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
label.on_top = on top
label.include_linked_features = Include {0} features
label.include_linked_tooltip = Include visible {0} features<br>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
++
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
--import javax.swing.JOptionPane;
--
/**
* GUI related routines for associating PDB files with sequences
*
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;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
--import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
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.
import java.util.ArrayList;
import java.util.Hashtable;
--import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.event.ListSelectionEvent;
*/
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;
import java.io.InputStreamReader;
import java.net.URL;
--import javax.swing.JOptionPane;
--
public class UserQuestionnaireCheck implements Runnable
{
/**
import java.util.Vector;
import javax.swing.JLabel;
--import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTable;
import javax.swing.JTextField;
*/
package jalview.io;
--import jalview.api.AlignExportSettingI;
--import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignmentViewPanel;
--import jalview.api.FeatureSettingsModelI;
--import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
public interface AlignmentFileWriterI
*/
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;
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("<br>").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
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;
--- /dev/null
+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<String, InputType> iparams = new Hashtable<String, InputType>();
+ 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);
+ }
+
+}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
--import jalview.gui.JvOptionPane;
import jalview.io.FastaFile;
import java.io.File;
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
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;
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;
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;
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;
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
{
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")
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
{
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
- import jalview.viewmodel.AlignmentViewport;
--
import java.awt.Color;
import java.util.ArrayList;
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;
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;
git://source.jalview.org / jalview.git / commitdiff