From 11512ebf0340c0814660287f7b124cd4eaa0665c Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 15 Jul 2010 14:07:26 +0000
Subject: [PATCH] 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 | 6 +++---
modules/gui/pymod/init_context_menu.py | 20 ++++++++++++++------
2 files changed, 17 insertions(+), 9 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 955897190..56fd10a8a 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/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')
diff --git a/modules/gui/pymod/init_context_menu.py b/modules/gui/pymod/init_context_menu.py
index 6bb6db853..b66ab38b0 100644
--- a/modules/gui/pymod/init_context_menu.py
+++ b/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)
\ No newline at end of file
--
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