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+org.eclipse.jdt.core.formatter.lineSplit=76
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.tabulation.char=space
+org.eclipse.jdt.core.formatter.tabulation.size=2
+org.eclipse.jdt.core.formatter.use_on_off_tags=true
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
--- /dev/null
+eclipse.preferences.version=1
+editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
+formatter_profile=_Jalview
+formatter_settings_version=12
+sp_cleanup.add_default_serial_version_id=true
+sp_cleanup.add_generated_serial_version_id=false
+sp_cleanup.add_missing_annotations=true
+sp_cleanup.add_missing_deprecated_annotations=true
+sp_cleanup.add_missing_methods=false
+sp_cleanup.add_missing_nls_tags=false
+sp_cleanup.add_missing_override_annotations=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
+sp_cleanup.add_serial_version_id=false
+sp_cleanup.always_use_blocks=true
+sp_cleanup.always_use_parentheses_in_expressions=false
+sp_cleanup.always_use_this_for_non_static_field_access=false
+sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
+sp_cleanup.convert_to_enhanced_for_loop=false
+sp_cleanup.correct_indentation=false
+sp_cleanup.format_source_code=true
+sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
+sp_cleanup.make_local_variable_final=true
+sp_cleanup.make_parameters_final=false
+sp_cleanup.make_private_fields_final=true
+sp_cleanup.make_type_abstract_if_missing_method=false
+sp_cleanup.make_variable_declarations_final=false
+sp_cleanup.never_use_blocks=false
+sp_cleanup.never_use_parentheses_in_expressions=true
+sp_cleanup.on_save_use_additional_actions=true
+sp_cleanup.organize_imports=true
+sp_cleanup.qualify_static_field_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
+sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
+sp_cleanup.remove_trailing_whitespaces=false
+sp_cleanup.remove_trailing_whitespaces_all=true
+sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unused_imports=true
+sp_cleanup.remove_unused_local_variables=false
+sp_cleanup.remove_unused_private_fields=true
+sp_cleanup.remove_unused_private_members=false
+sp_cleanup.remove_unused_private_methods=true
+sp_cleanup.remove_unused_private_types=true
+sp_cleanup.sort_members=false
+sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
+sp_cleanup.use_blocks=true
+sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=true
+sp_cleanup.use_parentheses_in_expressions=false
+sp_cleanup.use_this_for_non_static_field_access=false
+sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
+sp_cleanup.use_this_for_non_static_method_access=false
+sp_cleanup.use_this_for_non_static_method_access_only_if_necessary=true
+sp_cleanup.use_type_arguments=false
area (below the sequence ID area).
</p>
<ul>
- <li>Add New Row<br>
+ <li><strong>Add New Row</strong><br>
<em>Adds a new, named annotation row (a dialog box will pop up for you to
enter the label for the new row). </em> </li>
- <li>Hide Row<br>
+ <li><strong>Edit Label/Description</strong><br>
+ <em>This opens a dialog where you can change the name (displayed label), or the description
+ (as shown on the label tooltip) of the clicked annotation. </em> </li>
+ <li><strong>Hide This Row</strong><br>
<em>Hides the annotation row whose label was clicked in order to bring up
the menu.</em> </li>
- <li>Delete Row<br>
+ <li><strong>Hide All <em><label></em></strong><br>
+ <em>Hides all annotation rows whose label matches the one clicked.
+ (This option is only shown for annotations that relate to individual sequences,
+ not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
+ <li><strong>Delete This Row</strong><br>
<em>Deletes the annotation row whose label was clicked in order to bring up
the menu.</em> </li>
- <li>Show All Hidden Rows<br>
+ <li><strong>Show All Hidden Rows</strong><br>
<em>Shows all hidden annotation rows.</em> </li>
<li><strong>Export Annotation</strong> <em>(Application only)</em><br>
<em>Annotations can be saved to file or output to a text window in either the
<tr>
<td width="17%">FASTA</td>
<td width="60%">>SequenceName<br>
-THISISASEQENCE<br></td>
+THISISASEQUENCE<br></td>
<td width="23%">.fa, .fasta</td>
</tr><tr><td width="17%">MSF</td>
<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
>Seq2</td>
<td width="23%">.blc</td>
</tr><tr><td width="17%">PFAM</td>
-<td width="60%">SequenceName THISISASEQENCE</td>
+<td width="60%">SequenceName THISISASEQUENCE</td>
<td width="23%">.pfam</td>
</tr><tr>
<td width="17%">Stockholm</td>
</li>
<li><strong>Load Associated Tree<br> </strong><em>Jalview
can <a href="../calculations/treeviewer.html">view trees</a>
- stored in the Newick file format, and associate them with the
+ stored in the Newick file format, and associate them with the
alignment. Note: the ids of the tree file and your alignment MUST
be the same.</em></li>
<li><strong>Load Features / Annotations<br> </strong><em>Load
conservation calculation, quality calculation and consensus values
as bar charts. </em>
</li>
+ <li><strong>Show All Annotations</strong><em><br>
+ Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide All Annotations</strong><em><br>
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
<li><strong>Autocalculated Annotation<br> </strong><em>Settings
for the display of autocalculated annotation.</em>
<ul>
<li><strong>Show Sequence Features</strong><br> <em>Show
or hide sequence features on this alignment.</em>
</li>
- <li><strong><a href="../features/featuresettings.html">Seqence
+ <li><strong><a href="../features/featuresettings.html">Sequence
Feature Settings...</a> </strong><em><br> <em>Opens the
Sequence Feature Settings dialog box to control the colour and
display of sequence features on the alignment, and configure and
<li><strong> Add New Row</strong><br>
<em>Adds a new, named annotation row (a dialog box will pop up for you
to enter the label for the new row). </em> </li>
- <li><strong>Hide Row</strong><br>
- <em>Hides the annotation row whose label was clicked in order to bring
- up the menu.</em> </li>
+ <li><strong>Edit Label/Description</strong><br>
+ <em>This opens a dialog where you can change the name (displayed label), or the description
+ (as shown on the label tooltip) of the clicked annotation. </em> </li>
+ <li><strong>Hide This Row</strong><br>
+ <em>Hides the annotation row whose label was clicked in order to bring up
+ the menu.</em> </li>
+ <li><strong>Hide All <em><label></em></strong><br>
+ <em>Hides all annotation rows whose label matches the one clicked.
+ (This option is only shown for annotations that relate to individual sequences,
+ not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
<li><strong>Delete Row</strong><br>
<em>Deletes the annotation row whose label was clicked in order to bring
up the menu.</em> </li>
</strong><em>If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
calculation, quality calculation and consensus values as bar charts. </em></li>
+ <li><strong>Show All Annotations</strong><em><br>
+ Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide All Annotations</strong><em><br>
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
<li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
<ul><li>
<strong>Apply to all groups<br></strong>
</li>
<li><strong>Show Sequence Features</strong><br>
<em>Show or hide sequence features on this alignment.</em></li>
- <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
+ <li><strong><a href="../features/featuresettings.html">Sequence Feature Settings...</a></strong><em><br>
Opens the Sequence Feature Settings dialog box to control the colour and display
of sequence features on the alignment, and configure and retrieve features
from DAS annotation servers.</em></li>
<ul>
<li><strong>Selection</strong>
<ul>
- <li><a name="sqreport"><strong>Sequence Details ...<br>
+ <li><a name="sqreport"><strong>Sequence Details...<br>
</strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
- and database cross references</a> normally shown in the sequence's
+ and database cross references</a> normally shown in the sequence's
tooltip.</em></li>
+ <li><strong>Show Annotations...<br>
+ </strong><em>Choose to show (unhide) either All or
+ a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide Annotations...<br>
+ </strong><em>Choose to hide either All or
+ a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Add Reference Annotations...<br>
+ </strong><em>Add to the alignment window any annotations on the selected sequences
+ which have been read from reference sources or calculated (for example,
+ secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
<li><strong>Edit </strong>
<ul>
<li><strong>Copy</strong><br>
- <em>Copys the selected region. In the applet version, the copied sequences
+ <em>Copies the selected region. In the applet version, the copied sequences
are not available to the system clipboard.</em></li>
<li><strong>Cut<br>
</strong><em>Cuts the selected region from the alignment. In the applet
(The View representative structures option was introduced in
Jalview 2.8.1)</em></li>
</ul>
- <br> <li>
-
- </li>
+ <br>
</ul>
</li>
<li><strong>Hide Sequences</strong><br>
label.average_distance_bloslum62 = Average Distance Using BLOSUM62
label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
label.show_annotations = Show annotations
+label.hide_annotations = Hide annotations
+label.show_all_annotations = Show all annotations
+label.hide_all_annotations = Hide all annotations
+label.hide_all = Hide all
+label.add_reference_annotations = Add reference annotations
+label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).<br>Accepts regular expressions - search Help for 'regex' for details.
label.colour_text = Colour Text
label.show_non_conversed = Show nonconserved
label.overview_window = Overview Window
label.cut_paste_alignmen_file = Cut & Paste Alignment File
label.enter_redundancy_thereshold = Enter the redundancy thereshold
label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>
-label.select_feature_colour = Select Feature Colour
\ No newline at end of file
+label.select_feature_colour = Select Feature Colour
+label.delete_all = Delete all sequences
+warn.delete_all = <html>Deleting all sequences will close the alignment window.<br>Confirm deletion or Cancel.
+label.add_annotations_for = Add annotations for
+label.choose_annotations = Choose annotations
+label.find = Find
+label.invalid_search = Search string invalid
+error.invalid_regex = Invalid regular expression
import jalview.util.MessageManager;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
package jalview.datamodel;
-import jalview.util.MessageManager;
-
import java.util.*;
public class AlignmentOrder
{
if (!identity)
{
- throw new Error(MessageManager.getString("error.weak_sequencei_equivalence_not_yet_implemented"));
+ throw new Error("Weak sequenceI equivalence not yet implemented.");
}
else
{
}
if (!identity)
{
- throw new Error(MessageManager.getString("error.weak_sequencei_equivalence_not_yet_implemented"));
+ throw new Error("Weak sequenceI equivalence not yet implemented.");
}
else
{
import jalview.analysis.AlignSeq;
+import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
for (int r = 0; r < ret.length; r++)
{
- ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+ ret[r] = annotation.elementAt(r);
}
return ret;
return anns;
}
+ /**
+ * Returns a list of any annotations on the sequence that match the given
+ * calcId (source) and label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @return
+ */
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ if (annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (ann.calcId != null && ann.calcId.equals(calcId)
+ && ann.label != null && ann.label.equals(label))
+ {
+ result.add(ann);
+ }
+ }
+ }
+ return result;
+ }
+
public boolean updatePDBIds()
{
if (datasetSequence != null)
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.List;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.schemes.*;
+import java.util.Map;
+import java.util.Vector;
/**
* Collects a set contiguous ranges on a set of sequences
return eres;
}
+ @Override
public List<SequenceI> getSequences()
{
return sequences;
}
+ @Override
public List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
SequenceI seq;
for (int i = 0; i < sequences.size(); i++)
{
- seq = (SequenceI) sequences.elementAt(i);
+ seq = sequences.elementAt(i);
allSequences.addElement(seq);
if (hiddenReps.containsKey(seq))
{
*
* @return the first column selected by this group. Runs from 0<=i<N_cols
*/
+ @Override
public int getStartRes()
{
return startRes;
*
* @return the groups last selected column. Runs from 0<=i<N_cols
*/
+ @Override
public int getEndRes()
{
return endRes;
*/
public SequenceI getSequenceAt(int i)
{
- return (SequenceI) sequences.elementAt(i);
+ return sequences.elementAt(i);
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
// MC This needs to get reset when characters are inserted and deleted
if (sequences.size() > 0)
{
- width = ((SequenceI) sequences.elementAt(0)).getLength();
+ width = sequences.elementAt(0).getLength();
}
for (int i = 1; i < sequences.size(); i++)
{
- SequenceI seq = (SequenceI) sequences.elementAt(i);
+ SequenceI seq = sequences.elementAt(i);
if (seq.getLength() > width)
{
// TODO add in other methods like 'getAlignmentAnnotation(String label),
// etc'
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
- for (SequenceI seq : (Vector<SequenceI>) sequences)
+ for (SequenceI seq : sequences)
{
AlignmentAnnotation[] aa = seq.getAnnotation();
if (aa != null)
return aa;
}
+ /**
+ * Answer true if any annotation matches the calcId passed in (if not null).
