diff --git a/moose-gui/.travis.yml b/moose-gui/.travis.yml
index 5e29a4846ea26d48637ce99e46e52b124fc4abb7..15779bf198d587255777bc0c0afe4c636ee06f89 100644
--- a/moose-gui/.travis.yml
+++ b/moose-gui/.travis.yml
@@ -11,12 +11,13 @@ install:
- sudo apt-key add - < Release.key
- sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_12.04/ /' >> /etc/apt/sources.list.d/moose.list"
- sudo apt-get -y update
- - sudo apt-get install python3
- - sudo apt-get -y install moose
+ - sudo apt-get -y --force-yes install python3 python-pip
+ - sudo apt-get -y --force-yes install moose
+ - sudo pip install python-libsbml
script:
- # Making sure no python incompatible file is added.
- python -m compileall -q .
- python -c 'import moose'
- - python -c 'import moogli'
+ - #python -c 'import moogli'
- # More tests here for gui.
diff --git a/moose-gui/defaults.py b/moose-gui/defaults.py
index 6551d2d9eb2cc5ba6d79bf396de8b1d5c81bebfc..458f7b389e3f566a83ce0e2fc6c98cfaa3e1ac74 100644
--- a/moose-gui/defaults.py
+++ b/moose-gui/defaults.py
@@ -10,6 +10,7 @@ PLOT_FIELDS={
}
FIELD_UNITS={
'volume':'m3',
+ 'Kd' : 'mM',
'Km':'mM',
'kcat':'s-1',
'Vm':'V',
diff --git a/moose-gui/mgui.py b/moose-gui/mgui.py
index ede1ba954889a588d8ef37f41645daa6d0f0ec13..9f201303e2db36f325e27661637b37fbcfb7504a 100644
--- a/moose-gui/mgui.py
+++ b/moose-gui/mgui.py
@@ -1130,7 +1130,24 @@ class MWindow(QtGui.QMainWindow):
self.setPlugin(pluginName, ret['model'].path)
if pluginName == 'kkit':
QtCore.QCoreApplication.sendEvent(self.plugin.getEditorView().getCentralWidget().view, QtGui.QKeyEvent(QtCore.QEvent.KeyPress, Qt.Qt.Key_A, Qt.Qt.NoModifier))
-
+
+ noOfCompt = len(moose.wildcardFind(ret['model'].path+'/##[ISA=ChemCompt]'))
+ grp = 0
+ for c in moose.wildcardFind(ret['model'].path+'/##[ISA=ChemCompt]'):
+ noOfGrp = moose.wildcardFind(moose.element(c).path+'/#[TYPE=Neutral]')
+ grp = grp+len(noOfGrp)
+
+ noOfPool = len(moose.wildcardFind(ret['model'].path+'/##[ISA=PoolBase]'))
+ noOfFunc = len(moose.wildcardFind(ret['model'].path+'/##[ISA=Function]'))
+ noOfReac = len(moose.wildcardFind(ret['model'].path+'/##[ISA=ReacBase]'))
+ noOfEnz = len(moose.wildcardFind(ret['model'].path+'/##[ISA=EnzBase]'))
+ noOfStimtab = len(moose.wildcardFind(ret['model'].path+'/##[ISA=StimulusTable]'))
+
+ reply = QtGui.QMessageBox.information(self,"Model Info","Model has : \n %s Compartment \t \n %s Group \t \n %s Pool \t \n %s Function \t \n %s reaction \t \n %s Enzyme \t \n %s StimulusTable" %(noOfCompt, grp, noOfPool, noOfFunc, noOfReac, noOfEnz, noOfStimtab))
+ if reply == QtGui.QMessageBox.Ok:
+ QtGui.QApplication.restoreOverrideCursor()
+ return
+
def checkPlugin(self,dialog):
fileNames = dialog.selectedFiles()
for fileName in fileNames:
diff --git a/moose-gui/mload.py b/moose-gui/mload.py
index b91e2888592a75138554a28521cb0f1fea98c218..257daa9410909a3fb8eb877afdf8ef7ff7d125b5 100644
--- a/moose-gui/mload.py
+++ b/moose-gui/mload.py
@@ -55,6 +55,7 @@ from os.path import splitext
from PyQt4 import QtGui, QtCore, Qt
from plugins.setsolver import *
from moose.SBML import *
+from plugins.kkitOrdinateUtil import *
def loadGenCsp(target,filename,solver="gsl"):
target = target.replace(" ", "")
@@ -146,7 +147,26 @@ def loadFile(filename, target, solver="gsl", merge=True):
if modeltype == 'genesis':
if subtype == 'kkit' or subtype == 'prototype':
model,modelpath = loadGenCsp(target,filename,solver)
+ xcord,ycord = [],[]
if moose.exists(moose.element(modelpath).path):
+ mObj = moose.wildcardFind(moose.element(modelpath).path+'/##[ISA=PoolBase]'+','+
+ moose.element(modelpath).path+'/##[ISA=ReacBase]'+','+
+ moose.element(modelpath).path+'/##[ISA=EnzBase]'+','+
+ moose.element(modelpath).path+'/##[ISA=StimulusTable]')
+ for p in mObj:
+ if not isinstance(moose.element(p.parent),moose.CplxEnzBase):
+ xcord.append(moose.element(p.path+'/info').x)
+ ycord.append(moose.element(p.path+'/info').y)
+ recalculatecoordinatesforKkit(mObj,xcord,ycord)
+
+ for ememb in moose.wildcardFind(moose.element(modelpath).path+'/##[ISA=EnzBase]'):
+ objInfo = ememb.path+'/info'
+ #Enzyme's textcolor (from kkit) will be bgcolor (in moose)
+ if moose.exists(objInfo):
+ bgcolor = moose.element(objInfo).color
+ moose.element(objInfo).color = moose.element(objInfo).textColor
