X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=ee4ef797679b034e96475ebb3234c9823849c194;hb=45922d35b5dc6c73b3d0c55ef2ab884079723782;hp=3ea8e4d41e902dd3ba2eaec320548647a035a008;hpb=7aef14d879f7bfb8af464a6b7700a99413eab0c6;p=jalview.git diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 3ea8e4d..ee4ef79 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -20,11 +20,15 @@ */ package jalview.gui; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.JalviewVarnaBinding; +import jalview.structure.AtomSpec; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; -import java.awt.Font; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; @@ -54,43 +58,16 @@ import javax.swing.event.ListSelectionListener; import fr.orsay.lri.varna.VARNAPanel; import fr.orsay.lri.varna.components.ReorderableJList; import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; +import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm; import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; import fr.orsay.lri.varna.models.FullBackup; import fr.orsay.lri.varna.models.VARNAConfig; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.JalviewVarnaBinding; -import jalview.structure.AtomSpec; -import jalview.util.MessageManager; - public class AppVarnaBinding extends JalviewVarnaBinding { public VARNAPanel vp; - // remove unused (commented out) fields? - // protected JPanel _tools = new JPanel(); - // - // private JPanel _input = new JPanel(); - // - // private JPanel _strPanel = new JPanel(); - // - // private JTextField _str = new JTextField(); - // - // private JTextField _seq = new JTextField(); - // - // private JLabel _strLabel = new JLabel( - // MessageManager.getString("label.str")); - // - // private JButton _updateButton = new JButton( - // MessageManager.getString("action.update")); - // - // private JButton _deleteButton = new JButton( - // MessageManager.getString("action.delete")); - // - // private JButton _duplicateButton = new JButton( - // MessageManager.getString("action.snapshot")); - // protected JPanel _listPanel = new JPanel(); private ReorderableJList _sideList = null; @@ -136,7 +113,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding _sideList.addMouseListener(new MouseAdapter() { @Override - public void mouseClicked(MouseEvent e) { + public void mouseClicked(MouseEvent e) + { AppVarnaBinding.this.mouseClicked(e); } }); @@ -165,48 +143,6 @@ public class AppVarnaBinding extends JalviewVarnaBinding vp.setBackground(_backgroundColor); - Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); - - // MC commented out stuff not added to panel - remove? - // _seq.setFont(textFieldsFont); - // if (!rnaList.isEmpty()) - // { - // _seq.setText(rnaList.get(0).getSeq()); - // } - - // _updateButton.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // FullBackup sel = (FullBackup) _sideList.getSelectedValue(); - // sel.rna.setSequence("A"); - // } - // }); - // - // _strLabel.setPreferredSize(new Dimension(marginTools, 15)); - // _strLabel.setHorizontalTextPosition(JLabel.LEFT); - // _str.setFont(textFieldsFont); - // _strPanel.setLayout(new BorderLayout()); - // _strPanel.add(_strLabel, BorderLayout.WEST); - // _strPanel.add(_str, BorderLayout.CENTER); - // - // _input.setLayout(new GridLayout(1, 0)); - // _input.add(_strPanel); - // - // JPanel goPanel = new JPanel(); - // goPanel.setLayout(new BorderLayout()); - // - // _tools.setLayout(new BorderLayout()); - // _tools.add(_input, BorderLayout.CENTER); - // _tools.add(goPanel, BorderLayout.EAST); - // - // goPanel.add(_updateButton, BorderLayout.CENTER); - // - // JPanel ops = new JPanel(); - // ops.setLayout(new GridLayout(1, 2)); - // ops.add(_deleteButton); - // ops.add(_duplicateButton); - JLabel j = new JLabel( MessageManager.getString("label.structures_manager"), JLabel.CENTER); @@ -215,7 +151,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding _listPanel.add(j, BorderLayout.NORTH); _listPanel.add(listScroller, BorderLayout.CENTER); - new DropTarget(vp, new DropTargetAdapter() { + new DropTarget(vp, new DropTargetAdapter() + { @Override public void drop(DropTargetDropEvent dtde) { @@ -263,8 +200,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding public String[][] getParameterInfo() { - String[][] info = - { + String[][] info = { // Parameter Name Kind of Value Description, { "sequenceDBN", "String", "A raw RNA sequence" }, { "structureDBN", "String", @@ -345,14 +281,15 @@ public class AppVarnaBinding extends JalviewVarnaBinding String name = r.getName(); if (name.equals("")) { - name = path.substring(path - .lastIndexOf(File.separatorChar) + 1); + name = path.substring( + path.lastIndexOf(File.separatorChar) + 1); } if (mdls.size() > 1) { name += " (Model " + mn++ + ")"; } - _rnaList.add(varnaPanel.getConfig().clone(), r, name, true); + _rnaList.add(varnaPanel.getConfig().clone(), r, name, + true); } } } @@ -437,9 +374,9 @@ public class AppVarnaBinding extends JalviewVarnaBinding _sideList.ensureIndexIsVisible(index); /* - * TODO Object newName = JOptionPane.showInputDialog( this, + * TODO Object newName = JvOptionPane.showInputDialog( this, * "Specify a new name for this RNA", "Rename RNA", - * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if + * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if * (newName!=null) { item.name = newName.toString(); * this._sideList.repaint(); } */ @@ -447,7 +384,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding } @Override - public String[] getPdbFile() + public String[] getStructureFiles() { return null; } @@ -531,12 +468,9 @@ public class AppVarnaBinding extends JalviewVarnaBinding } /* - * switch display if not already shown + * switch display */ - if (sel.rna != rna) - { - vp.showRNA(model.rna, model.config); - } + vp.showRNA(model.rna, model.config); try { @@ -547,13 +481,10 @@ public class AppVarnaBinding extends JalviewVarnaBinding vp.toXML(filePath); /* - * restore the previous display if needed + * restore the previous display */ - if (sel.rna != rna) - { - vp.showRNA(sel.rna, sel.config); - } - + vp.showRNA(sel.rna, sel.config); + return filePath; } catch (IOException e) { @@ -571,7 +502,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding * * @param evt */ - protected void changeSelectedStructure_actionPerformed(ListSelectionEvent evt) + protected void changeSelectedStructure_actionPerformed( + ListSelectionEvent evt) { if (!evt.getValueIsAdjusting()) { @@ -596,7 +528,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding * * @param selectedRna */ - public void setSelectedIndex(int selectedRna) + public void setSelectedIndex(final int selectedRna) { /* * note this does nothing if, say, selecting item 3 when only 1 has been @@ -604,7 +536,6 @@ public class AppVarnaBinding extends JalviewVarnaBinding */ _sideList.setSelectedIndex(selectedRna); // TODO ? need a worker thread to get this to happen properly - showSelectedStructure(); } /** @@ -622,9 +553,25 @@ public class AppVarnaBinding extends JalviewVarnaBinding * @param rna * @param config */ - protected void addStructure(RNA rna, VARNAConfig config) + protected void addStructure(final RNA rna, final VARNAConfig config) { - rna.drawRNARadiate(config); + drawRna(rna, config); _rnaList.add(config, rna, rna.getName()); } + + /** + * @param rna + * @param config + */ + protected void drawRna(final RNA rna, final VARNAConfig config) + { + try + { + rna.drawRNA(rna.getDrawMode(), config); + } catch (ExceptionNAViewAlgorithm e) + { + // only throwable for draw mode = 3 NAView + System.err.println("Error drawing RNA: " + e.getMessage()); + } + } }