From c45ff77fed27bdee9025cca9b16a3c03d8e21674 Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Fri, 1 Jul 2011 16:57:01 +0200
Subject: [PATCH] JAL-842; Give Varna frames name for window organizer; always
 display the consensus structure and the 'trimmed' structure
 for a sequence;

Change-Id: If4e9b054455de3c0f43967e27fb399df4c23b751
---
 src/jalview/gui/AppVarna.java        |   46 +++++++++++++++++++------
 src/jalview/gui/AppVarnaBinding.java |   63 ++++++++++++++++++++--------------
 src/jalview/gui/PopupMenu.java       |    2 ++
 3 files changed, 76 insertions(+), 35 deletions(-)

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 7a1e206..012d0d1 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -48,7 +48,7 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 
   VARNAPanel varnaPanel;
   
-  String name;
+  public String name;
   
   /*public AppVarna(){
 	  vab = new AppVarnaBinding(); 
@@ -60,36 +60,62 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 	  RNA rna1 = new RNA(name);
 	  try {
 		  rna1.setRNA(seq,struc);
-	 } catch (ExceptionUnmatchedClosingParentheses e2) {
+	  } catch (ExceptionUnmatchedClosingParentheses e2) {
 		e2.printStackTrace();
 	  } catch (ExceptionFileFormatOrSyntax e3) {
 		e3.printStackTrace();
 	  }
 	  rnaList.add(rna1);
+	  rnaList.add(trimRNA(rna1));
 	  
 	  vab = new AppVarnaBinding(rnaList);
 	  //vab = new AppVarnaBinding(seq,struc);
-	  name=this.name;
+	  //System.out.println("Hallo: "+name);
+	  this.name=name;
 	  initVarna();	  
   }
   
   public void initVarna(){
-	  //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
 	  //vab.setFinishedInit(false);
 	  varnaPanel=vab.get_varnaPanel();
 	  setBackground(Color.white);
+	  JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
 	  getContentPane().setLayout(new BorderLayout());
-	  getContentPane().add(varnaPanel, BorderLayout.CENTER);
-	  
+	  getContentPane().add(split, BorderLayout.CENTER);
+	  //getContentPane().add(vab.getTools(), BorderLayout.NORTH);	
 	  varnaPanel.addVARNAListener(this);
-	  jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+	  jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
 	  this.pack();
-	  this.setVisible(true);
-	  //showPanel(true);
+	  showPanel(true);
   }
   
+  public RNA trimRNA(RNA rna){
+	  RNA rnaTrim = new RNA(rna.getName()+"_trim");
+	  String seq=rna.getSeq();
+	  String struc=rna.getStructDBN();
+	  String newSeq="";
+	  String newStruc="";
+	  for(int i=0;i<seq.length();i++){
+		  if(seq.substring(i, i+1).compareTo("-")!=0){
+			  newSeq=newSeq+seq.substring(i, i+1);
+			  newStruc=newStruc+struc.substring(i,i+1);
+		  }
+	  }
+	  try {
+		rnaTrim.setRNA(newSeq,newStruc);
+	} catch (ExceptionUnmatchedClosingParentheses e) {
+		// TODO Auto-generated catch block
+		e.printStackTrace();
+	} catch (ExceptionFileFormatOrSyntax e) {
+		// TODO Auto-generated catch block
+		e.printStackTrace();
+	}
+	//System.out.println(newSeq+"\t"+newStruc);
+	return rnaTrim;
+  }
+
   public void showPanel(boolean show){
-	  varnaPanel.setVisible(show);
+	  this.setVisible(show);
   }
   
   private boolean _started = false;
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 54ca3b3..092e850 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -80,12 +80,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 	 */
 	//private static final long serialVersionUID = -790155708306987257L;
 
-	//private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
-	//private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
-	//private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
+	private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
+	private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
+	private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
 	public VARNAPanel vp;
 