+ moose.element(objInfo).textColor = bgcolor
+
moose.Annotator(moose.element(modelpath).path+'/info').modeltype = "kkit"
else:
print " path doesn't exists"
@@ -156,6 +176,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
elif modeltype == 'cspace':
model,modelpath = loadGenCsp(target,filename)
+
if moose.exists(modelpath):
moose.Annotator((moose.element(modelpath).path+'/info')).modeltype = "cspace"
addSolver(modelpath,'gsl')
@@ -184,13 +205,21 @@ def loadFile(filename, target, solver="gsl", merge=True):
# moose.move("cells/", cell.path)
elif subtype == 'sbml':
- if target != '/':
- if moose.exists(target):
- moose.delete(target)
- model = mooseReadSBML(filename,target)
- if moose.exists(moose.element(model).path):
- moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
- addSolver(target,'gsl')
+ foundLibtaSBML_ = False
+ try:
+ import libsbml
+ foundLibSBML_ = True
+ except ImportError:
+ pass
+ if foundLibSBML_:
+ if target != '/':
+ if moose.exists(target):
+ moose.delete(target)
+ model = mooseReadSBML(filename,target)
+ if moose.exists(moose.element(model).path):
+ moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
+ addSolver(target,'gsl')
+ libsfound = foundLibSBML_
else:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
@@ -203,6 +232,5 @@ def loadFile(filename, target, solver="gsl", merge=True):
'model': model}
-
#
# mload.py ends here
diff --git a/moose-gui/objectedit.py b/moose-gui/objectedit.py
index 2545a1e2a562c60ab88cc3cb2a3197ab933d2594..a98294cc3f3fa619651e8ccf70f011bba1122810 100644
--- a/moose-gui/objectedit.py
+++ b/moose-gui/objectedit.py
@@ -6,7 +6,7 @@
# Maintainer:
# Created: Wed Jun 30 11:18:34 2010 (+0530)
# Version:
-# Last-Updated: Wed Aug 3 15:55:59 2016 (+0530)
+# Last-Updated: Friday May 17 23:45:59 2017 (+0530)
# By: Harsha
# Update #:
# URL:
@@ -38,8 +38,10 @@
#
# Fri Apr 19 15:05:53 IST 2013 - Subhasis added undo redo
# feature. Create ObjectEditModel as part of ObjectEditView.
-#
-
+# Tue Mar 7 16:10:54 IST 2017 - Harsha now Pool or BufPool can be interchangable
+# by setting/unsetting isbuffered field
+# Fri May 17 23:45:59 2017 (+0530) - Harsha added, notes header,
+# Kd is calculated for the second order reaction and value is displayed
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
@@ -172,13 +174,16 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
#harsha: For signalling models will be pulling out notes field from Annotator
# can updates if exist for other types also
if ( isinstance(self.mooseObject, moose.PoolBase)
- #or isinstance(self.mooseObject,moose.ReacBase)
or isinstance(self.mooseObject,moose.EnzBase) ) :
self.fields.append("Color")
- # self.fields.append("Notes")
flag = QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable
self.fieldFlags[fieldName] = flag
+ if ( isinstance(self.mooseObject, moose.ReacBase) ) :
+ self.fields.append("Kd")
+ flag = QtCore.Qt.ItemIsEnabled
+ self.fieldFlags[fieldName] = flag
+
def rowCount(self, parent):
return len(self.fields)
@@ -320,7 +325,18 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
try:
if (str(field) =="Color" ):
return QtGui.QPushButton("Press Me!")
- if ( (str(field) != "Notes") and (str(field) != "className")):
+ if (str(field) =="Kd" ):
+ #ret = self.mooseObject.getField(str(field))
+ Kd = 0
+
+ if self.mooseObject.className == "ZombieReac" or self.mooseObject.className == "Reac":
+ if self.mooseObject.numSubstrates > 1 or self.mooseObject.numProducts > 1:
+ if self.mooseObject.Kf != 0:
+ Kd = self.mooseObject.Kb/self.mooseObject.Kf
+
+ #Kd = QtCore.QVariant(QtCore.QString(str(ret)))
+ ret = QtCore.QVariant(QtCore.QString(str(Kd)))
+ if ( (str(field) != "Notes") and (str(field) != "className") and (str(field) != "Kd")):
ret = self.mooseObject.getField(str(field))
ret = QtCore.QVariant(QtCore.QString(str(ret)))
elif(str(field) == "className"):
@@ -465,7 +481,10 @@ class ObjectEditDockWidget(QtGui.QDockWidget):
base.setOrientation(PyQt4.QtCore.Qt.Vertical)
layout = QVBoxLayout()
layout.addWidget(view)#, 0, 0)
-
+ lineedit = QtGui.QLineEdit("Notes:")
+ lineedit.setReadOnly(True)
+ layout.addWidget(lineedit)
+
if ( isinstance(mobj, moose.PoolBase)
or isinstance(mobj,moose.ReacBase)
or isinstance(mobj,moose.EnzBase)
diff --git a/moose-gui/plugins/kkit.py b/moose-gui/plugins/kkit.py
