source/provider from matching the annotation description and PDB entry.
Implementation of Show secondary structure menu option. Updated
calculation of secondary structure consensus.
label.norm_consensus_logo = Normalise Consensus Logo
label.apply_all_groups = Apply to all groups
label.autocalculated_annotation = Autocalculated Annotation
-label.select_secondary_structure_preference = Secondary Structure Preference
+label.show_secondary_structure = Show Secondary Structure
label.show_first = Show first
label.show_last = Show last
label.struct_from_pdb = Process secondary structure from PDB
}
char c = sequences[row].getCharAt(column);
- AlignmentAnnotation[] aa = sequences[row].getAnnotation(Constants.SS_ANNOTATION_LABEL);
- if(aa == null) {
- aa = sequences[row].getAnnotation(Constants.SS_ANNOTATION_FROM_JPRED_LABEL);
- }
+ AlignmentAnnotation aa = AlignmentUtils.getDisplayedAlignmentAnnotation(sequences[row]);
if(aa!=null) {
ssCount++;
}
import java.util.Set;
import java.util.SortedMap;
import java.util.TreeMap;
+import java.util.Vector;
import jalview.api.AlignCalcWorkerI;
import jalview.bin.Console;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.IncompleteCodonException;
import jalview.datamodel.Mapping;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
return Color.gray;
}
- public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation[] aa,
+ public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation aa,
int seqPosition)
{
char ss = '*';
if (aa != null) {
- if (aa[0].getAnnotationForPosition(seqPosition) != null) {
- Annotation a = aa[0].getAnnotationForPosition(seqPosition);
+ if (aa.getAnnotationForPosition(seqPosition) != null) {
+ Annotation a = aa.getAnnotationForPosition(seqPosition);
ss = a.secondaryStructure;
//There is no representation for coil and it can be either ' ' or null.
return ss;
}
- public static String getSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations)
- {
- String ssSource = null;
+
+ public static List<String> extractSSSourceInAlignmentAnnotation(AlignmentAnnotation[] annotations) {
+
+ List<String> ssSources = new ArrayList<>();
+ Set<String> addedSources = new HashSet<>(); // to keep track of added sources
+
+
+ for (AlignmentAnnotation aa: annotations) {
+
+ String ssSource = extractSSSourceFromAnnotationDescription(aa);
+
+ if (ssSource!= null && !addedSources.contains(ssSource)) {
+ ssSources.add(ssSource);
+ addedSources.add(ssSource);
+ }
+
+ }
+ Collections.sort(ssSources);
+
+ return ssSources;
+
+ }
+
+ public static String extractSSSourceFromAnnotationDescription(AlignmentAnnotation aa) {
+
+
+ for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) {
+
+ if (label.equals(aa.label)) {
+
+ //For JPred
+ if(aa.label.equals(Constants.SS_ANNOTATION_FROM_JPRED_LABEL)){
+
+ return (Constants.SECONDARY_STRUCTURE_LABELS.get(aa.label));
+
+ }
+
+ //For input with secondary structure
+ if(aa.label.equals(Constants.SS_ANNOTATION_LABEL)
+ && aa.description.equals(Constants.SS_ANNOTATION_LABEL)){
+
+ return (Constants.SECONDARY_STRUCTURE_LABELS.get(aa.label));
+
+ }
+
+ //For other sources
+ if(aa.sequenceRef==null) {
+ return null;
+ }
+ else if(aa.sequenceRef.getDatasetSequence()==null) {
+ return null;
+ }
+ Vector<PDBEntry> pdbEntries = aa.sequenceRef.getDatasetSequence().getAllPDBEntries();
+
+ for (PDBEntry entry : pdbEntries){
+
+ String entryProvider = entry.getProvider();
+ if(entryProvider == null) {
+ entryProvider = "PDB";
+ }
+
+ // Trim the string from first occurrence of colon
+ String entryID = entry.getId();
+ int index = entryID.indexOf(':');
+
+ // Check if colon exists
+ if (index != -1) {
+
+ // Trim the string from first occurrence of colon
+ entryID = entryID.substring(0, index);
+
+ }
+
+ if(entryProvider == "PDB" && aa.description.toLowerCase().contains
+ ("secondary structure for " + entryID.toLowerCase())){
+
+ return entryProvider;
+
+ }
+
+ else if (entryProvider != "PDB" && aa.description.toLowerCase().contains(entryID.toLowerCase())){
+
+ return entryProvider;
+
+ }
+
+ }
+
+ }
+ }
+
+ return null;
+
+ }
+
+ //to do set priority for labels
+ public static AlignmentAnnotation getDisplayedAlignmentAnnotation(SequenceI seq){
