action.by_conservation = By Conservation
action.wrap = Wrap
action.show_gaps = Show Gaps
-action.show_occupancy = Show Occupancy
action.show_hidden_markers = Show Hidden Markers
action.find = Find
action.undefine_groups = Undefine Groups
label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
+label.quality_descr = Alignment Quality based on Blosum62 scores
+label.conservation_descr = Conservation of total alignment less than {0}% gaps
+label.consensus_descr = PID
+label.complement_consensus_descr = PID for cDNA
+label.strucconsensus_descr = PID for base pairs
+label.occupancy_descr = Number of aligned positions
\ No newline at end of file
label.score_model_enhconservation = Conservación de las propiedades físico-químicas
label.status_bar = Barra de estado
label.out_to_textbox = Generar cuadro de texto
+label.occupancy = Ocupación
label.clustal = Clustal
# label.colourScheme_<schemeName> as in JalviewColourScheme
label.colourScheme_clustal = Clustalx
label.updating_vamsas_session = Actualizando sesión VAMSAS
label.loading_file = Cargando fichero: {0}
label.edit_params = Editar {0}
+label.as_percentage = Como Porcentaje
error.not_implemented = No implementado
error.no_such_method_as_clone1_for = No existe ese método como un clone1 de {0}
error.null_from_clone1 = Nulo de clone1!
final int gapped = profile.getNonGapped();
- String description = "";
+ String description = "" + gapped;
- gaprow.annotations[i] = new Annotation(description, description,
+ gaprow.annotations[i] = new Annotation("", description,
'\0', gapped, jalview.util.ColorUtils.bleachColour(
Color.DARK_GRAY, (float) scale * gapped));
}
}
populateThresholdComboBox(threshold);
-
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
// restore Object state from the previous session if one exists
- if (av.getAnnotationColumnSelectionState() != null)
+ if (lastChooser != null)
{
- currentSearchPanel = av.getAnnotationColumnSelectionState()
+ currentSearchPanel = lastChooser
.getCurrentSearchPanel();
- currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.select(av.getAnnotationColumnSelectionState()
+ annotations.select(lastChooser
.getAnnotations().getSelectedIndex());
- threshold.select(av.getAnnotationColumnSelectionState()
+ threshold.select(lastChooser
.getThreshold().getSelectedIndex());
- actionOption = av.getAnnotationColumnSelectionState()
+ actionOption = lastChooser
.getActionOption();
+ percentThreshold.setState(lastChooser.percentThreshold.getState());
}
try
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.setTitle("Threshold Filter");
- thresholdPanel.add(percentThreshold);
thresholdPanel.add(getThreshold());
thresholdPanel.add(slider);
thresholdPanel.add(thresholdValue);
+ thresholdPanel.add(percentThreshold);
actionPanel.add(ok);
actionPanel.add(cancel);
{
if (!adjusting)
{
- thresholdValue.setText((slider.getValue() / 1000f) + "");
+ setThresholdValueText();
valueChanged(!sliderDragging);
}
}
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ percentThreshold.setEnabled(true);
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
+ percentThreshold.setEnabled(false);
// build filter params
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
// slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ percentThreshold.setEnabled(true);
adjusting = false;
// build filter params
@Override
public void actionPerformed(ActionEvent evt)
{
- if (evt.getSource() == thresholdValue)
- {
- try
- {
- float f = new Float(thresholdValue.getText()).floatValue();
- slider.setValue((int) (f * 1000));
- adjustmentValueChanged(null);
- } catch (NumberFormatException ex)
- {
- }
- }
- else if (evt.getSource() == ok)
+ if (evt.getSource() == ok)
{
ok_actionPerformed(null);
}
updateView();
}
+ /**
+ * update the text field from the threshold slider. preserves state of
+ * 'adjusting' so safe to call in init.
