JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / applications / newGUI / VARNAGUITreeModel.java

diff --git a/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITreeModel.java b/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITreeModel.java
deleted file mode 100644 (file)
index e307543..0000000
--- a/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITreeModel.java
+++ /dev/null
@@ -1,169 +0,0 @@
-package fr.orsay.lri.varna.applications.newGUI;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.PriorityQueue;
-import java.util.TreeSet;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreePath;
-
-public class VARNAGUITreeModel extends DefaultTreeModel{
-       
-  private TreeSet<String> _folders = new TreeSet<String>();
-  private TreeSet<String> _ids = new TreeSet<String>();
-  private Hashtable<String,TreeSet<VARNAGUIModel>> _criterionToFiles = new Hashtable<String,TreeSet<VARNAGUIModel>>();
-  private Hashtable<String,DefaultMutableTreeNode> _criterionToNodes = new Hashtable<String,DefaultMutableTreeNode>();
-  private ArrayList<DefaultMutableTreeNode> _fileNodes = new ArrayList<DefaultMutableTreeNode>();
-  
-  public enum SORT_MODE{
-         PATH,
-         ID
-  }
-  
-  private SORT_MODE _mode = SORT_MODE.PATH; 
-       
-  public VARNAGUITreeModel()
-  {
-         super(new DefaultMutableTreeNode("Folders"));
-  }
-
-
-  public void removeFolder(String path)
-  {
-         if (_mode==SORT_MODE.PATH)
-         {
-                 int pos = _folders.headSet(path).size();
-                 DefaultMutableTreeNode parent = (DefaultMutableTreeNode) getRoot().getChildAt(pos);
-                 parent.removeAllChildren();
-                 reload(parent);
-                 getRoot().remove(parent);
-                 _criterionToNodes.remove(path);
-                 _criterionToFiles.remove(path);
-         }
-         else if (_mode==SORT_MODE.ID)
-         {
-                 ArrayList<DefaultMutableTreeNode> toBeRemoved = new ArrayList<DefaultMutableTreeNode>(); 
-                 for(DefaultMutableTreeNode leafNode : _fileNodes)
-                 {
-                         VARNAGUIModel m = (VARNAGUIModel)leafNode.getUserObject();
-                         if (m.getFolder().equals(path))
-                         {
-                                 toBeRemoved.add(leafNode);
-                         }
-                 }
-                 for(DefaultMutableTreeNode leafNode : toBeRemoved)
-                 {
-                         _fileNodes.remove(leafNode);
-                         DefaultMutableTreeNode parent = (DefaultMutableTreeNode) leafNode.getParent();
-                         parent.remove(leafNode);
-                 }
-         }
-         _folders.remove(path);
-  }
-  
-  
-  public DefaultMutableTreeNode insertGroupNode(String crit, TreeSet<String> t)
-  {
-         DefaultMutableTreeNode groupNode = new DefaultMutableTreeNode(crit);
-         DefaultMutableTreeNode parent = getRoot();
-         int pos = t.headSet(crit).size();
-         parent.insert(groupNode, pos);         
-         reload(groupNode);
-         return groupNode;
-  }
-
-  public void insertLeafNode(DefaultMutableTreeNode parent, VARNAGUIModel m, TreeSet<VARNAGUIModel> t)
-  {
-         DefaultMutableTreeNode leafNode = new DefaultMutableTreeNode(m);
-         int pos = t.headSet(m).size();
-         parent.insert(leafNode, pos);
-         _fileNodes.add(leafNode);
-  }
-
-  public DefaultMutableTreeNode addFolder(String path)
-  {
-         DefaultMutableTreeNode groupNode = null;
-         try {
-                 if (!_folders.contains(path))
-                 {
-                         System.out.println("Folder: "+path);
-                         File dir = new File(path);
-                         if (dir.isDirectory())
-                         {
-                                 path = dir.getCanonicalPath();
-                                 _folders.add(path);
-                                 if (_mode==SORT_MODE.PATH)
-                                 {
-                                         System.out.println("  Adding: "+path);
-                                         groupNode = insertGroupNode(path, _folders);
-                                         _criterionToNodes.put(path,groupNode);
-                                         _criterionToFiles.put(path, new TreeSet<VARNAGUIModel>());
-                                 }
-                                 for(File f:dir.listFiles(_f))
-                                 {
-                                         addFile(path,f.getCanonicalPath());
-                                 }
-                         }
-                 }
-         } catch (IOException e) {
-                 e.printStackTrace();
-         }
-         return groupNode;
-  }
-    
-  private void addFile(String folder, String path)
-  {
-         System.out.println("  => "+path);
-         VARNAGUIModel m = new VARNAGUIModel(folder,path);
-         if (_mode==SORT_MODE.PATH)
-         {
-                 addFolder(folder);
-                 insertLeafNode(_criterionToNodes.get(folder), m, _criterionToFiles.get(folder));
-         }
-         else if (_mode==SORT_MODE.ID)
-         {
-                 String id = m.getID();
-                 if (!_criterionToNodes.containsKey(id))
-                 {
-                         _criterionToNodes.put(id, insertGroupNode(id, _ids));
-                 }
-                 insertLeafNode(_criterionToNodes.get(id), m, _criterionToFiles.get(id));
-         }
-  }
-  
-  public DefaultMutableTreeNode getRoot()
-  {
-         return (DefaultMutableTreeNode) super.getRoot();
-  }
-  
-  public ArrayList<String> getFolders()
-  {
-         ArrayList<String> result = new ArrayList<String>(_folders);
-         return result;
-  }
-  
-  
-   FilenameFilter _f = new FilenameFilter(){
-               public boolean accept(File dir, String name) {
-                       return name.toLowerCase().endsWith(".dbn") 
-                       || name.toLowerCase().endsWith(".ct")
-                       || name.toLowerCase().endsWith(".bpseq")
-                       || name.toLowerCase().endsWith(".rnaml");       
-               }};
-         
-  public FilenameFilter getFileNameFilter()
-  {
-       return _f;
-  }
-
-  public void setFileNameFilter(FilenameFilter f)
-  {
-       _f = f;
-  }
-
-}