index 5b79ea6fa2514f7fa9968b412d210f904cfdf03f..68bfd85ee77dcfb1a38c00ffea00e794363bc74a 100644
--- a/moose-gui/plugins/kkit.py
+++ b/moose-gui/plugins/kkit.py
@@ -1,3 +1,13 @@
+
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Mar 7 2017"
+import math
import sys
from PyQt4 import QtGui, QtCore, Qt
from default import *
@@ -21,6 +31,7 @@ import RunWidget
from os.path import expanduser
from setsolver import *
+
class KkitPlugin(MoosePlugin):
"""Default plugin for MOOSE GUI"""
def __init__(self, *args):
@@ -89,37 +100,25 @@ class KkitPlugin(MoosePlugin):
elif filters[str(filter_)] == 'Genesis':
mdtype = moose.Annotator(self.modelRoot+'/info')
self.coOrdinates = {}
- xycord = []
- self.sceneObj = KkitEditorView(self).getCentralWidget().mooseId_GObj
- #Here get x,y coordinates from the Annotation, to save layout position
- # into genesis
- for k,v in self.sceneObj.items():
+ ss = KkitEditorView(self).getCentralWidget().mooseId_GObj
+ for k,v in ss.items():
if moose.exists(moose.element(k).path+'/info'):
annoInfo = Annotator(k.path+'/info')
- self.coOrdinates[k] = {'x':annoInfo.x, 'y':annoInfo.y}
- if mdtype.modeltype != "kkit":
- #If coordinates come from kkit then directly transfering the co-ordinates
- # else zoomed in factor is applied before saving it to genesis form
- for k,v in self.coOrdinates.items():
- xycord.append(v['x'])
- xycord.append(v['y'])
- cmin = min(xycord)
- cmax = max(xycord)
- for k,v in self.coOrdinates.items():
- x = v['x']
- xprime = int((20*(float(v['x']-cmin)/float(cmax-cmin)))-10)
- v['x'] = xprime
- y = v['y']
- yprime = int((20*(float(v['y']-cmin)/float(cmax-cmin)))-10)
- v['y'] = -yprime
-
- filename = filename
- writeerror = mooseWriteKkit(self.modelRoot,str(filename),self.coOrdinates)
- if writeerror == False:
+ #co-ordinates will be in decimals converting to int which should be b/w 0 to 10
+ x = annoInfo.x *10
+ y = -annoInfo.y *10
+ self.coOrdinates[k] = {'x':x, 'y':y}
+
+ error,writen = mooseWriteKkit(self.modelRoot,str(filename),self.coOrdinates)
+ if writen == False:
QtGui.QMessageBox.information(None,'Could not save the Model','\nCheck the file')
else:
- QtGui.QMessageBox.information(None,'Saved the Model','\n File saved to \'{filename}\''.format(filename =filename+'.g'),QtGui.QMessageBox.Ok)
-
+ if error == "":
+ QtGui.QMessageBox.information(None,'Saved the Model','\n File saved to \'{filename}\''.format(filename =filename+'.g'),QtGui.QMessageBox.Ok)
+ else:
+ status = QtCore.QString("File saved but %2").arg(error);
+ QtGui.QMessageBox.information(None,'Saved the Model but ...','{error}'.format(error=error),QtGui.QMessageBox.Ok)
+
def getPreviousPlugin(self):
return None
@@ -168,13 +167,6 @@ class KkitPlugin(MoosePlugin):
graphView.layout().addWidget(self.currentRunView,0,0,2,1)
return self.view
-# class AnotherKkitRunViewsCentralWidget(QWidget):
-
-# def __init__():
-# QWidget.__init__()
-
-# def
-
class AnotherKkitRunView(RunView):
def __init__(self, modelRoot, plugin,*args):
@@ -335,22 +327,25 @@ class KineticsWidget(EditorWidgetBase):
self.comptPen = 5
self.iconScale = 1
self.arrowsize = 2
- self.defaultComptsize = 5
- self.noPositionInfo = True
- self.xyCord = {}
self.reset()
- self.qGraCompt = {}
- self.mooseId_GObj = {}
+
+ self.defaultSceneheight = 500
+ self.defaultScenewidth = 1000
+ self.positionInfoExist = True
+ self.defaultComptsize = 5
self.srcdesConnection = {}
+
+ self.mooseId_GObj = {}
+ self.qGraCompt = {}
+ self.xyCord = {}
self.editor = None
- self.xmin = 0.0
- self.xmax = 1.0
- self.ymin = 0.0
- self.ymax = 1.0
- self.xratio = 1.0
- self.yratio = 1.0
-
-
+ # self.xmin = 0.0
+ # self.xmax = 1.0
+ # self.ymin = 0.0
+ # self.ymax = 1.0
+ # self.xratio = 1.0
+ # self.yratio = 1.0
+
def reset(self):
self.createdItem = {}
#This are created at drawLine
@@ -371,16 +366,16 @@ class KineticsWidget(EditorWidgetBase):
def updateModelView(self):
self.getMooseObj()
- minmaxratiodict = {'xmin':self.xmin,'xmax':self.xmax,'ymin':self.ymin,'ymax':self.ymax,'xratio':self.xratio,'yratio':self.yratio}
+ #minmaxratiodict = {'xmin':self.xmin,'xmax':self.xmax,'ymin':self.ymin,'ymax':self.ymax,'xratio':self.xratio,'yratio':self.yratio}
if not self.m:
#At the time of model building
