<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>
<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
action.merge_results = Merge Results
action.load_scheme = Load scheme
action.save_scheme = Save scheme
-label.scheme_changed = Changes to scheme {0} have not been saved.<br><br>Save changes, or continue without saving to make a new colour scheme.
+label.scheme_changed = Changes to scheme ''{0}'' have not been saved.<br><br>Save changes, or continue without saving to make a new colour scheme.
label.save_changes = Save Changes
label.dont_save_changes = Don't Save
action.save_image = Save Image
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.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!
warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
-<<<<<<< HEAD
label.phyre2_model_prediction = 3D Protein Model prediction with Phyre2
label.run_phyre2_prediction = Run Phyre2 Prediction
status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
-=======
label.urllinks = Links
->>>>>>> develop
action.merge_results = Unificar resultados
action.load_scheme = Cargar esquema
action.save_scheme = Guardar esquema
+label.scheme_changed = Cambios en el esquema ''{0}'' no se han guardado.<br><br>Guardar cambios, o continuar sin guardar para hacer un nuevo esquema.
+label.save_changes = Guardar cambios
+label.dont_save_changes = No guardar
action.save_image = Guardar imagen
action.paste = Pegar
action.show_html_source = Mostrar código HTML
label.nuc_alignment_colour=Color del Alineamiento Nucleotídico
label.copy_format_from=Copiar formato de
label.chimera=Chimera
+label.create_chimera_attributes = Escribir características de Jalview
+label.create_chimera_attributes_tip = Establecer atributos en Chimera para características visibles
+label.attributes_set = {0} valores de atributos establecidos en Chimera
label.open_split_window=Abrir ventana dividida
label.open_split_window?=¿Quieres abrir ventana dividida, con cDNA y proteína vinculadas?
status.searching_for_pdb_structures=Buscando Estructuras PDB
info.change_threshold_mode_to_enable=Cambiar Modo de Umbral para Habilitar
label.separate_multiple_query_values=Introducir uno o mas {0}s separados por punto y coma ";"
label.let_chimera_manage_structure_colours=Deja que Chimera maneje colores de estructuras
+label.fetch_chimera_attributes = Buscar atributos desde Chimera
+label.fetch_chimera_attributes_tip = Copiar atributo de Chimera a característica de Jalview
label.view_rna_structure=Estructura 2D VARNA
label.scale_protein_to_cdna_tip=Hacer a los residuos de proteínas de la misma anchura que los codones en ventanas divididas
label.colour_with_chimera=Colorear con Chimera
+label.superpose_structures = Superponer estructuras
+error.superposition_failed = Superposición fallido: {0}
+label.insufficient_residues = Residuos alineados ({0}) insuficentes para superponer
label.show_pdbstruct_dialog=Datos de Estructura 3D...
label.hide_all=Ocultar todos
label.invert=Invertir
*/
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 = "";
gaprow.annotations[i] = new Annotation(description, description,
- '\0',
- gapped);
+ '\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()));
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());
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.setTitle("Threshold Filter");
+ thresholdPanel.add(percentThreshold);
thresholdPanel.add(getThreshold());
thresholdPanel.add(slider);
thresholdPanel.add(thresholdValue);
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);
{
threshold_actionPerformed(null);
}
+ else if (e.getSource() == percentThreshold)
+ {
+ if (!adjusting)
+ {
+ percentageValue_actionPerformed();
+ }
+
+ }
}
public void selectedAnnotationChanged()
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();
}
+ protected void setThresholdValueText()
+ {
+ adjusting = true;
+ if (percentThreshold.getState())
+ {
+ double scl = slider.getMaximum() - slider.getMinimum();
+ scl = (slider.getValue() - slider.getMinimum()) / scl;
+ thresholdValue.setText(100 * scl + "");
+ }
+ else
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ }
+ thresholdValue.setCaretPosition(0);
+ adjusting = false;
+ }
+
public void thresholdValue_actionPerformed(ActionEvent e)
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
+ if (percentThreshold.getState())
+ {
+ 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 populateThresholdComboBox(Choice threshold)
{
threshold.addItem(MessageManager
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
if (av.isShowAnnotation())
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * avcharWidth
- - 1, (endSeq - startSeq) * avcharHeight
+ - 1, (endSeq - startSeq + 1) * avcharHeight
+ offset);
}
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);
}
*/
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);
}
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- refreshGUI();
}
return true;
} catch (Exception q)
if (foundDataRow != null && foundDataRow.length > 0)
{
result = new ArrayList<FTSData>();
- String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
- .getWantedFields());
- // System.out.println(">>>>Title row : " + titleRow);
+ boolean firstRow = true;
for (String dataRow : foundDataRow)
