<td>Default is true.</td>
</tr>
<tr>
+ <td>showOccupancy</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
<td>sortBy</td>
<td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
<td> Sorts the alignment on startup</td>
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_B outlineColour=red colour=None
PROPERTIES Group_C colour=Clustal
<p>
<em>Show Annotations</em> - If this is selected the new window will
display an annotation panel below the sequences. This annotation
- panel may have several rows describing the whole alignment. The 3
- standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- for the alignment may be shown or hidden by default using the
- checkboxes below.
+ panel may have several rows describing the whole alignment. The 4
+ standard annotations <em>Conservation</em>, <em>Quality</em>,
+ <em>Occupancy</em> and <em>Consensus</em> for the alignment may
+ be shown or hidden by default using the checkboxes adjacent and
+ below.
</p>
<p>
<em>Show group: Conservation and Consensus</em> controls the display
label.score_model_enhconservation = Physicochemical property conservation
label.status_bar = Status bar
label.out_to_textbox = Output to Textbox
+label.occupancy = Occupancy
# delete Clustal - use FileFormat name instead
label.clustal = Clustal
# label.colourScheme_<schemeName> as in JalviewColourScheme
label.updating_vamsas_session = Updating vamsas session
label.loading_file = Loading File: {0}
label.edit_params = Edit {0}
+label.as_percentage = As Percentage
error.not_implemented = Not implemented
error.no_such_method_as_clone1_for = No such method as clone1 for {0}
error.null_from_clone1 = Null from clone1!
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!
*/
package jalview.analysis;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.util.MappingUtils;
import jalview.util.QuickSort;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
/**
* Takes in a vector or array of sequences and column start and column end and
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
// always set ranges again
gaprow.graphMax = nseq;
gaprow.graphMin = 0;
+ double scale = 0.8/nseq;
for (int i = startCol; i < endCol; i++)
{
ProfileI profile = profiles.get(i);
final int gapped = profile.getNonGapped();
- String description = String.valueOf(gapped);
+ String description = "" + gapped;
- gaprow.annotations[i] = new Annotation(description, description,
- '\0',
- gapped);
+ gaprow.annotations[i] = new Annotation("", description,
+ '\0', gapped, jalview.util.ColorUtils.bleachColour(
+ Color.DARK_GRAY, (float) scale * gapped));
}
}
showConsensus = applet.getDefaultParameter("showConsensus",
showConsensus);
+ showOccupancy = applet.getDefaultParameter("showOccupancy",
+ showOccupancy);
+
setShowUnconserved(applet.getDefaultParameter("showUnconserved",
getShowUnconserved()));
}
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
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
+ thresholdValue.setCaretPosition(0);
ok.addActionListener(this);
cancel.addActionListener(this);
// thresholdPanel.setFont(JvSwingUtils.getLabelFont());
// thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ percentThreshold.setLabel("As percentage");
+ percentThreshold.addItemListener(this);
+
actionPanel.setBackground(Color.white);
// actionPanel.setFont(JvSwingUtils.getLabelFont());
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.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ setThresholdValueText();
// slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ percentThreshold.setEnabled(true);
adjusting = false;
// build filter params
{
threshold_actionPerformed(null);
}
+ else if (e.getSource() == percentThreshold)
+ {
+ if (!adjusting)
+ {
+ percentageValue_actionPerformed();
+ }
+
+ }
}
public void selectedAnnotationChanged()
@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);
}
import java.awt.Scrollbar;
import java.awt.TextField;
import java.awt.event.ActionEvent;
-import java.util.Vector;
@SuppressWarnings("serial")
public abstract class AnnotationRowFilter extends Panel
protected Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+ protected Checkbox percentThreshold = new Checkbox();
+
protected TextField thresholdValue = new TextField(20);
protected Frame frame;
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(100f * scl + "");
+ }
+ else
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ }
+ thresholdValue.setCaretPosition(0);
+ adjusting = oldadj;
+ }
+
public void thresholdValue_actionPerformed(ActionEvent e)
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- updateView();
+ if (percentThreshold.getState())
+ {
+ int pos = slider.getMinimum()
+ + (int) ((slider.getMaximum() - slider.getMinimum()) * f / 100f);
+ slider.setValue(pos);
+ }
+ else
+ {
+ slider.setValue((int) (f * 1000));
+ }
+ valueChanged(false);
} catch (NumberFormatException ex)
{
}
}
+ protected void percentageValue_actionPerformed()
+ {
+ setThresholdValueText();
+ }
+
protected void populateThresholdComboBox(Choice threshold)
{
threshold.addItem(MessageManager
return aa;
}
- /**
- * Returns an iterable collection of any annotations that match on given
- * sequence ref, calcId and label (ignoring null values).
