X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c61c7995addc84ae5c1ec23ff2a06f0dfe6fc528;hb=62df38e7204f2903d1b4e5aaef7762acf96f317d;hp=b714aea53cabf9b96dea336328ca497d1ca28d14;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b714aea..c61c799 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -44,7 +44,7 @@ import java.awt.dnd.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements ClipboardOwner, DropTargetListener
+    extends GAlignFrame implements DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -54,9 +54,6 @@ public class AlignFrame
   AlignmentPanel alignPanel;
   AlignViewport viewport;
 
-  Vector viewports = new Vector();
-  Vector alignPanels = new Vector();
-
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
   Stack historyList = new Stack();
@@ -72,7 +69,6 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
-    viewports.add(viewport);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
@@ -88,7 +84,6 @@ public class AlignFrame
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanels.add(alignPanel);
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
@@ -195,11 +190,32 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");
   }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+  }
+
 
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -263,7 +279,7 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);
       }
 
-      Jalview2XML.SaveAlignment(this, file, shortName);
+      new Jalview2XML().SaveAlignment(this, file, shortName);
 
       // USE Jalview2XML to save this file
       return true;
@@ -285,6 +301,7 @@ public class AlignFrame
 
         out.print(output);
         out.close();
+        this.setTitle(file);
         return true;
       }
       catch (Exception ex)
@@ -360,6 +377,27 @@ public class AlignFrame
     thread.start();
   }
 
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
+    }
+
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -450,42 +488,8 @@ public class AlignFrame
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
-    }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -555,10 +559,6 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void lostOwnership(Clipboard clipboard, Transferable contents)
-  {
-    Desktop.jalviewClipboard = null;
-  }
 
 
   /**
@@ -639,12 +639,16 @@ public class AlignFrame
       seqs[i].setDBRef(seq.getDBRef());
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
       seqs[i].setDatasetSequence(seq.getDatasetSequence());
-
+      if(seq.getAnnotation()!=null)
+      {
+        for(int a=0; a<seq.getAnnotation().length; a++)
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+      }
     }
 
     FastaFile ff = new FastaFile();
     ff.addJVSuffix( viewport.showJVSuffix );
-    c.setContents(new StringSelection( ff.print(seqs)), this);
+    c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);
     Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
   }
 
@@ -705,69 +709,91 @@ public class AlignFrame
        sequences = new FormatAdapter().readFile(str, "Paste", format);
      }
 
+     AlignmentI alignment = null;
+
       if (newAlignment)
       {
-
-        Alignment alignment = new Alignment(sequences);
+        alignment = new Alignment(sequences);
 
