X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=82ce8359874e9964066a88f7d468c3544eaf4c2c;hb=9a05eeccaf18e0c82cd183f0b84a8be42bf181c7;hp=9a0def1eabe77ae26d42083e6007c3894ff47ead;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 9a0def1..82ce835 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,6 +21,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import MCview.*; @@ -37,7 +38,7 @@ import jalview.util.UrlLink; * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.118 $ */ public class PopupMenu extends JPopupMenu { @@ -68,6 +69,10 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -156,8 +161,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, - Vector groupLinks) + public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links, + final Vector groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -182,6 +187,8 @@ public class PopupMenu extends JPopupMenu colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(purinePyrimidineColour); + //colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -228,33 +235,11 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - Vector seqs = new Vector(); - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - Vector pdbs = ap.av.alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - - for (int p = 0; p < pdbs.size(); p++) - { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) - { - if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) - seqs.addElement(ap.av.alignment.getSequenceAt(i)); - - continue; - } - } - } - - SequenceI[] seqs2 = new SequenceI[seqs.size()]; - seqs.toArray(seqs2); - - new AppJmol(pdb, seqs2, null, ap); + // 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 PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } + }); viewStructureMenu.add(menuItem); @@ -268,10 +253,40 @@ public class PopupMenu extends JPopupMenu } } else - { - structureMenu.remove(viewStructureMenu); + { + if(ap.av.alignment.isNucleotide()==false){ + structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } + + if(ap.av.alignment.isNucleotide()==true){ + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + String rnastruc=new String(); + for(int i=0; i pdbe=new Hashtable(); + for (SequenceI sq: ap.av.getSequenceSelection()) + { + Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); + if (pes!=null) { + for (PDBEntry pe: pes) + { + pdbe.put(pe.getId(), pe); + } + } + } + if (pdbe.size()>0) + { + final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); + final JMenuItem gpdbview; + structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures.")); + gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); + gpdbview.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + } } else { @@ -452,9 +504,9 @@ public class PopupMenu extends JPopupMenu { // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq - .getDBRef(), new String[] - { urlLink.getTarget() }); + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { urlLink.getTarget() }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); @@ -658,8 +710,8 @@ public class PopupMenu extends JPopupMenu Object[] urlset = null; try { - urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview" - + System.currentTimeMillis(), false); + urlset = urlLink.makeUrlStubs(ids, seqstr, + "FromJalview" + System.currentTimeMillis(), false); } catch (UrlStringTooLongException e) { } @@ -987,6 +1039,8 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + colourMenu.add(purinePyrimidineColour); + //colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1138,6 +1192,23 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + /* + covariationColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + covariationColour_actionPerformed(); + } + });*/ + conservationMenuItem.setText("Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -1175,9 +1246,9 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg - .getSequences(ap.av.hiddenRepSequences), ap.av.alignment - .getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } @@ -1276,7 +1347,19 @@ public class PopupMenu extends JPopupMenu getGroup().cs = new NucleotideColourScheme(); refresh(); } - + + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + /* + protected void covariationColour_actionPerformed() + { + getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]); + refresh(); + } +*/ /** * DOCUMENT ME! * @@ -1293,9 +1376,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1347,9 +1430,9 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -1365,9 +1448,9 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -1401,9 +1484,9 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1); + ResidueProperties.propHash, 3, + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); @@ -1430,8 +1513,8 @@ public class PopupMenu extends JPopupMenu return; } - AnnotationColourGradient acg = new AnnotationColourGradient(sequence - .getAnnotation()[0], null, + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); acg.predefinedColours = true; @@ -1450,9 +1533,10 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); - EditNameDialog dialog = new EditNameDialog(sg.getName(), sg - .getDescription(), " Group Name ", "Group Description ", - "Edit Group Name/Description", ap.alignFrame); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " Group Name ", + "Group Description ", "Edit Group Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1489,9 +1573,10 @@ public class PopupMenu extends JPopupMenu */ void sequenceName_actionPerformed() { - EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence - .getDescription(), " Sequence Name ", - "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame); + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " Sequence Name ", + "Sequence Description ", "Edit Sequence Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1681,8 +1766,8 @@ public class PopupMenu extends JPopupMenu caseChange = ChangeCaseCommand.TO_LOWER; } - ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg - .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1697,8 +1782,8 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); String[] omitHidden = null; @@ -1710,7 +1795,8 @@ public class PopupMenu extends JPopupMenu omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); - if (nala!=null) { + if (nala != null) + { for (int i = 0; i < nala.length; i++) { AlignmentAnnotation na = nala[i]; @@ -1727,47 +1813,16 @@ public class PopupMenu extends JPopupMenu jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Select a PDB file"); - chooser.setToolTipText("Load a PDB file"); + chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false)); + chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'"); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - PDBEntry entry = new PDBEntry(); String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - try - { - MCview.PDBfile pdbfile = new MCview.PDBfile(choice, - jalview.io.AppletFormatAdapter.FILE); - - if (pdbfile.id == null) - { - String reply = JOptionPane - .showInternalInputDialog( - Desktop.desktop, - "Couldn't find a PDB id in the file supplied." - + "Please enter an Id to identify this structure.", - "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); - if (reply == null) - { - return; - } - - entry.setId(reply); - } - else - { - entry.setId(pdbfile.id); - } - } catch (java.io.IOException ex) - { - ex.printStackTrace(); - } - - entry.setFile(choice); - sequence.getDatasetSequence().addPDBId(entry); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); } } @@ -1853,8 +1908,7 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = jalview.structure.StructureSelectionManager - .getStructureSelectionManager().colourSequenceFromStructure( + Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure( sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", @@ -1880,17 +1934,18 @@ public class PopupMenu extends JPopupMenu if (sequence == null) sequence = (Sequence) sg.getSequenceAt(0); - EditNameDialog dialog = new EditNameDialog(sequence - .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame); + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, "Edit Sequence ", null, + "Edit Sequence", ap.alignFrame); if (dialog.accept) { EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), sg - .getSequencesAsArray(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); ap.alignFrame.addHistoryItem(editCommand);