JAL-3541 selectively merged build.gradle and gradle.properties

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

diff --git a/srcjar/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java b/srcjar/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java
new file mode 100644 (file)
index 0000000..edfd56f
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java
@@ -0,0 +1,142 @@
+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);
+}
+  
+
+  
+}