# when we want an empty GraphicView while creating new model,
# then remove all the view and add an empty view
if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):
self.layout().removeWidget(self.view)
- #self.sceneContainer.setSceneRect(-self.width()/2,-self.height()/2,self.width(),self.height())
- self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
-
+ #self.sceneContainer.setSceneRect(-self.width()/2,-self.height()/2,self.width(),self.height())
+ #self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
+ self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem)
if isinstance(self,kineticEditorWidget):
self.view.setRefWidget("editorView")
self.view.setAcceptDrops(True)
@@ -397,7 +392,8 @@ class KineticsWidget(EditorWidgetBase):
#self.drawLine_arrow()
if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):
self.layout().removeWidget(self.view)
- self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
+ # self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
+ self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem)
if isinstance(self,kineticEditorWidget):
#self.getMooseObj()
self.mooseObjOntoscene()
@@ -422,44 +418,23 @@ class KineticsWidget(EditorWidgetBase):
# setupItem
self.m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
if self.m:
- # self.xmin = 0.0
- # self.xmax = 1.0
- # self.ymin = 0.0
- # self.ymax = 1.0
- self.autoCordinatepos = {}
self.srcdesConnection = {}
-
#self.meshEntry.clear= {}
# Compartment and its members are setup
- self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot)
- self.autocoordinates = False
+ #self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot)
+
+ self.meshEntry,xcord,ycord = setupMeshObj(self.modelRoot)
+ self.positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
+ and len(np.nonzero(ycord)[0]) == 0)
+
if self.srcdesConnection:
self.srcdesConnection.clear()
else:
self.srcdesConnection = {}
setupItem(self.modelRoot,self.srcdesConnection)
- if not self.noPositionInfo:
- self.autocoordinates = True
-
- self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection)
- # TODO: size will be dummy at this point, but size I need the availiable size from the Gui
- self.size= QtCore.QSize(1000 ,550)
-
- if self.xmax-self.xmin != 0:
- self.xratio = (self.size.width()-10)/(self.xmax-self.xmin)
- else: self.xratio = self.size.width()-10
-
- if self.ymax-self.ymin:
- self.yratio = (self.size.height()-10)/(self.ymax-self.ymin)
- else: self.yratio = (self.size.height()-10)
-
- self.xratio = int(self.xratio)
- self.yratio = int(self.yratio)
- if self.xratio == 0:
- self.xratio = 1
- if self.yratio == 0:
- self.yratio = 1
-
+ if not self.positionInfoExist:
+ autoCoordinates(self.meshEntry,self.srcdesConnection)
+
def sizeHint(self):
return QtCore.QSize(800,400)
@@ -561,7 +536,6 @@ class KineticsWidget(EditorWidgetBase):
# compartment's rectangle size is calculated depending on children
self.comptChilrenBoundingRect()
-
def comptChilrenBoundingRect(self):
for k, v in self.qGraCompt.items():
@@ -582,6 +556,11 @@ class KineticsWidget(EditorWidgetBase):
# we are not using these colors for displaying the object so just passing dummy color white
if( objClass == "reaction" or objClass == "cplx" or objClass == "Function" or objClass == "StimulusTable"):
textcolor,bgcolor = QColor("white"),QColor("white")
+ elif(objClass == "enzyme"):
+ textcolor,bgcolor = getColor(info)
+ if bgcolor.name() == "#ffffff" or bgcolor == "white":
+ bgcolor = getRandColor()
+ Annoinfo.color = str(bgcolor.name())
else:
textcolor,bgcolor = getColor(info)
if bgcolor.name() == "#ffffff" or bgcolor == "white":
@@ -616,31 +595,13 @@ class KineticsWidget(EditorWidgetBase):
#Annoinfo.y = ypos
def positioninfo(self,iteminfo):
- Anno = moose.Annotator(self.modelRoot+'/info')
- if not self.noPositionInfo:
- try:
- # kkit does exist item's/info which up querying for parent.path gives the information of item's parent
- x,y = self.autoCordinatepos[(element(iteminfo).parent).path]
- except:
- # But in Cspace reader doesn't create item's/info, up on querying gives me the error which need to change\
- # in ReadCspace.cpp, at present i am taking care b'cos i don't want to pass just the item where I need to check\
- # type of the object (rea,pool,enz,cplx,tab) which I have already done.