+ *
+ * @param calcId
+ * @return
+ */
+ public boolean hasAnnotation(String calcId)
+ {
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
public void clear()
{
sequences.clear();
*/
package jalview.datamodel;
-import java.util.Vector;
+import java.util.List;
import fr.orsay.lri.varna.models.rna.RNA;
public AlignmentAnnotation[] getAnnotation(String label);
/**
+ * Return a list of any annotations which match the given calcId (source) and
+ * label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @return
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
* references on the sequence onto the dataset. It will also make a duplicate
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
case KeyEvent.VK_F1:
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
- "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
scaleLeft.setVisible(av.wrapAlignment);
scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
+ /*
+ * Show/hide all annotations only enabled if annotation panel is shown
+ */
+ showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
return;
}
- Vector seqs = new Vector();
+ List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
SequenceI seq;
for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
+ seqs.add(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ // If the cut affects all sequences, warn, remove highlighted columns
if (sg.getSize() == viewport.getAlignment().getHeight())
{
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
- cut[i] = (SequenceI) seqs.elementAt(i);
+ cut[i] = seqs.get(i);
}
/*
}
/**
- * DOCUMENT ME!
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllAnnotations.setEnabled(setVisible);
+ this.hideAllAnnotations.setEnabled(setVisible);
}
@Override
tm.setText(title);//
tm.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
NewTreePanel(type, (String) pwtype, title);
// object broker mechanism.
final Vector<JMenu> wsmenu = new Vector<JMenu>();
final IProgressIndicator af = me;
- final JMenu msawsmenu = new JMenu(MessageManager.getString("label.alignment"));
- final JMenu secstrmenu = new JMenu(MessageManager.getString("label.secondary_structure_prediction"));
- final JMenu seqsrchmenu = new JMenu(MessageManager.getString("label.sequence_database_search"));
- final JMenu analymenu = new JMenu(MessageManager.getString("label.analysis"));
- final JMenu dismenu = new JMenu(MessageManager.getString("label.protein_disorder"));
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ final JMenu analymenu = new JMenu("Analysis");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // final JMenu msawsmenu = new
+ // JMenu(MessageManager.getString("label.alignment"));
+ // final JMenu secstrmenu = new
+ // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ // final JMenu seqsrchmenu = new
+ // JMenu(MessageManager.getString("label.sequence_database_search"));
+ // final JMenu analymenu = new
+ // JMenu(MessageManager.getString("label.analysis"));
+ // final JMenu dismenu = new
+ // JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
trimrs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
}
+
+ /**
+ * Action on selection of menu option to Show or Hide all annotations.
+ *
+ * @param visibile
+ */
+ @Override
+ protected void setAllAnnotationsVisibility(boolean visible)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ aa.visible = visible;
+ }
+ this.alignPanel.paintAlignment(true);
+ }
}
class PrintThread extends Thread
--- /dev/null
+package jalview.gui;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Checkbox;
+import java.awt.CheckboxGroup;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+
+/**
+ * A panel that allows the user to select which sequence-associated annotation
+ * rows to show or hide.
+ *
+ * @author gmcarstairs
+ *
+ */
+@SuppressWarnings("serial")
+public class AnnotationChooser extends JPanel
+{
+
+ private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD, 12);
+
+ private static final int MY_FRAME_WIDTH = 600;
+
+ private static final int MY_FRAME_HEIGHT = 250;
+
+ private JInternalFrame frame;
+
+ private AlignmentPanel ap;
+
+ private SequenceGroup sg;
+
+ // all annotation rows' original visible state
+ private boolean[] resetState = null;
+
+ // is 'Show' selected?
+ private boolean showSelected;
+
+ // apply settings to selected (or all) sequences?
+ private boolean applyToSelectedSequences;
+
+ // apply settings to unselected (or all) sequences?
+ private boolean applyToUnselectedSequences;
+
+ // currently selected 'annotation type' checkboxes
+ private Map<String, String> selectedTypes = new HashMap<String, String>();
+
+ /**
+ * Constructor.
+ *
+ * @param alignPane
+ */
+ public AnnotationChooser(AlignmentPanel alignPane)
+ {
+ super();
+ this.ap = alignPane;
+ this.sg = alignPane.av.getSelectionGroup();
+ saveResetState(alignPane.getAlignment());
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ showFrame();
+ }
+
+ /**
+ * Save the initial show/hide state of all annotations to allow a Cancel
+ * operation.
+ *
+ * @param alignment
+ */
+ protected void saveResetState(AlignmentI alignment)
+ {
+ AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+ final int count = annotations.length;
+ this.resetState = new boolean[count];
+ for (int i = 0; i < count; i++)
+ {
+ this.resetState[i] = annotations[i].visible;
+ }
+ }
+
+ /**
+ * Populate this frame with:
+ * <p>
+ * checkboxes for the types of annotation to show or hide (i.e. any annotation
+ * type shown for any sequence in the whole alignment)
+ * <p>
+ * option to show or hide selected types
+ * <p>
+ * option to show/hide for the currently selected group, or its inverse
+ * <p>
+ * OK and Cancel (reset) buttons
+ */
+ protected void jbInit()
+ {
+ setLayout(new GridLayout(3, 1));
+ add(buildAnnotationTypesPanel());
+ add(buildShowHideOptionsPanel());
+ add(buildActionButtonsPanel());
+ validate();
+ }
+
+ /**
+ * Construct the panel with checkboxes for annotation types.
+ *
+ * @return
+ */
+ protected JPanel buildAnnotationTypesPanel()
+ {
+ JPanel jp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+
+ List<String> annotationTypes = getAnnotationTypes(
+ this.ap.getAlignment(), true);
+
+ for (final String type : annotationTypes)
+ {
+ final Checkbox check = new Checkbox(type);
+ check.setFont(CHECKBOX_FONT);
+ check.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
+ AnnotationChooser.this.selectedTypes.put(type, type);
+ }
+ else
+ {
+ AnnotationChooser.this.selectedTypes.remove(type);
+ }
+ changeTypeSelected_actionPerformed(type);
+ }
+ });
+ jp.add(check);
+ }
+ return jp;
+ }
+
+ /**
+ * Update display when scope (All/Selected sequences/Unselected) is changed.
+ * <p>
+ * Set annotations (with one of the selected types) to the selected Show/Hide
+ * visibility, if they are in the new application scope. Set to the opposite
+ * if outside the scope.
+ * <p>
+ * Note this only affects sequence-specific annotations, others are left
+ * unchanged.
+ */
+ protected void changeApplyTo_actionPerformed()
+ {
+ setAnnotationVisibility(true);
+
+ // copied from AnnotationLabel.actionPerformed (after show/hide row)...
+ // TODO should drive this functionality into AlignmentPanel
+ ap.updateAnnotation();
+ // this.ap.annotationPanel.adjustPanelHeight();
+ // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
+ // this.ap.annotationPanel.getSize().height);
+ // this.ap.validate();
+ this.ap.paintAlignment(true);
+ }
+
+ /**
+ * Update display when an annotation type is selected or deselected.
+ * <p>
+ * If the type is selected, set visibility of annotations of that type which
+ * are in the application scope (all, selected or unselected sequences).
+ * <p>
+ * If the type is unselected, set visibility to the opposite value. That is,
+ * treat select/deselect as a 'toggle' operation.
+ *
+ * @param type
+ */
+ protected void changeTypeSelected_actionPerformed(String type)
+ {
+ boolean typeSelected = this.selectedTypes.containsKey(type);
+ for (AlignmentAnnotation aa : this.ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (aa.sequenceRef != null && type.equals(aa.label)
+ && isInActionScope(aa))
+ {
+ aa.visible = typeSelected ? this.showSelected : !this.showSelected;
+ }
+ }
+ ap.updateAnnotation();
+ // // this.ap.annotationPanel.adjustPanelHeight();
+ // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
+ // this.ap.annotationPanel.getSize().height);
+ // this.ap.validate();
+ this.ap.paintAlignment(true);
+ }
+
+ /**
+ * Update display on change of choice of Show or Hide
+ * <p>
+ * For annotations of any selected type, set visibility of annotations of that
+ * type which are in the application scope (all, selected or unselected
+ * sequences).
+ *
+ * @param type
+ */
+ protected void changeShowHide_actionPerformed()
+ {
+ setAnnotationVisibility(false);
+
+ this.ap.updateAnnotation();
+ // this.ap.annotationPanel.adjustPanelHeight();
+ this.ap.paintAlignment(true);
+ }
+
+ /**
+ * Update visibility flags on annotation rows as per the current user choices.
+ *
+ * @param updateAllRows
+ */
+ protected void setAnnotationVisibility(boolean updateAllRows)
+ {
+ for (AlignmentAnnotation aa : this.ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (aa.sequenceRef != null)
+ {
+ setAnnotationVisibility(aa, updateAllRows);
+ }
+ }
+ }
+
+ /**
+ * Determine and set the visibility of the given annotation from the currently
+ * selected options.
+ * <p>
+ * Only update annotations whose type is one of the selected types.
+ * <p>
+ * If its sequence is in the selected application scope
+ * (all/selected/unselected sequences), then we set its visibility according
+ * to the current choice of Show or Hide.
+ * <p>
+ * If force update of all rows is wanted, then set rows not in the sequence
+ * selection scope to the opposite visibility to those in scope.
+ *
+ * @param aa
+ * @param updateAllRows
+ */
+ protected void setAnnotationVisibility(AlignmentAnnotation aa,
+ boolean updateAllRows)
+ {
+ if (this.selectedTypes.containsKey(aa.label))
+ {
+ if (isInActionScope(aa))
+ {
+ aa.visible = this.showSelected;
+ }
+ else if (updateAllRows)
+ {
+ aa.visible = !this.showSelected;
+ }
+ }
+ // TODO force not visible if associated sequence is hidden?
+ // currently hiding a sequence does not hide its annotation rows
+ }
+
+ /**
+ * Answers true if the annotation falls in the current selection criteria for
+ * show/hide.
+ * <p>
+ * It must be in the sequence selection group (for 'Apply to selection'), or
+ * not in it (for 'Apply except to selection'). No check needed for 'Apply to
+ * all'.
+ *
+ * @param aa
+ * @return
+ */
+ protected boolean isInActionScope(AlignmentAnnotation aa)
+ {
+ boolean result = false;
+ if (this.applyToSelectedSequences && this.applyToUnselectedSequences)
+ {
+ // we don't care if the annotation's sequence is selected or not
+ result = true;
+ }
+ else if (this.sg == null)
+ {
+ // shouldn't happen - defensive programming
+ result = true;
+ }
+ else if (this.sg.getSequences().contains(aa.sequenceRef))
+ {
+ // annotation is for a member of the selection group
+ result = this.applyToSelectedSequences ? true : false;
+ }
+ else
+ {
+ // annotation is not associated with the selection group
+ result = this.applyToUnselectedSequences ? true : false;
+ }
+ return result;
+ }
+
+ /**
+ * Get annotation 'types' for an alignment, optionally restricted to
+ * sequence-specific annotations only. The label is currently used for 'type'.
