From: Jim Procter Date: Mon, 23 Jul 2018 07:56:57 +0000 (+0100) Subject: Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7692386ccfe778075dd83a753d30a7a27fe507be;p=jalview.git Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950 merging refactored wsui with mchmmer to get latest service parameters goodness. --- 7692386ccfe778075dd83a753d30a7a27fe507be diff --cc help/html/features/preferences.html index 52e88db,5bca358..cbbca28 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@@ -62,9 -62,15 +62,11 @@@ sequence alignments and EPS files.
  • The "Editing" - Preferences tab contains settings affecting the export of - sequence alignments and EPS files. + Preferences tab contains settings affecting the behaviour of alignments as you edit them. +
    • +
  • The "HMMER" + Preferences tab allows you to configure locally installed HMMER tools.
    • -
  • The "DAS - Settings" Preferences tab allows you to select which DAS - sources to use when fetching DAS Features. -
  • The "Web Service" Preferences tab allows you to configure the JABAWS diff --cc src/jalview/jbgui/GPreferences.java index 6807382,a3921f6..4e909f1 --- a/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 test/jalview/ws/gui/Jws2ParamView.java index 80b48c3,134fbd1..b56c10c --- a/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 prl = null; Preset pr = null; diff --cc test/jalview/ws/jabaws/DisorderAnnotExportImport.java index e8b6c2b,e8b6c2b..6698ed1 --- a/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(); ++ 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 toremove = new ArrayList(); ++ List toremove = new ArrayList<>(); for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) { if (aa.autoCalculated) diff --cc test/jalview/ws/jabaws/RNAStructExportImport.java index 089c29f,089c29f..ee07335 --- a/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 aal = new ArrayList(); ++ List aal = new ArrayList<>(); for (AlignmentAnnotation rna : af.getViewport().getAlignment() .getAlignmentAnnotation()) { @@@ -259,7 -259,7 +259,7 @@@ @Test(groups = { "Network" }) public void testRnaalifoldSettingsRecovery() { -- List opts = new ArrayList(); ++ List opts = new ArrayList<>(); for (Argument rg : (List) rnaalifoldws.getRunnerConfig() .getArguments()) { diff --cc test/jalview/ws/jws2/ParameterUtilsTest.java index 7876522,c0aa2ee..66ce169 --- a/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 serviceTests = new ArrayList(); ++ private static List 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" })