*/
package jalview.appletgui;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+ import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
UrlProviderI urlProvider = null;
-- public IdPanel(AlignViewport av, AlignmentPanel parent)
++ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
-- this.av = av;
++ this.av = viewport;
alignPanel = parent;
-- idCanvas = new IdCanvas(av);
++ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
// make a list of label,url pairs
HashMap<String, String> urlList = new HashMap<String, String>();
-- if (av.applet != null)
++ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
-- label = av.applet.getParameter("linkLabel_" + i);
-- url = av.applet.getParameter("linkURL_" + i);
++ label = viewport.applet.getParameter("linkLabel_" + i);
++ url = viewport.applet.getParameter("linkURL_" + i);
// only add non-null parameters
if (label != null)
if (!urlList.isEmpty())
{
// set default as first entry in list
-- String defaultUrl = av.applet.getParameter("linkLabel_1");
++ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
UrlProviderFactoryI factory = new AppletUrlProviderFactory(
defaultUrl, urlList);
urlProvider = factory.createUrlProvider();
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- // look for non-pos features
StringBuffer tooltiptext = new StringBuffer();
- if (sequence != null)
+ if (sequence == null)
{
- if (sequence.getDescription() != null)
+ return;
+ }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
+ {
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
{
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
}
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ if (sf.getType() != null)
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
- {
- boolean nl = false;
- if (sf[sl].getFeatureGroup() != null)
- {
- tooltiptext.append(sf[sl].getFeatureGroup());
- nl = true;
- }
- ;
- if (sf[sl].getType() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getType());
- nl = true;
- }
- ;
- if (sf[sl].getDescription() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getDescription());
- nl = true;
- }
- ;
- if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
- {
- tooltiptext.append(" Score = ");
- tooltiptext.append(sf[sl].getScore());
- nl = true;
- }
- ;
- if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
- {
- tooltiptext.append(" (");
- tooltiptext.append(sf[sl].getStatus());
- tooltiptext.append(")");
- nl = true;
- }
- ;
- if (nl)
- {
- tooltiptext.append("\n");
- }
- }
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ if (nl)
+ {
+ tooltiptext.append("\n");
}
}
+
if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
String id = sq.getName();
// get the default url with the sequence details filled in
+ if (urlProvider == null)
+ {
+ return;
+ }
String url = urlProvider.getPrimaryUrl(id);
String target = urlProvider.getPrimaryTarget(id);
try
if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
- // build a new links menu based on the current links + any non-positional
- // features
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
- List<String> nlinks = urlProvider.getLinksForMenu();
+ List<String> nlinks;
+ if (urlProvider != null)
+ {
+ nlinks = urlProvider.getLinksForMenu();
+ }
+ else
+ {
+ nlinks = new ArrayList<String>();
+ }
- SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ if (sf.links != null)
{
- if (sf[sl].links != null && sf[sl].links.size() > 0)
+ for (String link : sf.links)
{
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
- {
- nlinks.add(sf[sl].links.elementAt(l));
- }
+ nlinks.add(link);
}
}
}
boolean up = true;
-- public ScrollThread(boolean up)
++ public ScrollThread(boolean isUp)
{
-- this.up = up;
++ this.up = isUp;
start();
}
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+ import jalview.io.FeaturesFile;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.event.MouseEvent;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.HashMap;
+ import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
AlignmentPanel ap;
/**
- * Creates a new FeatureRenderer object.
+ * Creates a new FeatureRenderer object
*
- * @param av
- * DOCUMENT ME!
+ * @param alignPanel
*/
- public FeatureRenderer(AlignmentPanel ap)
+ public FeatureRenderer(AlignmentPanel alignPanel)
{
- super(ap.av);
- this.ap = ap;
- if (ap != null && ap.getSeqPanel() != null
- && ap.getSeqPanel().seqCanvas != null
- && ap.getSeqPanel().seqCanvas.fr != null)
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
{
- transferSettings(ap.getSeqPanel().seqCanvas.fr);
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
}
}
int featureIndex = 0;
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features, boolean newFeatures,
- final AlignmentPanel ap)
+ /**
+ * Presents a dialog allowing the user to add new features, or amend or delete
+ * existing features. Currently this can be on
+ * <ul>
+ * <li>double-click on a sequence - Amend/Delete features at position</li>
+ * <li>Create sequence feature from pop-up menu on selected region</li>
+ * <li>Create features for pattern matches from Find</li>
+ * </ul>
+ *
+ * @param sequences
+ * the sequences features are to be created on (if creating
+ * features), or a single sequence (if amending features)
+ * @param features
+ * the current features at the position (if amending), or template