- return ssSource;
+ for(String ssLabel : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) {
+
+ AlignmentAnnotation[] aa = seq.getAnnotation(ssLabel);
+ if(aa!=null) {
+
+ for (AlignmentAnnotation annot: aa) {
+ if(annot.visible) {
+ return annot;
+ }
+ }
+ }
+ }
+
+ return null;
}
if(!gap1 && !undefinedSS1) {
//fetch the position in sequence for the column and finds the
//corresponding secondary structure annotation
- //TO DO - consider based on priority
+ //TO DO - consider based on priority and displayed
int seqPosition = seqs[i].findPosition(cpos);
AlignmentAnnotation[] aa = seqs[i].getRefSeq().getAnnotation(selectedSSSource);
+ if(aa!=null)
ss1 =
- AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
+ AlignmentUtils.findSSAnnotationForGivenSeqposition(aa[0], seqPosition);
}
if(!gap2 && !undefinedSS2) {
int seqPosition = seqs[j].findPosition(cpos);
AlignmentAnnotation[] aa = seqs[j].getRefSeq().getAnnotation(selectedSSSource);
- ss2 =
- AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
+ if(aa!=null)
+ ss2 =
+ AlignmentUtils.findSSAnnotationForGivenSeqposition(aa[0], seqPosition);
}
if ((!gap1 && !gap2) || params.includeGaps())
import java.util.Locale;
import java.util.Vector;
+import javax.swing.AbstractButton;
import javax.swing.ButtonGroup;
+import javax.swing.ButtonModel;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.Constants;
import jalview.util.HttpUtils;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.imagemaker.BitmapImageSizing;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
+import jalview.workers.SecondaryStructureConsensusThread;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
alignPanel.paintAlignment(false, false);
}
+
+ @Override
+ protected void updateShowSSRadioButtons(JMenu showSS, ButtonGroup ssButtonGroup){
+
+ List<String> ssSources = new ArrayList<String>();
+ AlignmentAnnotation[] anns = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(anns);
+
+ // Get the currently selected radio button
+ String selectedButtonModelName = getSelectedRadioButtonDisplayString(ssButtonGroup);
+ boolean selectedButtonModel = false;
+
+ // Clear existing radio buttons
+ showSS.removeAll();
+ JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem("All");
+ radioButtonAllSS.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed("All");
+ }
+ });
+ ssButtonGroup.add(radioButtonAllSS);
+ showSS.add(radioButtonAllSS);
+
+ JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem("None");
+ radioButtonNoneSS.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed("None");
+ }
+ });
+ ssButtonGroup.add(radioButtonNoneSS);
+ showSS.add(radioButtonNoneSS);
+ showSS.addSeparator();
+
+ for(String ssSource : ssSources) {
+
+ JRadioButtonMenuItem radioButton = new JRadioButtonMenuItem(ssSource);
+ radioButton.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ showSS_actionPerformed(ssSource);
+ }
+ });
+ ssButtonGroup.add(radioButton);
+ showSS.add(radioButton);
+
+ // Check if this radio button's name matches the selected radio button's name
+ if (ssSource.equals(selectedButtonModelName)) {
+ radioButton.setSelected(true); // Select this radio button
+ selectedButtonModel = true;
+ }
+
+ }
+
+ if (selectedButtonModelName == "None") {
+ // If no radio button was previously selected, select "All"
+ ssButtonGroup.setSelected(radioButtonNoneSS.getModel(), true);
+ selectedButtonModel = true;
+ }
+ if (!selectedButtonModel) {
+ // If no radio button was previously selected, select "All"
+ ssButtonGroup.setSelected(radioButtonAllSS.getModel(), true);
+ }
+ }
+
+ @Override
+ protected void showSS_actionPerformed(String ssSourceSelection){
+
+
+ AlignmentAnnotation[] annotations = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+
+ for (AlignmentAnnotation aa: annotations) {
+
+ for (String label : Constants.SECONDARY_STRUCTURE_LABELS.keySet()) {
+
+ if (label.equals(aa.label)) {
+
+ aa.visible = false;
+
+ if(ssSourceSelection == "All") {
+ aa.visible = true;
+ }
+
+ else {
+ String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa);
+ if(ssSource.equals(ssSourceSelection)) {
+ aa.visible = true;
+ }
+
+
+ }
+ }
+ }
+
+ }
+
+
