structure in the alignment. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.<br>
+ trace.<br/><br/>
</em></li>
- </ul></li>
- <li><strong>Help<br>
+ <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
+ <em>
+ These are only available if the <strong>Tools→Enable
+ Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
+ <ul>
+ <li><strong>Write Jalview features</strong><br /> <em>Selecting
+ this option will create new residue attributes for any
+ features currently visible in the associated alignment
+ views, allowing those positions to be selected and
+ analysed with via Chimera's 'Render by Attribute' tool
+ (found in the Tools submenu called Structure Analysis).<br />
+ <br />If you use this option, please remember to select
+ the <em>Refresh Menus</em> option in Chimera's Render by
+ Attribute dialog box in order to see the attributes
+ derived from Jalview sequence features.
+ </em><br />
+ <a href="https://issues.jalview.org/browse/JAL-2295">View
+ this function's issue in Jalview's bug tracker</a></li>
+ <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
+ submenu lists available Chimera residue attributes that
+ can be imported as Jalview features on associated
+ sequences.<br />This is particularly useful for
+ transferring quantitative positional annotation. For
+ example, structure similarity for an alignment can be
+ visualised by transferring the local RMSD attributes
+ generated by Chimera's Match->Align tool onto aligned
+ sequences and displayed with a <a
+ href="featureschemes.html">Graduated feature colour
+ scheme</a>.
+ </em><a href="https://issues.jalview.org/browse/JAL-2296">View
+ this function's issue in Jalview's bug tracker</a></li>
+ </ul></li>
+ <li><strong>Help<br>
</strong>
<ul>
<li><strong>Chimera Help<br>
the <a href="../features/groovy.html">Groovy Console</a> for
interactive scripting.
</em><strong><br></strong></li>
+ <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em>
</ul></li>
<li><strong>Vamsas</strong> <em>For more details, read the
<ul>
<li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
<li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
- <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
</ul>
<em>Application</em>
<ul>
- <li><!-- --></li>
+ <li>
+ <!-- JAL-2447 -->
+ Experimental Features Checkbox in Desktop's Tools
+ menu to hide or show untested features in the application.
+ </li>
+ <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
<li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
<li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
</ul>
+ <em>Experimental features</em>
+ <ul>
+ <li>
+ <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa.
+ </li>
+ </ul>
<em>Applet</em>
<ul>
<li><!-- --></li>
</ul>
+ <em>Test Suite</em>
+ <li><!-- JAL-2474 -->Added PrivelegedAccessor to test suite</li>
+ <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
+ <li><!-- -->
+ </ul>
</div></td><td><div align="left">
<em>General</em>
<ul>
<strong>What's new in Jalview 2.10.2 ?</strong>
</p>
<p>
- Full details about Jalview 2.10.2 are in the <a href="releases.html#Jalview.2.10.2">
- Release Notes</a>, but the highlights are below.</p>
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
+ </p>
+ <ul>
+ <li>
+ <li>New preferences for <a href="webServices/urllinks.html">opening
+ web pages for database cross-references</a> via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+ </li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development. To
+ access the features described below, please first enable the
+ <strong>Tools→Enable Experimental Features</strong> option, and then restart Jalview.
+ </p>
<ul>
- <li>
- <li>New preferences for <a href="webServices/urllinks.html">opening web pages for database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM database and identifiers.org services.</li>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in the Chimera viewer's Chimera menu</a> allow positional
+ annotation to be exchanged between Chimera and Jalview.
+ </li>
</ul>
-
</body>
</html>
label.complement_consensus_descr = PID for cDNA
label.strucconsensus_descr = PID for base pairs
label.occupancy_descr = Number of aligned positions
+label.show_experimental = Enable experimental features
+label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
+label.warning_hidden = Warning: {0} {1} is currently hidden
label.strucconsensus_descr = % Identidad para pares de bases
label.occupancy_descr = Número de posiciones alineadas
label.togglehidden = Show hidden regions
+label.warning_hidden = Advertencia: {0} {1} está actualmente oculto
seqs = rseqs;
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap, null))
+ features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
ap.av.setShowSequenceFeatures(true);
import java.awt.Choice;
import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Font;
+import java.awt.Frame;
import java.awt.Graphics;
import java.awt.GridLayout;
import java.awt.Label;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.awt.event.TextEvent;
+import java.awt.event.TextListener;
import java.util.Hashtable;
/**
public class FeatureRenderer extends
jalview.renderer.seqfeatures.FeatureRenderer
{
+ /*
+ * creating a new feature defaults to the type and group as
+ * the last one created
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
// Holds web links for feature groups and feature types
// in the form label|link
}
- static String lastFeatureAdded;
-
- static String lastFeatureGroupAdded;
-
- static String lastDescriptionAdded;
-
int featureIndex = 0;
boolean deleteFeature = false;
/**
* Shows a dialog allowing the user to create, or amend or delete, sequence
- * features.