+ * new features with start/end position set (if creating)
+ * @param create
+ * true to create features, false to amend or delete
+ * @param featureType
+ * the feature type to set on new features; if null, defaults to the
+ * type of the last new feature created if any, failing that to
+ * "feature_1"
+ * @param alignPanel
+ * @return
+ */
+ protected boolean amendFeatures(final List<SequenceI> sequences,
+ final List<SequenceFeature> features, boolean create,
+ final AlignmentPanel alignPanel, String featureType)
{
featureIndex = 0;
- final JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox overlaps;
+ final JPanel mainPanel = new JPanel(new BorderLayout());
final JTextField name = new JTextField(25);
final JTextField source = new JTextField(25);
final JTextArea description = new JTextArea(3, 25);
if (col != null)
{
fcol = new FeatureColour(col);
- updateColourButton(bigPanel, colour, new FeatureColour(col));
+ updateColourButton(mainPanel, colour, new FeatureColour(col));
}
}
else
{
if (fcc == null)
{
- final String type = features[featureIndex].getType();
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
fcc = new FeatureColourChooser(me, type);
fcc.setRequestFocusEnabled(true);
fcc.requestFocus();
fcol = fcc.getLastColour();
fcc = null;
setColour(type, fcol);
- updateColourButton(bigPanel, colour, fcol);
+ updateColourButton(mainPanel, colour, fcol);
}
});
}
}
});
- JPanel tmp = new JPanel();
- JPanel panel = new JPanel(new GridLayout(3, 1));
+ JPanel gridPanel = new JPanel(new GridLayout(3, 1));
- // /////////////////////////////////////
- // /MULTIPLE FEATURES AT SELECTED RESIDUE
- if (!newFeatures && features.length > 1)
+ if (!create && features.size() > 1)
{
- panel = new JPanel(new GridLayout(4, 1));
- tmp = new JPanel();
- tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+ /*
+ * more than one feature at selected position - add a drop-down
+ * to choose the feature to amend
+ */
+ gridPanel = new JPanel(new GridLayout(4, 1));
+ JPanel choosePanel = new JPanel();
+ choosePanel.add(new JLabel(MessageManager
+ .getString("label.select_feature")
+ ":"));
- overlaps = new JComboBox();
- for (int i = 0; i < features.length; i++)
+ final JComboBox<String> overlaps = new JComboBox<String>();
+ for (SequenceFeature sf : features)
{
- overlaps.addItem(features[i].getType() + "/"
- + features[i].getBegin() + "-" + features[i].getEnd()
- + " (" + features[i].getFeatureGroup() + ")");
+ String text = sf.getType() + "/" + sf.getBegin() + "-"
+ + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+ overlaps.addItem(text);
}
-
- tmp.add(overlaps);
+ choosePanel.add(overlaps);
overlaps.addItemListener(new ItemListener()
{
if (index != -1)
{
featureIndex = index;
- name.setText(features[index].getType());
- description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
+ SequenceFeature sf = features.get(index);
+ name.setText(sf.getType());
+ description.setText(sf.getDescription());
+ source.setText(sf.getFeatureGroup());
+ start.setValue(new Integer(sf.getBegin()));
+ end.setValue(new Integer(sf.getEnd()));
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequences[0], features[index].getBegin(),
- features[index].getEnd());
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
- ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
}
FeatureColourI col = getFeatureStyle(name.getText());
.createColourFromName(name.getText()));
}
oldcol = fcol = col;
- updateColourButton(bigPanel, colour, col);
+ updateColourButton(mainPanel, colour, col);
}
});
- panel.add(tmp);
+ gridPanel.add(choosePanel);
}
// ////////
// ////////////////////////////////////
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.name:"),
+ JPanel namePanel = new JPanel();
+ gridPanel.add(namePanel);
+ namePanel.add(new JLabel(MessageManager.getString("label.name:"),
JLabel.RIGHT));
- tmp.add(name);
+ namePanel.add(name);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group:"),
+ JPanel groupPanel = new JPanel();
+ gridPanel.add(groupPanel);
+ groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
JLabel.RIGHT));
- tmp.add(source);
+ groupPanel.add(source);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.colour"),
+ JPanel colourPanel = new JPanel();
+ gridPanel.add(colourPanel);
+ colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
JLabel.RIGHT));
- tmp.add(colour);
+ colourPanel.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
colour.setForeground(Color.black);
colour.setVerticalAlignment(SwingConstants.CENTER);
colour.setHorizontalTextPosition(SwingConstants.CENTER);
colour.setVerticalTextPosition(SwingConstants.CENTER);
- bigPanel.add(panel, BorderLayout.NORTH);
+ mainPanel.add(gridPanel, BorderLayout.NORTH);
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description:"),
+ JPanel descriptionPanel = new JPanel();
+ descriptionPanel.add(new JLabel(MessageManager
+ .getString("label.description:"),
JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
- panel.add(new JScrollPane(description));
+ descriptionPanel.add(new JScrollPane(description));
- if (!newFeatures)
+ if (!create)
{
- bigPanel.add(panel, BorderLayout.SOUTH);
+ mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
- panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.start"),
+ JPanel startEndPanel = new JPanel();
+ startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(MessageManager.getString("label.end"),