- parent, child = posixpath.split(iteminfo)
- x,y = self.autoCordinatepos[parent]
- ypos = (y-self.ymin)*self.yratio
- else:
- x = float(element(iteminfo).getField('x'))
- y = float(element(iteminfo).getField('y'))
- #Qt origin is at the top-left corner. The x values increase to the right and the y values increase downwards \
- #as compared to Genesis codinates where origin is center and y value is upwards, that is why ypos is negated
- # if Anno.modeltype == "kkit":
- # ypos = 1.0-(y-self.ymin)*self.yratio
- # else:
- # ypos = (y-self.ymin)*self.yratio
- ypos = 1.0 - (y-self.ymin)*self.yratio
- xpos = (x-self.xmin)*self.xratio
- return(xpos,ypos)
-
+ '''By this time, model loaded from kkit,cspace,SBML would have info field created and co-ordinates are added
+ either by autocoordinates (for cspace,SBML(unless it is not saved from moose)) or from kkit
+ '''
+ x = self.defaultScenewidth * float(element(iteminfo).getField('x'))
+ y = self.defaultSceneheight *float(element(iteminfo).getField('y'))
+ return(x,y)
+
def drawLine_arrow(self, itemignoreZooming=False):
for inn,out in self.srcdesConnection.items():
#print "inn ",inn, " out ",out
diff --git a/moose-gui/plugins/kkitOrdinateUtil.py b/moose-gui/plugins/kkitOrdinateUtil.py
index 03484f19ca5e61d3e56921e89e99ab8edd06c037..27ac35d62e5ad383816001e12b5adeb4b590d961 100644
--- a/moose-gui/plugins/kkitOrdinateUtil.py
+++ b/moose-gui/plugins/kkitOrdinateUtil.py
@@ -1,13 +1,5 @@
from moose import *
import numpy as np
-import networkx as nx
-from collections import Counter
-
-def xyPosition(objInfo,xory):
- try:
- return(float(element(objInfo).getField(xory)))
- except ValueError:
- return (float(0))
def setupMeshObj(modelRoot):
''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
@@ -15,11 +7,6 @@ def setupMeshObj(modelRoot):
value is key2:list where key2 represents moose object type,list of objects of a perticular type
e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
'''
- xmin = 0.0
- xmax = 1.0
- ymin = 0.0
- ymax = 1.0
- positionInfoExist = True
meshEntry = {}
if meshEntry:
meshEntry.clear()
@@ -47,17 +34,8 @@ def setupMeshObj(modelRoot):
for m in mol_cpl:
if isinstance(element(m.parent),CplxEnzBase):
cplxlist.append(m)
- objInfo = m.parent.path+'/info'
elif isinstance(element(m),moose.PoolBase):
mollist.append(m)
- objInfo =m.path+'/info'
- xcord.append(xyPosition(objInfo,'x'))
- ycord.append(xyPosition(objInfo,'y'))
-
- getxyCord(xcord,ycord,funclist)
- getxyCord(xcord,ycord,enzlist)
- getxyCord(xcord,ycord,realist)
- getxyCord(xcord,ycord,tablist)
meshEntry[meshEnt] = {'enzyme':enzlist,
'reaction':realist,
@@ -66,28 +44,18 @@ def setupMeshObj(modelRoot):
'table':tablist,
'function':funclist
}
- xmin = min(xcord)
- xmax = max(xcord)
- ymin = min(ycord)
- ymax = max(ycord)
- positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
- and len(np.nonzero(ycord)[0]) == 0)
- return(meshEntry,xmin,xmax,ymin,ymax,positionInfoExist)
+
+ for mert in [mollist,enzlist,realist,tablist]:
+ for merts in mert:
+ objInfo = merts.path+'/info'
+ if exists(objInfo):
+ xcord.append(element(objInfo).x)
+ ycord.append(element(objInfo).y)
+ return(meshEntry,xcord,ycord)
def sizeHint(self):
return QtCore.QSize(800,400)
-def getxyCord(xcord,ycord,list1):
- for item in list1:
- # if isinstance(item,Function):
- # objInfo = moose.element(item.parent).path+'/info'
- # else:
- # objInfo = item.path+'/info'
- if not isinstance(item,Function):
- objInfo = item.path+'/info'
- xcord.append(xyPosition(objInfo,'x'))
- ycord.append(xyPosition(objInfo,'y'))
-
def setupItem(modelPath,cntDict):
'''This function collects information of what is connected to what. \
eg. substrate and product connectivity to reaction's and enzyme's \
@@ -145,20 +113,6 @@ def setupItem(modelPath,cntDict):
prdlist.append((element(funcpar),'stp',countuniqItem[funcpar]))
cntDict[items] = sublist,prdlist
- # elif baseObj == 'Function':
- # #ZombieSumFunc adding inputs
- # inputlist = []
- # outputlist = []
- # funplist = []
- # nfunplist = []
- # for items in wildcardFind(path):
- # for funplist in moose.element(items).neighbors['valueOut']:
- # for func in funplist:
- # funcx = moose.element(items.path+'/x[0]')
- # uniqItem,countuniqItem = countitems(funcx,'input')
- # for inPut in uniqItem:
- # inputlist.append((inPut,'st',countuniqItem[inPut]))
- # cntDict[func] = inputlist
else:
for tab in wildcardFind(path):
tablist = []
@@ -169,17 +123,41 @@ def setupItem(modelPath,cntDict):
def countitems(mitems,objtype):
items = []
- #print "mitems in countitems ",mitems,objtype
items = element(mitems).neighbors[objtype]
uniqItems = set(items)
- countuniqItems = Counter(items)
+ #countuniqItemsauto = Counter(items)
+ countuniqItems = dict((i, items.count(i)) for i in items)
return(uniqItems,countuniqItems)
+def recalculatecoordinatesforKkit(mObjlist,xcord,ycord):
+
+ positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
+ and len(np.nonzero(ycord)[0]) == 0)
+
+ if positionInfoExist:
+ #Here all the object has been taken now recalculate and reassign back x and y co-ordinates
+ xmin = min(xcord)
+ xmax = max(xcord)
+ ymin = min(ycord)
+ ymax = max(ycord)
+ for merts in mObjlist:
+ objInfo = merts.path+'/info'
+ if moose.exists(objInfo):
+ Ix = (xyPosition(objInfo,'x')-xmin)/(xmax-xmin)
+ Iy = (ymin-xyPosition(objInfo,'y'))/(ymax-ymin)
+ element(objInfo).x = Ix