+ * features. If null in the supplied feature(s), feature type and group
+ * default to those for the last feature created (with initial defaults of
+ * "feature_1" and "Jalview").
*
* @param sequences
* @param features
* @param create
* @param ap
- * @param featureType
* @return
*/
boolean amendFeatures(final SequenceI[] sequences,
final SequenceFeature[] features, boolean create,
- final AlignmentPanel ap, String featureType)
+ final AlignmentPanel ap)
{
- Panel bigPanel = new Panel(new BorderLayout());
+ final Panel bigPanel = new Panel(new BorderLayout());
final TextField name = new TextField(16);
- final TextField source = new TextField(16);
+ final TextField group = new TextField(16);
final TextArea description = new TextArea(3, 35);
final TextField start = new TextField(8);
final TextField end = new TextField(8);
Button deleteButton = new Button("Delete");
deleteFeature = false;
+ name.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfTypeHidden(ap.alignFrame, name.getText());
+ }
+ });
+ group.addTextListener(new TextListener()
+ {
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ warnIfGroupHidden(ap.alignFrame, group.getText());
+ }
+ });
colourPanel = new FeatureColourPanel();
colourPanel.setSize(110, 15);
final FeatureRenderer fr = this;
featureIndex = index;
name.setText(features[index].getType());
description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
+ group.setText(features[index].getFeatureGroup());
start.setText(features[index].getBegin() + "");
end.setText(features[index].getEnd() + "");
tmp = new Panel();
panel.add(tmp);
tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
- tmp.add(source);
+ tmp.add(group);
tmp = new Panel();
panel.add(tmp);
bigPanel.add(panel, BorderLayout.CENTER);
}
- if (featureType != null)
- {
- lastFeatureAdded = featureType;
- }
- else
- {
- if (lastFeatureAdded == null)
- {
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (features[0].featureGroup != null)
- {
- lastFeatureGroupAdded = features[0].featureGroup;
- }
- else
- {
- lastFeatureAdded = "Jalview";
- }
- }
+ /*
+ * use defaults for type and group (and update them on Confirm) only
+ * if feature type has not been supplied by the caller
+ * (e.g. for Amend, or create features from Find)
+ */
+ boolean useLastDefaults = features[0].getType() == null;
+ String featureType = useLastDefaults ? lastFeatureAdded : features[0]
+ .getType();
+ String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : features[0].getFeatureGroup();
String title = create ? MessageManager
.getString("label.create_new_sequence_features")
dialog.setMainPanel(bigPanel);
- if (create)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
- }
- else
+ name.setText(featureType);
+ group.setText(featureGroup);
+
+ if (!create)
{
dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
dialog.setVisible(false);
}
});
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
}
start.setText(features[0].getBegin() + "");
FeaturesFile ffile = new FeaturesFile();
- if (dialog.accept)
+ /*
+ * only update default type and group if we used defaults
+ */
+ if (dialog.accept && useLastDefaults)
{
lastFeatureAdded = name.getText().trim();
- lastFeatureGroupAdded = source.getText().trim();
- lastDescriptionAdded = description.getText().replace('\n', ' ');
- }
-
- if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
- {
- lastFeatureGroupAdded = null;
+ lastFeatureGroupAdded = group.getText().trim();
}
if (!create)
{
-
SequenceFeature sf = features[featureIndex];
if (dialog.accept)
{
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
+ sf.type = name.getText().trim();
+ sf.featureGroup = group.getText().trim();
+ if (sf.featureGroup != null && sf.featureGroup.length() < 1)
+ {
+ sf.featureGroup = null;
+ }
+ sf.description = description.getText().replace('\n', ' ');
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
sf.end = Integer.parseInt(end.getText());
} catch (NumberFormatException ex)
{
+ //
}
+ boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
+ .equals(sf.featureGroup));
ffile.parseDescriptionHTML(sf, false);
- setVisible(lastFeatureAdded); // if user edited name then make sure new
- // type is visible
+ if (typeOrGroupChanged)
+ {
+ featuresAdded();
+ }
}
if (deleteFeature)
{
sequences[0].deleteFeature(sf);
+ // ensure Feature Settings reflects removal of feature / group
+ featuresAdded();
}
-
}
else
{
+ /*
+ * adding feature(s)
+ */
if (dialog.accept && name.getText().length() > 0)
{
for (int i = 0; i < sequences.length; i++)
{
- features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
+ features[i].type = name.getText().trim();
+ features[i].featureGroup = group.getText().trim();
+ features[i].description = description.getText()
+ .replace('\n', ' ');
sequences[i].addSequenceFeature(features[i]);
ffile.parseDescriptionHTML(features[i], false);
}
Color newColour = colourPanel.getBackground();
// setColour(lastFeatureAdded, fcol);
- if (lastFeatureGroupAdded != null)
- {
- setGroupVisibility(lastFeatureGroupAdded, true);
- }
setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
- setVisible(lastFeatureAdded);
- findAllFeatures(false); // different to original applet behaviour ?