+ */
protected void setThresholdValueText()
{
+ boolean oldadj = adjusting;
adjusting = true;
if (percentThreshold.getState())
{
double scl = slider.getMaximum() - slider.getMinimum();
scl = (slider.getValue() - slider.getMinimum()) / scl;
- thresholdValue.setText(100 * scl + "");
+ thresholdValue.setText(100f * scl + "");
}
else
{
thresholdValue.setText((slider.getValue() / 1000f) + "");
}
thresholdValue.setCaretPosition(0);
- adjusting = false;
+ adjusting = oldadj;
}
public void thresholdValue_actionPerformed(ActionEvent e)
float f = Float.parseFloat(thresholdValue.getText());
if (percentThreshold.getState())
{
- slider.setValue(slider.getMinimum()
- + ((int) ((f / 100f) * (slider.getMaximum() - slider
- .getMinimum()))));
+ int pos = slider.getMinimum()
+ + (int) ((slider.getMaximum() - slider.getMinimum()) * f / 100f);
+ slider.setValue(pos);
}
else
{
slider.setValue((int) (f * 1000));
}
- updateView();
+ valueChanged(false);
} catch (NumberFormatException ex)
{
}
/*
* update these constants when Jalview has been checked / updated for
- * changes to Ensembl REST API
+ * changes to Ensembl REST API (ref JAL-2105)
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.8";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.8";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
if (laterVersion)
{
- System.err.println(String.format(
- "Expected %s REST version %s but found %s, see %s",
- getDbSource(), expected, version, REST_CHANGE_LOG));
+ System.err
+ .println(String
+ .format("EnsemblRestClient expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version,
+ REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
protected HashSet<String> paginatorCart = new HashSet<String>();
+ private static final int MIN_WIDTH = 670;
+
+ private static final int MIN_HEIGHT = 300;
+
protected static final DecimalFormat totalNumberformatter = new DecimalFormat(
"###,###");
try
{
jbInit();
+ mainFrame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
mainFrame.addFocusListener(new FocusAdapter()
{
@Override
private JCheckBox thresholdIsMin = new JCheckBox();
+ protected static final int MIN_WIDTH = 500;
+
+ protected static final int MIN_HEIGHT = 240;
+
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.colour_by_annotation"), 520,
215);
-
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
private ColumnSelection oldColumnSelection;
+ protected int MIN_WIDTH = 420;
+
+ protected int MIN_HEIGHT = 430;
+
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.select_by_annotation"), 520,
215);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
-
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
// restore Object state from the previous session if one exists
- if (av.getAnnotationColumnSelectionState() != null)
+ if (lastChooser != null)
{
- currentSearchPanel = av.getAnnotationColumnSelectionState()
+ currentSearchPanel = lastChooser
.getCurrentSearchPanel();
- currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ annotations.setSelectedIndex(lastChooser
.getAnnotations().getSelectedIndex());
- threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ threshold.setSelectedIndex(lastChooser
.getThreshold().getSelectedIndex());
- actionOption = av.getAnnotationColumnSelectionState()
+ actionOption = lastChooser
.getActionOption();
+ percentThreshold.setSelected(lastChooser.percentThreshold
+ .isSelected());
}
try
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- if (percentThreshold.isSelected())
- {
- thresholdValue
- .setText(""
- + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
- }
- else
- {
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
- }
+ setThresholdValueText();
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
});
}
+ /**
+ * update the text field from the threshold slider. preserves state of
+ * 'adjusting' so safe to call in init.
+ */
protected void setThresholdValueText()
{
+ boolean oldadj = adjusting;
adjusting = true;
if (percentThreshold.isSelected())
{
{
thresholdValue.setText((slider.getValue() / 1000f) + "");
}
- adjusting = false;
+ adjusting = oldadj;
}
protected void addSliderMouseListeners()
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- if (percentThreshold.isEnabled())
+ if (percentThreshold.isSelected())
{
slider.setValue(slider.getMinimum()
+ ((int) ((f / 100f) * (slider.getMaximum() - slider
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
+import javax.swing.DefaultComboBoxModel;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
{
ok.setEnabled(false);
}
+ updateScoreModels(comboBox, tips);
}
/**
}
return false;
}
+
+ final JComboBox<String> comboBox = new JComboBox<String>();
+
+ final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
+
+ List<String> tips = new ArrayList<String>();
+
/**
* A rather elaborate helper method (blame Swing, not me) that builds a
* drop-down list of score models (by name) with descriptions as tooltips.
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> comboBox = new JComboBox<String>();
- ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
comboBox.setRenderer(renderer);
- final List<String> tips = new ArrayList<String>();
/*
* show tooltip on mouse over the combobox
* note the listener has to be on the components that make up
* the combobox, doesn't work if just on the combobox
*/
- MouseAdapter mouseListener = new MouseAdapter()
+ final MouseAdapter mouseListener = new MouseAdapter()
{
@Override
public void mouseEntered(MouseEvent e)
c.addMouseListener(mouseListener);
}
+ updateScoreModels(comboBox, tips);
+
+ /*
+ * set the list of tooltips on the combobox's renderer
+ */
+ renderer.setTooltips(tips);
+
+ return comboBox;
+ }
+
+ private void updateScoreModels(JComboBox comboBox, List<String> tips)
+ {
+ Object curSel = comboBox.getSelectedItem();
+ tips.clear();
+ DefaultComboBoxModel model = new DefaultComboBoxModel();
+
/*
* now we can actually add entries to the combobox,
* remembering their descriptions for tooltips
*/
ScoreModels scoreModels = ScoreModels.getInstance();
+ boolean selectedIsPresent = false;
for (ScoreModelI sm : scoreModels.getModels())
{
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
{
- comboBox.addItem(sm.getName());
+ if (curSel != null && sm.getName().equals(curSel))
+ {
+ selectedIsPresent = true;
+ curSel = sm.getName();
+ }
+ model.addElement(sm.getName());
/*
* tooltip is description if provided, else text lookup with
}
tips.add(tooltip);
}
-
- /*
- * set the list of tooltips on the combobox's renderer
- */
- renderer.setTooltips(tips);
}
-
- return comboBox;
+ if (selectedIsPresent)
+ {
+ model.setSelectedItem(curSel);
+ }
+ // finally, update the model
+ comboBox.setModel(model);
}
/**
// are we attached to some parent Desktop
Desktop parent = null;
+ private int MIN_WIDTH = 300;
+
+ private int MIN_HEIGHT = 250;
+
public Console()
{
// create all components and add them
.getLocalGraphicsEnvironment();
String[] fontNames = ge.getAvailableFontFamilyNames();
for (int n = 0; n < fontNames.length; n++)
+ {
System.out.println(fontNames[n]);
+ }
// Testing part: simple an error thrown anywhere in this JVM will be printed
// on the Console
// We do it with a seperate Thread becasue we don't wan't to break a Thread
JFrame frame = new JFrame(string);
frame.setName(string);
if (x == -1)
- x = (int) (i / 2);
+ {
+ x = i / 2;
+ }
if (y == -1)
- y = (int) (j / 2);
+ {
+ y = j / 2;
+ }
frame.setBounds(x, y, i, j);
return frame;
}
frame = initFrame("Jalview Java Console", bounds.width,
bounds.height, bounds.x, bounds.y);
}
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
// desktop.add(frame);
initConsole(false);
JalviewAppender jappender = new JalviewAppender();
// System.exit(0);
}
+ @Override
public synchronized void windowClosed(WindowEvent evt)
{
frame.setVisible(false);
}
}
+ @Override
public synchronized void windowClosing(WindowEvent evt)
{
frame.setVisible(false); // default behaviour of JFrame
// frame.dispose();
}
+ @Override
public synchronized void actionPerformed(ActionEvent evt)
{
trimBuffer(true);
// textArea.setText("");
}
+ @Override
public synchronized void run()
{
try
// lines++;
}
if (quit)
+ {
return;
+ }
}
while (Thread.currentThread() == reader2)
// lines++;
}
if (quit)
+ {
return;
+ }
}
while (Thread.currentThread() == textAppender)
{
long time = System.nanoTime();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
displayPipe.append(input); // change to stringBuffer
{
int available = in.available();
if (available == 0)
+ {
break;
+ }
byte b[] = new byte[available];
in.read(b);
input = input + new String(b, 0, b.length);
DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
+ private static int DEFAULT_MIN_WIDTH = 300;
+
+ private static int DEFAULT_MIN_HEIGHT = 250;
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
openFrameCount++;
+ frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
+ DEFAULT_MIN_HEIGHT));
frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
JPanel transPanel = new JPanel(new GridLayout(1, 2));
+ private static final int MIN_WIDTH = 400;
+
+ private static final int MIN_HEIGHT = 400;
+
public FeatureSettings(AlignFrame af)
{
this.af = af;
MessageManager.getString("label.sequence_feature_settings"),
400, 450);
}
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.Vector;
import javax.swing.JComponent;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
-import javax.swing.JOptionPane;
import javax.swing.KeyStroke;
/**
*/
public class Finder extends GFinder
{
- private static final int HEIGHT = 110;
+ private static final int HEIGHT = 120;
- private static final int WIDTH = 340;
+ private static final int WIDTH = 400;
AlignmentViewport av;
AlignmentPanel ap;
+ private static final int MIN_WIDTH = 350;
+
+ private static final int MIN_HEIGHT = 120;
+
JInternalFrame frame;
int seqIndex = 0;
addEscapeHandler();
Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
WIDTH, HEIGHT);
-
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
textfield.requestFocus();
}
import jalview.util.MessageManager;
import java.awt.Container;
+import java.awt.Dimension;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
{
frame.setSize(width, height);
}
+ int minWidth = width - 100;
+ int minHeight = height - 100;
+ frame.setMinimumSize(new Dimension(minWidth, minHeight));
frame.setContentPane(content);
this.block = block;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
PCAModel pcaModel;
+ private static final int MIN_WIDTH = 470;
+
+ private static final int MIN_HEIGHT = 250;
+
int top = 0;
/**
addKeyListener(rc);
Desktop.addInternalFrame(this, MessageManager
.getString("label.principal_component_analysis"), 475, 450);
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
}
import javax.swing.JCheckBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
{
initRNAStructure();
}
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
initGapCounts();
if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
+ MessageManager
+ .getString("label.complement_consensus_descr"),
+ new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
initConsensus(complementConsensus);
return true;
if (showOccupancy)
{
gapcounts = new AlignmentAnnotation("Occupancy",
- "Number of aligned positions", new Annotation[1], 0f,
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f,
alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
gapcounts.hasText = true;
gapcounts.autoCalculated = true;
if (conservation == null)
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps", new Annotation[1],
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()), new Annotation[1],
0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
if (quality == null)
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
+ MessageManager.getString("label.quality_descr"),
new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
{
if (alignment.hasRNAStructure() && strucConsensus == null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.ext.ensembl.EnsemblGenomes;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.uniprot.UniProtFTSRestClient;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+/**
+ * A class to verify that remotely fetched data has an expected format and can
+ * be successfully processed by Jalview. This is intended as a first line of
+ * defence and early warning of service affecting changes to data fetched
+ * externally.
+ * <p>
+ * This is class is not intended to cover remote services e.g. alignment. Nor
+ * should it duplicate tests already provided by other classes (such as
+ * PDBFTSRestClientTest). Or maybe we will relocate those tests here...
+ */
+public class RemoteFormatTest
+{
+ SequenceFetcher sf;
+
+ @BeforeTest(alwaysRun = true)
+ public void setUp() throws Exception
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ // ensure 'add annotation from structure' is selected
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+
+ sf = new SequenceFetcher(false);
+ }
+
+ @DataProvider(name = "AccessionData")
+ protected Object[][] getAccessions()
+ {
+ return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
+ { DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
+ { DBRefSource.EMBLCDS, "CAA37824" },
+ { DBRefSource.ENSEMBL, "ENSG00000157764" },
+ { new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
+ { new PfamFull().getDbSource(), "PF03760" },
+ { new PfamSeed().getDbSource(), "PF03760" },
+ { new RfamSeed().getDbSource(), "RF00014" } };
+ }
+
+ @Test(groups = "Network", dataProvider = "AccessionData")
+ public void testFetchAccession(String dbSource, String accessionId)
+ throws Exception
+ {
+ System.out.println("Fetching " + accessionId + " from " + dbSource);
+ List<DbSourceProxy> sps = sf.getSourceProxy(dbSource);
+ assertFalse(sps.isEmpty());
+ AlignmentI al = sps.get(0).getSequenceRecords(accessionId);
+ assertNotNull(al);
+ assertTrue(al.getHeight() > 0);
+ SequenceI sq = al.getSequenceAt(0);
+ // suppress this check as only Uniprot and PDB acquire PDB refs
+ // assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
+ assertTrue(sq.getDBRefs().length > 0, "No DBRef on sequence.");
+ // suppress this test as only certain databases provide 'primary' dbrefs
+ // assertFalse(sq.getPrimaryDBRefs().isEmpty());
+ int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
+ .length();
+ assertEquals(sq.getEnd() - sq.getStart() + 1, length,
+ "Sequence start/end doesn't match number of residues in sequence");
+ }
+
+ @Test(groups = { "Network" })
+ public void testUniprotFreeTextSearch() throws Exception
+ {
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ FTSRestClientI client = UniProtFTSRestClient.getInstance();
+ wantedFields.add(client.getDataColumnByNameOrCode("id"));
+ wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
+ wantedFields.add(client.getDataColumnByNameOrCode("organism"));
+ wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
+ wantedFields.add(client.getDataColumnByNameOrCode("length"));
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("Search All");
+ request.setSearchTerm("metanephrops"); // lobster!
+ request.setWantedFields(wantedFields);
+
+ FTSRestResponse response;
+ response = client.executeRequest(request);
+ assertTrue(response.getNumberOfItemsFound() > 20);
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getSearchSummary().size() > 20);
+ // verify we successfully filtered out the header row (JAL-2485)
+ FTSData header = response.getSearchSummary().iterator().next();
+ assertFalse(
+ header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"),
+ "Failed to filter out summary header row");
+ }
+}
git://source.jalview.org / jalview.git / commitdiff