+ element(objInfo).y = Iy
+
+def xyPosition(objInfo,xory):
+ try:
+ return(float(element(objInfo).getField(xory)))
+ except ValueError:
+ return (float(0))
+
+
def autoCoordinates(meshEntry,srcdesConnection):
- xmin = 0.0
- xmax = 1.0
- ymin = 0.0
- ymax = 1.0
+ print " kkit Ordinatesutil autoCoordinates "
+
G = nx.Graph()
for cmpt,memb in meshEntry.items():
for enzObj in find_index(memb,'enzyme'):
@@ -218,6 +196,7 @@ def autoCoordinates(meshEntry,srcdesConnection):
else:
for items in (items for items in out ):
G.add_edge(element(items[0]).path,inn.path)
+<<<<<<< HEAD
position = nx.spring_layout(G)
#nx.draw(G,pos=nx.spring_layout(G))
#position = nx.spring_layout(G)
@@ -231,20 +210,38 @@ def autoCoordinates(meshEntry,srcdesConnection):
xcord = []
ycord = []
+=======
+
+ position = graphviz_layout(G)
+ xcord, ycord = [],[]
+>>>>>>> 320e525a5a34fbd3f1cb572b6de38eca0c0876f0
for item in position.items():
xy = item[1]
- ann = moose.Annotator(item[0]+'/info')
- ann.x = xy[0]
- xcord.append(xy[0])
- ann.y = xy[1]
- ycord.append(xy[1])
+ xroundoff = round(xy[0],0)
+ yroundoff = round(xy[1],0)
+ xcord.append(xroundoff)
+ ycord.append(yroundoff)
+<<<<<<< HEAD
if xcord and ycord:
xmin = min(xcord)
xmax = max(xcord)
ymin = min(ycord)
ymax = max(ycord)
return(xmin,xmax,ymin,ymax,position)
+=======
+ xmin = min(xcord)
+ xmax = max(xcord)
+ ymin = min(ycord)
+ ymax = max(ycord)
+ for item in position.items():
+ xy = item[1]
+ anno = Annotator(item[0]+'/info')
+ Ax = (xy[0]-xmin)/(xmax-xmin)
+ Ay = (xy[1]-ymin)/(ymax-ymin)
+ anno.x = round(Ax,1)
+ anno.y = round(Ay,1)
+>>>>>>> 320e525a5a34fbd3f1cb572b6de38eca0c0876f0
def find_index(value, key):
""" Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """
diff --git a/moose-gui/plugins/kkitQGraphics.py b/moose-gui/plugins/kkitQGraphics.py
index 27ddbe3555d0bff5f9672ba9db5dd2b15b3dc7c6..b0bb4338871e106d8cee4094dc8c187d1ac22454 100644
--- a/moose-gui/plugins/kkitQGraphics.py
+++ b/moose-gui/plugins/kkitQGraphics.py
@@ -48,7 +48,6 @@ class KineticsDisplayItem(QtGui.QGraphicsWidget):
# self.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj)
if change == QtGui.QGraphicsItem.ItemSelectedChange and value == True:
self.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),element(self.mobj))
- #print " itemChange ",self.mobj,change,value
return QtGui.QGraphicsItem.itemChange(self,change,value)
class FuncItem(KineticsDisplayItem):
diff --git a/moose-gui/plugins/kkitViewcontrol.py b/moose-gui/plugins/kkitViewcontrol.py
index c5c74b54c770e7d01ce640f4796a6821f633fa51..c9541743f847dcd8b049ab5aed3440b8845d2210 100644
--- a/moose-gui/plugins/kkitViewcontrol.py
+++ b/moose-gui/plugins/kkitViewcontrol.py
@@ -10,9 +10,9 @@ from moose import utils
class GraphicalView(QtGui.QGraphicsView):
- def __init__(self, modelRoot,parent,border,layoutPt,createdItem,minmaxratio):
+ def __init__(self, modelRoot,parent,border,layoutPt,createdItem):
QtGui.QGraphicsView.__init__(self,parent)
- self.minmaxratioDict = minmaxratio
+
self.state = None
self.move = False
self.resetState()
@@ -99,7 +99,6 @@ class GraphicalView(QtGui.QGraphicsView):
return (item, ITEM)
if item.name == COMPARTMENT:
solution = (item, self.resolveCompartmentInteriorAndBoundary(item, position))
-
if solution is None:
return (None, EMPTY)
return solution
@@ -171,15 +170,29 @@ class GraphicalView(QtGui.QGraphicsView):
iInfo = itemPath+'/info'
anno = moose.Annotator(iInfo)
modelAnno = moose.Annotator(self.modelRoot+'/info')
+ x = item.parent().scenePos().x()/self.layoutPt.defaultScenewidth
+ y = item.parent().scenePos().y()/self.layoutPt.defaultSceneheight
+ anno.x = x
+ anno.y = y
+ '''
if modelAnno.modeltype == "kkit":
- x = ((self.mapToScene(event.pos()).x())+(self.minmaxratioDict['xmin']*self.minmaxratioDict['xratio']))/self.minmaxratioDict['xratio']
- y = (1.0 - self.mapToScene(event.pos()).y()+(self.minmaxratioDict['ymin']*self.minmaxratioDict['yratio']))/self.minmaxratioDict['yratio']
+ # x = ((self.mapToScene(event.pos()).x())+(self.minmaxratioDict['xmin']*self.minmaxratioDict['xratio']))/self.minmaxratioDict['xratio']
+ # y = (1.0 - self.mapToScene(event.pos()).y()+(self.minmaxratioDict['ymin']*self.minmaxratioDict['yratio']))/self.minmaxratioDict['yratio']
+ # anno.x = x
+ # anno.y = y
+ print " kvc CONNECTOR ",item.parent().mobj, displacement.x(), " y ",displacement.y()
+ print "scenePos CONNECTOR",item.parent().scenePos().x(),item.parent().scenePos().y(),
+ print "dive x ",item.parent().scenePos().x()/1000, " y ",item.parent().scenePos().y()/500
+ #item.parent().update()
+ #self.updateScale(1)
+ x = item.parent().scenePos().x()/1000
+ y = item.parent().scenePos().y()/500
anno.x = x
anno.y = y
elif(modelAnno.modeltype == "new_kkit" or modelAnno.modeltype == "sbml" or modelAnno.modeltype == "cspace"):
anno.x = self.mapToScene(event.pos()).x()
anno.y = self.mapToScene(event.pos()).y()
-
+ '''
#if not isinstance(item.parent(),FuncItem) and not isinstance(item.parent(),CplxItem):
if not isinstance(item.parent(),CplxItem):
self.removeConnector()
@@ -1102,17 +1115,28 @@ class GraphicalView(QtGui.QGraphicsView):
if ( isinstance(moose.element(src),PoolBase) and ( (isinstance(moose.element(des),ReacBase) ) or isinstance(moose.element(des),EnzBase) )):
#If one to tries to connect pool to Reac/Enz (substrate to Reac/Enz), check if already (product to Reac/Enz) exist.