+ *
+ * TODO refactor to helper class. See
+ * AnnotationColourChooser.getAnnotationItems() for another client
+ *
+ * @param alignment
+ * @param sequenceSpecific
+ * @return
+ */
+ public static List<String> getAnnotationTypes(AlignmentI alignment,
+ boolean sequenceSpecificOnly)
+ {
+ List<String> result = new ArrayList<String>();
+ for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
+ {
+ if (!sequenceSpecificOnly || aa.sequenceRef != null)
+ {
+ String label = aa.label;
+ if (!result.contains(label))
+ {
+ result.add(label);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Construct the panel with options to:
+ * <p>
+ * show or hide the selected annotation types
+ * <p>
+ * do this for the current selection group or its inverse
+ *
+ * @return
+ */
+ protected JPanel buildShowHideOptionsPanel()
+ {
+ JPanel jp = new JPanel();
+ jp.setLayout(new BorderLayout());
+
+ JPanel showHideOptions = buildShowHidePanel();
+ jp.add(showHideOptions, BorderLayout.CENTER);
+
+ JPanel applyToOptions = buildApplyToOptionsPanel();
+ jp.add(applyToOptions, BorderLayout.SOUTH);
+
+ return jp;
+ }
+
+ /**
+ * Build a panel with radio buttons options for sequences to apply show/hide
+ * to. Options are all, current selection, all except current selection.
+ * Initial state has 'current selection' selected.
+ * <p>
+ * If the sequence group is null, then we are acting on the whole alignment,
+ * and only 'all sequences' is enabled (and selected).
+ *
+ * @return
+ */
+ protected JPanel buildApplyToOptionsPanel()
+ {
+ final boolean wholeAlignment = this.sg == null;
+ JPanel applyToOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ CheckboxGroup actingOn = new CheckboxGroup();
+
+ String forAll = MessageManager.getString("label.all_sequences");
+ final Checkbox allSequences = new Checkbox(forAll, actingOn,
+ wholeAlignment);
+ allSequences.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED) {
+ AnnotationChooser.this.setApplyToSelectedSequences(true);
+ AnnotationChooser.this.setApplyToUnselectedSequences(true);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
+ }
+ }
+ });
+ applyToOptions.add(allSequences);
+
+ String forSelected = MessageManager
+ .getString("label.selected_sequences");
+ final Checkbox selectedSequences = new Checkbox(forSelected, actingOn,
+ !wholeAlignment);
+ selectedSequences.setEnabled(!wholeAlignment);
+ selectedSequences.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
+ AnnotationChooser.this.setApplyToSelectedSequences(true);
+ AnnotationChooser.this.setApplyToUnselectedSequences(false);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
+ }
+ }
+ });
+ applyToOptions.add(selectedSequences);
+
+ String exceptSelected = MessageManager
+ .getString("label.except_selected_sequences");
+ final Checkbox unselectedSequences = new Checkbox(exceptSelected, actingOn, false);
+ unselectedSequences.setEnabled(!wholeAlignment);
+ unselectedSequences.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
+ AnnotationChooser.this.setApplyToSelectedSequences(false);
+ AnnotationChooser.this.setApplyToUnselectedSequences(true);
+ AnnotationChooser.this.changeApplyTo_actionPerformed();
+ }
+ }
+ });
+ applyToOptions.add(unselectedSequences);
+
+ // set member variables to match the initial selection state
+ this.applyToSelectedSequences = selectedSequences.getState()
+ || allSequences.getState();
+ this.applyToUnselectedSequences = unselectedSequences.getState()
+ || allSequences.getState();
+
+ return applyToOptions;
+ }
+
+ /**
+ * Build a panel with radio button options to show or hide selected
+ * annotations.
+ *
+ * @return
+ */
+ protected JPanel buildShowHidePanel()
+ {
+ JPanel showHideOptions = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ CheckboxGroup showOrHide = new CheckboxGroup();
+
+ /*
+ * Radio button 'Show selected annotations' - initially unselected
+ */
+ String showLabel = MessageManager
+ .getString("label.show_selected_annotations");
+ final Checkbox showOption = new Checkbox(showLabel, showOrHide, false);
+ showOption.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED) {
+ AnnotationChooser.this.setShowSelected(true);
+ AnnotationChooser.this.changeShowHide_actionPerformed();
+ }
+ }
+ });
+ showHideOptions.add(showOption);
+
+ /*
+ * Radio button 'hide selected annotations'- initially selected
+ */
+ String hideLabel = MessageManager
+ .getString("label.hide_selected_annotations");
+ final Checkbox hideOption = new Checkbox(hideLabel, showOrHide, true);
+ hideOption.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getStateChange() == ItemEvent.SELECTED)
+ {
+ AnnotationChooser.this.setShowSelected(false);
+ AnnotationChooser.this.changeShowHide_actionPerformed();
+ }
+ }
+ });
+ showHideOptions.add(hideOption);
+
+ /*
+ * Set member variable to match initial selection state
+ */
+ this.showSelected = showOption.getState();
+
+ return showHideOptions;
+ }
+
+ /**
+ * Construct the panel with OK and Cancel buttons.
+ *
+ * @return
+ */
+ protected JPanel buildActionButtonsPanel()
+ {
+ JPanel jp = new JPanel();
+ final Font labelFont = JvSwingUtils.getLabelFont();
+
+ JButton ok = new JButton(MessageManager.getString("action.ok"));
+ ok.setFont(labelFont);
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed();
+ }
+ });
+ jp.add(ok);
+
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ cancel.setFont(labelFont);
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed();
+ }
+ });
+ jp.add(cancel);
+
+ return jp;
+ }
+
+ /**
+ * On 'Cancel' button, undo any changes.
+ */
+ protected void cancel_actionPerformed()
+ {
+ resetOriginalState();
+ this.ap.repaint();
+ close_actionPerformed();
+ }
+
+ /**
+ * Restore annotation visibility to their state on entry here, and repaint
+ * alignment.
+ */
+ protected void resetOriginalState()
+ {
+ int i = 0;
+ for (AlignmentAnnotation aa : this.ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ aa.visible = this.resetState[i++];
+ }
+ }
+
+ /**
+ * On 'Close' button, close the dialog.
+ */
+ protected void close_actionPerformed()
+ {
+ try
+ {
+ this.frame.setClosed(true);
+ } catch (Exception exe)
+ {
+ }
+ }
+
+ /**
+ * Render a frame containing this panel.
+ */
+ private void showFrame()
+ {
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.choose_annotations"),
+ MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
+ }
+
+ protected void setShowSelected(boolean showSelected)
+ {
+ this.showSelected = showSelected;
+ }
+
+ protected void setApplyToSelectedSequences(
+ boolean applyToSelectedSequences)
+ {
+ this.applyToSelectedSequences = applyToSelectedSequences;
+ }
+
+ protected void setApplyToUnselectedSequences(
+ boolean applyToUnselectedSequences)
+ {
+ this.applyToUnselectedSequences = applyToUnselectedSequences;
+ }
+
+ protected boolean isShowSelected()
+ {
+ return showSelected;
+ }
+
+ protected boolean isApplyToSelectedSequences()
+ {
+ return applyToSelectedSequences;
+ }
+
+ protected boolean isApplyToUnselectedSequences()
+ {
+ return applyToUnselectedSequences;
+ }
+
+}
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import net.miginfocom.swing.MigLayout;
-
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import net.miginfocom.swing.MigLayout;
public class AnnotationColourChooser extends JPanel
{
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
valueChanged(!sliderDragging);
}
}
super.mouseDragged(e);
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (sliderDragging)
if (!list.contains(label))
{
anmap[list.size()] = i;
- list.addElement(label);
+ list.add(label);
}
else
if (!isSeqAssociated)
{
anmap[list.size()] = i;
- list.addElement(label + "_" + (index++));
+ list.add(label + "_" + (index++));
}
}
}
seqAssociated.setEnabled(enableSeqAss);
- annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ this.annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
return list;
}
minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (minColour.isEnabled())
maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (maxColour.isEnabled())
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
});
threshold.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
threshold_actionPerformed(e);
});
thresholdValue.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
thresholdValue_actionPerformed(e);
.getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
currentColours_actionPerformed(e);
.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
thresholdIsMin_actionPerformed(actionEvent);
{
changeColour();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation);
ap.paintAlignment(false);
}
*/
package jalview.gui;
-import java.util.*;
-import java.util.regex.Pattern;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.image.BufferedImage;
+import java.util.Vector;
+import java.util.regex.Pattern;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.util.MessageManager;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
- image = (Image) bi;
+ image = bi;
addMouseListener(this);
addMouseMotionListener(this);
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
+ refresh();
+
+ }
+
+ /**
+ * Redraw sensibly.
+ */
+ protected void refresh()
+ {
ap.validateAnnotationDimensions(false);
ap.addNotify();
ap.repaint();
- // validate();
- // ap.paintAlignment(true);
}
/**
*/
public void mouseClicked(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
+ // JAL-1264 hide all sequence-specific annotations of this type
+ final String label = aa[selectedRow].label;
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ JMenuItem hideType = new JMenuItem();
+ String text = MessageManager.getString("label.hide_all") + " " + label;
+ hideType.setText(text);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ for (AlignmentAnnotation ann : ap.av.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef != null && ann.label != null
+ && ann.label.equals(label))
+ {
+ ann.visible = false;
+ }
+ }
+ refresh();
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
pop.add(item);
}
}
- else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ else if (label.indexOf("Consensus") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
import javax.swing.JProgressBar;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((int) (screenSize.width - 900) / 2,
- (int) (screenSize.height - 650) / 2, 900, 650);
+ setBounds((screenSize.width - 900) / 2,
+ (screenSize.height - 650) / 2, 900, 650);
}
jconsole = new Console(this, showjconsole);
// add essential build information
{
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
}
throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ final JPanel progressPanel = progressBars.get(new Long(id));
if (handler.canCancel())
{
JButton cancel = new JButton(
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-
-import javax.swing.*;
-import javax.swing.event.*;
-import javax.swing.table.*;
-
import jalview.analysis.AlignmentSorter;
import jalview.bin.Cache;
import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.AbstractCellEditor;
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSlider;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableCellEditor;
+import javax.swing.table.TableCellRenderer;
+
public class FeatureSettings extends JPanel
{
DasSourceBrowser dassourceBrowser;
(String) table.getValueAt(selectedRow, 0));
}
}
+
+ // isPopupTrigger fires on mouseReleased on Mac
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ selectedRow = table.rowAtPoint(evt.getPoint());
+ if (evt.isPopupTrigger())
+ {
+ popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
+ table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
+ evt.getY());
+ }
+ }
});
table.addMouseMotionListener(new MouseMotionAdapter()
file), "UTF-8");
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
- jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
+ jucs = jucs
.unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
public void stateChanged(ChangeEvent evt)
{
- fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
af.alignPanel.paintAlignment(true);
}
});
*/
package jalview.gui;
-import java.util.*;
-import java.awt.event.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
/**
- * DOCUMENT ME!
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ *
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
*
* @author $author$
* @version $Revision$
*/
public class Finder extends GFinder
{
+ private static final int HEIGHT = 110;
+
+ private static final int WIDTH = 340;
+
AlignViewport av;
AlignmentPanel ap;
SearchResults searchResults;
/**
- * Creates a new Finder object.
- *
- * @param av
- * DOCUMENT ME!
- * @param ap
- * DOCUMENT ME!
- * @param f
- * DOCUMENT ME!
+ * Creates a new Finder object with no associated viewport or panel.
*/
public Finder()
{
focusfixed = false;
}
+ /**
+ * Constructor given an associated viewport and alignment panel. Constructs
+ * and displays an internal frame where the user can enter a search string.
+ *
+ * @param viewport
+ * @param alignPanel
+ */
public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
{
av = viewport;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+ WIDTH, HEIGHT);
textfield.requestFocus();
}
/**
- * DOCUMENT ME!
+ * Performs the 'Find Next' action.
*
* @param e
- * DOCUMENT ME!
*/
public void findNext_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
+ * Performs the 'Find All' action.
*
* @param e
- * DOCUMENT ME!
*/
public void findAll_actionPerformed(ActionEvent e)
{
}
/**
- * incrementally search the alignment
+ * Search the alignment for the next or all matches. If 'all matches', a
+ * dialog is shown with the number of sequence ids and subsequences matched.
*
* @param findAll
- * true means find all results and raise a dialog box
*/
void doSearch(boolean findAll)
{
String searchString = textfield.getText().trim();
- if (searchString.length() < 1)
+ if (isInvalidSearchString(searchString))
{
return;
}
}
}
+
+ /**
+ * Displays an error dialog, and answers false, if the search string is
+ * invalid, else answers true.
