returning src2 -> srcjar

[jalview.git] / src2 / fr / orsay / lri / varna / applications / fragseq / FragSeqFileModel.java

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 (file)
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);
-         }
-         
-}