X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1c488fe5ec722791e505443576a939411eaf2d9f;hb=9862477ece665df66d95f54921796b8703cd7971;hp=1795c1a2ce708e057718512c98ccd54928441924;hpb=a57e62adb20b8c9be0172f2d5d1e767c3aa528ca;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1795c1a..1c488fe 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -587,10 +587,18 @@ public class AlignFrame
 
     validate();
   }
-
-
-
-
+  /**
+   * 
+   * @return true if any progress bars are still active
+   */
+  public boolean operationInProgress()
+  {
+    if (progressBars!=null && progressBars.size()>0)
+    {
+      return true;
+    }
+    return false;
+  }
   /*
    Added so Castor Mapping file can obtain Jalview Version
   */
@@ -696,10 +704,8 @@ public class AlignFrame
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
-        new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" },
-        new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" },
+        jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+        jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
         currentFileFormat,
         false);
 
@@ -781,7 +787,7 @@ public class AlignFrame
       String output = f.formatSequences(
           format,
           (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
-          omitHidden, f.getCacheSuffixDefault(format));
+          omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
       if (output == null)
       {
@@ -853,7 +859,7 @@ public class AlignFrame
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment,
-        omitHidden));
+        omitHidden, viewport.colSel));
   }
 
   /**
@@ -2860,7 +2866,7 @@ public class AlignFrame
   {
     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0));
+                              viewport.getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
                                     viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -3123,7 +3129,7 @@ public class AlignFrame
       public void actionPerformed(ActionEvent e)
       {
         SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
         alignPanel.paintAlignment(true);
       }
@@ -3424,6 +3430,11 @@ public class AlignFrame
    */
   public void BuildWebServiceMenu()
   {
+    // TODO: add support for context dependent disabling of services based on alignment and current selection
+    // TODO: refactor to allow list of AbstractName/Handler bindings to be stored or retrieved from elsewhere
+    // TODO: add additional serviceHandle parameter to specify abstract handler class independently of AbstractName
+    // TODO: add in rediscovery GUI function to restart discoverer
+    // TODO: group services by location as well as function and/or introduce object broker mechanism.
     if ( (Discoverer.services != null)
         && (Discoverer.services.size() > 0))
     {
@@ -3523,9 +3534,6 @@ public class AlignFrame
       resetWebServiceMenu();
       this.webService.add(this.webServiceNoServices);
     }
-    // TODO: add in rediscovery function
-    // TODO: reduce code redundancy.
-    // TODO: group services by location as well as function.
   }
 
 
@@ -3614,6 +3622,7 @@ public class AlignFrame
 
           public void actionPerformed(ActionEvent e)
           {
+            // TODO: new thread for this call with vis-delay
             af.showProductsFor(sel, ds, isRegSel, dna, source);
           }
           