+ *
+ * @param searchString
+ * @return
+ */
+ protected boolean isInvalidSearchString(String searchString)
+ {
+ String error = getSearchValidationError(searchString);
+ if (error == null)
+ {
+ return false;
+ }
+ JOptionPane.showInternalMessageDialog(this, error,
+ MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+ JOptionPane.ERROR_MESSAGE);
+ return true;
+ }
+
+ /**
+ * Returns an error message string if the search string is invalid, else
+ * returns null.
+ *
+ * Currently validation is limited to checking the string is not empty, and is
+ * a valid regular expression (simple searches for base sub-sequences will
+ * pass this test). Additional validations may be added in future if the
+ * search syntax is expanded.
+ *
+ * @param searchString
+ * @return
+ */
+ protected String getSearchValidationError(String searchString)
+ {
+ String error = null;
+ if (searchString == null || searchString.length() == 0)
+ {
+ error = MessageManager.getString("label.invalid_search");
+ }
+ try
+ {
+ Pattern.compile(searchString);
+ } catch (PatternSyntaxException e)
+ {
+ error = MessageManager.getString("error.invalid_regex") + ": "
+ + e.getDescription();
+ }
+ return error;
+ }
}
--- /dev/null
+package jalview.gui;
+
+import java.net.URL;
+
+import javax.help.HelpBroker;
+import javax.help.HelpSet;
+import javax.help.HelpSetException;
+
+/**
+ * Utility class to show the help documentation window.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class Help
+{
+
+ private static final long HALF_A_MO = 500; // half a second
+
+ private static long lastOpenedTime = 0L;
+
+ /**
+ * Not instantiable
+ */
+ private Help()
+ {
+
+ }
+
+ /**
+ * Show help text in a new window. But do nothing if within half a second of
+ * the last invocation.
+ *
+ * This is a workaround for issue JAL-914 - both Desktop and AlignFrame
+ * responding to F1 key, resulting in duplicate help windows opened.
+ *
+ * @throws HelpSetException
+ */
+ public static void showHelpWindow() throws HelpSetException
+ {
+ long timeNow = System.currentTimeMillis();
+
+ if (timeNow - lastOpenedTime > HALF_A_MO)
+ {
+ lastOpenedTime = timeNow;
+ ClassLoader cl = Desktop.class.getClassLoader();
+ URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
+ HelpSet hs = new HelpSet(cl, url);
+
+ HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ }
+}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.awt.BorderLayout;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
/**
- * DOCUMENT ME!
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
*
* @author $author$
* @version $Revision$
* Creates a new IdPanel object.
*
* @param av
- * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
*/
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
}
/**
- * DOCUMENT ME!
+ * Respond to mouse movement by constructing tooltip text for the sequence id
+ * under the mouse.
*
* @param e
* DOCUMENT ME!
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- StringBuffer tip = new StringBuffer();
+ StringBuffer tip = new StringBuffer(64);
seqAnnotReport
.createSequenceAnnotationReport(tip, sequence,
av.isShowDbRefs(), av.isShowNpFeats(),
}
/**
- * DOCUMENT ME!
+ * Responds to a mouse drag by selecting the sequences under the dragged
+ * region.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent e)
alignPanel.paintAlignment(true);
}
+ /**
+ * Response to the mouse wheel by scrolling the alignment panel.
+ */
@Override
public void mouseWheelMoved(MouseWheelEvent e)
{
if (e.isShiftDown())
{
alignPanel.scrollRight(true);
-
}
else
{
}
/**
- * DOCUMENT ME!
+ * Handle a mouse click event. Currently only responds to a double-click. The
+ * action is to try to open a browser window at a URL that searches for the
+ * selected sequence id. The search URL is configured in Preferences |
+ * Connections | URL link from Sequence ID. For example:
+ *
+ * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent e)
{
- if (e.getClickCount() < 2)
+ /*
+ * Ignore single click. Ignore 'left' click followed by 'right' click (user
+ * selects a row then its pop-up menu).
+ */
+ if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
{
return;
}
- java.util.Vector links = Preferences.sequenceURLLinks;
+ Vector links = Preferences.sequenceURLLinks;
if (links == null || links.size() < 1)
{
return;
MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
-
}
/**
}
/**
- * DOCUMENT ME!
+ * Respond to a mouse press. Does nothing for (left) double-click as this is
+ * handled by mouseClicked().
+ *
+ * Right mouse down - construct and show context menu.
+ *
+ * Ctrl-down or Shift-down - add to or expand current selection group if there
+ * is one.
+ *
+ * Mouse down - select this sequence.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent e)
{
- if (e.getClickCount() == 2)
+ if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
{
return;
}
int seq = alignPanel.seqPanel.findSeq(e);
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
+ if (SwingUtilities.isRightMouseButton(e))
{
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
// build a new links menu based on the current links + any non-positional
}
/**
- * DOCUMENT ME!
+ * Toggle whether the sequence is part of the current selection group.
*
* @param seq
- * DOCUMENT ME!
*/
void selectSeq(int seq)
{
}
/**
- * DOCUMENT ME!
+ * Add contiguous rows of the alignment to the current selection group. Does
+ * nothing if there is no selection group.
*
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
*/
void selectSeqs(int start, int end)
{
}
/**
- * DOCUMENT ME!
+ * Respond to mouse released. Refreshes the display and triggers broadcast of
+ * the new selection group to any listeners.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Highlight sequence ids that match the given list, and if necessary scroll
+ * to the start sequence of the list.
*
* @param list
- * DOCUMENT ME!
*/
public void highlightSearchResults(List<SequenceI> list)
{
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.AnnotationRenderer;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
import javax.swing.ButtonGroup;
*/
public class PopupMenu extends JPopupMenu
{
+ private static final String ALL_ANNOTATIONS = "All";
+
+ private static final String COMMA = ",";
+
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
JMenuItem sequenceSelDetails = new JMenuItem();
+ JMenuItem chooseAnnotations = new JMenuItem();
+
SequenceI sequence;
JMenuItem createGroupMenuItem = new JMenuItem();
JMenu outputMenu = new JMenu();
+ JMenu showAnnotationsMenu = new JMenu();
+
+ JMenu hideAnnotationsMenu = new JMenu();
+
+ JMenuItem addDatasequenceAnnotations = new JMenuItem();
+
JMenuItem sequenceFeature = new JMenuItem();
JMenuItem textColour = new JMenuItem();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
outputMenu.add(item);
}
+ /*
+ * Build menus for annotation types that may be shown or hidden.
+ */
+ buildAnnotationTypesMenus();
+
try
{
jbInit();
menuItem = new JMenuItem();
menuItem.setText(pdb.getId());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
- {
- // TODO re JAL-860: optionally open dialog or provide a menu entry
- // allowing user to open just one structure per sequence
- // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
- // { pdb })[0], null, ap);
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(pdb,
- ap.av.collateForPDB(new PDBEntry[]
- { pdb })[0], null, ap);
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ // TODO re JAL-860: optionally open dialog or provide a menu entry
+ // allowing user to open just one structure per sequence
+ // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+ // { pdb })[0], null, ap);
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(pdb,
+ ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
}
-
});
viewStructureMenu.add(menuItem);
"label.2d_rna_structure_line", new String[]
{ structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
-
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// System.out.println("1:"+structureLine);
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(false);
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(true);
MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showSequence(index);
MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showAllHiddenSeqs();
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
- Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
- .getPDBId();
+ Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
if (pes != null && pes.size() > 0)
{
reppdb.put(pes.get(0).getId(), pes.get(0));
}
}
+ /**
+ * Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection.
+ * <p>
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ */
+ protected void buildAnnotationTypesMenus()
+ {
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup == null)
+ {
+ // this menu option is only for a selection
+ return;
+ }
+
+ showAnnotationsMenu.removeAll();
+ hideAnnotationsMenu.removeAll();
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showAnnotationsMenu, "", all, true, true);
+ addAnnotationTypeToShowHide(hideAnnotationsMenu, "", all, true, false);
+ showAnnotationsMenu.addSeparator();
+ hideAnnotationsMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+ BitSet visibleGraphGroups = PopupMenu
+ .getVisibleLineGraphGroups(annotations);
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup.
+ */
+ Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, annotations, selectionGroup);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showAnnotationsMenu, calcId, type,
+ false, true);
+ }
+ }
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideAnnotationsMenu, calcId, type,
+ false, false);
+ }
+ }
+ }
+
+ /**
+ * Helper method to populate lists of annotation types for the Show/Hide
+ * Annotations menus. If sequenceGroup is not null, this is restricted to
+ * annotations which are associated with sequences in the selection group.
+ * <p/>
+ * If an annotation row is currently visible, its type (label) is added (once
+ * only per type), to the shownTypes list. If it is currently hidden, it is
+ * added to the hiddenTypesList.
+ * <p/>
+ * For rows that belong to a line graph group, so are always rendered
+ * together:
+ * <ul>
+ * <li>Treat all rows in the group as visible, if at least one of them is</li>
+ * <li>Build a comma-separated label with all the types that belong to the
+ * group</li>
+ * </ul>
+ *
+ * @param shownTypes
+ * a map, keyed by calcId (annotation source), whose entries are the
+ * lists of annotation types found for the calcId; each annotation
+ * type in turn may be a list (in the case of grouped annotations)
+ * @param hiddenTypes
+ * a map, similar to shownTypes, but for hidden annotation types
+ * @param visibleGraphGroups
+ * a lookup keyed by graphGroup identifier
+ * @param annotations
+ * the annotations on the alignment to scan
+ * @param sequenceGroup
+ * the sequence group to restrict search to
+ */
+ public static void getAnnotationTypesForShowHide(
+ Map<String, List<List<String>>> shownTypes,
+ Map<String, List<List<String>>> hiddenTypes,
+ BitSet visibleGraphGroups, AlignmentAnnotation[] annotations,
+ SequenceGroup sequenceGroup)
+ {
+ /*
+ * Build a lookup, by calcId (annotation source), of all annotation types in
+ * each graph group.
+ */
+ Map<String, Map<Integer, List<String>>> groupLabels = new HashMap<String, Map<Integer, List<String>>>();
+
+ // trackers for which calcId!label combinations we have dealt with
+ List<String> addedToShown = new ArrayList<String>();
+ List<String> addedToHidden = new ArrayList<String>();
+
+ for (AlignmentAnnotation aa : annotations)
+ {
+
+ if (sequenceGroup == null
+ || (aa.sequenceRef != null && sequenceGroup.getSequences()
+ .contains(aa.sequenceRef)))
+ {
+ String calcId = aa.getCalcId();
+
+ /*
+ * Build a 'composite label' for types in line graph groups.
+ */
+ final List<String> labelAsList = new ArrayList<String>();
+ final String displayLabel = aa.label;
+ labelAsList.add(displayLabel);
+ if (aa.graph == AlignmentAnnotation.LINE_GRAPH
+ && aa.graphGroup > -1)
+ {
+ if (!groupLabels.containsKey(calcId))
+ {
+ groupLabels.put(calcId, new HashMap<Integer, List<String>>());
+ }
+ Map<Integer, List<String>> groupLabelsForCalcId = groupLabels
+ .get(calcId);
+ if (groupLabelsForCalcId.containsKey(aa.graphGroup))
+ {
+ if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
+ displayLabel))
+ {
+ groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
+ }
+ }
+ else
+ {
+ groupLabelsForCalcId.put(aa.graphGroup, labelAsList);
+ }
+ }
+ else
+ /*
+ * 'Simple case' - not a grouped annotation type - list of one label
+ * only
+ */
+ {
+ String rememberAs = calcId + "!" + displayLabel;
+ if (aa.visible && !addedToShown.contains(rememberAs))
+ {
+ if (!shownTypes.containsKey(calcId))
+ {
+ shownTypes.put(calcId, new ArrayList<List<String>>());
+ }
+ shownTypes.get(calcId).add(labelAsList);
+ addedToShown.add(rememberAs);
+ }
+ else
+ {
+ if (!aa.visible && !addedToHidden.contains(rememberAs))
+ {
+ if (!hiddenTypes.containsKey(calcId))
+ {
+ hiddenTypes.put(calcId, new ArrayList<List<String>>());
+ }
+ hiddenTypes.get(calcId).add(labelAsList);
+ addedToHidden.add(rememberAs);
+ }
+ }
+ }
+ }
+ }
+ /*
+ * finally add the 'composite group labels' to the appropriate lists,
+ * depending on whether the group is identified as visible or hidden
+ */
+ for (String calcId : groupLabels.keySet())
+ {
+ for (int group : groupLabels.get(calcId).keySet())
+ {
+ final List<String> groupLabel = groupLabels.get(calcId).get(group);
+ if (visibleGraphGroups.get(group))
+ {
+ if (!shownTypes.containsKey(calcId))
+ {
+ shownTypes.put(calcId, new ArrayList<List<String>>());
+ }
+ shownTypes.get(calcId).add(groupLabel);
+ }
+ else
+ {
+ if (!hiddenTypes.containsKey(calcId))
+ {
+ hiddenTypes.put(calcId, new ArrayList<List<String>>());
+ }
+ hiddenTypes.get(calcId).add(groupLabel);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns a BitSet (possibly empty) of those graphGroups for line graph
+ * annotations, which have at least one member annotation row marked visible.
