Merge branch 'develop' into feature/JAL-3551Pymol

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

diff --git a/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java b/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java
new file mode 100644 (file)
index 0000000..6374db8
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java
@@ -0,0 +1,158 @@
+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);
+         }
+         
+}