- // findAllFeatures();
+ featuresAdded();
}
else
{
return true;
}
+
+ protected void warnIfGroupHidden(Frame frame, String group)
+ {
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ showWarning(frame, msg);
+ }
+ }
+
+ protected void warnIfTypeHidden(Frame frame, String type)
+ {
+ if (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ showWarning(frame, msg);
+ }
+ }
+ }
+
+ /**
+ * @param frame
+ * @param msg
+ */
+ protected void showWarning(Frame frame, String msg)
+ {
+ JVDialog d = new JVDialog(frame, "", true, 350, 200);
+ Panel mp = new Panel();
+ d.ok.setLabel(MessageManager.getString("action.ok"));
+ d.cancel.setVisible(false);
+ mp.setLayout(new FlowLayout());
+ mp.add(new Label(msg));
+ d.setMainPanel(mp);
+ d.setVisible(true);
+ }
}
{
fr.findAllFeatures(true); // was default - now true to make all visible
}
+ groupPanel = new Panel();
discoverAllFeatureData();
add(lowerPanel, BorderLayout.SOUTH);
- if (groupPanel != null)
- {
- groupPanel.setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
- // scaled on number of
- // visible groups. seems
- // broken
- groupPanel.validate();
+ groupPanel.setLayout(new GridLayout(
+ (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+ // scaled on number of
+ // visible groups. seems
+ // broken
+ groupPanel.validate();
+
+ add(groupPanel, BorderLayout.NORTH);
- add(groupPanel, BorderLayout.NORTH);
- }
frame = new Frame();
frame.add(this);
final FeatureSettings me = this;
if (fr.getAllFeatureColours() != null
&& fr.getAllFeatureColours().size() > 0)
{
- rebuildGroups();
+ // rebuildGroups();
}
resetTable(false);
}
/**
- * rebuilds the group panel
+ * Answers the visibility of the given group, and adds a checkbox for it if
+ * there is not one already
*/
- public void rebuildGroups()
+ public boolean checkGroupState(String group)
{
- boolean rdrw = false;
- if (groupPanel == null)
- {
- groupPanel = new Panel();
- }
- else
- {
- rdrw = true;
- groupPanel.removeAll();
- }
- // TODO: JAL-964 - smoothly incorporate new group entries if panel already
- // displayed and new groups present
- for (String group : fr.getFeatureGroups())
- {
- boolean vis = fr.checkGroupVisibility(group, false);
- Checkbox check = new MyCheckbox(group, vis, false);
- check.addMouseListener(this);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(groupItemListener);
- // note - visibility seems to correlate with displayed. ???wtf ??
- check.setVisible(vis);
- groupPanel.add(check);
- }
- if (rdrw)
+ boolean visible = fr.checkGroupVisibility(group, true);
+
+ /*
+ * is there already a checkbox for this group?