+ * The logic is that only one row in the group is marked visible, but when it
+ * is drawn, so are all the other rows in the same group.
+ * <p/>
+ * This lookup set allows us to check whether rows marked not visible are in
+ * fact shown.
+ *
+ * @see AnnotationRenderer#drawComponent
+ * @param annotations
+ * @return
+ */
+ public static BitSet getVisibleLineGraphGroups(
+ AlignmentAnnotation[] annotations)
+ {
+ // todo move to a utility class
+ BitSet result = new BitSet();
+ for (AlignmentAnnotation ann : annotations)
+ {
+ if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
+ {
+ int gg = ann.graphGroup;
+ if (gg > -1)
+ {
+ result.set(gg);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
+ String calcId, final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(types, allTypes, actionIsShow);
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ /**
+ * Action on selecting a list of annotation type (or the 'all types' values)
+ * to show or hide for the selection.
+ *
+ * @param types
+ * @param anyType
+ * @param doShow
+ */
+ protected void showHideAnnotation_actionPerformed(
+ Collection<String> types, boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ // TODO: select by calcId (source of annotation) as well as label
+ // e.g. by refactoring of buildAnnotationTypeMenus to as
+ // to construct the actionPerformed methods as the calcId/labels are found
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && ap.av.getSelectionGroup().getSequences()
+ .contains(aa.sequenceRef))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ refresh();
+ }
+
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
{ url }));
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
showLink(url);
// TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
.getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
+ chooseAnnotations.setText(MessageManager
+ .getString("label.choose_annotations") + "...");
+ chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
sequenceDetails.setText(MessageManager
.getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
createGroupMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createGroupMenuItem_actionPerformed();
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
.setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
});
outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ "...");
+ showAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ hideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ configureReferenceAnnotationsMenu();
sequenceFeature.setText(MessageManager
.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
+ "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
add(groupMenu);
add(sequenceMenu);
this.add(structureMenu);
+ // groupMenu.add(chooseAnnotations);
+ groupMenu.add(showAnnotationsMenu);
+ groupMenu.add(hideAnnotationsMenu);
+ groupMenu.add(addDatasequenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
JMenuItem item = new JMenuItem(userColours.nextElement().toString());
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
.getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed();
zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed();
.getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed();
turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed();
buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed();
.getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
.getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
.setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed();
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
});
}
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not on the alignment. If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an annotation that matches on
+ * sequenceRef.datasetSequence, calcId and label.
+ */
+ protected void configureReferenceAnnotationsMenu()
+ {
+ addDatasequenceAnnotations.setText(MessageManager
+ .getString("label.add_reference_annotations"));
+ addDatasequenceAnnotations.setEnabled(false);
+
+ /*
+ * Temporary store so we can write distinct calcId / type pairs on the
+ * tooltip.
+ */
+ Map<String, String> tipEntries = new HashMap<String, String>();
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ // this menu option only applies for a Selection
+ if (this.ap.av.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ /*
+ * For each sequence selected in the alignment, make a list of any
+ * annotations on the underlying dataset sequence which are not already on
+ * the sequence in the alignment.
+ *
+ * Build a map of { alignmentSequence, <List of annotations to add> }
+ */
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new HashMap<SequenceI, List<AlignmentAnnotation>>();
+ for (SequenceI seq : this.ap.av.getSelectionGroup().getSequences())
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * If the sequence has no annotation that matches this one, then add
+ * this one to the results list.
+ */
+ if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label)
+ .isEmpty())
+ {
+ result.add(dsann);
+ tipEntries.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ if (!candidates.isEmpty())
+ {
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ addDatasequenceAnnotations.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ addDatasequenceAnnotations.setToolTipText(tooltipText);
+
+ addDatasequenceAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ for (SequenceI seq : candidates.keySet())
+ {
+ for (AlignmentAnnotation ann : candidates.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ // add to the sequence (sets correct copyAnn.datasetSequence)
+ seq.addAlignmentAnnotation(copyAnn);
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ this.ap.getAlignment().addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ refresh();
+ }
+
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
}
/**
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
+ *
+ * @param e
+ */
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
+ {
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
// or we simply trust the user wants
// wysiwig behaviour
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), ap.av, true));
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ ap.av, true));
}
public void pdbFromFile_actionPerformed()
: ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
+ @Override
public void run()
{
if (sg != null)
{
if (sequence == null)
- sequence = (Sequence) sg.getSequenceAt(0);
+ sequence = sg.getSequenceAt(0);
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
*/
package jalview.jbgui;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
JMenuItem showAllhidden = new JMenuItem();
+ protected JMenuItem showAllAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAnnotations = new JMenuItem();
+
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
JMenuItem invertColSel = new JMenuItem();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
}
} catch (Exception e)
{
+ System.err.println(e.toString());
}
if (!new jalview.util.Platform().isAMac())
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
| java.awt.event.KeyEvent.SHIFT_MASK, false));
saveAs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
saveAs_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
closeMenuItem_actionPerformed(false);
selectAllSequenceMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
selectAllSequenceMenuItem_actionPerformed(e);
deselectAllSequenceMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deselectAllSequenceMenuItem_actionPerformed(e);
invertSequenceMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertSequenceMenuItem_actionPerformed(e);
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
makeGrpsFromSelection_actionPerformed(e);
remove2LeftMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2LeftMenuItem_actionPerformed(e);
remove2RightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2RightMenuItem_actionPerformed(e);
removeGappedColumnMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeGappedColumnMenuItem_actionPerformed(e);
removeAllGapsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeAllGapsMenuItem_actionPerformed(e);
justifyLeftMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
justifyLeftMenuItem_actionPerformed(e);
justifyRightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
justifyRightMenuItem_actionPerformed(e);
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewBoxesMenuItem_actionPerformed(e);
viewTextMenuItem.setState(true);
viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewTextMenuItem_actionPerformed(e);
showNonconservedMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showUnconservedMenuItem_actionPerformed(e);
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortPairwiseMenuItem_actionPerformed(e);
sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortIDMenuItem_actionPerformed(e);
sortLengthMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortLengthMenuItem_actionPerformed(e);
sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortGroupMenuItem_actionPerformed(e);
removeRedundancyMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeRedundancyMenuItem_actionPerformed(e);
pairwiseAlignmentMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pairwiseAlignmentMenuItem_actionPerformed(e);
.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PCAMenuItem_actionPerformed(e);
averageDistanceTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
averageDistanceTreeMenuItem_actionPerformed(e);
neighbourTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
neighbourTreeMenuItem_actionPerformed(e);
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed(e);
zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed(e);
taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed(e);
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed(e);
helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed(e);
.getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed(e);
turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed(e);
buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed(e);
.getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
.setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed(e);
.setText(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed(e);
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideColour_actionPerformed(e);
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed(e);
RNAInteractionColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
RNAInteractionColour_actionPerformed(e);
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
avTreeBlosumMenuItem_actionPerformed(e);
njTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
njTreeBlosumMenuItem_actionPerformed(e);
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText(MessageManager
.getString("label.show_annotations"));
- annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
- "SHOW_ANNOTATIONS", true));
- annotationPanelMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotationPanelMenuItem_actionPerformed(e);
- }
- });
+ annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+ true));
+ annotationPanelMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ /*
+ * Show/hide all annotations only enabled if annotation panel is shown
+ */
+ showAllAnnotations.setText(MessageManager
+ .getString("label.show_all_annotations"));
+ showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed();
+ }
+ });
+ hideAllAnnotations.setText(MessageManager
+ .getString("label.hide_all_annotations"));
+ hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed();
+ }
+ });
colourTextMenuItem.setText(MessageManager
.getString("label.colour_text"));
colourTextMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
colourTextMenuItem_actionPerformed(e);
htmlMenuItem.setText(MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
htmlMenuItem_actionPerformed(e);
.getString("label.overview_window"));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
overviewMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
undoMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
redoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed(e);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed(e);
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
wrapMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
printMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
printMenuItem_actionPerformed(e);
renderGapsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
renderGapsMenuItem_actionPerformed(e);
findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
findMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
findMenuItem_actionPerformed(e);
.getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDThreshold_actionPerformed(e);
.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
showSeqFeatures_actionPerformed(actionEvent);
showDbRefsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
showGroupConservation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
showConsensusHistogram.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
showSequenceLogo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
normaliseSequenceLogo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideColour_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteGroups_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
createGroup.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createGroup_actionPerformed(e);
| java.awt.event.KeyEvent.SHIFT_MASK, false));
unGroup.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroup_actionPerformed(e);
copy.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
cut.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed(e);
}
});
delete.setText(MessageManager.getString("action.delete"));
- delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
delete.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
delete_actionPerformed(e);
| java.awt.event.KeyEvent.SHIFT_MASK, false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteNew_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteThis_actionPerformed(e);
.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
applyToAllGroups_actionPerformed(e);
});
createPNG.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createPNG(null);
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
font_actionPerformed(e);
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
seqLimit_actionPerformed(e);
epsFile.setText("EPS");
epsFile.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createEPS(null);
.getString("label.load_associated_tree"));
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
LoadtreeMenuItem_actionPerformed(e);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleAbove_actionPerformed(e);
scaleLeft.setText(MessageManager.getString("action.scale_left"));
scaleLeft.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleLeft_actionPerformed(e);
scaleRight.setText(MessageManager.getString("action.scale_right"));
scaleRight.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleRight_actionPerformed(e);
centreColumnLabelsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
centreColumnLabels_actionPerformed(e);
followHighlightMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
modifyPID_actionPerformed(e);
modifyConservation
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
modifyConservation_actionPerformed(e);
sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
+ @Override
public void menuSelected(MenuEvent e)
{
buildTreeMenu();
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuCanceled(MenuEvent e)
{
}
sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
{
+ @Override
public void menuCanceled(MenuEvent e)
{
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuSelected(MenuEvent e)
{
buildSortByAnnotationScoresMenu();
.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
padGapsMenuitem_actionPerformed(e);
vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
vamsasStore_actionPerformed(e);
.getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showTranslation_actionPerformed(e);
+ "...");
extractScores.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
extractScores_actionPerformed(e);
.getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
featureSettings_actionPerformed(e);
.setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fetchSequence_actionPerformed(e);
.getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotationColour_actionPerformed(e);
.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
rnahelicesColour_actionPerformed(e);
.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
associatedData_actionPerformed(e);
"AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
autoCalculate_actionPerformed(e);
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortByTreeOption_actionPerformed(e);
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
listenToViewSelections_actionPerformed(e);
addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromFile_actionPerformed(e);
addFromText.setText(MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromText_actionPerformed(e);
addFromURL.setText(MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromURL_actionPerformed(e);
.getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportFeatures_actionPerformed(e);
.getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportAnnotations_actionPerformed(e);
.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showAllSeqs_actionPerformed(e);
.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showAllColumns_actionPerformed(e);
.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSelSequences_actionPerformed(e);
.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSelColumns_actionPerformed(e);
.getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideAllSelection_actionPerformed(e);
.getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideAllButSelection_actionPerformed(e);
.getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showAllhidden_actionPerformed(e);
}
});
-
hiddenMarkers.setText(MessageManager
.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hiddenMarkers_actionPerformed(e);
| java.awt.event.KeyEvent.ALT_MASK, false));
invertColSel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertColSel_actionPerformed(e);
});
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
JTabbedPane pane = (JTabbedPane) evt.getSource();
});
tabbedPane.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
tabbedPane_mousePressed(e);
});
tabbedPane.addFocusListener(new FocusAdapter()
{
+ @Override
public void focusGained(FocusEvent e)
{
tabbedPane_focusGained(e);
.getMenuShortcutKeyMask(), false));
save.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
reload_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
newView.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
+ "...");
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed(e);
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
idRightAlign_actionPerformed(e);
java.awt.event.KeyEvent.VK_G, 0, false));
gatherViews.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
gatherViews_actionPerformed(e);
java.awt.event.KeyEvent.VK_X, 0, false));
expandViews.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
expandViews_actionPerformed(e);
.setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pageSetup_actionPerformed(e);
.getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
alignmentProperties();
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
viewMenu.add(annotationPanelMenuItem);
+ viewMenu.add(showAllAnnotations);
+ viewMenu.add(hideAllAnnotations);
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
// selectMenu.add(listenToViewSelections);
}
+ /**
+ * Action on clicking Show all annotations.
