/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
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.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem pdbFromFile = new JMenuItem();
- // JBPNote: Commented these out - Should add these services via the web
- // services menu system.
- // JMenuItem ContraFold = new JMenuItem();
-
- // JMenuItem RNAFold = new JMenuItem();
-
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu seqHideAnnotationsMenu = new JMenu();
- JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenu groupShowAnnotationsMenu = new JMenu();
JMenu groupHideAnnotationsMenu = new JMenu();
- JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
JMenuItem sequenceFeature = new JMenuItem();
JMenu jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem pdbStructureDialog = new JMenuItem();
- JMenu viewStructureMenu = new JMenu();
+ JMenu rnaStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
-
JMenu groupLinksMenu;
JMenuItem hideInsertions = new JMenuItem();
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
makeReferenceSeq.setText("Mark as representative");
}
- if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size() > 0)
+ if (!ap.av.getAlignment().isNucleotide())
{
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
- .elements();
-
- while (e.hasMoreElements())
- {
- final PDBEntry pdb = (PDBEntry) e.nextElement();
-
- menuItem = new JMenuItem();
- menuItem.setText(pdb.getId());
- menuItem.addActionListener(new ActionListener()
- {
- @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);
-
- /*
- * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
- * menuItem.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * colourByStructure(pdb.getId()); } });
- * colStructureMenu.add(menuItem);
- */
- }
+ remove(rnaStructureMenu);
}
else
{
- if (ap.av.getAlignment().isNucleotide() == false)
- {
- structureMenu.remove(viewStructureMenu);
- }
- // structureMenu.remove(colStructureMenu);
- }
- if (ap.av.getAlignment().isNucleotide() == true)
- {
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ int origCount = rnaStructureMenu.getItemCount();
+ /*
+ * add menu items to 2D-render any alignment or sequence secondary
+ * structure annotation
+ */
+ AlignmentAnnotation[] aas = ap.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; aa != null && i < aa.length; i++)
+ if (aas != null)
{
- if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
+ for (final AlignmentAnnotation aa : aas)
{
- final String rnastruc = aa[i].getRNAStruc();
- final String structureLine = aa[i].label + " (alignment)";
- menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new String[]
- { structureLine }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ if (aa.isValidStruc() && aa.sequenceRef == null)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ /*
+ * valid alignment RNA secondary structure annotation
+ */
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new Object[]
+ { aa.label }));
+ menuItem.addActionListener(new java.awt.event.ActionListener()
{
- // // System.out.println("1:"+structureLine);
- // System.out.println("1:sname" + seq.getName());
- // System.out.println("2:seq" + seq);
- //
- // // System.out.println("3:"+seq.getSequenceAsString());
- // System.out.println("3:strucseq" + rnastruc);
- // // System.out.println("4:struc"+seq.getRNA());
- // System.out.println("5:name" + seq.getName());
- // System.out.println("6:ap" + ap);
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),
- rnastruc, seq.getName(), ap);
- // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
- // seq.getName(), ap);
- System.out.println("end");
- }
- });
- viewStructureMenu.add(menuItem);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq, aa, ap);
+ }
+ });
+ rnaStructureMenu.add(menuItem);
+ }
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
-
if (seq.getAnnotation() != null)
{
- AlignmentAnnotation seqAnno[] = seq.getAnnotation();
- for (int i = 0; i < seqAnno.length; i++)
+ AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+ for (final AlignmentAnnotation aa : seqAnns)
{
- if (seqAnno[i].isValidStruc())
+ if (aa.isValidStruc())
{
- final String rnastruc = seqAnno[i].getRNAStruc();
-
+ /*
+ * valid sequence RNA secondary structure annotation
+ */
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name", new String[]
+ "label.2d_rna_sequence_name", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
-
- new AppVarna(seq.getName() + " structure", seq, seq
- .getSequenceAsString(), rnastruc, seq.getName(),
- ap);
+ new AppVarna(seq, aa, ap);
}
});
- viewStructureMenu.add(menuItem);
+ rnaStructureMenu.add(menuItem);
}
}
}
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
}
menuItem = new JMenuItem(
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new String[]
+ new Object[]
{ sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
- if (pdbe.size() == 1)
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_structure_for", new String[]
- { sqass.getDisplayId(false) })));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_all_structures", new String[]
- { new Integer(pdbe.size()).toString() })));
- }
- gpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
- gpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pe, ap.av.collateForPDB(pe));
- }
- });
- if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
- {
- structureMenu.add(rpdbview = new JMenuItem(MessageManager
- .formatMessage(
- "label.view_all_representative_structures",
- new String[]
- { new Integer(reppdb.size()).toString() })));
- rpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
- rpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- }
- });
- }
}
}
else
if (seq == null)
{
sequenceMenu.setVisible(false);
- structureMenu.setVisible(false);
+ pdbStructureDialog.setVisible(false);
+ rnaStructureMenu.setVisible(false);
}
if (links != null && links.size() > 0)
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
- label = label.substring(1, label.length() - 1);
+ label = label.substring(1, label.length() - 1); // a, b, c
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, forSequences, allTypes,
- actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
}
});
showOrHideMenu.add(item);
}
- /**
- * Action on selecting a list of annotation type (or the 'all types' values)
- * to show or hide for the specified sequences.