#If exist then connection not allowed one need to delete the msg and try connecting back.
- found = False
+ #And in moose Enzyme can't have 2nd order reaction.
+ founds, foundp = False,False
+
+ if isinstance(moose.element(des),EnzBase):
+ print moose.element(des).neighbors["subOut"]
+ if len(moose.element(des).neighbors["subOut"]) > 0:
+ founds = True
+
for msg in des.msgOut:
if moose.element(msg.e2.path) == src:
if msg.srcFieldsOnE1[0] == "prdOut":
- found = True
- if found == False:
+ foundp = True
+
+ if foundp == False and founds == False:
# moose.connect(src, 'reac', des, 'sub', 'OneToOne')
moose.connect(des, 'sub', src, 'reac', 'OneToOne')
- else:
+ elif foundp:
srcdesString = srcClass+' is already connected as '+ '\'Product\''+' to '+desClass +' \n \nIf you wish to connect this object then first delete the exist connection'
QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
+ elif founds:
+ srcdesString = desClass+' has already connected to a'+ '\'Substrate\''+' \n \nIn moose Enzyme\'s can not have second order reaction. If you wish to connect this object then first delete the exist connection'
+ QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
elif (isinstance (moose.element(src),PoolBase) and (isinstance(moose.element(des),Function))):
numVariables = des.numVars
@@ -1153,15 +1177,22 @@ class GraphicalView(QtGui.QGraphicsView):
):
moose.connect(src, 'valueOut', des, 'setNumKf', 'OneToOne')
elif (((isinstance(moose.element(src),ReacBase))or (isinstance(moose.element(src),EnzBase))) and (isinstance(moose.element(des),PoolBase))):
- found = False
+ founds,foundp = False,False
+ if isinstance(moose.element(src),EnzBase):
+ if len(moose.element(src).neighbors["prdOut"]) > 0:
+ foundp = True
+
for msg in src.msgOut:
if moose.element(msg.e2.path) == des:
if msg.srcFieldsOnE1[0] == "subOut":
- found = True
- if found == False:
+ founds = True
+ if founds == False and foundp == False:
#moose.connect(src, 'prd', des, 'reac', 'OneToOne')
- moose.connect(src, 'prd', des, 'reac', 'OneToOne')
- else:
+ moose.connect(src, 'prd', des, 'reac', 'OneToOne')
+ elif foundp:
+ srcdesString = srcClass+' is already connected as '+ '\'Product\''+' to '+desClass +' \n \nIn moose Enzyme\'s can not have second order reaction. If you wish to connect this object then first delete the exist connection'
+ QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
+ elif founds:
srcdesString = desClass+' is already connected as '+'\'Substrate\''+' to '+srcClass +' \n \nIf you wish to connect this object then first delete the exist connection'
QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
# elif( isinstance(moose.element(src),ReacBase) and (isinstance(moose.element(des),PoolBase) ) ):
@@ -1180,4 +1211,4 @@ class GraphicalView(QtGui.QGraphicsView):
if callsetupItem:
self.layoutPt.getMooseObj()
setupItem(self.modelRoot,self.layoutPt.srcdesConnection)
- self.layoutPt.drawLine_arrow(False)
\ No newline at end of file
+ self.layoutPt.drawLine_arrow(False)
diff --git a/moose-gui/plugins/modelBuild.py b/moose-gui/plugins/modelBuild.py
index 471d8e9eaf63953343cb3a7e968e5e2135e27860..406e0d2a4360a08c0489f25c2f9a782839a3bb2d 100644
--- a/moose-gui/plugins/modelBuild.py
+++ b/moose-gui/plugins/modelBuild.py
@@ -28,13 +28,9 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
print "28 ",modelpath
if moose.exists(modelpath+'/info'):
mType = moose.Annotator((moose.element(modelpath+'/info'))).modeltype
- print " 1 event_pos ",event_pos
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
- print "2 ",itemAtView
pos = view.mapToScene(event_pos)
- print " 3 ",pos
modelpath = moose.element(modelpath)
- print " model path @34 ",modelpath
if num:
string_num = ret_string+str(num)
else:
@@ -73,15 +69,12 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('green'),bgcolor)
poolinfo.color = str(bgcolor.getRgb())
- #if mType == "new_kkit":
- poolinfo.x = posWrtComp.x()
- poolinfo.y = posWrtComp.y()
view.emit(QtCore.SIGNAL("dropped"),poolObj)
setupItem(modelpath.path,layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
- poolinfo.x = posWrtComp.x()
- poolinfo.y = posWrtComp.y()
-
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ poolinfo.x = x
+ poolinfo.y = y
#Dropping is on compartment then update Compart size
if isinstance(mobj,moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
@@ -94,8 +87,8 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
qGItem = ReacItem(reacObj,itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),"white", "white")
#if mType == "new_kkit":
- reacinfo.x = posWrtComp.x()
- reacinfo.y = posWrtComp.y()