+ */
+ protected void showAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(true);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ */
+ protected void hideAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(false);
+ }
+
+ /**
+ * Set the visibility of all annotations to true or false.
+ *
+ * @param visible
+ */
+ protected void setAllAnnotationsVisibility(boolean visible)
+ {
+
+ }
+
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
*/
package jalview.workers;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import java.util.ArrayList;
+import java.util.List;
+
public class ConservationThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
AlignmentI alignment = alignViewport.getAlignment();
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import java.util.Hashtable;
+
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
--- /dev/null
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Unit tests for Alignment datamodel.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AlignmentTest
+{
+ // @formatter:off
+ private static final String TEST_DATA =
+ "# STOCKHOLM 1.0\n" +
+ "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
+ "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
+ "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
+ "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
+ "#=GR D.melanogaster.1 SS ................((((\n" +
+ "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
+ "#=GR D.melanogaster.2 SS ................((((\n" +
+ "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
+ "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
+ "//";
+ // @formatter:on
+
+
+ private Alignment al;
+
+ /*
+ * Read in Stockholm format test data including secondary structure
+ * annotations.
+ */
+ @Before
+ public void setUp() throws IOException
+ {
+ al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ AppletFormatAdapter.PASTE, "STH");
+ for (int i = 0; i < al.getSequencesArray().length; ++i)
+ {
+ al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
+ al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
+ + al.getSequenceAt(i).getName());
+ }
+ }
+
+ /**
+ * Test method that returns annotations that match on calcId.
+ */
+ @Test
+ public void testFindAnnotation_byCalcId()
+ {
+ Iterable<AlignmentAnnotation> anns = al
+ .findAnnotation("CalcIdForD.melanogaster.2");
+ Iterator<AlignmentAnnotation> iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ AlignmentAnnotation ann = iter.next();
+ assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+ assertFalse(iter.hasNext());
+ }
+}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Checkbox;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FlowLayout;
+import java.awt.event.ItemEvent;
+import java.io.IOException;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JPanel;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Unit tests for AnnotationChooser
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AnnotationChooserTest
+{
+ // 4 sequences x 13 positions
+ final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+ + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ + "TIETHKEEELTA-\n";
+
+ AnnotationChooser testee;
+
+ AlignmentPanel parentPanel;
+
+ AlignFrame af;
+
+ @Before
+ public void setUp() throws IOException
+ {
+ AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ AppletFormatAdapter.PASTE, "FASTA");
+ af = new AlignFrame(al, 700, 500);
+ parentPanel = new AlignmentPanel(af, af.getViewport());
+ addAnnotations();
+ }
+
+ /**
+ * Add 4 annotations, 3 of them sequence-specific.
+ *
+ * <PRE>
+ * ann1 - for sequence 0 - label 'IUPRED'
+ * ann2 - not sequence related - label 'Beauty'
+ * ann3 - for sequence 3 - label 'JMol'
+ * ann4 - for sequence 2 - label 'IUPRED'
+ * ann5 - for sequence 1 - label 'JMol'
+ */
+ private void addAnnotations()
+ {
+ Annotation an = new Annotation(2f);
+ Annotation[] anns = new Annotation[]
+ { an, an, an };
+ AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ ann0.setSequenceRef(seqs[0]);
+ ann2.setSequenceRef(seqs[3]);
+ ann3.setSequenceRef(seqs[2]);
+ ann4.setSequenceRef(seqs[1]);
+ parentPanel.getAlignment().addAnnotation(ann0);
+ parentPanel.getAlignment().addAnnotation(ann1);
+ parentPanel.getAlignment().addAnnotation(ann2);
+ parentPanel.getAlignment().addAnnotation(ann3);
+ parentPanel.getAlignment().addAnnotation(ann4);
+ }
+
+ /**
+ * Test creation of panel with OK and Cancel buttons
+ */
+ @Test
+ public void testBuildActionButtonsPanel()
+ {
+ testee = new AnnotationChooser(parentPanel);
+ JPanel jp = testee.buildActionButtonsPanel();
+ assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
+
+ Component[] comps = jp.getComponents();
+ assertEquals("Not 2 action buttons", 2, comps.length);
+
+ final Component jb1 = comps[0];
+ final Component jb2 = comps[1];
+
+ assertEquals("Not 'OK' button", MessageManager.getString("action.ok"),
+ ((JButton) jb1).getText());
+ assertEquals("Wrong button font", JvSwingUtils.getLabelFont(),
+ jb1.getFont());
+
+ assertEquals("Not 'Cancel' button",
+ MessageManager.getString("action.cancel"),
+ ((JButton) jb2).getText());
+ assertEquals("Wrong button font", JvSwingUtils.getLabelFont(),
+ jb2.getFont());
+ }
+
+ /**
+ * Test 'Apply to' has 3 radio buttons enabled, 'Selected Sequences' selected,
+ * when there is a current selection group.
+ */
+ @Test
+ public void testBuildApplyToOptionsPanel_withSelectionGroup()
+ {
+ selectSequences(0, 2, 3);
+ testee = new AnnotationChooser(parentPanel);
+
+ JPanel jp = testee.buildApplyToOptionsPanel();
+ Component[] comps = jp.getComponents();
+ assertEquals("Not 3 radio buttons", 3, comps.length);
+
+ final Checkbox cb1 = (Checkbox) comps[0];
+ final Checkbox cb2 = (Checkbox) comps[1];
+ final Checkbox cb3 = (Checkbox) comps[2];
+
+ assertTrue("Not enabled", cb1.isEnabled());
+ assertTrue("Not enabled", cb2.isEnabled());
+ assertTrue("Not enabled", cb3.isEnabled());
+ assertEquals("Option not selected", cb2, cb2.getCheckboxGroup()
+ .getSelectedCheckbox());
+
+ // check state variables match checkbox selection
+ assertTrue(testee.isApplyToSelectedSequences());
+ assertFalse(testee.isApplyToUnselectedSequences());
+ }
+
+ /**
+ * Add a sequence group to the alignment with the specified sequences (base 0)
+ * in it
+ *
+ * @param i
+ * @param more
+ */
+ private void selectSequences(int... selected)
+ {
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ SequenceGroup sg = new SequenceGroup();
+ for (int i : selected)
+ {
+ sg.addSequence(seqs[i], false);
+ }
+ parentPanel.av.setSelectionGroup(sg);
+ }
+
+ /**
+ * Test 'Apply to' has 1 radio button enabled, 'All Sequences' selected, when
+ * there is no current selection group.
+ */
+ @Test
+ public void testBuildApplyToOptionsPanel_noSelectionGroup()
+ {
+ testee = new AnnotationChooser(parentPanel);
+ JPanel jp = testee.buildApplyToOptionsPanel();
+ verifyApplyToOptionsPanel_noSelectionGroup(jp);
+ }
+
+ protected void verifyApplyToOptionsPanel_noSelectionGroup(JPanel jp)
+ {
+ assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
+ Component[] comps = jp.getComponents();
+ assertEquals("Not 3 radio buttons", 3, comps.length);
+
+ final Checkbox cb1 = (Checkbox) comps[0];
+ final Checkbox cb2 = (Checkbox) comps[1];
+ final Checkbox cb3 = (Checkbox) comps[2];
+
+ assertTrue("Not enabled", cb1.isEnabled());
+ assertFalse("Enabled", cb2.isEnabled());
+ assertFalse("Enabled", cb3.isEnabled());
+ assertEquals("Not selected", cb1, cb1.getCheckboxGroup()
+ .getSelectedCheckbox());
+
+ // check state variables match checkbox selection
+ assertTrue(testee.isApplyToSelectedSequences());
+ assertTrue(testee.isApplyToUnselectedSequences());
+
+ assertEquals("Wrong text",
+ MessageManager.getString("label.all_sequences"), cb1.getLabel());
+ assertEquals("Wrong text",
+ MessageManager.getString("label.selected_sequences"),
+ cb2.getLabel());
+ assertEquals("Wrong text",
+ MessageManager.getString("label.except_selected_sequences"),
+ cb3.getLabel());
+ }
+
+ /**
+ * Test Show and Hide radio buttons created, with Hide initially selected.
+ */
+ @Test
+ public void testBuildShowHidePanel()
+ {
+ testee = new AnnotationChooser(parentPanel);
+ JPanel jp = testee.buildShowHidePanel();
+ verifyShowHidePanel(jp);
+
+ }
+
+ protected void verifyShowHidePanel(JPanel jp)
+ {
+ assertTrue("Wrong layout", jp.getLayout() instanceof FlowLayout);
+ Component[] comps = jp.getComponents();
+ assertEquals("Not 2 radio buttons", 2, comps.length);
+
+ final Checkbox cb1 = (Checkbox) comps[0];
+ final Checkbox cb2 = (Checkbox) comps[1];
+
+ assertTrue("Show not enabled", cb1.isEnabled());
+ assertTrue("Hide not enabled", cb2.isEnabled());
+
+ // Hide (button 2) selected; note this may change to none (null)
+ assertEquals("Not selected", cb2, cb2.getCheckboxGroup()
+ .getSelectedCheckbox());
+
+ assertTrue("Show is flagged", !testee.isShowSelected());
+
+ assertEquals("Wrong text",
+ MessageManager.getString("label.show_selected_annotations"),
+ cb1.getLabel());
+ assertEquals("Wrong text",
+ MessageManager.getString("label.hide_selected_annotations"),
+ cb2.getLabel());
+ }
+
+ /**
+ * Test construction of panel containing two sub-panels
+ */
+ @Test
+ public void testBuildShowHideOptionsPanel()
+ {
+ testee = new AnnotationChooser(parentPanel);
+ JPanel jp = testee.buildShowHideOptionsPanel();
+ assertTrue("Wrong layout", jp.getLayout() instanceof BorderLayout);
+ Component[] comps = jp.getComponents();
+ assertEquals("Not 2 sub-panels", 2, comps.length);
+
+ verifyShowHidePanel((JPanel) comps[0]);
+ verifyApplyToOptionsPanel_noSelectionGroup((JPanel) comps[1]);
+ }
+
+ /**
+ * Test that annotation types are (uniquely) identified.