+ */
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
- groupPanel.validate();
+ if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group))
+ {
+ ((Checkbox) groupPanel.getComponent(g)).setState(visible);
+ return visible;
+ }
}
+
+ /*
+ * add a new checkbox
+ */
+ Checkbox check = new MyCheckbox(group, visible, false);
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(groupItemListener);
+ groupPanel.add(check);
+
+ groupPanel.validate();
+ return visible;
}
// This routine adds and removes checkboxes depending on
void resetTable(boolean groupsChanged)
{
List<String> displayableTypes = new ArrayList<String>();
+ Set<String> foundGroups = new HashSet<String>();
+
AlignmentI alignment = av.getAlignment();
+
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI seq = alignment.getSequenceAt(i);
displayableTypes.addAll(types);
}
+ /*
+ * remove any checkboxes for groups not present
+ */
+ pruneGroups(foundGroups);
+
Component[] comps;
int cSize = featurePanel.getComponentCount();
MyCheckbox check;
}
/**
+ * Remove from the groups panel any checkboxes for groups that are not in the
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
+ *
+ * @param foundGroups
+ */
+ protected void pruneGroups(Set<String> foundGroups)
+ {
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ Checkbox checkbox = (Checkbox) groupPanel.getComponent(g);
+ if (!foundGroups.contains(checkbox.getLabel()))
+ {
+ groupPanel.remove(checkbox);
+ }
+ }
+ }
+
+ /**
* update the checklist of feature types with the given type
*
* @param groupsChanged
}
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap, searchString))
+ features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
av.setShowSequenceFeatures(true);
SequenceFeature[] featuresArray = features
.toArray(new SequenceFeature[features.size()]);
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence }, featuresArray, false, ap,
- null);
+ new SequenceI[] { sequence }, featuresArray, false, ap);
seqCanvas.highlightSearchResults(null);
}
}
if (nvismsa[0] != null)
{
- return new Object[] { nvismsa[0], new ColumnSelection() };
+ return new Object[] { nvismsa[0], new HiddenColumns() };
}
else
{
@Override
public boolean hasNext()
{
- return current + 1 <= last;
+ return next <= last;
}
@Override
public Integer next()
{
- if (current + 1 > last)
+ if (next > last)
{
throw new NoSuchElementException();
}
@Override
public boolean hasNext()
{
- return current + 1 <= last;
+ return next <= last;
}
@Override
public Integer next()
{
- if (current + 1 > last)
+ if (next > last)
{
throw new NoSuchElementException();
}
*/
package jalview.datamodel;
-import htsjdk.samtools.Cigar;
-
import java.util.List;
public class CigarArray extends CigarBase
}
/**
- * @see Cigar.getSequenceAndDeletions
+ * @see CigarBase.getSequenceAndDeletions
* @param GapChar
* char
* @return Object[][]
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
- MessageManager.getString("label.create_chimera_attributes"));
- writeFeatures.setToolTipText(MessageManager
- .getString("label.create_chimera_attributes_tip"));
- writeFeatures.addActionListener(new ActionListener()
+ /*
+ * exchange of Jalview features and Chimera attributes is for now
+ * an optionally enabled experimental feature
+ */
+ if (Desktop.instance.showExperimental())
{
- @Override
- public void actionPerformed(ActionEvent e)
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
{
- sendFeaturesToChimera();
- }
- });
- viewerActionMenu.add(writeFeatures);
-
- final JMenu fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
- fetchAttributes.setToolTipText(MessageManager
- .getString("label.fetch_chimera_attributes_tip"));
- fetchAttributes.addMouseListener(new MouseAdapter()
- {
-
- @Override
- public void mouseEntered(MouseEvent e)
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sendFeaturesToChimera();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
+
+ final JMenu fetchAttributes = new JMenu(
+ MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes.setToolTipText(MessageManager
+ .getString("label.fetch_chimera_attributes_tip"));
+ fetchAttributes.addMouseListener(new MouseAdapter()
{
- buildAttributesMenu(fetchAttributes);
- }
- });
- viewerActionMenu.add(fetchAttributes);
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
+ }
}
/**
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
+ af.setMenusForViewport();
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
if (cs != null)
private static int DEFAULT_MIN_HEIGHT = 250;
+ private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
instance = this;
doVamsasClientCheck();
- groovyShell = new JMenuItem();
- groovyShell.setText(MessageManager.getString("label.groovy_console"));
- groovyShell.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- groovyShell_actionPerformed();
- }
- });
- toolsMenu.add(groovyShell);
- groovyShell.setVisible(true);
-
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
showConsole(showjconsole);
showNews.setVisible(false);
+
+ experimentalFeatures.setSelected(showExperimental());
getIdentifiersOrgData();
});
}
+ /**
+ * Answers true if user preferences to enable experimental features is True
+ * (on), else false
+ *
+ * @return
+ */
+ public boolean showExperimental()
+ {
+ String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+ Boolean.FALSE.toString());
+ return Boolean.valueOf(experimental).booleanValue();
+ }
+
public void doConfigureStructurePrefs()
{
// configure services
}
- protected JMenuItem groovyShell;
-
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
*
/**
* Add Groovy Support to Jalview
*/
+ @Override
public void groovyShell_actionPerformed()
{
try
}
}
}
+
+ /**
+ * Sets the Preferences property for experimental features to True or False
+ * depending on the state of the controlling menu item
+ */
+ @Override
+ protected void showExperimental_actionPerformed(boolean selected)
+ {
+ Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
+ }
}
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
/**
* DOCUMENT ME!
public class FeatureRenderer extends
jalview.renderer.seqfeatures.FeatureRenderer
{
+ /*
+ * defaults for creating a new feature are the last created
+ * feature type and group
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
+
Color resBoxColour;
AlignmentPanel ap;
}
}
- // // /////////////
- // // Feature Editing Dialog
- // // Will be refactored in next release.
