From: Jim Procter Date: Thu, 23 Apr 2020 17:54:49 +0000 (+0100) Subject: Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release --- 3609d4b908fa64cab35f2348401baab3347188fc diff --cc resources/lang/Messages.properties index 2647c43,a4b24ed..b18f46f --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@@ -135,9 -131,9 +135,11 @@@ action.select_highlighted_columns = Sel tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns action.deselect_all = Deselect all action.invert_selection = Invert selection +action.filter_by_evalue = Filter by E-Value +action.filter_by_score = Filter by Score action.using_jmol = Using Jmol + action.undo_changes_to_feature_settings = Undo all unapplied changes to feature settings + action.undo_changes_to_feature_settings_and_close_the_dialog = Undo all pending changes and close the feature settings dialog action.link = Link action.group_link = Group Link action.show_chain = Show Chain @@@ -1489,3 -1410,5 +1495,6 @@@ label.show_linked_features = Show {0} f label.on_top = on top label.include_linked_features = Include {0} features label.include_linked_tooltip = Include visible {0} features
converted to local sequence coordinates + label.features_not_shown = {0} feature(s) not shown + label.no_features_to_sort_by = No features to sort by ++ diff --cc src/jalview/gui/AssociatePdbFileWithSeq.java index fe0aedf,fe0aedf..20e8dfe --- a/src/jalview/gui/AssociatePdbFileWithSeq.java +++ b/src/jalview/gui/AssociatePdbFileWithSeq.java @@@ -28,8 -28,8 +28,6 @@@ import jalview.io.StructureFile import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; --import javax.swing.JOptionPane; -- /** * GUI related routines for associating PDB files with sequences * diff --cc src/jalview/gui/CalculationChooser.java index 9abef1f,336a312..f972653 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@@ -29,8 -28,7 +29,6 @@@ import jalview.api.analysis.SimilarityP import jalview.bin.Cache; import jalview.datamodel.SequenceGroup; import jalview.util.MessageManager; - import jalview.viewmodel.AlignmentViewport; -- import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; diff --cc src/jalview/gui/EditNameDialog.java index 0ec4a87,0ec4a87..5045ecc --- a/src/jalview/gui/EditNameDialog.java +++ b/src/jalview/gui/EditNameDialog.java @@@ -28,7 -28,7 +28,6 @@@ import java.awt.Font import javax.swing.JButton; import javax.swing.JComponent; import javax.swing.JLabel; --import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JTextField; diff --cc src/jalview/gui/PopupMenu.java index 2034b3f,568f7f1..0fd5feb --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@@ -58,33 -81,6 +83,9 @@@ import jalview.util.StringUtils import jalview.util.UrlLink; import jalview.viewmodel.seqfeatures.FeatureRendererModel; - import java.awt.Color; - import java.awt.event.ActionEvent; - import java.awt.event.ActionListener; +import java.io.IOException; +import java.net.MalformedURLException; - import java.util.ArrayList; - import java.util.Arrays; - import java.util.BitSet; - import java.util.Collection; - import java.util.Collections; - import java.util.Hashtable; - import java.util.LinkedHashMap; - import java.util.List; - import java.util.Map; - import java.util.Objects; - import java.util.SortedMap; - import java.util.TreeMap; - import java.util.Vector; - - import javax.swing.ButtonGroup; - import javax.swing.JCheckBoxMenuItem; - import javax.swing.JColorChooser; - import javax.swing.JMenu; - import javax.swing.JMenuItem; - import javax.swing.JPopupMenu; - import javax.swing.JRadioButtonMenuItem; + /** * The popup menu that is displayed on right-click on a sequence id, or in the * sequence alignment. diff --cc src/jalview/gui/RestInputParamEditDialog.java index 8ae5408,8ae5408..50b84e7 --- a/src/jalview/gui/RestInputParamEditDialog.java +++ b/src/jalview/gui/RestInputParamEditDialog.java @@@ -30,7 -30,7 +30,6 @@@ import jalview.ws.rest.RestServiceDescr import java.util.ArrayList; import java.util.Hashtable; --import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.event.ListSelectionEvent; diff --cc src/jalview/gui/SplitFrame.java index a8a13a4,574cf04..c5a0083 --- a/src/jalview/gui/SplitFrame.java +++ b/src/jalview/gui/SplitFrame.java @@@ -20,8 -20,10 +20,11 @@@ */ package jalview.gui; +import jalview.api.AlignViewportI; + import jalview.api.AlignViewControllerGuiI; + import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; + import jalview.controller.FeatureSettingsControllerGuiI; import jalview.datamodel.AlignmentI; import jalview.jbgui.GAlignFrame; import jalview.jbgui.GSplitFrame; diff --cc src/jalview/gui/UserQuestionnaireCheck.java index ef86756,ef86756..8c3c76e --- a/src/jalview/gui/UserQuestionnaireCheck.java +++ b/src/jalview/gui/UserQuestionnaireCheck.java @@@ -26,8 -26,8 +26,6 @@@ import java.io.BufferedReader import java.io.InputStreamReader; import java.net.URL; --import javax.swing.JOptionPane; -- public class UserQuestionnaireCheck