From ca80a4b4aef307f1f4d60fa74d6279b54351afd6 Mon Sep 17 00:00:00 2001
From: BobHanson <hansonr@stolaf.edu>
Date: Thu, 28 May 2020 15:58:09 -0500
Subject: [PATCH] Varna fix for hashtable.remove(value) [unclear]

---
 .../applications/fragseq/FragSeqTreeModel.java     |   31 ++++++++++++--------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java b/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java
index 6586c04..70b858b 100644
--- a/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java
+++ b/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java
@@ -6,8 +6,6 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.PriorityQueue;
-import java.util.Random;
 import java.util.TreeSet;
 
 import javax.swing.event.TreeExpansionEvent;
@@ -22,11 +20,11 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
 	  private FragSeqNode _rootIDs = new FragSeqNode("IDs");
 	  private FragSeqNode _rootFolders = new FragSeqNode("Folders");
 
-	private TreeSet<String> _folders = new TreeSet<String>();
-  private Hashtable<String,FragSeqNode> _folderPathToFolderNode = new Hashtable<String,FragSeqNode>();
+	private TreeSet<String> _folders = new TreeSet<>();
+  private Hashtable<String,FragSeqNode> _folderPathToFolderNode = new Hashtable<>();
 
-  private Hashtable<String,FragSeqNode> _idsToNode = new Hashtable<String,FragSeqNode>();
-  private Hashtable<String,ArrayList<FragSeqNode>> _pathToIDFileNodes = new Hashtable<String,ArrayList<FragSeqNode>>();
+  private Hashtable<String,FragSeqNode> _idsToNode = new Hashtable<>();
+  private Hashtable<String,ArrayList<FragSeqNode>> _pathToIDFileNodes = new Hashtable<>();
   
   public enum SORT_MODE{
 	  PATH,
@@ -77,7 +75,10 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
 		  if (parent.getChildCount()==0)
 		  {
 			  parent.removeFromParent();
-			  _folderPathToFolderNode.remove(parent);
+        // BH was just parent --
+        System.out.println("Varna FragSeqTreeModel removing " + parent + " "
+                + parent.toString());
+        _folderPathToFolderNode.remove(parent.toString());
 			  if (parent.getUserObject() instanceof String)
 			  {
 				  String path = parent.getUserObject().toString();
@@ -105,7 +106,7 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
 
   public void removeFolder(String path)
   {
-	  ArrayList<FragSeqNode> toBeRemoved = new ArrayList<FragSeqNode>(); 
+	  ArrayList<FragSeqNode> toBeRemoved = new ArrayList<>(); 
 	  Enumeration en = _folderPathToFolderNode.get(path).children();
 	  while(en.hasMoreElements())
 	  {
@@ -168,6 +169,7 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
 	  insertFileNode(_folderPathToFolderNode.get(folder), m);
   }
   
+  @Override
   public FragSeqNode getRoot()
   {
 	  return (FragSeqNode) super.getRoot();
@@ -175,13 +177,14 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
   
   public ArrayList<String> getFolders()
   {
-	  ArrayList<String> result = new ArrayList<String>(_folders);
+	  ArrayList<String> result = new ArrayList<>(_folders);
 	  return result;
   }
   
   
    FilenameFilter _f = new FilenameFilter(){
-		public boolean accept(File dir, String name) {
+		@Override
+    public boolean accept(File dir, String name) {
 			return name.toLowerCase().endsWith(".dbn") 
 			|| name.toLowerCase().endsWith(".ct")
 			|| name.toLowerCase().endsWith(".bpseq")
@@ -199,7 +202,7 @@ public class FragSeqTreeModel extends DefaultTreeModel implements TreeWillExpand
   }
 
   
-private Hashtable<FragSeqNode,Boolean> _isExpanded = new Hashtable<FragSeqNode,Boolean>();
+private Hashtable<FragSeqNode,Boolean> _isExpanded = new Hashtable<>();
   
 public boolean isExpanded(FragSeqNode n)
 {
@@ -208,9 +211,12 @@ public boolean isExpanded(FragSeqNode n)
 	return _isExpanded.get(n);
   }
   else
-	  return false;
+  {
+    return false;
+  }
 }
 
+@Override
 public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException {
 	if (event.getSource() instanceof FragSeqTree)
 	{
@@ -242,6 +248,7 @@ public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException
 	}
 }
 
+@Override
 public void treeWillCollapse(TreeExpansionEvent event)
 		throws ExpandVetoException {
 	// TODO Auto-generated method stub
-- 
1.7.10.2