From: tcofoegbu Date: Thu, 28 May 2015 10:03:04 +0000 (+0100) Subject: JAL-1749 reinstated the ability to view RNA structures X-Git-Tag: Release_2_10_0~654^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9709ea1f5cfd18e119b0fdca9ead402fc53ddb8a;p=jalview.git JAL-1749 reinstated the ability to view RNA structures --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index e25fb93..1af3839 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1,4 +1,4 @@ -action.refresh_services = Refresh Services +label.view_structureaction.refresh_services = Refresh Services action.reset_services = Reset Services action.merge_results = Merge Results action.load_scheme = Load scheme @@ -675,6 +675,8 @@ label.discover_pdb_ids = Discover PDB ids label.text_colour = Text Colour label.structure = Structure label.view_structure = View Structure +label.view_protein_structure = View Protein Structure +label.view_rna_structure = View Nucleotide Structure label.clustalx_colours = Clustalx colours label.above_identity_percentage = Above % Identity label.create_sequence_details_report_annotation_for = Annotation for {0} diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 013f4d2..0d28a70 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -204,9 +204,9 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenuItem structureMenu = new JMenuItem(); + JMenuItem proteinStructureMenu = new JMenuItem(); - JMenu viewStructureMenu = new JMenu(); + JMenu rnaStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); @@ -322,51 +322,11 @@ public class PopupMenu extends JPopupMenu makeReferenceSeq.setText("Mark as representative"); } - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + if (ap.av.getAlignment().isNucleotide() == false) { - 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); - */ - } - } - else - { - if (ap.av.getAlignment().isNucleotide() == false) - { - structureMenu.remove(viewStructureMenu); - } + remove(rnaStructureMenu); } + if (ap.av.getAlignment().isNucleotide() == true) { AlignmentAnnotation[] aa = ap.av.getAlignment() @@ -391,7 +351,7 @@ public class PopupMenu extends JPopupMenu System.out.println("end"); } }); - viewStructureMenu.add(menuItem); + rnaStructureMenu.add(menuItem); } } @@ -422,7 +382,7 @@ public class PopupMenu extends JPopupMenu ap); } }); - viewStructureMenu.add(menuItem); + rnaStructureMenu.add(menuItem); } } } @@ -638,7 +598,8 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + proteinStructureMenu.setVisible(false); + rnaStructureMenu.setVisible(false); } if (links != null && links.size() > 0) @@ -1379,8 +1340,9 @@ public class PopupMenu extends JPopupMenu } }); jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.view_structure")); - structureMenu.addActionListener(new ActionListener() + proteinStructureMenu.setText(MessageManager + .getString("label.view_protein_structure")); + proteinStructureMenu.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) @@ -1395,8 +1357,9 @@ public class PopupMenu extends JPopupMenu } }); - viewStructureMenu.setText(MessageManager - .getString("label.view_structure")); + rnaStructureMenu.setText(MessageManager + .getString("label.view_rna_structure")); + // colStructureMenu.setText("Colour By Structure"); editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); @@ -1439,7 +1402,8 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - add(structureMenu); + add(rnaStructureMenu); + add(proteinStructureMenu); if (sequence!=null) { add(hideInsertions);