Align dialog fix show alignment

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2568 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/bindings/pymod/tmtools.py

@@ -28,7 +28,7 @@ tmalign: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
 Authors: Pascal Benkert, Marco Biasini
 """
 
-import subprocess, os, tempfile
+import subprocess, os, tempfile, platform
 from ost import settings, io, geom, seq
 
 def _SetupFiles(models):
@@ -66,9 +66,9 @@ def _ParseTmAlign(lines):
   seq1 = seq.CreateSequence("1",lines[20].strip())
   seq2 = seq.CreateSequence("2",lines[22].strip())
   alignment = seq.CreateAlignment()
-  alignment.AddSequence(seq1)
   alignment.AddSequence(seq2)
-  return TMAlignResult(rmsd, aln_length, tm_score, tf, seq1, alignment)
+  alignment.AddSequence(seq1)
+  return TMAlignResult(rmsd, aln_length, tm_score, tf, seq2, alignment)
 
 def _RunTmAlign(tmalign, tmp_dir):
   model1_filename=os.path.join(tmp_dir, 'model01.pdb')

modules/gui/pymod/init_context_menu.py

@@ -122,6 +122,7 @@ class ShowResultDialog(QtGui.QDialog):
     self.list.resizeColumnsToContents()
 
 class AlignmentContextMenu(QtCore.QObject):
+
   def __init__(self, context_menu):
     try:
       if platform.system() == "Windows":
@@ -133,6 +134,7 @@ class AlignmentContextMenu(QtCore.QObject):
       self.action = QtGui.QAction("Align", self)
       QtCore.QObject.connect(self.action,QtCore.SIGNAL("triggered()"), self.Align)
       context_menu.AddAction(self.action, gui.ContextActionType.ENTITY | gui.ContextActionType.MULTI)
+      self.seq_viewer = None
     except settings.FileNotFound:
       return
     
@@ -170,19 +172,25 @@ class AlignmentContextMenu(QtCore.QObject):
       
   def __DisplayAlignment(self, res_list):
     if(len(res_list)>0):
-      ref_seq = res_list[0].ref_sequence
+      ref_seq = seq.CreateSequence("REF",res_list[0].ref_sequence.GetGaplessString())
       aln_list = seq.AlignmentList()
       if(ref_seq.IsValid()):
         for res in res_list:
+          print res.alignment.GetSequence(0)
+          print res.alignment.GetSequence(1)
+          print "----------------"
           aln_list.append(res.alignment)
         alignment = alg.MergePairwiseAlignments(aln_list, ref_seq)
         gosty = gui.GostyApp.Instance()
         main_area = gosty.perspective.GetMainArea()
-        seq_viewer = gui.SequenceViewerV2(True)
-        gosty.AddWidgetToApp(str(ref_seq),seq_viewer)
-        seq_viewer.AddAlignment(alignment)
-        main_area.ShowSubWindow(seq_viewer)
-  
+        if self.seq_viewer:
+          main_area.RemoveWidget(self.seq_viewer)
+          self.seq_viewer.qobject.close()
+        self.seq_viewer = gui.SequenceViewer(True)
+        self.seq_viewer.AddAlignment(alignment)
+        self.seq_viewer.ChangeDisplayMode("Highlight conservation 1")
+        self.seq_viewer.Show()
+        
 def _InitContextMenu(app):
   cm=app.scene_win.GetContextMenu()
   AlignmentContextMenu(cm)
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