+ *
+ */
+ @Test
+ public void testGetAnnotationTypes()
+ {
+ selectSequences(1);
+ testee = new AnnotationChooser(parentPanel);
+ // selection group should make no difference to the result
+ // as all annotation types for the alignment are considered
+
+ List<String> types = AnnotationChooser.getAnnotationTypes(
+ parentPanel.getAlignment(), true);
+ assertEquals("Not two annotation types", 2, types.size());
+ assertTrue("IUPRED missing", types.contains("IUPRED"));
+ assertTrue("JMol missing", types.contains("JMol"));
+
+ types = AnnotationChooser.getAnnotationTypes(
+ parentPanel.getAlignment(), false);
+ assertEquals("Not six annotation types", 6, types.size());
+ assertTrue("IUPRED missing", types.contains("IUPRED"));
+ assertTrue("JMol missing", types.contains("JMol"));
+ assertTrue("Beauty missing", types.contains("Beauty"));
+ // These are added by viewmodel.AlignViewport.initAutoAnnotation():
+ assertTrue("Consensus missing", types.contains("Consensus"));
+ assertTrue("Quality missing", types.contains("Quality"));
+ assertTrue("Conservation missing", types.contains("Conservation"));
+ }
+
+ /**
+ * Test result of selecting an annotation type, with 'Hide for all sequences'.
+ *
+ * We expect all annotations of that type to be set hidden. Other annotations
+ * should be left visible.
+ */
+ @Test
+ public void testSelectType_hideForAll()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+ setSelected(hideCheckbox, true);
+
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
+ 1, 1, 0);
+ setSelected(allSequencesCheckbox, true);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[7].visible); // JMol for seq1
+
+ setSelected(getTypeCheckbox("JMol"), true);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertFalse(anns[5].visible); // JMol for seq3 - not selected but hidden
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertFalse(anns[7].visible); // JMol for seq1 - selected and hidden
+ }
+
+ /**
+ * Test result of selecting an annotation type, with 'Hide for selected
+ * sequences'.
+ *
+ * We expect the annotations of that type, linked to the sequence group, to be
+ * set hidden. Other annotations should be left visible.
+ */
+ @Test
+ public void testSelectType_hideForSelected()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+ setSelected(hideCheckbox, true);
+
+ /*
+ * Don't set the 'selected sequences' radio button since this would trigger
+ * an update, including unselected sequences / annotation types
+ */
+ // setSelected(getSelectedSequencesCheckbox());
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ assertTrue(anns[7].visible); // JMol for seq1
+
+ setSelected(getTypeCheckbox("JMol"), true);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3 not in selection group
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertFalse(anns[7].visible); // JMol for seq1 in selection group
+ }
+
+ /**
+ * Test result of deselecting an annotation type, with 'Hide for all
+ * sequences'.
+ *
+ * We expect all annotations of that type to be set visible. Other annotations
+ * should be left unchanged.
+ */
+ @Test
+ public void testDeselectType_hideForAll()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+ setSelected(hideCheckbox, true);
+
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
+ 1, 1, 0);
+ setSelected(allSequencesCheckbox, true);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ final Checkbox typeCheckbox = getTypeCheckbox("JMol");
+
+ // select JMol - all hidden
+ setSelected(typeCheckbox, true);
+ assertFalse(anns[5].visible); // JMol for seq3
+ assertFalse(anns[7].visible); // JMol for seq1
+
+ // deselect JMol - all unhidden
+ setSelected(typeCheckbox, false);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertTrue(anns[7].visible); // JMol for seq1
+ }
+
+ /**
+ * Test result of deselecting an annotation type, with 'Hide for selected
+ * sequences'.
+ *
+ * We expect the annotations of that type, linked to the sequence group, to be
+ * set visible. Other annotations should be left unchanged.
+ */
+ @Test
+ public void testDeselectType_hideForSelected()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+ setSelected(hideCheckbox, true);
+
+ /*
+ * Don't set the 'selected sequences' radio button since this would trigger
+ * an update, including unselected sequences / annotation types
+ */
+ // setSelected(getSelectedSequencesCheckbox());
+
+ setSelected(getTypeCheckbox("JMol"), true);
+ setSelected(getTypeCheckbox("JMol"), false);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3 not in selection group
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertTrue(anns[7].visible); // JMol for seq1 in selection group
+ }
+
+ /**
+ * Test result of selecting an annotation type, with 'Show for all sequences'.
+ *
+ * We expect all annotations of that type to be set visible. Other annotations
+ * should be left unchanged
+ */
+ @Test
+ public void testSelectType_showForAll()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
+ 1, 1, 0);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ // hide all JMol annotations
+ setSelected(allSequencesCheckbox, true);
+ setSelected(hideCheckbox, true);
+ setSelected(getTypeCheckbox("JMol"), true);
+ assertFalse(anns[5].visible); // JMol for seq3
+ assertFalse(anns[7].visible); // JMol for seq1
+ // ...now show them...
+ setSelected(showCheckbox, true);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertTrue(anns[7].visible); // JMol for seq1
+ }
+
+ /**
+ * Test result of selecting an annotation type, with 'Show for selected
+ * sequences'.
+ *
+ * We expect all annotations of that type, linked to the sequence group, to be
+ * set visible. Other annotations should be left unchanged
+ */
+ @Test
+ public void testSelectType_showForSelected()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+
+ final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent(
+ testee, 1, 1, 1);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ // hide all JMol annotations in the selection region (== annotation 7)
+ setSelected(selectedSequencesCheckbox, true);
+ setSelected(hideCheckbox, true);
+ setSelected(getTypeCheckbox("JMol"), true);
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertFalse(anns[7].visible); // JMol for seq1
+ // ...now show them...
+ setSelected(showCheckbox, true);
+
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertTrue(anns[7].visible); // JMol for seq1
+ }
+
+ /**
+ * Test result of deselecting an annotation type, with 'Show for all
+ * sequences'.
+ *
+ * We expect all annotations of that type to be set hidden. Other annotations
+ * should be left unchanged.
+ */
+ @Test
+ public void testDeselectType_showForAll()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+
+ final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
+ setSelected(showCheckbox, true);
+
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
+ 1, 1, 0);
+ setSelected(allSequencesCheckbox, true);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ final Checkbox typeCheckbox = getTypeCheckbox("JMol");
+ // select JMol - all shown
+ setSelected(typeCheckbox, true);
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[7].visible); // JMol for seq1
+
+ // deselect JMol - all hidden
+ setSelected(typeCheckbox, false);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertFalse(anns[5].visible); // JMol for seq3
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertFalse(anns[7].visible); // JMol for seq1
+ }
+
+ /**
+ * Test result of deselecting an annotation type, with 'Show for selected
+ * sequences'.
+ *
+ * We expect the annotations of that type, linked to the sequence group, to be
+ * set hidden. Other annotations should be left unchanged.
+ */
+ @Test
+ public void testDeselectType_showForSelected()
+ {
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+ final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
+ setSelected(showCheckbox, true);
+
+ /*
+ * Don't set the 'selected sequences' radio button since this would trigger
+ * an update, including unselected sequences / annotation types
+ */
+ // setSelected(getSelectedSequencesCheckbox());
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ // select JMol - should remain visible
+ setSelected(getTypeCheckbox("JMol"), true);
+ assertTrue(anns[5].visible); // JMol for seq3
+ assertTrue(anns[7].visible); // JMol for seq1
+
+ // deselect JMol - should be hidden for selected sequences only
+ setSelected(getTypeCheckbox("JMol"), false);
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertTrue(anns[3].visible); // IUPred for seq0
+ assertTrue(anns[4].visible); // Beauty
+ assertTrue(anns[5].visible); // JMol for seq3 not in selection group
+ assertTrue(anns[6].visible); // IUPRED for seq2
+ assertFalse(anns[7].visible); // JMol for seq1 in selection group
+ }
+
+ /**
+ * Helper method to drill down to a sub-component in a Container hierarchy.
+ *
+ * @param cont
+ * @param i
+ * @param j
+ * @param k
+ * @return
+ */
+ public static Component getComponent(Container cont, int... positions)
+ {
+ Component comp = cont;
+ for (int i : positions)
+ {
+ comp = ((Container) comp).getComponent(i);
+ }
+ return comp;
+ }
+
+ /**
+ * Helper method to set or unset a checkbox and fire its action listener.
+ *
+ * @param cb
+ * @param select
+ */
+ protected void setSelected(Checkbox cb, boolean select)
+ {
+ // TODO refactor to a test utility class
+ cb.setState(select);
+ // have to manually fire the action listener
+ cb.getItemListeners()[0].itemStateChanged(new ItemEvent(cb,
+ ItemEvent.ITEM_STATE_CHANGED, cb, select ? ItemEvent.SELECTED
+ : ItemEvent.DESELECTED));
+ }
+
+ /**
+ * Helper method to drill down to the 'Annotation type' checkbox with given
+ * label.
+ *
+ * @return
+ */
+ private Checkbox getTypeCheckbox(String forLabel)
+ {
+ Component[] cbs = ((JPanel) testee.getComponent(0)).getComponents();
+ for (Component comp : cbs)
+ {
+ final Checkbox cb = (Checkbox) comp;
+ if (cb.getLabel().equals(forLabel))
+ {
+ return cb;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Test isInActionScope for the case where the scope is selected sequences.
+ * Test cases include sequences in the selection group, and others not in the
+ * group.
+ */
+ @Test
+ public void testIsInActionScope_selectedScope()
+ {
+ // sequences 1 and 2 have annotations 4 and 3 respectively
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+
+ final Checkbox selectedSequencesCheckbox = (Checkbox) getComponent(
+ testee, 1, 1, 1);
+ setSelected(selectedSequencesCheckbox, true);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+ // remember 3 annotations to skip (Conservation/Quality/Consensus)
+ assertFalse(testee.isInActionScope(anns[3]));
+ assertFalse(testee.isInActionScope(anns[4]));
+ assertFalse(testee.isInActionScope(anns[5]));
+ assertTrue(testee.isInActionScope(anns[6]));
+ assertTrue(testee.isInActionScope(anns[7]));
+ }
+
+ /**
+ * Test isInActionScope for the case where the scope is unselected sequences.
+ * Test cases include sequences in the selection group, and others not in the
+ * group.
+ */
+ @Test
+ public void testIsInActionScope_unselectedScope()
+ {
+ // sequences 1 and 2 have annotations 4 and 3 respectively
+ selectSequences(1, 2);
+ testee = new AnnotationChooser(parentPanel);
+
+ final Checkbox unselectedSequencesCheckbox = (Checkbox) getComponent(
+ testee, 1, 1, 2);
+ setSelected(unselectedSequencesCheckbox, true);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+ // remember 3 annotations to skip (Conservation/Quality/Consensus)
+ assertTrue(testee.isInActionScope(anns[3]));
+ assertTrue(testee.isInActionScope(anns[4]));
+ assertTrue(testee.isInActionScope(anns[5]));
+ assertFalse(testee.isInActionScope(anns[6]));
+ assertFalse(testee.isInActionScope(anns[7]));
+ }
+
+ /**
+ * Test that the reset method restores previous visibility flags.