+ List<AlignCalcWorkerI> workers = viewport.getCalcManager()
+ .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty()) {
+
+ viewport.getCalcManager().startWorker(workers.remove(0));
+
+ }
+
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true, true);
+
+
+
+ }
+
+ protected String getSelectedRadioButtonDisplayString(ButtonGroup ssButtonGroup) {
+ Enumeration<AbstractButton> buttons = ssButtonGroup.getElements();
+ while (buttons.hasMoreElements()) {
+ AbstractButton button = buttons.nextElement();
+ if (button.isSelected()) {
+ return button.getText();
+ }
+ }
+ return null; // No radio button is selected
+}
/*
* (non-Javadoc)
AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
List<String> ssSources = AlignmentUtils.getSecondaryStructureSources(annotations);
+ //List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+
return ssSources;
}
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import javax.swing.BorderFactory;
import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
+import jalview.log.JLoggerLog4j;
import jalview.schemes.ResidueColourScheme;
+import jalview.util.Log4j;
import jalview.util.MessageManager;
import jalview.util.Platform;
};
addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
copyHighlighted.addActionListener(al);
+
+
+
+ ButtonGroup ssButtonGroup = new ButtonGroup();
+ final JRadioButtonMenuItem showAll = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_first"));
+ final JRadioButtonMenuItem showjPred = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_last"));
+ final JRadioButtonMenuItem show3DSS = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_last"));
+ ssButtonGroup.add(showAll);
+ ssButtonGroup.add(showjPred);
+ ssButtonGroup.add(show3DSS);
+ final boolean autoFirst1 = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAll.setSelected(autoFirst1);
+ setShowAutoCalculatedAbove(autoFirst);
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
- JMenu selectSS = new JMenu(
- MessageManager.getString("label.select_secondary_structure_preference"));
+ JMenu showSS = new JMenu(
+ MessageManager.getString("label.show_secondary_structure"));
+
+ showSS.addMouseListener(new MouseAdapter() {
+
+ @Override
+ public void mouseEntered(MouseEvent e) {
+
+ updateShowSSRadioButtons(showSS, ssButtonGroup); // Update radio buttons every time the menu is clicked
+
+ }
+ });
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
annotationsMenu.add(sortAnnBySequence);
annotationsMenu.add(sortAnnByLabel);
annotationsMenu.addSeparator();
+ annotationsMenu.add(showSS);
+ annotationsMenu.addSeparator();
autoAnnMenu.add(showAutoFirst);
autoAnnMenu.add(showAutoLast);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
- selectSS.add(threeDStructure);
- selectSS.add(jPred);
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
protected void showComplement_actionPerformed(boolean complement)
{
}
+
+ protected List<String> updateShowSSRadioButtons()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ protected void updateShowSSRadioButtons(JMenu showSS,
+ ButtonGroup ssButtonGroup)
+ {
+ // TODO Auto-generated method stub
+ }
+
+ protected void showSS_actionPerformed(String ssSourceSelection)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.SortedMap;
import java.util.TreeMap;
{annotations4, true}, // Annotations present from JPred secondary structure present
};
}
-//
-// @Test(dataProvider = "SSSourceFromAnnotationDescription")
-// public void testGetSSSourceFromAnnotationDescription(Map<SequenceI, List<AlignmentAnnotation>> annotations, String expectedSSSource) {
-// String actualSSSource = AlignmentUtils.getSSSourceFromAnnotationDescription(annotations);
-// Assert.assertEquals(actualSSSource, expectedSSSource);
-// }
+
+ @Test
+ public void testGetSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations, String expectedSSSource) {
+ List<String> actualSSSource = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+ Assert.assertEquals(actualSSSource, expectedSSSource);
+ }
@DataProvider(name = "SSSourceFromAnnotationDescription")
public static Object[][] provideSSSourceFromAnnotationDescription() {
git://source.jalview.org / jalview.git / commitdiff