28
--- 1/help/html/features/preferences.html
--- 2/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@@ -62,9 -62,15 +62,11 @@@
        sequence alignments and EPS files.
      </li>
      <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
-         Preferences</a> tab contains settings affecting the export of
-       sequence alignments and EPS files.
+         Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+     </li>
+     <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
+         Preferences</a> tab allows you to configure locally installed HMMER tools.
      </li>
 -    <li>The <a href="dassettings.html"><strong>&quot;DAS
 -          Settings&quot;</strong> Preferences</a> tab allows you to select which DAS
 -      sources to use when fetching DAS Features.
 -    </li>
      <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
            Service&quot;</strong> Preferences</a> tab allows you to configure the <a
        href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>

diff --cc src/jalview/bin/Jalview.java
Simple merge

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/Preferences.java
Simple merge

diff --cc src/jalview/gui/WsJobParameters.java
Simple merge

diff --cc src/jalview/jbgui/GPreferences.java
index 6807382,a3921f6..4e909f1
--- 1/src/jalview/jbgui/GPreferences.java
--- 2/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@@ -264,8 -274,29 +274,24 @@@ public class GPreferences extends JPane
  
    protected JCheckBox sortByTree = new JCheckBox();
  
+   /*
+    * hmmer tab and components
+    */
+   protected JPanel hmmerTab;
+ 
+   protected JCheckBox hmmrTrimTermini;
+ 
+   protected AbstractButton hmmerBackgroundUniprot;
+ 
+   protected AbstractButton hmmerBackgroundAlignment;
+ 
+   protected JTextField hmmerSequenceCount;
+ 
+   protected JTextField hmmerPath;
+ 
+   protected JTextField cygwinPath;
  
    /*
 -   * DAS Settings tab
 -   */
 -  protected JPanel dasTab = new JPanel();
 -
 -  /*
     * Web Services tab
     */
    protected JPanel wsTab = new JPanel();
@@@ -321,7 -354,15 +349,9 @@@
      tabbedPane.add(initEditingTab(),
              MessageManager.getString("label.editing"));
  
+     tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+ 
      /*
 -     * See DasSourceBrowser for the real work of configuring this tab.
 -     */
 -    dasTab.setLayout(new BorderLayout());
 -    tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 -
 -    /*
       * See WsPreferences for the real work of configuring this tab.
       */
      wsTab.setLayout(new BorderLayout());

diff --cc src/jalview/ws/jws2/Jws2Client.java
Simple merge

diff --cc test/jalview/ws/gui/Jws2ParamView.java
index 80b48c3,134fbd1..b56c10c
--- 1/test/jalview/ws/gui/Jws2ParamView.java
--- 2/test/jalview/ws/gui/Jws2ParamView.java
+++ b/test/jalview/ws/gui/Jws2ParamView.java
@@@ -91,7 -93,7 +93,7 @@@ public class Jws2ParamVie
      for (Jws2Instance service : disc.getServices())
      {
        if (serviceTests.size() == 0
--              || serviceTests.contains(service.serviceType.toLowerCase()))
++              || serviceTests.contains(service.getName().toLowerCase()))
        {
          List<Preset> prl = null;
          Preset pr = null;

diff --cc test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index e8b6c2b,e8b6c2b..6698ed1
--- 1/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
--- 2/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@@ -82,10 -82,10 +82,10 @@@ public class DisorderAnnotExportImpor
        Thread.sleep(100);
      }
  
--    iupreds = new ArrayList<Jws2Instance>();
++    iupreds = new ArrayList<>();
      for (Jws2Instance svc : disc.getServices())
      {
--      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
++      if (svc.getNameURI().toLowerCase().contains("iupredws"))
        {
          iupreds.add(svc);
        }
@@@ -129,7 -129,7 +129,7 @@@
      AlignmentI orig_alig = af.getViewport().getAlignment();
      // NOTE: Consensus annotation row cannot be exported and reimported
      // faithfully - so we remove them
--    List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
++    List<AlignmentAnnotation> toremove = new ArrayList<>();
      for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
      {
        if (aa.autoCalculated)

diff --cc test/jalview/ws/jabaws/RNAStructExportImport.java
index 089c29f,089c29f..ee07335
--- 1/test/jalview/ws/jabaws/RNAStructExportImport.java
--- 2/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@@ -98,7 -98,7 +98,7 @@@ public class RNAStructExportImpor
      for (Jws2Instance svc : disc.getServices())
      {
  
--      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
++      if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
        {
          rnaalifoldws = svc;
        }
@@@ -118,7 -118,7 +118,7 @@@
      assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
  
      // remove any existing annotation
--    List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
++    List<AlignmentAnnotation> aal = new ArrayList<>();
      for (AlignmentAnnotation rna : af.getViewport().getAlignment()
              .getAlignmentAnnotation())
      {
@@@ -259,7 -259,7 +259,7 @@@
    @Test(groups = { "Network" })
    public void testRnaalifoldSettingsRecovery()
    {
--    List<Argument> opts = new ArrayList<Argument>();
++    List<Argument> opts = new ArrayList<>();
      for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
              .getArguments())
      {

diff --cc test/jalview/ws/jws2/ParameterUtilsTest.java
index 7876522,c0aa2ee..66ce169
--- 1/test/jalview/ws/jws2/ParameterUtilsTest.java
--- 2/test/jalview/ws/jws2/ParameterUtilsTest.java
+++ b/test/jalview/ws/jws2/ParameterUtilsTest.java
@@@ -62,7 -61,7 +62,7 @@@ public class ParameterUtilsTes
     * To limit tests to specify services, add them to this list; leave list empty
     * to test all
     */
--  private static List<String> serviceTests = new ArrayList<String>();
++  private static List<String> serviceTests = new ArrayList<>();
  
    private static Jws2Discoverer disc = null;
  
@@@ -129,10 -128,10 +129,10 @@@
     * @param service
     * @return
     */
 -  public boolean isForTesting(Jws2Instance service)
 +  public boolean isForTesting(UIinfo service)
    {
      return serviceTests.size() == 0
--            || serviceTests.contains(service.serviceType.toLowerCase());
++            || serviceTests.contains(service.getName().toLowerCase());
    }
  
    @Test(groups = { "Network" })