From 9a05eeccaf18e0c82cd183f0b84a8be42bf181c7 Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Mon, 25 Jul 2011 12:58:33 +0200
Subject: [PATCH] JAL-882; VARNA crashed when non-standard gaps where in
 structure; the are now replaced with standard gaps before
 commiting to VARNA in AppVarna.java

Change-Id: I36b523fb7f1063dc2fa5924cb4569f15e0067df2
---
 src/jalview/gui/AnnotationPanel.java |   57 ++++++++++++++++++++++++++++------
 src/jalview/gui/AppVarna.java        |   17 ++++++++--
 2 files changed, 63 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 60d3e06..32f9514 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -93,6 +93,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
   boolean mouseDragging = false;
 
   boolean MAC = false;
+  
+  //for editing cursor
+  int cursorX = 0;
+  int cursorY = 0;
 
   /**
    * Creates a new AnnotationPanel object.
@@ -454,15 +458,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       }
 
       JPopupMenu pop = new JPopupMenu("Structure type");
-      JMenuItem item = new JMenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(STEM);
-      item.addActionListener(this);
-      pop.add(item);
+      JMenuItem item;
+      /*
+       * Just display the needed structure options
+       */
+      if(av.alignment.isNucleotide()==true){
+    	  item = new JMenuItem(STEM);
+    	  item.addActionListener(this);
+    	  pop.add(item); 
+      }else{
+    	  item = new JMenuItem(HELIX);
+    	  item.addActionListener(this);
+    	  pop.add(item);
+    	  item = new JMenuItem(SHEET);
+    	  item.addActionListener(this);
+    	  pop.add(item); 	  
+      }
       item = new JMenuItem(LABEL);
       item.addActionListener(this);
       pop.add(item);
@@ -655,7 +666,35 @@ public class AnnotationPanel extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
+	  if(activeRow !=-1){
+	    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();	    	   
+	    AlignmentAnnotation anot = aa[activeRow];
+	    
+	    if(anot.description.equals("secondary structure")){
+	    	System.out.println(anot.description+" "+anot.getRNAStruc());	   
+	    }
+	  }
   }
+	  
+	  public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1)
+	  {
+	    int pady = av.charHeight / 5;
+	    int charOffset = 0;
+	    graphics.setColor(Color.black);
+	    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+	    if (av.validCharWidth)
+	    {
+	      graphics.setColor(Color.white);
+
+	      char s = seq.getCharAt(res);
+
+	      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+	      graphics.drawString(String.valueOf(s), charOffset + x1,
+	              (y1 + av.charHeight) - pady);
+	    }
+
+	  }
 
   /**
    * DOCUMENT ME!
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 7617574..fe9292e 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -18,6 +18,8 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.awt.*;
 
 import javax.swing.*;
@@ -61,11 +63,13 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
 	  initVarna();
   }*/
   
+ 
+  
   public AppVarna(String seq,String struc,String name,AlignmentPanel ap){
 	  ArrayList<RNA> rnaList = new ArrayList<RNA>();
 	  RNA rna1 = new RNA(name);
 	  try {
-		  rna1.setRNA(seq,struc);
+		  rna1.setRNA(seq,replaceOddGaps(struc));
 	  } catch (ExceptionUnmatchedClosingParentheses e2) {
 		e2.printStackTrace();
 	  } catch (ExceptionFileFormatOrSyntax e3) {
@@ -99,10 +103,19 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
 	  showPanel(true);
   }
   
+  public String replaceOddGaps(String oldStr){
+	  String patternStr = "[^([{<>}])]";
+      String replacementStr = ".";
+      Pattern pattern = Pattern.compile(patternStr);
+      Matcher matcher = pattern.matcher(oldStr);
+      String newStr=matcher.replaceAll(replacementStr);
+	  return newStr;
+  }
+  
   public RNA trimRNA(RNA rna){
 	  RNA rnaTrim = new RNA("trim_"+rna.getName());
 	  try {
-		  rnaTrim.setRNA(rna.getSeq(),rna.getStructDBN());
+		  rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
 	  } catch (ExceptionUnmatchedClosingParentheses e2) {
 		e2.printStackTrace();
 	  } catch (ExceptionFileFormatOrSyntax e3) {
-- 
1.7.10.2