         if(Desktop.jalviewClipboard!=null)
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
            alignment.setDataset( null );
-
-
-        AlignFrame af = new AlignFrame(alignment);
-        String newtitle = new String("Copied sequences");
-
-        if (title.startsWith("Copied sequences"))
-        {
-          newtitle = title;
-        }
-        else
-        {
-          newtitle = newtitle.concat("- from " + title);
-        }
-
-        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                 NEW_WINDOW_HEIGHT);
       }
       else
       {
+        alignment = viewport.getAlignment();
+
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
         {
+
           Sequence newseq = new Sequence(sequences[i].getName(),
               sequences[i].getSequence(), sequences[i].getStart(),
               sequences[i].getEnd());
-          viewport.alignment.addSequence(newseq);
-          if(sequences[i].getDatasetSequence()==null)
-          {
-             ////////////////////////////
-            //Datset needs extension;
-            /////////////////////////////
-            Sequence ds = new Sequence(sequences[i].getName(),
-                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
-                                       sequences[i].getStart(),
-                                       sequences[i].getEnd());
-            newseq.setDatasetSequence(ds);
-            viewport.alignment.getDataset().addSequence(ds);
-          }
-          else
-          {
-            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
-            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
-            {
-              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
-              {
-                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
-              }
-            }
-          }
+
+          alignment.addSequence(newseq);
         }
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+        viewport.setEndSeq(alignment.getHeight());
+        alignment.getWidth();
+        viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
+
+      // Add any annotations attached to sequences
+      for (int i = 0; i < sequences.length; i++)
+     {
+       if (sequences[i].getAnnotation() != null)
+       {
+         for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+         {
+           AlignmentAnnotation newAnnot =
+               new AlignmentAnnotation(
+                   sequences[i].getAnnotation()[a].label,
+                   sequences[i].getAnnotation()[a].description,
+                   sequences[i].getAnnotation()[a].annotations,
+                   sequences[i].getAnnotation()[a].graphMin,
+                   sequences[i].getAnnotation()[a].graphMax,
+                   sequences[i].getAnnotation()[a].graph);
+
+           sequences[i].getAnnotation()[a] = newAnnot;
+           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+               sequenceMapping;
+           newAnnot.sequenceRef = sequences[i];
+           newAnnot.adjustForAlignment();
+           alignment.addAnnotation(newAnnot);
+           alignment.setAnnotationIndex(newAnnot, a);
+         }
+
+         alignPanel.annotationPanel.adjustPanelHeight();
+       }
+     }
+
+     if(newAlignment)
+     {
+       AlignFrame af = new AlignFrame(alignment);
+       String newtitle = new String("Copied sequences");
+
+
+       //>>>This is a fix for the moment, until a better solution is found!!<<<
+       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+       if (title.startsWith("Copied sequences"))
+       {
+         newtitle = title;
+       }
+       else
+       {
+         newtitle = newtitle.concat("- from " + title);
+       }
+
+       Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                                NEW_WINDOW_HEIGHT);
+
+     }
+
+
     }
     catch (Exception ex)
     {
@@ -810,7 +836,7 @@ public class AlignFrame
 
     //Jalview no longer allows deletion of residues.
     //Check here whether any residues are in selection area
-    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
       for (int i = 0; i < sg.sequences.size(); i++)
       {
@@ -831,7 +857,7 @@ public class AlignFrame
           j++;
         }while(j<=sg.getEndRes());
       }
-    }
+    }*/
 
 
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
@@ -921,6 +947,11 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
@@ -1143,7 +1174,10 @@ public class AlignFrame
 
  public void alignmentChanged()
  {
-   if(viewport.vconsensus!=null)
+   if(viewport.padGaps)
+     viewport.getAlignment().padGaps();
+
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
    {
      viewport.updateConsensus();
      viewport.updateConservation();
@@ -1205,8 +1239,11 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-    if (viewport.getAlignment().padGaps())
-      alignmentChanged();
+
+    viewport.padGaps = padGapsMenuitem.isSelected();
+
+   // if (viewport.padGaps)
+    alignmentChanged();
   }
 
   /**
@@ -1351,9 +1388,9 @@ public class AlignFrame
   {
     if (!viewport.alignment.isNucleotide())
     {
-      new SequenceFeatureFetcher(viewport.
-                                 alignment,
-                                 alignPanel);
+      new DasSequenceFeatureFetcher(viewport.
+                                    alignment,
+                                    alignPanel);
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
     }
@@ -1937,6 +1974,17 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if(viewport.autoCalculateConsensus)
+    {
+      alignmentChanged();
+    }
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1986,7 +2034,7 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 3))
@@ -2038,7 +2086,6 @@ public class AlignFrame
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2347,6 +2394,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2358,7 +2406,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2375,7 +2423,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }
 
@@ -2499,42 +2547,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations
       = viewport.alignment.getAlignmentAnnotation();
   int a, aSize;
-  for (int i = 0; i < annotations.length; i++)
+  if(annotations!=null)
   {
-
-    if (annotations[i].label.equals("Quality") ||
-        annotations[i].label.equals("Conservation") ||
-        annotations[i].label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
     {
-      continue;
-    }
-
+      if (annotations[i].label.equals("Quality") ||
+          annotations[i].label.equals("Conservation") ||
+          annotations[i].label.equals("Consensus"))
+      {
+        continue;
+      }
 
-    aSize = viewport.alignment.getWidth()/3;
-    jalview.datamodel.Annotation [] anots =
-        new jalview.datamodel.Annotation[aSize];
+      aSize = viewport.alignment.getWidth() / 3;
+      jalview.datamodel.Annotation[] anots =
+          new jalview.datamodel.Annotation[aSize];
 