- */
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
- && ann.sequenceRef != null && ann.sequenceRef == seq
- && ann.label != null && ann.label.equals(label))
+ if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+ .equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+ && (label == null || (ann.label != null && ann.label
+ .equals(label))))
{
aa.add(ann);
}
if (start < fwidth)
{
viscontigs[nvis] = start;
- viscontigs[nvis + 1] = fwidth; // end is inclusive
+ viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
nvis += 2;
}
return viscontigs;
}
else
{
- return new int[] { 0, width };
+ return new int[] { 0, width - 1 };
}
}
*/
Iterable<AlignmentAnnotation> findAnnotation(String calcId);
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ *
+ * @param seq
+ * null or reference sequence to select annotation for
+ * @param calcId
+ * null or the calcId to select annotation for
+ * @param label
+ * null or the label to select annotation for
+ */
Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label);
return aa;
}
- /**
- * Returns a list of annotations that match the specified sequenceRef, calcId
- * and label, ignoring null values.
- *
- * @return list of AlignmentAnnotation objects
- */
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
- && ann.sequenceRef != null && ann.sequenceRef == seq
- && ann.label != null && ann.label.equals(label))
+ if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+ .equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+ && (label == null || (ann.label != null && ann.label
+ .equals(label))))
{
aa.add(ann);
}
/*
* 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)
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
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
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ percentThreshold.setBackground(Color.white);
+ percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.add(getThreshold());
- thresholdPanel.add(thresholdValue, "wrap");
- thresholdPanel.add(slider, "grow, span, wrap");
+ thresholdPanel.add(percentThreshold, "wrap");
+ thresholdPanel.add(slider, "grow");
+ thresholdPanel.add(thresholdValue, "span, wrap");
actionPanel.add(ok);
actionPanel.add(cancel);
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.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+
+ setThresholdValueText();
+
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
protected JCheckBox seqAssociated = new JCheckBox();
+ protected JCheckBox percentThreshold = new JCheckBox();
+
protected JSlider slider = new JSlider();
protected JTextField thresholdValue = new JTextField(20);
{
if (!adjusting)
{
- thresholdValue.setText((slider.getValue() / 1000f) + "");
+ setThresholdValueText();
valueChanged(!sliderDragging);
}
}
});
}
+ /**
+ * 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() - slider.getMinimum())
+ * 100f / (slider.getMaximum() - slider.getMinimum()));
+ }
+ else
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ }
+ adjusting = oldadj;
+ }
protected void addSliderMouseListeners()
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
+ if (percentThreshold.isSelected())
+ {
+ slider.setValue(slider.getMinimum()
+ + ((int) ((f / 100f) * (slider.getMaximum() - slider
+ .getMinimum()))));
+ }
+ else
+ {
+ slider.setValue((int) (f * 1000));
+ }
updateView();
} catch (NumberFormatException ex)
{
}
}
+ protected void percentageValue_actionPerformed()
+ {
+ setThresholdValueText();
+ }
+
protected void thresholdIsMin_actionPerformed()
{
updateView();
}
});
+ percentThreshold.setText(MessageManager.getString("label.as_percentage"));
+ percentThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!adjusting)
+ {
+ percentageValue_actionPerformed();
+ }
+ }
+ });
slider.setPaintLabels(false);
slider.setPaintTicks(true);
slider.setBackground(Color.white);
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
false));
showGroupConservation.setSelected(Cache.getDefault(
Boolean.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Boolean.toString(showOccupancy.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
Boolean.toString(showGroupConsensus.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showOccupancy.setEnabled(annotations.isSelected());
showGroupConsensus.setEnabled(annotations.isSelected());
showGroupConservation.setEnabled(annotations.isSelected());
showConsensHistogram.setEnabled(annotations.isSelected()
*/
public class ViewDef
{
- public String viewname;
+ // TODO this class is not used - remove?
