fully integrate HMMER3 file format into Jalview

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a9a970f..2140ed9 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -72,6 +72,7 @@ import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
+import jalview.io.HMMFile;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.JPredFile;
@@ -167,7 +168,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public AlignViewControllerI avc;
 
-  List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
+  List<AlignmentPanel> alignPanels = new ArrayList<>();
 
   /**
    * Last format used to load or save alignments in this window
@@ -396,8 +397,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addKeyListener();
 
-    final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
-    final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+    final List<AlignmentPanel> selviews = new ArrayList<>();
+    final List<AlignmentPanel> origview = new ArrayList<>();
     final String menuLabel = MessageManager
             .getString("label.copy_format_from");
     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
@@ -410,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 origview.clear();
                 origview.add(alignPanel);
                 // make an array of all alignment panels except for this one
-                List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
+                List<AlignmentPanel> aps = new ArrayList<>(
                         Arrays.asList(Desktop.getAlignmentPanels(null)));
                 aps.remove(AlignFrame.this.alignPanel);
                 return aps.toArray(new AlignmentPanel[aps.size()]);
@@ -1732,7 +1733,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI> sg = new ArrayList<SequenceI>();
+    List<SequenceI> sg = new ArrayList<>();
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
@@ -1751,7 +1752,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    List<SequenceI> invertGroup = new ArrayList<SequenceI>();
+    List<SequenceI> invertGroup = new ArrayList<>();
 
     for (SequenceI seq : viewport.getAlignment().getSequences())
     {
@@ -1884,7 +1885,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ArrayList<int[]> hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
+      hiddenColumns = new ArrayList<>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
       for (int[] region : viewport.getAlignment().getHiddenColumns()
@@ -1994,7 +1995,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
-      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      ArrayList<Integer> newGraphGroups = new ArrayList<>();
       int fgroup = -1;
 
       if (newAlignment)
@@ -2826,7 +2827,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected List<String> getExistingViewNames(List<Component> comps)
   {
-    List<String> existingNames = new ArrayList<String>();
+    List<String> existingNames = new ArrayList<>();
     for (Component comp : comps)
     {
       if (comp instanceof AlignmentPanel)
@@ -3760,7 +3761,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     List<Component> comps = PaintRefresher.components.get(viewport
             .getSequenceSetId());
-    List<TreePanel> treePanels = new ArrayList<TreePanel>();
+    List<TreePanel> treePanels = new ArrayList<>();
     for (Component comp : comps)
     {
       if (comp instanceof TreePanel)
@@ -4020,7 +4021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void run()
       {
-        final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
+        final List<JMenuItem> legacyItems = new ArrayList<>();
         try
         {
           // System.err.println("Building ws menu again "
@@ -4035,7 +4036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // TODO: group services by location as well as function and/or
           // introduce
           // object broker mechanism.
-          final Vector<JMenu> wsmenu = new Vector<JMenu>();
+          final Vector<JMenu> wsmenu = new Vector<>();
           final IProgressIndicator af = me;
 
           /*
@@ -4403,8 +4404,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    List<String> files = new ArrayList<String>();
-    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
+    List<String> files = new ArrayList<>();
+    List<DataSourceType> protocols = new ArrayList<>();
 
     try
     {
@@ -4424,8 +4425,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         /**
          * Object[] { String,SequenceI}
          */
-        ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
-        ArrayList<String> filesnotmatched = new ArrayList<String>();
+        ArrayList<Object[]> filesmatched = new ArrayList<>();
+        ArrayList<String> filesnotmatched = new ArrayList<>();
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
@@ -4649,6 +4650,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                             "label.successfully_loaded_matrix",
                             sm.getMatrixName()));
           }
+          else if (FileFormat.HMMER3.equals(format))
+          {
+            HMMFile hmm = new HMMFile(new FileParse(file, sourceType));
+            hmm.parse();
+            System.out.println("successful");
+          }
           else if (FileFormat.Jnet.equals(format))
           {
             JPredFile predictions = new JPredFile(file, sourceType);
@@ -5416,7 +5423,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> cdnaSeqs = new ArrayList<>();
     for (SequenceI aaSeq : alignment.getSequences())
     {
       for (AlignedCodonFrame acf : mappings)