+ # reacinfo.x = posWrtComp.x()
+ # reacinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[reacObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"),reacObj)
setupItem(modelpath.path,layoutPt.srcdesConnection)
@@ -104,6 +97,9 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
if isinstance(mobj,moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ reacinfo.x = x
+ reacinfo.y = y
elif string == "StimulusTable":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
@@ -112,8 +108,8 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
qGItem = TableItem(tabObj,itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('white'),QtGui.QColor('white'))
#if mType == "new_kkit":
- tabinfo.x = posWrtComp.x()
- tabinfo.y = posWrtComp.y()
+ #tabinfo.x = posWrtComp.x()
+ #tabinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[tabObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"),tabObj)
setupItem(modelpath.path,layoutPt.srcdesConnection)
@@ -122,6 +118,10 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
if isinstance(mobj,moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ tabinfo.x = x
+ tabinfo.y = y
+
elif string == "Function":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
funcObj = moose.Function(mobj.path+'/'+string_num)
@@ -140,8 +140,8 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('red'),QtGui.QColor('green'))
layoutPt.mooseId_GObj[funcObj] = qGItem
#if mType == "new_kkit":
- funcinfo.x = posWrtComp.x()
- funcinfo.y = posWrtComp.y()
+ #funcinfo.x = posWrtComp.x()
+ #funcinfo.y = posWrtComp.y()
view.emit(QtCore.SIGNAL("dropped"),funcObj)
setupItem(modelpath.path,layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
@@ -150,6 +150,9 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
if isinstance(mooseCmpt,moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mooseCmpt)]
updateCompartmentSize(compt)
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ funcinfo.x = x
+ funcinfo.y = y
elif string == "Enz" or string == "MMenz":
#If 2 enz has same pool parent, then pos of the 2nd enz shd be displaced by some position, need to check how to deal with it
@@ -170,11 +173,16 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y()-40,QtGui.QColor('green'),bgcolor)
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ enzinfo.x = x
+ enzinfo.y = y
+ enzinfo.color = str(bgcolor.name())
+ enzinfo.textColor = str(QtGui.QColor('green').name())
#if mType == "new_kkit":
- enzinfo.x = posWrtComp.x()
- enzinfo.y = posWrtComp.y()
+ #enzinfo.x = posWrtComp.x()
+ #enzinfo.y = posWrtComp.y()
- enzinfo.color = str(bgcolor.name())
+ #enzinfo.color = str(bgcolor.name())
e = moose.Annotator(enzinfo)
#e.x = posWrtComp.x()
#e.y = posWrtComp.y()
@@ -187,8 +195,8 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
enzboundingRect = qGEnz.boundingRect()
moose.connect( enzObj, 'cplx', cplxItem, 'reac' )
qGItem.setDisplayProperties(enzboundingRect.height()/2,enzboundingRect.height()-40,QtGui.QColor('white'),QtGui.QColor('white'))
- cplxinfo.x = enzboundingRect.height()/2
- cplxinfo.y = enzboundingRect.height()-60
+ #cplxinfo.x = enzboundingRect.height()/2
+ #cplxinfo.y = enzboundingRect.height()-60
view.emit(QtCore.SIGNAL("dropped"),enzObj)
else:
@@ -199,13 +207,17 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y()-30,QtGui.QColor('green'),bgcolor)
- enzinfo.x = posWrtComp.x()
- enzinfo.y = posWrtComp.y()
+ #enzinfo.x = posWrtComp.x()
+ #enzinfo.y = posWrtComp.y()
enzinfo.color = str(bgcolor.name())
layoutPt.mooseId_GObj[enzObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"),enzObj)
+ x,y = roundoff(qGItem.scenePos(),layoutPt)
+ enzinfo.x = x
+ enzinfo.y = y
setupItem(modelpath.path,layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
+
#Dropping is on compartment then update Compart size
if isinstance(enzparent,moose.ChemCompt):
updateCompartmentSize(parentcompt)
@@ -280,6 +292,15 @@ def createObj(scene,view,modelpath,string,pos,layoutPt):
if ret_string != " ":
checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layoutPt)
+def roundoff(scenePos,layoutPt):
+ xtest = scenePos.x()/layoutPt.defaultScenewidth
+ xroundoff = round(xtest,1)
+
+ ytest = scenePos.y()/layoutPt.defaultSceneheight
+ yroundoff = round(ytest,1)
+
+ return(xroundoff,yroundoff)
+
def findUniqId(mobj,string,num):
if num == 0:
path = mobj.path+'/'+string;
@@ -297,4 +318,4 @@ def findCompartment(mooseObj):
elif isinstance(mooseObj,ChemCompt):
return (mooseObj)
else:
- return findCompartment(moose.element(mooseObj.parent))
\ No newline at end of file
+ return findCompartment(moose.element(mooseObj.parent))