+ */
+ @Test
+ public void testResetOriginalState()
+ {
+ testee = new AnnotationChooser(parentPanel);
+
+ AlignmentAnnotation[] anns = parentPanel.getAlignment()
+ .getAlignmentAnnotation();
+ // all start visible
+ for (int i = 0; i < anns.length; i++)
+ {
+ assertTrue(i + "'th sequence not visible", anns[i].visible);
+ }
+
+ final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
+ setSelected(hideCheckbox, true);
+
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
+ 1, 1, 0);
+ setSelected(allSequencesCheckbox, true);
+
+ setSelected(getTypeCheckbox("JMol"), true);
+ setSelected(getTypeCheckbox("IUPRED"), true);
+
+ assertTrue(anns[0].visible); // Conservation
+ assertTrue(anns[1].visible); // Quality
+ assertTrue(anns[2].visible); // Consensus
+ assertFalse(anns[3].visible); // IUPRED
+ assertTrue(anns[4].visible); // Beauty (not seq-related)
+ assertFalse(anns[5].visible); // JMol
+ assertFalse(anns[6].visible); // IUPRED
+ assertFalse(anns[7].visible); // JMol
+
+ // reset - should all be visible
+ testee.resetOriginalState();
+ for (int i = 0; i < anns.length; i++)
+ {
+ assertTrue(i + "'th sequence not visible", anns[i].visible);
+ }
+ }
+}
*/
package jalview.gui;
-import static org.junit.Assert.*;
import jalview.bin.Cache;
-import java.awt.Component;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JPanel;
import javax.swing.JTextArea;
import org.junit.AfterClass;
import org.junit.BeforeClass;
+import org.junit.Ignore;
import org.junit.Test;
public class JAL1353bugdemo
volatile boolean finish = false;
@Test
+ @Ignore
+ // comment out @Ignore to enable this test
public void test()
{
Cache.initLogger();
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.IOException;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Unit tests for PopupMenu
+ *
+ * @author gmcarstairs
+ *
+ */
+public class PopupMenuTest
+{
+ // 4 sequences x 13 positions
+ final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+ + "TIETHKEAELVG-\n"
+ + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+ + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+ + "TIETHKEEELTA-\n";
+
+ private static final int SEQ_ANN_COUNT = 10;
+
+ private static final int AUTO_ANNS = 3;
+
+ AlignmentI alignment;
+
+ AlignmentPanel parentPanel;
+
+ @Before
+ public void setUp() throws IOException
+ {
+ AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ AppletFormatAdapter.PASTE, "FASTA");
+ AlignFrame af = new AlignFrame(al, 700, 500);
+ parentPanel = new AlignmentPanel(af, af.getViewport());
+ alignment = parentPanel.getAlignment();
+
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
+ for (int i = 0; i < anns.length; i++)
+ {
+ anns[i] = new AlignmentAnnotation("Label" + i, null, 0d);
+ anns[i].setCalcId("CalcId" + i);
+ anns[i].visible = true;
+ alignment.addAnnotation(anns[i]);
+ }
+ }
+
+ /**
+ * Test method that determines visible graph groups.
+ */
+ @Test
+ public void testGetVisibleGraphGroups()
+ {
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ /*
+ * a bar graph group is not included
+ */
+ anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
+ anns[0].graphGroup = 1;
+ anns[0].visible = true;
+
+ /*
+ * a line graph group is included as long as one of its members is visible
+ */
+ anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[1].graphGroup = 5;
+ anns[1].visible = false;
+ anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[2].graphGroup = 5;
+ anns[2].visible = true;
+
+ /*
+ * a line graph group with no visible rows is not included
+ */
+ anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[3].graphGroup = 3;
+ anns[3].visible = false;
+
+ // a visible line graph with no graph group is not included
+ anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[4].graphGroup = -1;
+ anns[4].visible = true;
+
+ BitSet result = PopupMenu.getVisibleLineGraphGroups(anns);
+ assertTrue(result.get(5));
+ assertFalse(result.get(0));
+ assertFalse(result.get(1));
+ assertFalse(result.get(2));
+ assertFalse(result.get(3));
+ }
+
+ /**
+ * Test a mixture of show/hidden annotations in/outside selection group.
+ */
+ @Test
+ public void testGetAnnotationTypesForShowHide_forSelectionGroup()
+ {
+ Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ BitSet visibleGraphGroups = new BitSet();
+ selectSequences(0, 3);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+
+ /*
+ * Configure annotation properties for test (offsetting for auto-calculated
+ * rows).
+ */
+ // not in selection group (should be ignored):
+ // hidden annotation Label4 not in selection group
+ anns[AUTO_ANNS + 4].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 4].visible = false;
+ anns[AUTO_ANNS + 7].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 7].visible = true;
+
+ /*
+ * in selection group, hidden:
+ */
+ anns[AUTO_ANNS + 2].sequenceRef = seqs[3]; // CalcId2/Label2
+ anns[AUTO_ANNS + 2].visible = false;
+ anns[AUTO_ANNS + 3].sequenceRef = seqs[3]; // CalcId3/Label2
+ anns[AUTO_ANNS + 3].visible = false;
+ anns[AUTO_ANNS + 3].label = "Label2";
+ anns[AUTO_ANNS + 4].sequenceRef = seqs[3]; // CalcId2/Label3
+ anns[AUTO_ANNS + 4].visible = false;
+ anns[AUTO_ANNS + 4].label = "Label3";
+ anns[AUTO_ANNS + 4].setCalcId("CalcId2");
+ anns[AUTO_ANNS + 8].sequenceRef = seqs[0]; // CalcId9/Label9
+ anns[AUTO_ANNS + 8].visible = false;
+ anns[AUTO_ANNS + 8].label = "Label9";
+ anns[AUTO_ANNS + 8].setCalcId("CalcId9");
+ /*
+ * in selection group, visible
+ */
+ anns[AUTO_ANNS + 6].sequenceRef = seqs[0]; // CalcId6/Label6
+ anns[AUTO_ANNS + 6].visible = true;
+ anns[AUTO_ANNS + 9].sequenceRef = seqs[3]; // CalcId9/Label9
+ anns[AUTO_ANNS + 9].visible = true;
+
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
+
+ // check results; note CalcId9/Label9 is both hidden and shown (for
+ // different sequences) so should be in both
+ // shown: CalcId6/Label6 and CalcId9/Label9
+ assertEquals(2, shownTypes.size());
+ assertEquals(1, shownTypes.get("CalcId6").size());
+ assertEquals(1, shownTypes.get("CalcId6").get(0).size());
+ assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
+ assertEquals(1, shownTypes.get("CalcId9").size());
+ assertEquals(1, shownTypes.get("CalcId9").get(0).size());
+ assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));
+
+ // hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
+ assertEquals(3, hiddenTypes.size());
+ assertEquals(2, hiddenTypes.get("CalcId2").size());
+ assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
+ assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
+ assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
+ assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
+ assertEquals(1, hiddenTypes.get("CalcId3").size());
+ assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
+ assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
+ assertEquals(1, hiddenTypes.get("CalcId9").size());
+ assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
+ assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));
+
+ consoleDebug(shownTypes, hiddenTypes);
+ }
+
+ /**
+ * This output is not part of the test but may help make sense of it...
+ *
+ * @param shownTypes
+ * @param hiddenTypes
+ */
+ protected void consoleDebug(Map<String, List<List<String>>> shownTypes,
+ Map<String, List<List<String>>> hiddenTypes)
+ {
+ for (String calcId : shownTypes.keySet())
+ {
+ System.out.println("Visible annotation types for calcId=" + calcId);
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ System.out.println(" " + type);
+ }
+ }
+ for (String calcId : hiddenTypes.keySet())
+ {
+ System.out.println("Hidden annotation types for calcId=" + calcId);
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ System.out.println(" " + type);
+ }
+ }
+ }
+
+ /**
+ * Test case where there are 'grouped' annotations, visible and hidden, within
+ * and without the selection group.
+ */
+ @Test
+ public void testGetAnnotationTypesForShowHide_withGraphGroups()
+ {
+ final int GROUP_4 = 4;
+ final int GROUP_5 = 5;
+ final int GROUP_6 = 6;
+
+ Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ BitSet visibleGraphGroups = new BitSet();
+ visibleGraphGroups.set(GROUP_4);
+ visibleGraphGroups.set(GROUP_6);
+ selectSequences(0, 3);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+
+ /*
+ * Configure annotation properties for test (offsetting for auto-calculated
+ * rows).
+ */
+ // annotations for selection group and graph group
+ // hidden annotations Label2, Label3, in (hidden) group 5
+ anns[AUTO_ANNS + 2].sequenceRef = seqs[3];
+ anns[AUTO_ANNS + 2].visible = false;
+ anns[AUTO_ANNS + 2].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 2].graphGroup = GROUP_5; // not a visible group
+ anns[AUTO_ANNS + 3].sequenceRef = seqs[0];
+ anns[AUTO_ANNS + 3].visible = false;
+ anns[AUTO_ANNS + 3].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 3].graphGroup = GROUP_5;
+ // need to ensure annotations have the same calcId as well
+ anns[AUTO_ANNS + 3].setCalcId("CalcId2");
+
+ // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
+ anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
+ // being in a visible group should take precedence over this visibility
+ anns[AUTO_ANNS + 1].visible = false;
+ anns[AUTO_ANNS + 1].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 1].graphGroup = GROUP_6;
+ anns[AUTO_ANNS + 5].sequenceRef = seqs[0];
+ anns[AUTO_ANNS + 5].visible = true; // visibleGraphGroups overrides this
+ anns[AUTO_ANNS + 5].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 5].graphGroup = GROUP_6;
+ anns[AUTO_ANNS + 5].setCalcId("CalcId1");
+
+ // annotations outwith selection group - should be ignored
+ // hidden grouped annotations
+ anns[AUTO_ANNS + 6].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 6].visible = false;
+ anns[AUTO_ANNS + 6].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 6].graphGroup = GROUP_4;
+ anns[AUTO_ANNS + 8].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 8].visible = false;
+ anns[AUTO_ANNS + 8].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 8].graphGroup = GROUP_4;
+ // visible grouped annotations Label7, Label9
+ anns[AUTO_ANNS + 7].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 7].visible = true;
+ anns[AUTO_ANNS + 7].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 7].graphGroup = GROUP_4;
+ anns[AUTO_ANNS + 9].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 9].visible = true;
+ anns[AUTO_ANNS + 9].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 9].graphGroup = GROUP_4;
+
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
+
+ consoleDebug(shownTypes, hiddenTypes);
+
+ // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
+ assertEquals(1, shownTypes.get("CalcId1").size());
+ assertEquals(2, shownTypes.get("CalcId1").get(0).size());
+ assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
+ assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
+
+ // CalcId2 / Label2, Label3 (only) should be 'hidden'
+ assertEquals(1, hiddenTypes.get("CalcId2").size());
+ assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
+ assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
+ assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
+ }
+
+ /**
+ * Add a sequence group to the alignment with the specified sequences (base 0)
+ * in it
+ *
+ * @param i
+ * @param more
+ */
+ private void selectSequences(int... selected)
+ {
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ SequenceGroup sg = new SequenceGroup();
+ for (int i : selected)
+ {
+ sg.addSequence(seqs[i], false);
+ }
+ parentPanel.av.setSelectionGroup(sg);
+ }
+}
import java.util.ArrayList;
import java.util.List;
-import java.util.function.Consumer;
import org.junit.Test;
}
String jobid = msaservice.align(iseqs);
- if (jobid != null) {
- JobStatus js = null;
- do {
- try {
- Thread.sleep(500);
- } catch (InterruptedException q) {
- }
- ;
- js = msaservice.getJobStatus(jobid);
- } while (!js.equals(JobStatus.FAILED)
- && !js.equals(JobStatus.CANCELLED)
- && !js.equals(JobStatus.FINISHED));
- assertEquals("Trial alignment failed. State was " + js.name(),
- js, JobStatus.FINISHED);
- assertEquals(
- "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
- msaservice.getResult(jobid).getSequences().size(),
- iseqs.size());
- msaservice.getResult(jobid).getSequences()
- .forEach(new Consumer<FastaSequence>() {
- @Override
- public void accept(FastaSequence t) {
- System.out.println(">"+t.getId());
- System.out.println(t.getFormattedFasta());
- }
- });
+ if (jobid != null)
+ {
+ JobStatus js = null;
+ do
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ js = msaservice.getJobStatus(jobid);
+ } while (!js.equals(JobStatus.FAILED)
+ && !js.equals(JobStatus.CANCELLED)
+ && !js.equals(JobStatus.FINISHED));
+ assertEquals("Trial alignment failed. State was " + js.name(), js,
+ JobStatus.FINISHED);
+ assertEquals(
+ "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
+ msaservice.getResult(jobid).getSequences().size(),
+ iseqs.size());
+ for (FastaSequence t : msaservice.getResult(jobid).getSequences())
+ {
+ System.out.println(">" + t.getId());
+ System.out.println(t.getFormattedFasta());
+ }
+ // .forEach(new Consumer<FastaSequence>() {
+ // @Override
+ // public void accept(FastaSequence t) {
+ // System.out.println(">"+t.getId());
+ // System.out.println(t.getFormattedFasta());
+ // }
+ // });
}
}
git://source.jalview.org / jalview.git / commitdiff