implements Runnable { /** diff --cc src/jalview/gui/WsPreferences.java index 5186a26,5186a26..0f776c6 --- a/src/jalview/gui/WsPreferences.java +++ b/src/jalview/gui/WsPreferences.java @@@ -37,7 -37,7 +37,6 @@@ import java.util.List import java.util.Vector; import javax.swing.JLabel; --import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JTable; import javax.swing.JTextField; diff --cc src/jalview/io/AlignmentFileReaderI.java index a471d9b,a471d9b..1c42896 --- a/src/jalview/io/AlignmentFileReaderI.java +++ b/src/jalview/io/AlignmentFileReaderI.java @@@ -20,8 -20,8 +20,6 @@@ */ package jalview.io; --import jalview.api.AlignExportSettingI; --import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; diff --cc src/jalview/io/AlignmentFileWriterI.java index 6af4d1e,6af4d1e..d329344 --- a/src/jalview/io/AlignmentFileWriterI.java +++ b/src/jalview/io/AlignmentFileWriterI.java @@@ -22,8 -22,8 +22,6 @@@ package jalview.io import jalview.api.AlignExportSettingI; import jalview.api.AlignmentViewPanel; --import jalview.api.FeatureSettingsModelI; --import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; public interface AlignmentFileWriterI diff --cc src/jalview/io/SequenceAnnotationReport.java index 66db038,27c1652..bf3cd45 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@@ -20,8 -20,14 +20,15 @@@ */ package jalview.io; + import java.util.Arrays; + import java.util.Collection; + import java.util.Comparator; + import java.util.LinkedHashMap; + import java.util.List; + import java.util.Map; + import jalview.api.FeatureColourI; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.GeneLociI; @@@ -377,10 -478,9 +479,10 @@@ public class SequenceAnnotationRepor if (sequence.getDescription() != null) { tmp = sequence.getDescription(); - sb.append("
").append(tmp); + sb.append(tmp); maxWidth = Math.max(maxWidth, tmp.length()); } + SequenceI ds = sequence; while (ds.getDatasetSequence() != null) { diff --cc src/jalview/jbgui/GCutAndPasteTransfer.java index 94a4677,94a4677..3dc4111 --- a/src/jalview/jbgui/GCutAndPasteTransfer.java +++ b/src/jalview/jbgui/GCutAndPasteTransfer.java @@@ -25,7 -25,7 +25,6 @@@ import jalview.util.MessageManager import java.awt.BorderLayout; import java.awt.Font; --import java.awt.Toolkit; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; diff --cc src/jalview/ws/rest/clientdefs/ShmrRestClient.java index a10931b,0000000..986d760 mode 100644,000000..100644 --- a/src/jalview/ws/rest/clientdefs/ShmrRestClient.java +++ b/src/jalview/ws/rest/clientdefs/ShmrRestClient.java @@@ -1,58 -1,0 +1,54 @@@ +package jalview.ws.rest.clientdefs; + +import jalview.io.packed.DataProvider.JvDataType; +import jalview.util.MessageManager; +import jalview.ws.rest.InputType; +import jalview.ws.rest.RestClient; +import jalview.ws.rest.RestServiceDescription; - import jalview.ws.rest.params.Alignment; - import jalview.ws.rest.params.JobConstant; - import jalview.ws.rest.params.SeqGroupIndexVector; - +import java.util.Hashtable; + +public class ShmrRestClient +{ + + public static RestClient makeShmmrRestClient() + { + String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager + .getString("label.multiharmony"); + Hashtable iparams = new Hashtable(); + jalview.ws.rest.params.JobConstant toolp; + // toolp = new jalview.ws.rest.JobConstant("tool","jalview"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr"); + // iparams.put(toolp.token, toolp); + // toolp = new + // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("start_search","1"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("blast","0"); + // iparams.put(toolp.token, toolp); + + jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment(); + // SHMR server has a 65K limit for content pasted into the 'ali' parameter, + // so we always upload our files. + aliinput.token = "ali_file"; + aliinput.writeAsFile = true; + iparams.put(aliinput.token, aliinput); + jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector(); + sgroups.setMinsize(2); + sgroups.min = 2;// need at least two group defined to make a partition + iparams.put("groups", sgroups); + sgroups.token = "groups"; + sgroups.sep = " "; + RestServiceDescription shmrService = new RestServiceDescription( + action, + description, + name, + "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1", + "?tool=jalview", iparams, true, false, '-'); + // a priori knowledge of the data returned from the service + shmrService.addResultDatatype(JvDataType.ANNOTATION); + return new RestClient(shmrService); + } + +} diff --cc test/jalview/analysis/AlignmentGenerator.java index 9d3877c,9d3877c..4974a88 --- a/test/jalview/analysis/AlignmentGenerator.java +++ b/test/jalview/analysis/AlignmentGenerator.java @@@ -24,7 -24,7 +24,6 @@@ import jalview.datamodel.Alignment import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; --import jalview.gui.JvOptionPane; import jalview.io.FastaFile; import java.io.File; @@@ -33,8 -33,8 +32,6 @@@ import java.io.PrintStream import java.util.Arrays; import java.util.Random; --import org.testng.annotations.BeforeClass; -- /** * Generates, and outputs in Fasta format, a random peptide or nucleotide alignment for given * sequence length and count. Will regenerate the same alignment each time if diff --cc test/jalview/analysis/AlignmentUtilsTests.java index 128bc5c,128bc5c..a28efdf --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@@ -27,7 -27,7 +27,6 @@@ import static org.testng.AssertJUnit.as import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; --import jalview.analysis.AlignmentUtils.DnaVariant; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@@ -41,7 -41,7 +40,6 @@@ import jalview.datamodel.SearchResultsI import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; --import jalview.datamodel.features.SequenceFeatures; import jalview.gui.JvOptionPane; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; @@@ -55,7 -55,7 +53,6 @@@ import jalview.util.MappingUtils import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; --import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.TreeMap; diff --cc test/jalview/gui/AlignViewportTest.java index 977e901,4e15dba..bd36a08 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@@ -27,7 -27,14 +27,15 @@@ import static org.testng.AssertJUnit.as import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.AlignViewportI; + import java.util.ArrayList; + import java.util.List; + + import org.testng.Assert; + import org.testng.annotations.BeforeClass; + import org.testng.annotations.BeforeMethod; + import org.testng.annotations.Test; + import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; @@@ -47,17 -54,8 +55,9 @@@ import jalview.schemes.ColourSchemeI import jalview.schemes.PIDColourScheme; import jalview.structure.StructureSelectionManager; import jalview.util.MapList; +import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; - import java.util.ArrayList; - import java.util.List; - - import org.testng.Assert; - import org.testng.annotations.BeforeClass; - import org.testng.annotations.BeforeMethod; - import org.testng.annotations.Test; - public class AlignViewportTest { diff --cc test/jalview/gui/PairwiseAlignmentPanelTest.java index 1ea0ba1,3322ee8..4457eea --- a/test/jalview/gui/PairwiseAlignmentPanelTest.java +++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java @@@ -7,14 -6,13 +7,12 @@@ import jalview.datamodel.AlignmentI import jalview.datamodel.SequenceGroup; import jalview.io.DataSourceType; import jalview.io.FileLoader; - import jalview.viewmodel.AlignmentViewport; -- import javax.swing.JTextArea; -import junit.extensions.PA; - import org.testng.annotations.Test; +import junit.extensions.PA; + public class PairwiseAlignmentPanelTest { @Test(groups = "Functional") diff --cc test/jalview/project/Jalview2xmlTests.java index 47b8aea,77dee71..8916d7a --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@@ -75,23 -90,6 +90,8 @@@ import jalview.util.matcher.Condition import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; - import java.awt.Color; - import java.io.File; - import java.io.IOException; - import java.util.ArrayList; - import java.util.HashMap; - import java.util.List; - import java.util.Map; - - import javax.swing.JInternalFrame; - - import org.testng.Assert; - import org.testng.AssertJUnit; - import org.testng.annotations.BeforeClass; - import org.testng.annotations.Test; - +import junit.extensions.PA; + @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase { diff --cc test/jalview/renderer/OverviewResColourFinderTest.java index d01e53f,1687516..e44dbe0 --- a/test/jalview/renderer/OverviewResColourFinderTest.java +++ b/test/jalview/renderer/OverviewResColourFinderTest.java @@@ -34,8 -33,7 +34,6 @@@ import jalview.gui.JvOptionPane import jalview.schemes.ColourSchemeI; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; - import jalview.viewmodel.AlignmentViewport; -- import java.awt.Color; import java.util.ArrayList; diff --cc test/jalview/renderer/ResidueColourFinderTest.java index 24f653c,81fb2c0..da50e8f --- a/test/jalview/renderer/ResidueColourFinderTest.java +++ b/test/jalview/renderer/ResidueColourFinderTest.java @@@ -31,8 -30,7 +31,6 @@@ import jalview.gui.AlignViewport import jalview.gui.JvOptionPane; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; - import jalview.viewmodel.AlignmentViewport; -- import java.awt.Color; import org.testng.annotations.BeforeClass; diff --cc test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java index f488c55,6b1fbd2..d82d847 --- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java @@@ -11,8 -10,7 +11,6 @@@ import jalview.api.FeatureColourI import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; --import jalview.gui.AlignViewport; - import jalview.gui.FeatureRenderer; import jalview.io.DataSourceType; import jalview.io.FileLoader; import jalview.schemes.FeatureColour;