- *
- * @param types
- * @param forSequences
- * @param anyType
- * @param doShow
- */
- protected void showHideAnnotation_actionPerformed(
- Collection<String> types, List<SequenceI> forSequences,
- boolean anyType, boolean doShow)
- {
- for (AlignmentAnnotation aa : ap.getAlignment()
- .getAlignmentAnnotation())
- {
- if (anyType || types.contains(aa.label))
- {
- if ((aa.sequenceRef != null)
- && forSequences.contains(aa.sequenceRef))
- {
- aa.visible = doShow;
- }
- }
- }
- refresh();
- }
-
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
addshowLink(linkMenus[type], label
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_param", new String[]
+ "label.open_url_param", new Object[]
{ url }));
item.addActionListener(new java.awt.event.ActionListener()
{
pdbFromFile_actionPerformed();
}
});
- // RNAFold.setText("From RNA Fold with predict2D");
- // RNAFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // RNAFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
- // ContraFold.setText("From Contra Fold with predict2D");
- // ContraFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // ContraFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
+
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
- viewStructureMenu.setText(MessageManager
- .getString("label.view_structure"));
+ pdbStructureDialog.setText(MessageManager
+ .getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
+ rnaStructureMenu.setText(MessageManager
+ .getString("label.view_rna_structure"));
+
// colStructureMenu.setText("Colour By Structure");
editSequence.setText(MessageManager.getString("label.edit_sequence")
+ "...");
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
- add(structureMenu);
+ add(rnaStructureMenu);
+ add(pdbStructureDialog);
if (sequence!=null)
{
add(hideInsertions);
if (ap.getAlignment().isNucleotide())
{
// JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
- // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
protected void configureReferenceAnnotationsMenu(
JMenuItem menuItem, List<SequenceI> forSequences)
{
- menuItem.setText(MessageManager
- .getString("label.add_reference_annotations"));
menuItem.setEnabled(false);
- if (forSequences == null)
- {
- return;
- }
/*
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
Map<String, String> tipEntries = new TreeMap<String, String>();
- StringBuilder tooltip = new StringBuilder(64);
- tooltip.append(MessageManager.getString("label.add_annotations_for"));
-
- /*
- * For each sequence selected in the alignment, make a list of any
- * annotations on the underlying dataset sequence which are not already on
- * the alignment.
- *
- * Build a map of { alignmentSequence, <List of annotations to add> }
- */
- AlignmentI al = this.ap.av.getAlignment();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
- for (SequenceI seq : forSequences)
- {
- 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)
- {
- /*
- * Find matching annotations on the alignment.
- */
- final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
- .findAnnotations(seq, dsann.getCalcId(),
- dsann.label);
- if (!matchedAlignmentAnnotations.iterator().hasNext())
- {
- result.add(dsann);
- tipEntries.put(dsann.getCalcId(), dsann.label);
- }
- }
- /*
- * Save any addable annotations for this sequence
- */
- if (!result.isEmpty())
- {
- candidates.put(seq, result);
- }
- }
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
if (!candidates.isEmpty())
{
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
/*
* Found annotations that could be added. Enable the menu item, and
* configure its tooltip and action.
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- /*
- * Add annotations at the top of the annotation, in the same order as their
- * related sequences.
- */
- 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 copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- this.ap.getAlignment().addAnnotation(copyAnn);
- copyAnn.visible = true;
- }
- }
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
refresh();
}
+ MessageManager
.formatMessage(
"label.create_sequence_details_report_annotation_for",
- new String[]
+ new Object[]
{ seq.getDisplayId(true) }) + "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequece_details_for",
- (sequences.length == 1 ? new String[]
- { sequences[0].getDisplayId(true) } : new String[]
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) } : new Object[]
{ MessageManager.getString("label.selection") })), 500, 400);
}
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
}
int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
+ SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
ap.av.hideSequence(hseqs);
// refresh(); TODO: ? needed ?
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(),
sg.getEndRes() + 1);
String description;
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
+ "label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
// or we simply trust the user wants
// wysiwig behaviour
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- ap.av, true));
+ cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
+ ap, true));
}
public void pdbFromFile_actionPerformed()
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
+ "label.select_pdb_file_for", new Object[]
{ sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
+ "label.load_pdb_file_associate_with_sequence", new Object[]
{ sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
}
- // JBNote: commented out - these won't be instantiated here...!
- // public void RNAFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromRNAFold("toto");
- // }
- //
- // public void ContraFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromContraFold("toto");
- // }
+
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,