X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=32a50cfbfa30c359defac13060d2ebab1b8adf1b;hb=e4dca3706ab423352c26ac100f3ca5a3e7c3d2c4;hp=7921ed23bb7d71b097ba36f195326980f606b56e;hpb=e44514b727077d5cd7edb5d8184ab85cbc2eed13;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7921ed2..32a50cf 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -125,11 +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. */
@@ -224,19 +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");
@@ -377,6 +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
@@ -1386,14 +1402,11 @@ public class AlignFrame
 
   public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
-    if (!viewport.alignment.isNucleotide())
-    {
       new DasSequenceFeatureFetcher(viewport.
                                     alignment,
                                     alignPanel);
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-    }
   }
 
 
@@ -2621,93 +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)
@@ -2788,12 +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";