-
- static String lastFeatureAdded;
-
- static String lastFeatureGroupAdded;
-
- static String lastDescriptionAdded;
-
FeatureColourI oldcol, fcol;
int featureIndex = 0;
* <li>Create sequence feature from pop-up menu on selected region</li>
* <li>Create features for pattern matches from Find</li>
* </ul>
+ * If the supplied feature type is null, show (and update on confirm) the type
+ * and group of the last new feature created (with initial defaults of
+ * "feature_1" and "Jalview").
*
* @param sequences
* the sequences features are to be created on (if creating
* features), or a single sequence (if amending features)
* @param features
* the current features at the position (if amending), or template
- * new features with start/end position set (if creating)
+ * new feature(s) with start/end position set (if creating)
* @param create
* true to create features, false to amend or delete
- * @param featureType
- * the feature type to set on new features; if null, defaults to the
- * type of the last new feature created if any, failing that to
- * "feature_1"
* @param alignPanel
* @return
*/
protected boolean amendFeatures(final List<SequenceI> sequences,
final List<SequenceFeature> features, boolean create,
- final AlignmentPanel alignPanel, String featureType)
+ final AlignmentPanel alignPanel)
{
-
featureIndex = 0;
final JPanel mainPanel = new JPanel(new BorderLayout());
+
final JTextField name = new JTextField(25);
- final JTextField source = new JTextField(25);
+ name.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+ });
+
+ final JTextField group = new JTextField(25);
+ group.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+ });
+
final JTextArea description = new JTextArea(3, 25);
final JSpinner start = new JSpinner();
final JSpinner end = new JSpinner();
SequenceFeature sf = features.get(index);
name.setText(sf.getType());
description.setText(sf.getDescription());
- source.setText(sf.getFeatureGroup());
+ group.setText(sf.getFeatureGroup());
start.setValue(new Integer(sf.getBegin()));
end.setValue(new Integer(sf.getEnd()));
gridPanel.add(choosePanel);
}
- // ////////
- // ////////////////////////////////////
JPanel namePanel = new JPanel();
gridPanel.add(namePanel);
gridPanel.add(groupPanel);
groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
JLabel.RIGHT));
- groupPanel.add(source);
+ groupPanel.add(group);
JPanel colourPanel = new JPanel();
gridPanel.add(colourPanel);
mainPanel.add(descriptionPanel, BorderLayout.CENTER);
}
+ /*
+ * default feature type and group to that of the first feature supplied,
+ * or to the last feature created if not supplied (null value)
+ */
SequenceFeature firstFeature = features.get(0);
- if (featureType != null)
- {
- lastFeatureAdded = featureType;
- }
- else
- {
- if (lastFeatureAdded == null)
- {
- if (firstFeature.type != null)
- {
- lastFeatureAdded = firstFeature.type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (firstFeature.featureGroup != null)
- {
- lastFeatureGroupAdded = firstFeature.featureGroup;
- }
- else
- {
- lastFeatureGroupAdded = "Jalview";
- }
- }
-
- if (create)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
- }
- else
- {
- name.setText(firstFeature.getType());
- source.setText(firstFeature.getFeatureGroup());
- }
+ boolean useLastDefaults = firstFeature.getType() == null;
+ final String featureType = useLastDefaults ? lastFeatureAdded
+ : firstFeature.getType();
+ final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : firstFeature.getFeatureGroup();
+ name.setText(featureType);
+ group.setText(featureGroup);
start.setValue(new Integer(firstFeature.getBegin()));
end.setValue(new Integer(firstFeature.getEnd()));
if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
{
- lastFeatureAdded = name.getText().trim();
- lastFeatureGroupAdded = source.getText().trim();
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");
- // TODO: determine if the null feature group is valid
- if (lastFeatureGroupAdded.length() < 1)
+ /*
+ * update default values only if creating using default values
+ */
+ if (useLastDefaults)
{
- lastFeatureGroupAdded = null;
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = group.getText().trim();
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
}
}
* NO_OPTION corresponds to the Delete button
*/
sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ // update Feature Settings for removal of feature / group
+ featuresAdded();
}
else if (reply == JvOptionPane.YES_OPTION)
{
/*
* YES_OPTION corresponds to the Amend button
+ * need to refresh Feature Settings if type, group or colour changed
*/
- boolean typeChanged = !lastFeatureAdded.equals(sf.type);
- String newType = lastFeatureAdded;
- String newFeatureGroup = lastFeatureGroupAdded;
- String newDescription = lastDescriptionAdded;
-
+ String newType = name.getText().trim();
+ String newFeatureGroup = group.getText().trim();
+ String newDescription = description.getText().replaceAll("\n", " ");
+ boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
+ .equals(sf.featureGroup));
+ refreshSettings |= (fcol != oldcol);
setColour(newType, fcol);
