jal-842; sequence transmitting to Varna included

[jalview.git] / src / jalview / gui / AppVarnaBinding.java

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index ac9a880..389efd1 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -87,7 +87,7 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
        // private static final String DEFAULT_STRUCTURE2 =
        // "((((..(((....)))..))))";
 
-       private VARNAPanel _vp;
+       public VARNAPanel vp;
 
        private JPanel _tools = new JPanel();
        private JPanel _input = new JPanel();
@@ -130,6 +130,11 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
        }
        
+       public AppVarnaBinding(String seq){
+               super("VARNA in Jalview");
+               initVarna(seq,this.DEFAULT_STRUCTURE1);
+       }
+       
        
        
        private void initVarna(String seq, String str){
@@ -151,8 +156,8 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                                if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
                                {
                                        FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
-                                       Mapping map = Mapping.DefaultOutermostMapping(_vp.getRNA().getSize(), sel.rna.getSize());
-                                       _vp.showRNAInterpolated(sel.rna,sel.config,map);
+                                       Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
+                                       vp.showRNAInterpolated(sel.rna,sel.config,map);
                                        _seq.setText(sel.rna.getSeq());
                                        _str.setText(sel.rna.getStructDBN());
                                }
@@ -163,27 +168,27 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                RNA _RNA1 = new RNA("User defined 1");
                
                try {
-                       _vp = new VARNAPanel("0",".");
+                       vp = new VARNAPanel("0",".");
                        _RNA1.setRNA(seq, str);
-                       _RNA1.drawRNARadiate(_vp.getConfig());
+                       _RNA1.drawRNARadiate(vp.getConfig());
                } catch (ExceptionNonEqualLength e) {
-                       _vp.errorDialog(e);
+                       vp.errorDialog(e);
                } catch (ExceptionUnmatchedClosingParentheses e2) {
                e2.printStackTrace();
                } catch (ExceptionFileFormatOrSyntax e3) {
                e3.printStackTrace();
                }
-               _vp.setPreferredSize(new Dimension(400, 400));
-               _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
+               vp.setPreferredSize(new Dimension(400, 400));
+               _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 
                setBackground(_backgroundColor);
-               _vp.setBackground(_backgroundColor);
+               vp.setBackground(_backgroundColor);
 
                getContentPane().setLayout(new BorderLayout());
-               getContentPane().add(_vp, BorderLayout.CENTER);
+               getContentPane().add(vp, BorderLayout.CENTER);
 
                setVisible(true);
-               _vp.addVARNAListener(this);
+               vp.addVARNAListener(this);
        }
 
        private void RNAPanelDemoInit() 
@@ -209,8 +214,8 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                                if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
                                {
                                        FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
-                                       Mapping map = Mapping.DefaultOutermostMapping(_vp.getRNA().getSize(), sel.rna.getSize());
-                                       _vp.showRNAInterpolated(sel.rna,sel.config,map);
+                                       Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
+                                       vp.showRNAInterpolated(sel.rna,sel.config,map);
                                        _seq.setText(sel.rna.getSeq());
                                        _str.setText(sel.rna.getStructDBN());
                                }
@@ -221,27 +226,27 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                RNA _RNA1 = new RNA("User defined 1");
                RNA _RNA2 = new RNA("User defined 2");
                try {
-                       _vp = new VARNAPanel("0",".");
+                       vp = new VARNAPanel("0",".");
                        _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
-                       _RNA1.drawRNARadiate(_vp.getConfig());
+                       _RNA1.drawRNARadiate(vp.getConfig());
                        _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
-                       _RNA2.drawRNARadiate(_vp.getConfig());
+                       _RNA2.drawRNARadiate(vp.getConfig());
                } catch (ExceptionNonEqualLength e) {
-                       _vp.errorDialog(e);
+                       vp.errorDialog(e);
                } catch (ExceptionUnmatchedClosingParentheses e2) {
                e2.printStackTrace();
                } catch (ExceptionFileFormatOrSyntax e3) {
                e3.printStackTrace();
                }
-               _vp.setPreferredSize(new Dimension(400, 400));
-           _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName());
-           _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
+               vp.setPreferredSize(new Dimension(400, 400));
+           _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
+           _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 
            JScrollPane listScroller = new JScrollPane(_sideList);
            listScroller.setPreferredSize(new Dimension(150, 0));
 
                setBackground(_backgroundColor);
-               _vp.setBackground(_backgroundColor);
+               vp.setBackground(_backgroundColor);
 
 
                Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
@@ -256,12 +261,12 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                                try {
                                RNA nRNA = new RNA(generateDefaultName());
                                nRNA.setRNA(_seq.getText(), _str.getText());
-                               nRNA.drawRNARadiate(_vp.getConfig());
+                               nRNA.drawRNARadiate(vp.getConfig());
                                _rnaList.add(new VARNAConfig(),nRNA,true);
                                } catch (ExceptionUnmatchedClosingParentheses e1) {
-                                       JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
+                                       JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
                                } catch (ExceptionFileFormatOrSyntax e1) {
-                                       JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
+                                       JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
                                }
                        }
                });
@@ -297,7 +302,7 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                });
                _duplicateButton.addActionListener(new ActionListener() {
                        public void actionPerformed(ActionEvent e) {
-                                       _rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true); 
+                                       _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true); 
                        }});
                
                JPanel ops = new JPanel();
@@ -314,15 +319,15 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
 
                goPanel.add(_createButton, BorderLayout.CENTER);
 
-               JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,_vp);
+               JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
                getContentPane().setLayout(new BorderLayout());
                getContentPane().add(split, BorderLayout.CENTER);
                getContentPane().add(_tools, BorderLayout.NORTH);
 
                setVisible(true);
-               DropTarget dt = new DropTarget(_vp, this);
+               DropTarget dt = new DropTarget(vp, this);
                
-               _vp.addVARNAListener(this);
+               vp.addVARNAListener(this);
        }
        
        public static String generateDefaultName()
@@ -347,7 +352,7 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
        }
 
        public void init() {
-               _vp.setBackground(_backgroundColor);
+               vp.setBackground(_backgroundColor);
                _error = true;
        }
 
@@ -367,11 +372,11 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
        }
 
        public VARNAPanel get_varnaPanel() {
-               return _vp;
+               return vp;
        }
 
        public void set_varnaPanel(VARNAPanel surface) {
-               _vp = surface;
+               vp = surface;
        }
 
 
@@ -559,8 +564,8 @@ public class AppVarnaBinding extends JFrame implements DropTargetListener, Inter
                                  } catch (ExceptionUnmatchedClosingParentheses e1) {
                                  } catch (ExceptionFileFormatOrSyntax e1) {
                                  }
-                                 _vp.showRNA(r);
-                                 _vp.repaint();
+                                 vp.showRNA(r);
+                                 vp.repaint();
                          }
                          else
                          {