-	private JPanel _tools = new JPanel();
+	protected JPanel _tools = new JPanel();
 	private JPanel _input = new JPanel();
 
 	private JPanel _seqPanel = new JPanel();
@@ -99,7 +99,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 	private JButton _deleteButton = new JButton("Delete");
 	private JButton _duplicateButton = new JButton("Snapshot");
 	
-	private JPanel _listPanel = new JPanel();
+	protected JPanel _listPanel = new JPanel();
 	private ReorderableJList _sideList = null;
 
 
@@ -131,9 +131,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		initVarna(seq,struc);
 	}
 	
-	public AppVarnaBinding(ArrayList<RNA> rnalist){
+	public AppVarnaBinding(ArrayList<RNA> rnaList){
 		//super("VARNA in Jalview");
-		initVarnaEdit(rnalist);
+		initVarnaEdit(rnaList);
 	}
 	
 	
@@ -195,7 +195,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 	    DefaultListModel dlm = new DefaultListModel(); 
 	    
 
-		int marginTools = 40;
+		//int marginTools = 40;
 
 	    DefaultListSelectionModel m = new DefaultListSelectionModel();
 	    m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
@@ -215,13 +215,14 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 					FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 					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());
+					//_seq.setText(sel.rna.getSeq());
+					//_str.setText(sel.rna.getStructDBN());
 				}
 			}
 	    });
-
+	    
 	    _rnaList = new BackupHolder(dlm,_sideList);
+	   		
 		try {
 			vp = new VARNAPanel("0",".");
 			for(int i=0;i<rnaInList.size();i++){
@@ -232,18 +233,22 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		} 
 		vp.setPreferredSize(new Dimension(400, 400));
 		for(int i=0;i<rnaInList.size();i++){
-			_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName(),true);
+			if(i<rnaInList.size()-1){
+				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName());
+			}else{
+				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName(),true);
+			}
 		}
+
 	    /*_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));
 
-		//TODO setBackground(_backgroundColor);
 		vp.setBackground(_backgroundColor);
-
-
+		
+		/*
 		Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 
 		_seqLabel.setHorizontalTextPosition(JLabel.LEFT);
@@ -265,8 +270,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 				}
 			}
 		});
-
-
+		
 		_seqPanel.setLayout(new BorderLayout());
 		_seqPanel.add(_seqLabel, BorderLayout.WEST);
 		_seqPanel.add(_seq, BorderLayout.CENTER);
@@ -299,7 +303,8 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 			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); 
 			}});
-		
+		goPanel.add(_createButton, BorderLayout.CENTER);
+		*/
 		JPanel ops = new JPanel();
 		ops.setLayout(new GridLayout(1,2));
 		ops.add(_deleteButton);
@@ -312,9 +317,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		_listPanel.add(j,BorderLayout.NORTH);
 		_listPanel.add(listScroller,BorderLayout.CENTER);
 
-		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);
 		/**TODO
 		getContentPane().setLayout(new BorderLayout());
 		getContentPane().add(split, BorderLayout.CENTER);
@@ -326,9 +331,17 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		
 		vp.addVARNAListener(this);
 	}
+	
+	public JPanel getTools(){
+		return _tools;
+	}
+	
+	public JPanel getListPanel(){
+		return _listPanel;
+	}
 
-
-	/*private void RNAPanelDemoInit() 
+	/*
+	private void RNAPanelDemoInit() 
 	{
 	    DefaultListModel dlm = new DefaultListModel(); 
 	    
@@ -465,8 +478,8 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		DropTarget dt = new DropTarget(vp, this);
 		
 		vp.addVARNAListener(this);
-	}*/
-	
+	}
+	*/
 	public static String generateDefaultName()
 	{
 		return "User file #"+_nextID++;
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2ac304b..a4808cf 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -269,6 +269,8 @@ public class PopupMenu extends JPopupMenu
     			  break;
     		  }
     	  }
+    	  
+    	  SequenceGroup a = aa[0].groupRef;
 
     	  //TODO: make rnastrucF a bit more nice
     	  final String rnastrucF=rnastruc;
-- 
1.7.10.2