- getFeaturesDisplayed().setVisible(newType);
+/*?*/ getFeaturesDisplayed().setVisible(newType);
int newBegin = sf.begin;
int newEnd = sf.end;
try
// amend features only gets one sequence to act on
sequences.get(0).addSequenceFeature(newSf);
- if (typeChanged)
+ if (refreshSettings)
{
- findAllFeatures();
+ featuresAdded();
}
}
}
for (int i = 0; i < sequences.size(); i++)
{
SequenceFeature sf = features.get(i);
- sf.type = lastFeatureAdded;
+ sf.type = name.getText().trim();
// fix for JAL-1538 - always set feature group here
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
+ sf.featureGroup = group.getText().trim();
+ sf.description = description.getText().replaceAll("\n", " ");
sequences.get(i).addSequenceFeature(sf);
ffile.parseDescriptionHTML(sf, false);
}
- if (lastFeatureGroupAdded != null)
- {
- setGroupVisibility(lastFeatureGroupAdded, true);
- }
setColour(lastFeatureAdded, fcol);
- setVisible(lastFeatureAdded);
- findAllFeatures(false);
+ featuresAdded();
alignPanel.paintAlignment(true);
}
/**
+ * Show a warning message if the entered type is one that is currently hidden
+ *
+ * @param panel
+ * @param type
+ */
+ protected void warnIfTypeHidden(JPanel panel, String type)
+ {
+ if (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
+ }
+ }
+ }
+
+ /**
+ * Show a warning message if the entered group is one that is currently hidden
+ *
+ * @param panel
+ * @param group
+ */
+ protected void warnIfGroupHidden(JPanel panel, String group)
+ {
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
+ }
+ }
+
+ /**
* update the amend feature button dependent on the given style
*
* @param bigPanel
private static final int MIN_HEIGHT = 400;
+ /**
+ * Constructor
+ *
+ * @param af
+ */
public FeatureSettings(AlignFrame af)
{
this.af = af;
{
boolean visible = fr.checkGroupVisibility(group, true);
- if (groupPanel == null)
- {
- groupPanel = new JPanel();
- }
-
- boolean alreadyAdded = false;
for (int g = 0; g < groupPanel.getComponentCount(); g++)
{
if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
{
- alreadyAdded = true;
((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
- break;
+ return visible;
}
}
- if (alreadyAdded)
- {
-
- return visible;
- }
final String grp = group;
final JCheckBox check = new JCheckBox(group, visible);
check.setFont(new Font("Serif", Font.BOLD, 12));
// rather than float
Set<String> displayableTypes = new HashSet<String>();
+ Set<String> foundGroups = new HashSet<String>();
/*
* determine which feature types may be visible depending on
visibleGroups.add(group);
}
}
+ foundGroups.addAll(groups);
/*
* get distinct feature types for visible groups
System.arraycopy(data[i], 0, originalData[i], 0, 3);
}
}
+ else
+ {
+ updateOriginalData(data);
+ }
table.setModel(new FeatureTableModel(data));
table.getColumnModel().getColumn(0).setPreferredWidth(200);
- if (groupPanel != null)
- {
- groupPanel.setLayout(new GridLayout(
- fr.getFeatureGroupsSize() / 4 + 1, 4));
-
- groupPanel.validate();
- bigPanel.add(groupPanel, BorderLayout.NORTH);
- }
+ groupPanel.setLayout(new GridLayout(fr.getFeatureGroupsSize() / 4 + 1,
+ 4));
+ pruneGroups(foundGroups);
+ groupPanel.validate();
updateFeatureRenderer(data, groupChanged != null);
resettingTable = false;
}
/**
+ * Updates 'originalData' (used for restore on Cancel) if we detect that
+ * changes have been made outwith this dialog
+ * <ul>
+ * <li>a new feature type added (and made visible)</li>
+ * <li>a feature colour changed (in the Amend Features dialog)</li>
+ * </ul>
+ *
+ * @param foundData
+ */
+ protected void updateOriginalData(Object[][] foundData)
+ {
+ // todo LinkedHashMap instead of Object[][] would be nice
+
+ Object[][] currentData = ((FeatureTableModel) table.getModel())
+ .getData();
+ for (Object[] row : foundData)
+ {
+ String type = (String) row[0];
+ boolean found = false;
+ for (Object[] current : currentData)
+ {
+ if (type.equals(current[0]))
+ {
+ found = true;
+ /*
+ * currently dependent on object equality here;
+ * really need an equals method on FeatureColour
+ */
+ if (!row[1].equals(current[1]))
+ {
+ /*
+ * feature colour has changed externally - update originalData
+ */
+ for (Object[] original : originalData)
+ {
+ if (type.equals(original[0]))
+ {
+ original[1] = row[1];
+ break;
+ }
+ }
+ }
+ break;
+ }
+ }
+ if (!found)
+ {
+ /*
+ * new feature detected - add to original data (on top)
+ */
+ Object[][] newData = new Object[originalData.length + 1][3];
+ for (int i = 0; i < originalData.length; i++)
+ {
+ System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3);
+ }
+ newData[0] = row;
+ originalData = newData;
+ }
+ }
+ }
+
+ /**
+ * Remove from the groups panel any checkboxes for groups that are not in the
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
+ *
+ * @param foundGroups
+ */
+ protected void pruneGroups(Set<String> foundGroups)
+ {
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g);
+ if (!foundGroups.contains(checkbox.getText()))
+ {
+ groupPanel.remove(checkbox);
+ }
+ }
+ }
+
+ /**
* reorder data based on the featureRenderers global priority list.
