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

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

diff --git a/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java b/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java
deleted file mode 100644 (file)
index edfd56f..0000000
--- a/src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java
+++ /dev/null
@@ -1,142 +0,0 @@
-package fr.orsay.lri.varna.applications.newGUI;
-
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.datatransfer.UnsupportedFlavorException;
-import java.io.File;
-import java.io.FileFilter;
-import java.io.FileNotFoundException;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.Collection;
-import java.util.Date;
-import java.util.regex.Pattern;
-
-import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-public class VARNAGUIModel implements Comparable<VARNAGUIModel> {
-  private Date _lastModified;
-  private boolean _outOfSync = false;
-  private RNA _r = null;
-  private String _caption = "";
-  private String _path = "";
-  private String _folder = "";
-
-  
-  public static Date lastModif(String path)
-  {
-        return new Date(new File(path).lastModified()) ;
-  }
-  
-  public VARNAGUIModel(String folder, String path)
-  {
-       this(folder,path,lastModif(path));
-  }
-  
-  public VARNAGUIModel(String folder, String path,Date lastModified)
-  {
-         _lastModified = lastModified;
-         _outOfSync = false;
-         _folder =folder;
-         _path = path;
-         String[] s = path.split(Pattern.quote(File.separator));
-         if (s.length>0)
-           _caption = s[s.length-1];
-  }
-  
-  public boolean hasChanged()
-  {
-         return _outOfSync;
-  }
-  
-  public boolean checkForModifications()
-  {
-       if (!lastModif(_path).equals(_lastModified) && !_outOfSync)
-       {
-               _outOfSync = true;
-                 return true;
-       }
-       return false;
-  }
-  
-  
-  public RNA getRNA()
-  {
-         if (_r ==null)
-         {
-                 try {
-                       createRNA();
-               } catch (ExceptionUnmatchedClosingParentheses e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               } catch (ExceptionFileFormatOrSyntax e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               } catch (FileNotFoundException e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               } catch (ExceptionExportFailed e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               } catch (ExceptionPermissionDenied e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               } catch (ExceptionLoadingFailed e) {
-                       // TODO Auto-generated catch block
-                       e.printStackTrace();
-               }
-         }
-         return _r;
-  }
-  
-  private RNA createRNA() throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed
-  {
-         Collection<RNA> r = RNAFactory.loadSecStr(_path);
-         if (r.size()>0)
-         {
-                 _r = r.iterator().next();
-                 _r.drawRNARadiate();
-         }
-         else
-         {
-                 throw new ExceptionFileFormatOrSyntax("No valid RNA defined in this file.");
-         }
-         return _r;
-  }
-  
-  public String toString()
-  {
-         return _caption + (this._outOfSync?"*":"");
-  }
-  
-  public String getID()
-  {
-         return getRNA().getID();
-  }
-  
-  public String getCaption()
-  {
-         return _caption;
-  }
-
-  public String getFolder()
-  {
-         return _folder;
-  }
-
-  public static DataFlavor Flavor = new DataFlavor(VARNAGUIModel.class, "VARNA Object");
-
-
-public int compareTo(VARNAGUIModel o) {
-       return _caption.compareTo(o._caption);
-}
-  
-
-  
-}