From f92024c0fce83d3aa2b48a248accd246596ea2fc Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 15 Jul 2010 14:07:23 +0000
Subject: [PATCH] Align in SceneWin show alignment
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2566 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/tmtools.py | 15 ++++++--
modules/gui/pymod/export_main_area.cc | 18 ++++++++-
modules/gui/pymod/init_context_menu.py | 53 ++++++++++++++++++++------
3 files changed, 70 insertions(+), 16 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 9117b675d..955897190 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -28,8 +28,8 @@ tmalign: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
Authors: Pascal Benkert, Marco Biasini
"""
-import subprocess, os, tempfile, platform
-from ost import settings, io, geom
+import subprocess, os, tempfile
+from ost import settings, io, geom, seq
def _SetupFiles(models):
# create temporary directory
@@ -43,11 +43,13 @@ def _CleanupFiles(dir_name):
shutil.rmtree(dir_name)
class TMAlignResult:
- def __init__(self, rmsd, tm_score, aligned_length, transform):
+ def __init__(self, rmsd, tm_score, aligned_length, transform, ref_sequence, alignment):
self.rmsd=rmsd
self.tm_score=tm_score
self.aligned_length=aligned_length
self.transform=transform
+ self.ref_sequence =ref_sequence
+ self.alignment=alignment
def _ParseTmAlign(lines):
info_line=lines[11].split(',')
@@ -61,7 +63,12 @@ def _ParseTmAlign(lines):
tf2[4], tf3[2], tf3[3], tf3[4])
tf=geom.Mat4(rot)
tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
- return TMAlignResult(rmsd, aln_length, tm_score, tf)
+ 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)
def _RunTmAlign(tmalign, tmp_dir):
model1_filename=os.path.join(tmp_dir, 'model01.pdb')
diff --git a/modules/gui/pymod/export_main_area.cc b/modules/gui/pymod/export_main_area.cc
index 5a9dfed58..4e6b793b5 100644
--- a/modules/gui/pymod/export_main_area.cc
+++ b/modules/gui/pymod/export_main_area.cc
@@ -142,6 +142,20 @@ void main_area_hide_sub_window(MainArea* m, const SipHandlerBase& sh)
}
+void main_area_show_sub_window_b(MainArea* m, object py_object)
+{
+ if(QWidget* widget = get_cpp_qobject<QWidget>(py_object)){
+ m->ShowSubWindow(widget);
+ }
+}
+
+void main_area_hide_sub_window_b(MainArea* m, object py_object)
+{
+ if(QWidget* widget = get_cpp_qobject<QWidget>(py_object)){
+ m->HideSubWindow(widget);
+ }
+}
+
void export_MainArea()
{
class_<MainArea, boost::noncopyable>("MainArea", no_init)
@@ -161,8 +175,10 @@ void export_MainArea()
.def("width", &MainArea::width)
.def("height", &MainArea::height)
.def("ShowSubWindow", &MainArea::ShowSubWindow)
- .def("ShowSubWindow", &main_area_show_sub_window)
+ .def("ShowSubWindow", &main_area_show_sub_window)
+ .def("ShowSubWindow", &main_area_show_sub_window_b)
.def("HideSubWindow", &MainArea::HideSubWindow)
+ .def("HideSubWindow", &main_area_hide_sub_window_b)
.def("HideSubWindow", &main_area_hide_sub_window)
.def("EnableTabbedMode", &MainArea::EnableTabbedMode, arg("flag")=true)
.def("GetQObject",&get_py_qobject<MainArea>)
diff --git a/modules/gui/pymod/init_context_menu.py b/modules/gui/pymod/init_context_menu.py
index 7cd032ca2..6bb6db853 100644
--- a/modules/gui/pymod/init_context_menu.py
+++ b/modules/gui/pymod/init_context_menu.py
@@ -2,9 +2,12 @@ import platform
from PyQt4 import QtCore, QtGui
-from ost import geom, gfx, gui
+import sip
+
+from ost import geom, gfx, gui, seq
from ost import settings
from ost.bindings import tmtools
+from ost.seq import alg
class SelectRefDialog(QtGui.QDialog):
def __init__(self, ent_list, parent=None):
@@ -23,6 +26,14 @@ class SelectRefDialog(QtGui.QDialog):
self.list.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
vb.addWidget(self.label)
vb.addWidget(self.list)
+ self.show_scores = QtGui.QCheckBox(self)
+ self.show_scores.setText("Show Scores")
+ self.show_scores.setChecked(True)
+ vb.addWidget(self.show_scores)
+ self.show_alignment = QtGui.QCheckBox(self)
+ self.show_alignment.setText("Display Alignment")
+ self.show_alignment.setChecked(False)
+ vb.addWidget(self.show_alignment)
hb = QtGui.QHBoxLayout()
hb.setDirection(QtGui.QBoxLayout.LeftToRight)
cancel_btn = QtGui.QPushButton("Cancel", self)
@@ -58,7 +69,13 @@ class SelectRefDialog(QtGui.QDialog):
self.ent_list_.remove(ent)
self.ent_list_.insert(0,ent)
self.accept()
-
+
+ def GetShowScores(self):
+ return self.show_scores.isChecked()
+
+ def GetDisplayAlignment(self):
+ return self.show_alignment.isChecked()
+
def GetEntities(self):
return self.ent_list_
@@ -124,14 +141,11 @@ class AlignmentContextMenu(QtCore.QObject):
ent_list = list()
for i in range(0,scene_selection.GetActiveNodeCount()):
ent_list.append(scene_selection.GetActiveNode(i))
- if len(ent_list) == 2:
- self.__Align(ent_list)
- elif len(ent_list) > 2:
- sd = SelectRefDialog(ent_list)
- if(sd.exec_()):
- self.__Align(sd.GetEntities())
+ sd = SelectRefDialog(ent_list)
+ if(sd.exec_()):
+ self.__Align(sd.GetEntities(),sd.GetShowScores(), sd.GetDisplayAlignment())
- def __Align(self, ent_list):
+ def __Align(self, ent_list,show_scores=True, display_alignment=False):
node = ent_list[0]
res_list = list()
if isinstance(node, gfx.Entity):
@@ -141,7 +155,10 @@ class AlignmentContextMenu(QtCore.QObject):
if isinstance(node, gfx.Entity):
res_list.append(tmtools.TMAlign(node.view.handle, ref))
node.UpdatePositions()
- self.__ShowScore(ent_list, res_list)
+ if show_scores:
+ self.__ShowScore(ent_list, res_list)
+ if display_alignment:
+ self.__DisplayAlignment(res_list)
def __ShowScore(self, ent_list, res_list):
if(len(res_list)==1):
@@ -151,7 +168,21 @@ class AlignmentContextMenu(QtCore.QObject):
elif(len(res_list)>1):
ShowResultDialog(ent_list, res_list).exec_()
-
+ def __DisplayAlignment(self, res_list):
+ if(len(res_list)>0):
+ ref_seq = res_list[0].ref_sequence
+ aln_list = seq.AlignmentList()
+ if(ref_seq.IsValid()):
+ for res in res_list:
+ 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)
+
def _InitContextMenu(app):
cm=app.scene_win.GetContextMenu()
AlignmentContextMenu(cm)
\ No newline at end of file
--
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