@@ -3631,33 +3640,61 @@ public class AlignFrame
   }
 protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source)
   {
-  ds = this.getViewport().alignment.getDataset(); // update our local dataset reference
-  Alignment prods = CrossRef.findXrefSequences(sel, dna, source, ds);
-  if (prods!=null)
-  {
-    SequenceI[] sprods = new SequenceI[prods.getHeight()];
-    for (int s=0; s<sprods.length;s++)
-    {
-      sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
-      if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
-        ds.addSequence(sprods[s].getDatasetSequence());
-    }
-    Alignment al = new Alignment(sprods);
-    AlignedCodonFrame[] cf = prods.getCodonFrames();
-    for (int s=0; cf!=null && s<cf.length; s++)
+  final boolean fisRegSel = isRegSel;
+  final boolean fdna = dna;
+  final String fsrc = source;
+  final AlignFrame ths = this;
+  final SequenceI[] fsel = sel;
+  Runnable foo = new Runnable() {
+
+    public void run()
     {
-      al.addCodonFrame(cf[s]);
-      cf[s] = null;
+      final long sttime = System.currentTimeMillis();
+      ths.setProgressBar("Searching for sequences from "+fsrc, sttime);
+      try {
+        Alignment ds = ths.getViewport().alignment.getDataset(); // update our local dataset reference
+      Alignment prods = CrossRef.findXrefSequences(fsel, fdna, fsrc, ds);
+      if (prods!=null)
+      {
+        SequenceI[] sprods = new SequenceI[prods.getHeight()];
+        for (int s=0; s<sprods.length;s++)
+        {
+          sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+          if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
+            ds.addSequence(sprods[s].getDatasetSequence());
+          sprods[s].updatePDBIds();
+        }
+        Alignment al = new Alignment(sprods);
+        AlignedCodonFrame[] cf = prods.getCodonFrames();
+        for (int s=0; cf!=null && s<cf.length; s++)
+        {
+          al.addCodonFrame(cf[s]);
+          cf[s] = null;
+        }
+        al.setDataset(ds);
+        AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+        String newtitle =""+((fdna) ? "Proteins " : "Nucleotides ") + " for "+((fisRegSel) ? "selected region of " : "")
+                + getTitle();
+        Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+                DEFAULT_HEIGHT);
+      } else {
+        System.err.println("No Sequences generated for xRef type "+fsrc);
+      }
+      }
+      catch (Exception e)
+      {
+        jalview.bin.Cache.log.error("Exception when finding crossreferences",e);
+      }
+      catch (Error e)
+      {
+        jalview.bin.Cache.log.error("Error when finding crossreferences",e);
+      }
+      ths.setProgressBar("Finished searching for sequences from "+fsrc, sttime);
     }
-    al.setDataset(ds);
-    AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    String newtitle =""+((dna) ? "Proteins " : "Nucleotides ") + " for "+((isRegSel) ? "selected region of " : "")
-            + getTitle();
-    Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
-            DEFAULT_HEIGHT);
-  } else {
-    System.err.println("No Sequences generated for xRef type "+source);
-  }
+    
+  };
+  Thread frunner = new Thread(foo);
+  frunner.start();
   }
 
 
@@ -3732,9 +3769,10 @@ public void showTranslation_actionPerformed(ActionEvent e)
 }
 
 /**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
+ * Try to load a features file onto the alignment.
+ * @param file contents or path to retrieve file 
+ * @param type access mode of file (see jalview.io.AlignFile)
+ * @return true if features file was parsed corectly.
  */
 public boolean parseFeaturesFile(String file, String type)
 {
@@ -3835,12 +3873,15 @@ public void drop(DropTargetDropEvent evt)
     }
 }
 
-  // This method will attempt to load a "dropped" file first by testing
-  // whether its and Annotation file, then features file. If both are
-  // false then the user may have dropped an alignment file onto this
-  // AlignFrame
+  /**     
+   * Attempt to load a "dropped" file: First by testing
+   * whether it's and Annotation file, then a JNet file, and finally a features file. If all are
+   * false then the user may have dropped an alignment file onto this
+   * AlignFrame.
+   * @param file either a filename or a URL string.
+   */
    public void loadJalviewDataFile(String file)
-  {
+   {
     try
     {
       String protocol = "File";
@@ -3855,34 +3896,37 @@ public void drop(DropTargetDropEvent evt)
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,protocol);
-        if (!isGroupsFile)
+        // try to see if its a JNet 'concise' style annotation file *before* we try to parse it as a features file
+        String format = new IdentifyFile().Identify(file, protocol);
+        if(format.equalsIgnoreCase("JnetFile"))
         {
-          String format = new IdentifyFile().Identify(file, protocol);
-
-          if(format.equalsIgnoreCase("JnetFile"))
-          {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                file, protocol);
-            new JnetAnnotationMaker().add_annotation(predictions,
+          jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                  file, protocol);
+          new JnetAnnotationMaker().add_annotation(predictions,
                 viewport.getAlignment(),
                 0, false);
-            alignPanel.adjustAnnotationHeight();
-            alignPanel.paintAlignment(true);
-          }
-          else
+          isAnnotation=true;
+        }
+        else
+        {
+          // try to parse it as a features file
+          boolean isGroupsFile = parseFeaturesFile(file,protocol);
+          // if it wasn't a features file then we just treat it as a general alignment file to load into the current view.
+          if (!isGroupsFile)
           {
             new FileLoader().LoadFile(viewport, file, protocol, format);
+          } else {
+            alignPanel.paintAlignment(true);
+          }
         }
       }
-      }
-      else
+      if (isAnnotation)
       {
-        // (isAnnotation)
+        
         alignPanel.adjustAnnotationHeight();
         buildSortByAnnotationScoresMenu();
+        alignPanel.paintAlignment(true);
       }
-
     }
     catch (Exception ex)
     {