-    for(a=0; a<viewport.alignment.getWidth(); a++)
-    {
-     if( annotations[i].annotations[a]==null
-      || annotations[i].annotations[a]==null)
-       continue;
+      for (a = 0; a < viewport.alignment.getWidth(); a++)
+      {
+        if (annotations[i].annotations[a] == null
+            || annotations[i].annotations[a] == null)
+          continue;
 
-      anots[a/3] = new Annotation(
-     annotations[i].annotations[a].displayCharacter,
-     annotations[i].annotations[a].description,
-     annotations[i].annotations[a].secondaryStructure,
-     annotations[i].annotations[a].value,
-     annotations[i].annotations[a].colour);
-    }
+        anots[a / 3] = new Annotation(
+            annotations[i].annotations[a].displayCharacter,
+            annotations[i].annotations[a].description,
+            annotations[i].annotations[a].secondaryStructure,
+            annotations[i].annotations[a].value,
+            annotations[i].annotations[a].colour);
+      }
 
-    jalview.datamodel.AlignmentAnnotation aa
+      jalview.datamodel.AlignmentAnnotation aa
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-       annotations[i].description, anots );
-     al.addAnnotation(aa);
+          annotations[i].description, anots);
+      al.addAnnotation(aa);
+    }
   }
 
-
     AlignFrame af = new AlignFrame(al);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              NEW_WINDOW_WIDTH,
@@ -2575,11 +2623,12 @@ public void showTranslation_actionPerformed(ActionEvent e)
  */
 public boolean parseGroupsFile(String file)
 {
+    String line = null;
     try
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
       SequenceI seq = null;
-      String line, type, desc, token;
+      String type, desc, token;
 
       int index, start, end;
       StringTokenizer st;
@@ -2641,8 +2690,7 @@ public boolean parseGroupsFile(String file)
             alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end);
-          sf.setFeatureGroup(featureGroup);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }
@@ -2650,8 +2698,9 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
+      System.out.println(line);
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex);
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
       return false;
     }
 
@@ -2715,57 +2764,59 @@ public void drop(DropTargetDropEvent evt)
     {
       e.printStackTrace();
     }
-
     if (files != null)
     {
       try
       {
-        boolean isAnnotation = false;
 
         for (int i = 0; i < files.size(); i++)
         {
-          String file = files.get(i).toString();
-
-          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
-
-          if( !isAnnotation )
-          {
-            boolean isGroupsFile = parseGroupsFile(file);
-            if (!isGroupsFile)
-            {
-              String protocol = "File";
-              String format = new IdentifyFile().Identify(file, protocol);
-              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
-
-              FastaFile ff = new FastaFile();
-              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-              c.setContents(new StringSelection(ff.print(sequences)), this);
-
-              this.paste(false);
-
-            }
-          }
+          loadJalviewDataFile(files.get(i).toString());
         }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+}
 
-        if(isAnnotation)
+  // 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
+   public void loadJalviewDataFile(String file)
+  {
+    try{
+      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
+          alignment, file);
+
+      if (!isAnnotation)
+      {
+        boolean isGroupsFile = parseGroupsFile(file);
+        if (!isGroupsFile)
         {
-          int height = alignPanel.annotationPanel.adjustPanelHeight();
-          alignPanel.annotationScroller.setPreferredSize(
-              new Dimension(alignPanel.annotationScroller.getWidth(),
-                            height));
+          String protocol = "File";
+          String format = new IdentifyFile().Identify(file, protocol);
+          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,
+              format);
 
-          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              alignPanel.annotationSpaceFillerHolder.getWidth(),
-              height));
+          FastaFile ff = new FastaFile();
+          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+          c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);
 
-          alignPanel.addNotify();
+          this.paste(false);
         }
       }
-      catch (Exception ex)
+      else
       {
-        ex.printStackTrace();
+        // (isAnnotation)
+        alignPanel.adjustAnnotationHeight();
       }
-    }
-}
 
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
 }