{
- if (dataRow.equalsIgnoreCase(titleRow))
+ // The first data row is usually the header data. This should be
+ // filtered out from the rest of the data See: JAL-2485
+ if (firstRow)
{
- // System.out.println(">>>>>>>>>> matched!!!");
+ firstRow = false;
continue;
}
// System.out.println(dataRow);
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
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 + "");
+
+ if (percentThreshold.isSelected())
+ {
+ thresholdValue
+ .setText(""
+ + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
+ }
+ else
+ {
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ }
+
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
ap.paintAlignment(true);
}
+
public ColumnSelection getOldColumnSelection()
{
return oldColumnSelection;
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);
}
}
});
}
+ protected void setThresholdValueText()
+ {
+ adjusting = true;
+ if (percentThreshold.isSelected())
+ {
+ thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
+ * 100f / (slider.getMaximum() - slider.getMinimum()));
+ }
+ else
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ }
+ adjusting = false;
+ }
protected void addSliderMouseListeners()
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
+ if (percentThreshold.isEnabled())
+ {
+ 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()
(int) clip.getBounds().getHeight());
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
if (av.isShowAnnotation())
{
g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
- (endSeq - startSeq) * charHeight + offset);
+ (endSeq - startSeq + 1) * charHeight + offset);
}
g1.translate(-screenY * charWidth, 0);
}
}
}
- globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+ globalColourScheme = (viewport.getGlobalColourScheme() == null) ? ResidueColourScheme.NONE
+ : viewport.getGlobalColourScheme().getSchemeName();
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);
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;
consensus = new AlignmentAnnotation("Consensus", "PID",
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();
}
// 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",
+ "Number of aligned positions", 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);
}
}
.getDbResNum());
} catch (NumberFormatException nfe)
{
- resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb
+ if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+ {
+ resNum = UNASSIGNED;
+ continue;
+ }
+ resNum = Integer.valueOf(pdbRefDb
.getDbResNum().split("[a-zA-Z]")[0]);
continue;
}
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 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 };
import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueColourScheme;
import java.io.IOException;
import java.util.ArrayList;
private JSONFile jf;
+ private AlignExportSettingI exportSettings;
+
@BeforeTest(alwaysRun = true)
public void setup() throws Exception
{
TEST_ANOT_HEIGHT = expectedAnnots.size();
TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ exportSettings = new AlignExportSettingI()
{
@Override
public boolean isExportHiddenSequences()
}
@Test(groups = { "Functional" })
+ /**
+ * Test for bug JAL-2489, NPE when exporting BioJSON with global colour scheme set as 'None'
+ */
+ public void testBioJSONRoundTripWithGlobalColourSchemeSetAsNone()
+ {
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
+
+ Alignment _alignment;
+ try
+ {
+ // load example BioJSON file
+ _alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ DataSourceType.FILE, FileFormat.Json);
+ JSONFile bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ AlignFrame alignFrame = new AlignFrame(_alignment,
+ bioJsonFile.getHiddenSequences(),
+ bioJsonFile.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ // Change colour scheme to 'None' and perform round trip
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ ResidueColourScheme.NONE, _alignment);
+ alignFrame.changeColour(cs);
+ alignFrame.getViewport().setFeaturesDisplayed(
+ bioJsonFile.getDisplayedFeatures());
+ formatAdapter = new AppletFormatAdapter(alignFrame.alignPanel,
+ exportSettings);
+ // export BioJSON string
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ alignFrame.alignPanel.getAlignment(), false);
+ // read back Alignment from BioJSON string
+ formatAdapter = new AppletFormatAdapter();
+ formatAdapter.readFile(jsonOutput, DataSourceType.PASTE,
+ FileFormat.Json);
+ // assert 'None' colour scheme is retained after round trip
+ JSONFile _bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ Assert.assertEquals(_bioJsonFile.getGlobalColourScheme(),
+ ResidueColourScheme.NONE);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Test(groups = { "Functional" })
public void isShowSeqFeaturesSet()
{
Assert.assertTrue(testJsonFile.isShowSeqFeatures(),
PIR_MODELLER=false
GAP_SYMBOL=-
SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
SHOW_GROUP_CONSERVATION=false
SHOW_JWS2_SERVICES=true
SHOW_NPFEATS_TOOLTIP=true
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testWriteParameterSet() throws WrongParameterException
{
for (Jws2Instance service : disc.getServices())
git://source.jalview.org / jalview.git / commitdiff