X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=32a50cfbfa30c359defac13060d2ebab1b8adf1b;hb=e4dca3706ab423352c26ac100f3ca5a3e7c3d2c4;hp=87cd9a967b27b41045cc3cc0be5e3440cdeb742c;hpb=4c5be7222caa476ab4ae8f390dae5720a7f27217;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 87cd9a9..32a50cf 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");
 
@@ -130,11 +125,17 @@ public class AlignFrame
    });
 
 
-  if (Desktop.desktop != null)
-  {
-    addServiceListeners();
-    setGUINucleotide(al.isNucleotide());
-  }
+    if (Desktop.desktop != null)
+    {
+      addServiceListeners();
+      setGUINucleotide(al.isNucleotide());
+    }
+
+    if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+    {
+      wrapMenuItem.setSelected(true);
+      wrapMenuItem_actionPerformed(null);
+    }
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
@@ -205,6 +206,22 @@ public class AlignFrame
   {
     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!
    *
@@ -213,19 +230,15 @@ public class AlignFrame
   public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
+        getProperty( "LAST_DIRECTORY"),
         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
+        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
         new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, currentFileFormat);
+        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+        currentFileFormat,
+        false);
+
 
-    chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
@@ -290,6 +303,7 @@ public class AlignFrame
 
         out.print(output);
         out.close();
+        this.setTitle(file);
         return true;
       }
       catch (Exception ex)
@@ -365,6 +379,20 @@ public class AlignFrame
     thread.start();
   }
 
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+    new AnnotationExporter().exportFeatures(alignPanel);
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+    new AnnotationExporter().exportAnnotations(
+      alignPanel,
+      viewport.alignment.getAlignmentAnnotation()
+        );
+  }
+
+
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -547,10 +575,6 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void lostOwnership(Clipboard clipboard, Transferable contents)
-  {
-    Desktop.jalviewClipboard = null;
-  }
 
 
   /**
@@ -631,12 +655,16 @@ 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()};
   }
 
@@ -697,74 +725,91 @@ 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");
-
-        //>>>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);
       }
       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)
     {
@@ -1279,7 +1324,7 @@ public class AlignFrame
    *
    * @param e DOCUMENT ME!
    */
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setWrapAlignment(wrapMenuItem.isSelected());
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
@@ -1357,14 +1402,11 @@ public class AlignFrame
 
   public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
-    if (!viewport.alignment.isNucleotide())
-    {
-      new SequenceFeatureFetcher(viewport.
-                                 alignment,
-                                 alignPanel);
+      new DasSequenceFeatureFetcher(viewport.
+                                    alignment,
+                                    alignPanel);
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-    }
   }
 
 
@@ -1949,6 +1991,10 @@ public class AlignFrame
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if(viewport.autoCalculateConsensus)
+    {
+      alignmentChanged();
+    }
   }
 
 
@@ -2514,42 +2560,42 @@ 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,
@@ -2588,93 +2634,27 @@ public void showTranslation_actionPerformed(ActionEvent e)
  *
  * @param String DOCUMENT ME!
  */
-public boolean parseGroupsFile(String file)
+public boolean parseFeaturesFile(String file, String type)
 {
-    String line = null;
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      int lineNo = 0;
-      String featureGroup = null;
-      while ( (line = in.readLine()) != null)
-      {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          if (type.equalsIgnoreCase("startgroup"))
-          {
-            featureGroup = st.nextToken();
-          }
-          else if (type.equalsIgnoreCase("endgroup"))
-          {
-            //We should check whether this is the current group,
-            //but at present theres no way of showing more than 1 group
-            st.nextToken();
-            featureGroup = null;
-          }
-          else
-          {
-            UserColourScheme ucs = new UserColourScheme(st.nextToken());
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
-                ucs.findColour("A"));
-          }
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-
-          type = st.nextToken();
-
-          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
-          }
-
-          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
-
-          seq.getDatasetSequence().addSequenceFeature(sf);
-        }
-      }
+    boolean featuresFile = false;
+    try{
+      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment,
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours);
     }
-    catch (Exception ex)
+    catch(Exception ex)
     {
-      System.out.println(line);
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex +"\n"+line);
-      return false;
     }
 
-    viewport.showSequenceFeatures = true;
-    showSeqFeatures.setSelected(true);
-    alignPanel.repaint();
-    return true;
+    if(featuresFile)
+    {
+      viewport.showSequenceFeatures = true;
+      showSeqFeatures.setSelected(true);
+      alignPanel.repaint();
+    }
+
+    return featuresFile;
 }
 
 public void dragEnter(DropTargetDragEvent evt)
@@ -2755,12 +2735,13 @@ public void drop(DropTargetDropEvent evt)
    public void loadJalviewDataFile(String file)
   {
     try{
-      boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
+      boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
           alignment, file);
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseGroupsFile(file);
+        boolean isGroupsFile = parseFeaturesFile(file,
+                                                AppletFormatAdapter.FILE);
         if (!isGroupsFile)
         {
           String protocol = "File";
@@ -2770,24 +2751,15 @@ public void drop(DropTargetDropEvent evt)
 
           FastaFile ff = new FastaFile();
           Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-          c.setContents(new StringSelection(ff.print(sequences)), this);
+          c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);
 
           this.paste(false);
         }
       }
-
-      if (isAnnotation)
+      else
       {
-        int height = alignPanel.annotationPanel.adjustPanelHeight();
-        alignPanel.annotationScroller.setPreferredSize(
-            new Dimension(alignPanel.annotationScroller.getWidth(),
-                          height));
-
-        alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            alignPanel.annotationSpaceFillerHolder.getWidth(),
-            height));
-
-        alignPanel.addNotify();
+        // (isAnnotation)
+        alignPanel.adjustAnnotationHeight();
       }
 
     }catch(Exception ex)