+ startEndPanel.add(start);
+ startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
JLabel.RIGHT));
- panel.add(end);
- bigPanel.add(panel, BorderLayout.CENTER);
+ startEndPanel.add(end);
+ mainPanel.add(startEndPanel, BorderLayout.CENTER);
}
else
{
- bigPanel.add(panel, BorderLayout.CENTER);
+ mainPanel.add(descriptionPanel, BorderLayout.CENTER);
}
- if (lastFeatureAdded == null)
+ SequenceFeature firstFeature = features.get(0);
+ if (featureType != null)
{
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
+ lastFeatureAdded = featureType;
+ }
+ else
+ {
+ if (lastFeatureAdded == null)
{
- lastFeatureAdded = "feature_1";
+ if (firstFeature.type != null)
+ {
+ lastFeatureAdded = firstFeature.type;
+ }
+ else
+ {
+ lastFeatureAdded = "feature_1";
+ }
}
}
if (lastFeatureGroupAdded == null)
{
- if (features[0].featureGroup != null)
+ if (firstFeature.featureGroup != null)
{
- lastFeatureGroupAdded = features[0].featureGroup;
+ lastFeatureGroupAdded = firstFeature.featureGroup;
}
else
{
}
}
- if (newFeatures)
+ if (create)
{
name.setText(lastFeatureAdded);
source.setText(lastFeatureGroupAdded);
}
else
{
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
+ name.setText(firstFeature.getType());
+ source.setText(firstFeature.getFeatureGroup());
}
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- description.setText(features[0].getDescription());
- updateColourButton(bigPanel, colour,
+ start.setValue(new Integer(firstFeature.getBegin()));
+ end.setValue(new Integer(firstFeature.getEnd()));
+ description.setText(firstFeature.getDescription());
+ updateColourButton(mainPanel, colour,
(oldcol = fcol = getFeatureStyle(name.getText())));
Object[] options;
- if (!newFeatures)
+ if (!create)
{
- options = new Object[] { "Amend", "Delete", "Cancel" };
+ options = new Object[] { MessageManager.getString("label.amend"),
+ MessageManager.getString("action.delete"),
+ MessageManager.getString("action.cancel") };
}
else
{
- options = new Object[] { "OK", "Cancel" };
+ options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
}
- String title = newFeatures ? MessageManager
+ String title = create ? MessageManager
.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences[0].getName() });
+ new String[] { sequences.get(0).getName() });
+ /*
+ * show the dialog
+ */
int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+ mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
JvOptionPane.QUESTION_MESSAGE, null, options,
MessageManager.getString("action.ok"));
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+ FeaturesFile ffile = new FeaturesFile();
if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
{
}
}
- if (!newFeatures)
+ if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
if (reply == JvOptionPane.NO_OPTION)
{
- sequences[0].getDatasetSequence().deleteFeature(sf);
+ /*
+ * NO_OPTION corresponds to the Delete button
+ */
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
}
else if (reply == JvOptionPane.YES_OPTION)
{
+ /*
+ * YES_OPTION corresponds to the Amend button
+ */
+ boolean typeChanged = !lastFeatureAdded.equals(sf.type);
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
-
- setColour(sf.type, fcol);
- getFeaturesDisplayed().setVisible(sf.type);
-
+ String newType = lastFeatureAdded;
+ String newFeatureGroup = lastFeatureGroupAdded;
+ String newDescription = lastDescriptionAdded;
+
+ setColour(newType, fcol);
+ getFeaturesDisplayed().setVisible(newType);
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = ((Integer) start.getValue()).intValue();
- sf.end = ((Integer) end.getValue()).intValue();
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
} catch (NumberFormatException ex)
{
+ // JSpinner doesn't accept invalid format data :-)
+ }
+
+ /*
+ * replace the feature by deleting it and adding a new one
+ * (to ensure integrity of SequenceFeatures data store)
+ */
- sequences[0].deleteFeature(sf);
++ sequences.get(0).deleteFeature(sf);
+ SequenceFeature newSf = new SequenceFeature(newType,
+ newDescription, newBegin, newEnd, sf.getScore(),
+ newFeatureGroup);
+ // ensure any additional properties are copied
+ if (sf.otherDetails != null)
+ {
+ newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
+ }
+ ffile.parseDescriptionHTML(newSf, false);
+ // add any additional links not parsed from description
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ newSf.addLink(link);
+ }
}
+ // amend features only gets one sequence to act on
- sequences[0].addSequenceFeature(newSf);
++ sequences.get(0).addSequenceFeature(newSf);
+
- ffile.parseDescriptionHTML(sf, false);
+ if (typeChanged)
+ {
+ findAllFeatures();
+ }
}
}
else
{
if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
+ for (int i = 0; i < sequences.size(); i++)
{
- features[i].type = lastFeatureAdded;
+ SequenceFeature sf = features.get(i);
+ sf.type = lastFeatureAdded;
// fix for JAL-1538 - always set feature group here
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ sequences.get(i).addSequenceFeature(sf);
+ ffile.parseDescriptionHTML(sf, false);
}
if (lastFeatureGroupAdded != null)
findAllFeatures(false);
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
}
}
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true);
return true;
}
git://source.jalview.org / jalview.git / commitdiff