X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2Ffragseq%2FFragSeqFileModel.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2Ffragseq%2FFragSeqFileModel.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=6374db87526b4b5f7f332b0a178f322c0e783ec8;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java b/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java
deleted file mode 100644
index 6374db8..0000000
--- a/src2/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package fr.orsay.lri.varna.applications.fragseq;
-
-import java.awt.datatransfer.DataFlavor;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Date;
-import java.util.Random;
-import java.util.regex.Pattern;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-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 FragSeqFileModel implements Comparable<FragSeqFileModel> {
-	private ArrayList<FragSeqModel> _models = new ArrayList<FragSeqModel>();
-	  protected Date _lastModified;
-	  protected boolean _outOfSync = false;
-	  protected String _caption = "";
-	  protected String _path = "";
-	  protected String _folder = "";
-	  protected boolean _cached = false;
-
-	  
-	  public static Date lastModif(String path)
-	  {
-		 return new Date(new File(path).lastModified()) ;
-	  }
-	  
-	  public FragSeqFileModel(String folder, String path)
-	  {
-		this(folder,path,lastModif(path));
-	  }
-	  
-	  
-	  private static Random _rnd = new Random();
-	  
-	  public FragSeqFileModel(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 void load()
-	  {
-		  ArrayList<RNA> rnas = null;
-		  try {
-			  rnas = createRNAs();
-			for (RNA r: rnas)
-			{  
-				this.addModel(new FragSeqRNASecStrModel(r));
-				  int nb =_rnd.nextInt(5); 
-				  for(int i=0;i<nb;i++)
-				  {
-					  FragSeqAnnotationDataModel data = new FragSeqAnnotationDataModel(r.getID(),""+i+"-"+r.getID());
-					  FragSeqAnnotationDataModel.addRandomAnnotations(r,data);
-					  addModel(data);
-				  }		  
-			}
-		} catch (ExceptionUnmatchedClosingParentheses e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (FileNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (ExceptionFileFormatOrSyntax 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();
-		}
-		  _cached = true;
-	  }
-	  
-	  public boolean hasChanged()
-	  {
-		  return _outOfSync;
-	  }
-	  
-	  public boolean checkForModifications()
-	  {
-		if (!lastModif(_path).equals(_lastModified) && !_outOfSync)
-		{
-			_outOfSync = true;
-			  return true;
-		}
-		return false;
-	  }
-	  
-	  
-	  public String toString()
-	  {
-		  return _caption + (this._outOfSync?"*":"");
-	  }
-	  
-	  
-	  public String getCaption()
-	  {
-		  return _caption;
-	  }
-
-	  public String getFolder()
-	  {
-		  return _folder;
-	  }
-
-	  public String getPath()
-	  {
-		  return _path;
-	  }
-
-
-	public int compareTo(FragSeqFileModel o) {
-		return _caption.compareTo(o._caption);
-	}
-	  
-	public ArrayList<FragSeqModel> getModels()
-	{
-		if (!_cached)
-		{  load();  }
-		return _models;
-	}
-	public void addModel(FragSeqModel f)
-	{
-		_models.add(f);
-	}
-
-	
-	private ArrayList<RNA> createRNAs() throws ExceptionUnmatchedClosingParentheses, ExceptionFileFormatOrSyntax, FileNotFoundException, ExceptionExportFailed, ExceptionPermissionDenied, ExceptionLoadingFailed
-	  {
-		  Collection<RNA> r = RNAFactory.loadSecStr(_path);
-		  for (RNA r2 : r)
-		  {
-			  r2.drawRNARadiate();
-		  }
-		  return new ArrayList<RNA>(r);
-	  }
-	  
-}