*
* @param data
settingsPane.setLayout(borderLayout2);
dasSettingsPane.setLayout(borderLayout3);
bigPanel.setLayout(borderLayout4);
+
+ groupPanel = new JPanel();
+ bigPanel.add(groupPanel, BorderLayout.NORTH);
+
invert.setFont(JvSwingUtils.getLabelFont());
invert.setText(MessageManager.getString("label.invert_selection"));
invert.addActionListener(new ActionListener()
}
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap, searchString))
+ features, true, ap))
{
/*
* ensure feature display is turned on to show the new features,
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
- features.add(new SequenceFeature(null, null, null, start, end,
- "Jalview"));
+ features.add(new SequenceFeature(null, null, null, start, end, null));
}
}
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap, null))
+ features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
* @param evt
* @return
*/
- int findRes(MouseEvent evt)
+ int findColumn(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
}
int seq = findSeq(evt);
- int res = findRes(evt);
+ int res = findColumn(evt);
if (seq < 0 || res < 0)
{
mouseDragged(evt);
}
- int res = findRes(evt);
+ final int column = findColumn(evt);
int seq = findSeq(evt);
- int pos;
- if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res >= sequence.getLength())
+ if (column >= sequence.getLength())
{
return;
}
- pos = setStatusMessage(sequence, res, seq);
+ /*
+ * set status bar message, returning residue position in sequence
+ */
+ final int pos = setStatusMessage(sequence, column, seq);
if (ssm != null && pos > -1)
{
- mouseOverSequence(sequence, res, pos);
+ mouseOverSequence(sequence, column, pos);
}
tooltipText.setLength(6); // Cuts the buffer back to <html>
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
}
}
- // use aa to see if the mouse pointer is on a
if (av.isShowSequenceFeatures())
{
- int rpos;
List<SequenceFeature> features = ap.getFeatureRenderer()
- .findFeaturesAtRes(sequence.getDatasetSequence(),
- rpos = sequence.findPosition(res));
- seqARep.appendFeatures(tooltipText, rpos, features,
+ .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+ seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) // <html>
// avcontroller or viewModel
/**
- * Set status message in alignment panel
+ * Sets the status message in alignment panel, showing the sequence number
+ * (index) and id, residue and residue position for the given sequence and
+ * column position. Returns the calculated residue position in the sequence.
*
* @param sequence
* aligned sequence object
- * @param res
+ * @param column
* alignment column
* @param seq
* index of sequence in alignment
* @return position of res in sequence
*/
- int setStatusMessage(SequenceI sequence, int res, int seq)
+ int setStatusMessage(SequenceI sequence, final int column, int seq)
{
StringBuilder text = new StringBuilder(32);
/*
* Try to translate the display character to residue name (null for gap).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(res));
+ final String displayChar = String.valueOf(sequence.getCharAt(column));
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
}
int pos = -1;
+ pos = sequence.findPosition(column);
if (residue != null)
{
- pos = sequence.findPosition(res);
text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
return;
}
- int res = findRes(evt);
+ int res = findColumn(evt);
if (res < 0)
{
List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ sequence.findPosition(findColumn(evt)));
if (!features.isEmpty())
{
*/
List<SequenceI> seqs = Collections.singletonList(sequence);
seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
- ap, null);
+ ap);
seqCanvas.highlightSearchResults(null);
}
}
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
- final int res = findRes(evt);
+ final int res = findColumn(evt);
final int seq = findSeq(evt);
oldSeq = seq;
needOverviewUpdate = false;
if (av.cursorMode)
{
- seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorX = findColumn(evt);
seqCanvas.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
*/
void showPopupMenu(MouseEvent evt)
{
- final int res = findRes(evt);
+ final int res = findColumn(evt);
final int seq = findSeq(evt);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
+ int res = findColumn(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