+ public final String viewname;
- public HiddenSequences hidseqs;
+ public final HiddenSequences hidseqs;
- public HiddenColumns hiddencols;
+ public final HiddenColumns hiddencols;
- public Vector visibleGroups;
+ public final Hashtable hiddenRepSeqs;
- public Hashtable hiddenRepSeqs;
-
- public ViewDef(String viewname, HiddenSequences hidseqs,
- HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs,
+ HiddenColumns hcols, Hashtable hRepSeqs)
{
- this.viewname = viewname;
- this.hidseqs = hidseqs;
- this.hiddencols = hiddencols;
- this.hiddenRepSeqs = hiddenRepSeqs;
+ this.viewname = vname;
+ this.hidseqs = hseqs;
+ this.hiddencols = hcols;
+ this.hiddenRepSeqs = hRepSeqs;
}
}
}
if (list == null)
{
- list = view.visibleGroups;
+ // list = view.visibleGroups;
}
if (cs == null)
{
return false;
}
- public void printGroups(List<SequenceGroup> list)
+ protected void printGroups(List<SequenceGroup> list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
if (sg.cs != null)
{
text.append("colour=");
- text.append(sg.cs.toString());
+ text.append(ColourSchemeProperty.getColourName(sg.cs
+ .getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
{
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
seqGrpPojo.setGroupName(seqGrp.getName());
- seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
- .getSchemeName());
+ seqGrpPojo.setColourScheme(ColourSchemeProperty
+ .getColourName(seqGrp.getColourScheme()));
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
}
}
}
- globalColourScheme = (viewport.getGlobalColourScheme() == null) ? ResidueColourScheme.NONE
- : viewport.getGlobalColourScheme().getSchemeName();
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
+ .getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
protected JComboBox<String> fontNameCB = new JComboBox<String>();
+ protected JCheckBox showOccupancy = new JCheckBox();
+
protected JCheckBox showUnconserved = new JCheckBox();
protected JCheckBox idItalics = new JCheckBox();
identity.setHorizontalTextPosition(SwingConstants.LEFT);
identity.setSelected(true);
identity.setText(MessageManager.getString("label.consensus"));
+ showOccupancy.setFont(LABEL_FONT);
+ showOccupancy.setEnabled(false);
+ showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
+ showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
+ showOccupancy.setSelected(true);
+ showOccupancy.setText(MessageManager.getString("label.occupancy"));
+
JLabel showGroupbits = new JLabel();
showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
.getString("label.database_references"));
annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);
annotations.setSelected(true);
annotations.setText(MessageManager.getString("label.show_annotations"));
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ // annotations.setBounds(new Rectangle(169, 12, 200, 23));
annotations.addActionListener(new ActionListener()
{
@Override
sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
JPanel annsettingsPanel = new JPanel();
- annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
+ annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
annsettingsPanel.setBorder(new EtchedBorder());
visualTab.add(annsettingsPanel);
Border jb = new EmptyBorder(1, 1, 4, 5);
+ annotations.setBorder(jb);
+ showOccupancy.setBorder(jb);
quality.setBorder(jb);
conservation.setBorder(jb);
identity.setBorder(jb);
showConsensLogo.setBorder(jb);
JPanel autoAnnotSettings = new JPanel();
- autoAnnotSettings.setLayout(new GridLayout(3, 3));
annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.setLayout(new GridLayout(0, 2));
+ autoAnnotSettings.add(annotations);
autoAnnotSettings.add(quality);
+ // second row of autoannotation box
+ autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+
+ autoAnnotSettings.setLayout(new GridLayout(0, 3));
autoAnnotSettings.add(conservation);
autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showOccupancy);
autoAnnotSettings.add(showGroupbits);
autoAnnotSettings.add(showGroupConservation);
autoAnnotSettings.add(showGroupConsensus);
autoAnnotSettings.add(showConsensbits);
autoAnnotSettings.add(showConsensHistogram);
autoAnnotSettings.add(showConsensLogo);
+
+
JPanel tooltipSettings = new JPanel();
tooltipSettings.setBorder(new TitledBorder(MessageManager
jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
visualTab.add(jPanel2);
- visualTab.add(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
visualTab.add(sortAnnBy);
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;
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensus)
{
return;
}
protected boolean showConsensus = true;
+ protected boolean showOccupancy = true;
+
private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
{
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);
- gapcounts = new AlignmentAnnotation("Occupancy",
- "Number of aligned positions",
- new Annotation[1], 0f, alignment.getHeight(),
- AlignmentAnnotation.BAR_GRAPH);
- initGapCounts(gapcounts);
+ initGapCounts();
initComplementConsensus();
}
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;
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts(AlignmentAnnotation counts)
+ private void initGapCounts()
{
- counts.hasText = false;
- counts.autoCalculated = true;
- counts.graph = AlignmentAnnotation.BAR_GRAPH;
-
- if (showConsensus)
+ if (showOccupancy)
{
- alignment.addAnnotation(counts);
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
}
}
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;
.equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
{
- String resNumIndexString = cRefDb.getDbResNum()
- .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
- : cRefDb.getDbResNum();
- try
- {
- currSeqIndex = Integer.valueOf(resNumIndexString);
- } catch (NumberFormatException nfe)
- {
- currSeqIndex = Integer.valueOf(resNumIndexString
- .split("[a-zA-Z]")[0]);
- continue;
- }
+ currSeqIndex = getLeadingIntegerValue(
+ cRefDb.getDbResNum(), UNASSIGNED);
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
}
if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
- int resNum;
- try
- {
- resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb
- .getDbResNum());
- } catch (NumberFormatException nfe)
- {
- if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
- {
- resNum = UNASSIGNED;
- continue;
- }
- resNum = Integer.valueOf(pdbRefDb
- .getDbResNum().split("[a-zA-Z]")[0]);
- continue;
- }
+
+ int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
+ residue.getDbResNum(), UNASSIGNED)
+ : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+ UNASSIGNED);
if (isResidueObserved(residue)
|| seqCoordSys == CoordinateSys.UNIPROT)
}
/**
+ * Get the leading integer part of a string that begins with an integer.
+ *
+ * @param input
+ * - the string input to process
+ * @param failValue
+ * - value returned if unsuccessful
+ * @return
+ */
+ static int getLeadingIntegerValue(String input, int failValue)
+ {
+ if (input == null)
+ {
+ return failValue;
+ }
+ String[] parts = input.split("(?=\\D)(?<=\\d)");
+ if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+ {
+ return Integer.valueOf(parts[0]);
+ }
+ return failValue;
+ }
+
+
+ /**
*
* @param chainId
* Target chain to populate mapping of its atom positions.
assertFalse(iter.hasNext());
}
+ /**
+ * Test method that returns annotations that match on reference sequence,
+ * label, or calcId.
+ */
+ @Test(groups = { "Functional" })
+ public void testFindAnnotations_bySeqLabelandorCalcId()
+ {
+ // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+ /* Note - this is an incomplete test - need to check null or
+ * non-null [ matches, not matches ] behaviour for each of the three
+ * parameters..*/
+
+ // search for a single, unique calcId with wildcards on other params
+ Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+ "CalcIdForD.melanogaster.2", null);
+ Iterator<AlignmentAnnotation> iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ AlignmentAnnotation ann = iter.next();
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+ assertFalse(iter.hasNext());
+
+ // save reference to test sequence reference parameter
+ SequenceI rseq = ann.sequenceRef;
+
+ // search for annotation associated with a single sequence
+ anns = al.findAnnotations(rseq, null, null);
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ ann = iter.next();
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+ assertFalse(iter.hasNext());
+
+ // search for annotation with a non-existant calcId
+ anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+ iter = anns.iterator();
+ assertFalse(iter.hasNext());
+
+ // search for annotation with a particular label - expect three
+ anns = al.findAnnotations(null, null, "secondary structure");
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ iter.next();
+ assertTrue(iter.hasNext());
+ iter.next();
+ assertTrue(iter.hasNext());
+ iter.next();
+ // third found.. so
+ assertFalse(iter.hasNext());
+
+ // null on all parameters == find all annotations
+ anns = al.findAnnotations(null, null, null);
+ iter = anns.iterator();
+ int n = al.getAlignmentAnnotation().length;
+ while (iter.hasNext())
+ {
+ n--;
+ iter.next();
+ }
+ assertTrue("Found " + n + " fewer annotations from search.", n == 0);
+ }
+
@Test(groups = { "Functional" })
public void testDeleteAllAnnotations_includingAutocalculated()
{
import static org.testng.Assert.assertEquals;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
.getSequenceAsString(), "A$$CDE");
}
+
+ @Test(groups = { "Functional" })
+ public void testGetVisibleContigs()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">s1\n0123456789\n", DataSourceType.PASTE);
+ AlignViewport av = af.getViewport();
+ AlignmentView view = av.getAlignmentView(true);
+
+ /*
+ * verify getVisibleContigs returns inclusive [start, end] ranges
+ *
+ * no columns hidden
+ */
+ int[] contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 0, 9 });
+
+ /*
+ * hide 3 internal columns
+ */
+ av.hideColumns(5, 7);
+ // the old AlignmentView is now stale!
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 0, 9 });
+ // get a fresh AlignmentView
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 0, 4, 8, 9 });
+
+ // hide first 2 columns
+ av.hideColumns(0, 1);
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 2, 4, 8, 9 });
+
+ // hide last column
+ av.hideColumns(9, 9);
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 2, 4, 8, 8 });
+
+ // unhide columns 5-7
+ av.showColumn(5);
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 2, 8 });
+
+ // hide columns 2-7
+ av.hideColumns(2, 7);
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 8, 8 });
+
+ // hide column 8
+ av.hideColumns(8, 8);
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] {});
+
+ // unhide all
+ av.showAllHiddenColumns();
+ view = av.getAlignmentView(true);
+ contigs = view.getVisibleContigs();
+ assertEquals(contigs, new int[] { 0, 9 });
+ }
}
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;
Boolean.TRUE.toString());
Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+ Boolean.FALSE.toString());
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
av.setSelectionGroup(sg2);
assertSame(sg2.getContext(), sg1); // unchanged
}
+ /**
+ * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
+ */
+ @Test(groups = { "Functional" })
+ public void testShowOrDontShowOccupancy()
+ {
+ // disable occupancy
+ jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewport av = af.getViewport();
+ Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ int c = 0;
+ for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+ null, "Occupancy"))
+ {
+ c++;
+ }
+ Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
+
+ // enable occupancy
+ jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ av = af.getViewport();
+ Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ c = 0;
+ for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+ null, av.getAlignmentGapAnnotation().label))
+ {
+ c++;
+ }
+ ;
+ Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
+
+ }
}
assertEquals("Cached PDB Entries", filterOpt.getName());
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
DataSourceType.FILE));
AnnotationFile aff = new AnnotationFile();
+ // ViewDef is not used by Jalview
ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
new Hashtable());
String anfileout = new AnnotationFile().printAnnotations(
expectedSeqs.put(seq.getName(), seq);
}
- // create and add sequence groups
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ // create and add a sequence group
+ List<SequenceI> grpSeqs = new ArrayList<SequenceI>();
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs,
+ "JGroup:1883305585",
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
"Zappo colour scheme expected!");
}
- @Test(groups = { "Functional" })
/**
- * Test for bug JAL-2489, NPE when exporting BioJSON with global colour scheme set as 'None'
+ * Test for bug JAL-2489, NPE when exporting BioJSON with global colour
+ * scheme, and a group colour scheme, set as 'None'
*/
- public void testBioJSONRoundTripWithGlobalColourSchemeSetAsNone()
+ @Test(groups = { "Functional" })
+ public void testBioJSONRoundTripWithColourSchemeNone()
{
AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
bioJsonFile.getHiddenSequences(),
bioJsonFile.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // Change colour scheme to 'None' and perform round trip
+
+ /*
+ * Create a group on the alignment;
+ * Change global and group colour scheme to 'None' and perform round trip
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(_alignment.getSequenceAt(0), false);
+ sg.setColourScheme(null);
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
ResidueColourScheme.NONE, _alignment);
alignFrame.changeColour(cs);
// System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
return matched;
}
+
+ /**
+ * Test group roundtrip with null (None) group colour scheme
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testGrpParsed_colourNone() throws IOException
+ {
+ AlignmentI copy = new Alignment(testAlignment);
+ SequenceGroup sg = testAlignment.getGroups().get(0);
+ SequenceGroup copySg = new SequenceGroup(new ArrayList<SequenceI>(),
+ sg.getName(),
+ null, sg.getDisplayBoxes(), sg.getDisplayText(),
+ sg.getColourText(), sg.getStartRes(), sg.getEndRes());
+ for (SequenceI seq : sg.getSequences())
+ {
+ int seqIndex = testAlignment.findIndex(seq);
+ copySg.addSequence(copy.getSequenceAt(seqIndex), false);
+ }
+ copy.addGroup(copySg);
+
+ AlignFrame af = new AlignFrame(copy, copy.getWidth(), copy.getHeight());
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter(
+ af.alignPanel);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ copy, false);
+ formatAdapter = new AppletFormatAdapter();
+ AlignmentI newAlignment = formatAdapter.readFile(jsonOutput,
+ DataSourceType.PASTE, FileFormat.Json);
+
+ Assert.assertNotNull(newAlignment.getGroups());
+ for (SequenceGroup seqGrp : newAlignment.getGroups())
+ {
+ SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
+ AssertJUnit.assertTrue(
+ "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
+ isGroupMatched(expectedGrp, seqGrp));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
+ TEST_GRP_HEIGHT, passedCount);
+ }
}
PIR_MODELLER=false
GAP_SYMBOL=-
SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
SHOW_GROUP_CONSERVATION=false
SHOW_JWS2_SERVICES=true
SHOW_NPFEATS_TOOLTIP=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");
+ }
+}
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testWriteParameterSet() throws WrongParameterException
{
for (Jws2Instance service : disc.getServices())
Assert.assertNull(entityP);
}
+
+ @Test(groups = { "Network" })
+ public void getLeadingIntegerFromString()
+ {
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("1234abcd", -1), 1234);
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("1234", -1),
+ 1234);
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("abcd1234", -1), -1);
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("None", -1), -1);
+ Assert.assertEquals(
+ SiftsClient.getLeadingIntegerValue("Null", -1), -1);
+ }
}
git://source.jalview.org / jalview.git / commitdiff