import jalview.api.AlignmentViewPanel;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.FlowLayout;
import java.awt.Toolkit;
JMenuItem garbageCollect = new JMenuItem();
+ protected JMenuItem groovyShell;
+
+ protected JCheckBoxMenuItem experimentalFeatures;
+
protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
e.printStackTrace();
}
- if (!new jalview.util.Platform().isAMac())
+ if (!Platform.isAMac())
{
FileMenu.setMnemonic('F');
inputLocalFileMenuItem.setMnemonic('L');
showNews_actionPerformed(e);
}
});
+ groovyShell = new JMenuItem();
+ groovyShell.setText(MessageManager.getString("label.groovy_console"));
+ groovyShell.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ groovyShell_actionPerformed();
+ }
+ });
+ experimentalFeatures = new JCheckBoxMenuItem();
+ experimentalFeatures.setText(MessageManager
+ .getString("label.show_experimental"));
+ experimentalFeatures.setToolTipText(MessageManager
+ .getString("label.show_experimental_tip"));
+ experimentalFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showExperimental_actionPerformed(experimentalFeatures.isSelected());
+ }
+ });
+
snapShotWindow.setText(MessageManager.getString("label.take_snapshot"));
snapShotWindow.addActionListener(new ActionListener()
{
toolsMenu.add(showConsole);
toolsMenu.add(showNews);
toolsMenu.add(garbageCollect);
+ toolsMenu.add(groovyShell);
+ toolsMenu.add(experimentalFeatures);
// toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
inputMenu.add(inputURLMenuItem);
// inputMenu.add(vamsasLoad);
}
+ protected void showExperimental_actionPerformed(boolean selected)
+ {
+ }
+
+ protected void groovyShell_actionPerformed()
+ {
+ }
+
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
}
}
-
+ // <<<<<<< HEAD
+ //
+ // =======
+ // if (minmax == null)
+ // {
+ // minmax = new Hashtable<String, float[][]>();
+ // }
+ //
+ // Set<String> oldGroups = new HashSet<String>(featureGroups.keySet());
+ // >>>>>>> refs/heads/develop
AlignmentI alignment = av.getAlignment();
List<String> allfeatures = new ArrayList<String>(); // or HashSet?
SequenceI asq = alignment.getSequenceAt(i);
for (String group : asq.getFeatures().getFeatureGroups(true))
{
+ // <<<<<<< HEAD
/*
* features in null group are always displayed; other groups
* keep their current visibility; new groups as 'newMadeVisible'
*/
boolean groupDisplayed = true;
if (group != null)
+ // =======
+ // continue;
+ // }
+ //
+ // int index = 0;
+ // while (index < features.length)
+ // {
+ // String fgrp = features[index].getFeatureGroup();
+ // oldGroups.remove(fgrp);
+ // if (!featuresDisplayed.isRegistered(features[index].getType()))
+ // >>>>>>> refs/heads/develop
{
+ // <<<<<<< HEAD
if (featureGroups.containsKey(group))
+ // =======
+ // if (fgrp != null)
+ // >>>>>>> refs/heads/develop
{
groupDisplayed = featureGroups.get(group);
}
}
/*
+ //<<<<<<< HEAD
* mark any new feature types as visible
*/
Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
setOrder(type, 0);
}
}
+ // =======
+ // * oldGroups now consists of groups that no longer
+ // * have any feature in them - remove these
+ // */
+ // for (String grp : oldGroups)
+ // {
+ // featureGroups.remove(grp);
+ // >>>>>>> refs/heads/develop
}
updateRenderOrder(allfeatures);
AllColsIterator it = new AllColsIterator(0, 3, hiddenCols);
it.remove();
}
+
+ /*
+ * Test iterator behaves correctly when there is only one element in the collection
+ */
+ @Test(groups = { "Functional" })
+ public void testOneElement()
+ {
+ HiddenColumns hidden = new HiddenColumns();
+ AllColsIterator it = new AllColsIterator(0, 0, hidden);
+ int count = 0;
+ while (it.hasNext())
+ {
+ it.next();
+ count++;
+ }
+ assertTrue(count == 1, "hasNext() is false after 1 iteration");
+ }
}
{
AlignmentI al;
- Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
@BeforeClass
public void setup()
hiddenRepSequences.put(allseqs[start], theseSeqs);
}
+
+ /*
+ * Test iterator behaves correctly when there is only one element in the collection
+ */
+ @Test(groups = { "Functional" })
+ public void testOneElement()
+ {
+ AllRowsIterator it = new AllRowsIterator(0, 0, al);
+ int count = 0;
+ while (it.hasNext())
+ {
+ it.next();
+ count++;
+ }
+ assertTrue(count == 1, "hasNext() is false after 1 iteration");
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff