def __init__(self,expdat): super(CorrelationWindow, self).__init__() uic.loadUi(hs.get_data_path('correlation.py','ui'), self) self.cexp=expdat self.cField.addItems(expdat.fields) self.bFieldValues1.clicked.connect(self.fieldvalues1) self.tNewName.setText(self.cexp.studyname+'_de')
def __init__(self): super(LoadWindow, self).__init__() uic.loadUi(hs.get_data_path('load.py','ui'), self) self.bLoadBrowseTable.clicked.connect(self.browsetable) self.bLoadBrowseMap.clicked.connect(self.browsemap) self.bLoadLoad.clicked.connect(self.load) self.bLoadCancel.clicked.connect(self.cancel)
def __init__(self,expdat): super(FilterSimilarSamplesWindow, self).__init__() uic.loadUi(hs.get_data_path('filtersimilarsamples.py','ui'), self) self.cexp=expdat self.cField.addItems(expdat.fields) self.bFieldValues1.clicked.connect(self.fieldvalues1) self.tNewName.setText(self.cexp.studyname+'_fss')
def __init__(self,expdat): super(PlotGUIWindow, self).__init__() hs.Debug(1,hs.get_data_path('plotguiwindow.py','ui')) uic.loadUi(os.path.join(hs.heatsequerdir,'ui/plotguiwindow.py'), self) self.bGetSequence.clicked.connect(self.getsequence) self.bExport.clicked.connect(self.export) self.bView.clicked.connect(self.view) self.bSave.clicked.connect(self.save) self.bDBSave.clicked.connect(self.dbsave) self.bEnrich.clicked.connect(self.enrich) self.bExpInfo.clicked.connect(self.expinfo) self.bSampleInfo.clicked.connect(self.sampleinfo) self.connect(self.cSampleField, QtCore.SIGNAL('activated(QString)'), self.samplefield) self.FigureTab.connect(self.FigureTab, QtCore.SIGNAL("currentChanged(int)"),self.tabchange) self.cSampleField.setCurrentIndex(0) self.cexp=expdat self.selectionlines={} self.selection=[] self.setWindowTitle(self.cexp.studyname) for cfield in self.cexp.fields: self.cSampleField.addItem(cfield) self.cPlotXField.addItem(cfield) if self.cexp.seqdb: ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb) for conto in ontofields: # for conto in self.cexp.seqdb.OntoGraph.keys(): self.cOntology.addItem(conto) self.dc=None self.createaddplot(useqt=True)
def __init__(self,expdat,cdb=False,bdb=False): super(BiClusterWindow, self).__init__() uic.loadUi(hs.get_data_path('bicluster.py','ui'), self) self.cexp=expdat self.cooldb=cdb self.bactdb=bdb self.lStudy.setText(self.cexp.studyname) self.bBiCluster.clicked.connect(self.bicluster) self.bView.clicked.connect(self.view)
def __init__(self,expdat): super(FilterSamplesWindow, self).__init__() uic.loadUi(hs.get_data_path('filtersamples.py','ui'), self) self.cexp=expdat self.cField.addItems(expdat.fields) self.bOK.clicked.connect(self.OK) self.bFieldValues.clicked.connect(self.fieldvalues) self.cOverwrite.stateChanged.connect(self.overwrite) self.bCancel.clicked.connect(self.cancel) self.tNewName.setText(self.cexp.studyname+'_f')
def __init__(self, expdat): super(DiffExpWindow, self).__init__() uic.loadUi(hs.get_data_path("diffexp.py", "ui"), self) self.cexp = expdat self.cField.addItems(expdat.fields) self.bFieldValues1.clicked.connect(self.fieldvalues1) self.bFieldValues2.clicked.connect(self.fieldvalues2) self.cAll.stateChanged.connect(self.allvalues) # self.cField.stateChanged.connect(self.fieldchanged) self.tNewName.setText(self.cexp.studyname + "_de")
def __init__(self,expdat): super(ClassifyWindow, self).__init__() uic.loadUi(hs.get_data_path('classifier.py','ui'), self) self.cexp=expdat self.cField.addItems(expdat.fields) self.bFieldValues1.clicked.connect(self.fieldvalues1) self.bFieldValues2.clicked.connect(self.fieldvalues2) self.cAll.stateChanged.connect(self.allvalues) # self.cField.stateChanged.connect(self.fieldchanged) self.tNewName.setText(self.cexp.studyname+'_de')
def __init__(self,expdat): super(AdvPlotWindow, self).__init__() uic.loadUi(hs.get_data_path('advplot.py','ui'), self) self.cexp=expdat self.cField.addItems(expdat.fields) self.bOK.clicked.connect(self.OK) self.bFieldValues.clicked.connect(self.fieldvalues) self.bMetaData.clicked.connect(self.metadata) self.cSort.stateChanged.connect(self.usesort) self.bCancel.clicked.connect(self.cancel)
def __init__(self,listdata=[],listname=''): """ create a list window with items in the list and the listname as specified input: listdata - the data to show in the list (a list) listname - name to display above the list """ super(ListWindow, self).__init__() uic.loadUi(hs.get_data_path('listwindow.py','ui'), self) for citem in listdata: self.lList.addItem(citem) if listname: self.lLabel.setText(listname)
def __init__(self,expdat): super(MetaDataWindow, self).__init__() uic.loadUi(hs.get_data_path('plotmetadata.py','ui'), self) self.cexp=expdat self.mddict={} for cmeta in expdat.plotmetadata: cname="%s;%s;%s;%s;%s" % (cmeta[0],cmeta[1],cmeta[2],cmeta[3],cmeta[4]) self.lMetaData.addItem(cname) self.mddict[cname]=cmeta self.bAdd.clicked.connect(self.add) # the main list right mouse menu self.lMetaData.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) self.lMetaData.connect(self.lMetaData, QtCore.SIGNAL("customContextMenuRequested(QPoint)"),self.listItemRightClicked)
def __init__(self,expdat): super(PlotGUIWindow, self).__init__() uic.loadUi(hs.get_data_path('plotguiwindow.py','ui'), self) # uic.loadUi('ui/plotguiwindow.py', self) self.bGetSequence.clicked.connect(self.getsequence) self.bExport.clicked.connect(self.export) self.bView.clicked.connect(self.view) self.bSave.clicked.connect(self.save) self.bDBSave.clicked.connect(self.dbsave) self.bEnrich.clicked.connect(self.enrich) self.bSampleInfo.clicked.connect(self.sampleinfo) self.connect(self.cSampleField, QtCore.SIGNAL('activated(QString)'), self.samplefield) self.FigureTab.connect(self.FigureTab, QtCore.SIGNAL("currentChanged(int)"),self.tabchange) self.cSampleField.setCurrentIndex(0) self.cexp=expdat self.selectionlines={} self.selection=[] self.setWindowTitle(self.cexp.studyname) for cfield in self.cexp.fields: self.cSampleField.addItem(cfield) self.cPlotXField.addItem(cfield) if self.cexp.seqdb: ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb) for conto in ontofields: # for conto in self.cexp.seqdb.OntoGraph.keys(): self.cOntology.addItem(conto) # add the matplotlib figure self.frame = QtGui.QWidget(self) self.dc = MyMplCanvas(self.frame, width=5, height=4, dpi=100) # add it to an hboxlayout to make it resize with window layout = QtGui.QHBoxLayout(self) layout.insertSpacing(0,250) # layout.addWidget(self.dc) # self.setLayout(layout) layout2 = QtGui.QVBoxLayout() layout.addLayout(layout2) layout2.addWidget(self.dc) self.mpl_toolbar = NavigationToolbar(self.dc, self) layout2.addWidget(self.mpl_toolbar) self.setLayout(layout)
def __init__(self,expdat): super(PlotGUIWindow, self).__init__() hs.Debug(1,hs.get_data_path('plotguiwindow.py','ui')) uic.loadUi(os.path.join(hs.heatsequerdir,'ui/plotguiwindow.py'), self) self.bGetSequence.clicked.connect(self.getsequence) self.bExport.clicked.connect(self.export) self.bView.clicked.connect(self.view) self.bSave.clicked.connect(self.save) self.bDBSave.clicked.connect(self.dbsave) self.bEnrich.clicked.connect(self.enrich) self.bExpInfo.clicked.connect(self.expinfo) self.bSampleInfo.clicked.connect(self.sampleinfo) self.lCoolDB.doubleClicked.connect(self.showannotation) self.cSampleField.activated.connect(self.samplefield) self.FigureTab.currentChanged.connect(self.tabchange) self.cSampleField.setCurrentIndex(0) self.cexp=expdat self.selectionlines={} self.selection=[] self.setWindowTitle(self.cexp.studyname) for cfield in self.cexp.fields: self.cSampleField.addItem(cfield) self.cPlotXField.addItem(cfield) if self.cexp.seqdb: ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb) for conto in ontofields: # for conto in self.cexp.seqdb.OntoGraph.keys(): self.cOntology.addItem(conto) self.dc=None self.createaddplot(useqt=True) # right click menu self.lCoolDB.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) self.lCoolDB.customContextMenuRequested.connect(self.listItemRightClicked)
def __init__(self,expdat): super(JoinWindow, self).__init__() uic.loadUi(hs.get_data_path('joinfields.py','ui'), self) self.cexp=expdat self.cField1.addItems(expdat.fields) self.cField2.addItems(expdat.fields)
def __init__(self,expdat): super(MetaDataDetailsWindow, self).__init__() uic.loadUi(hs.get_data_path('metadatadetails.py','ui'), self) self.cexp=expdat self.bFieldValues.clicked.connect(self.values) self.cField.addItems(expdat.fields)
def __init__(self): super(AppWindow, self).__init__() uic.loadUi(hs.get_data_path('appwindow.py','ui'), self) self.bMainLoadNew.clicked.connect(self.load) self.bPickleLoad.clicked.connect(self.pickleload) self.bMainPlot.clicked.connect(self.plot) self.bMainAdvancedPlot.clicked.connect(self.advplot) self.bMainFilterSamples.clicked.connect(self.filtersamples) self.bDiffExp.clicked.connect(self.diffexp) self.bCorrelation.clicked.connect(self.correlation) self.bFilterSimilarSamples.clicked.connect(self.filtersimilarsamples) self.bClassifier.clicked.connect(self.classify) self.bFilterOrigReads.clicked.connect(self.filterorigreads) self.bMainSortSamples.clicked.connect(self.sortsamples) self.bMainClusterBacteria.clicked.connect(self.clusterbacteria) self.bMainFilterMinReads.clicked.connect(self.filterminreads) self.bMainFilterTaxonomy.clicked.connect(self.filtertaxonomy) self.bFilterAnnotation.clicked.connect(self.filterannotation) self.bFilterPresence.clicked.connect(self.filterpresence) self.bFilterMean.clicked.connect(self.filtermean) self.bSortAbundance.clicked.connect(self.sortabundance) self.bJoinFields.clicked.connect(self.joinfields) self.bJoinExps.clicked.connect(self.joinexps) self.bBicluster.clicked.connect(self.bicluster) self.bEnrichment.clicked.connect(self.enrichment) self.bFilterFasta.clicked.connect(self.filterfasta) self.bRenormalize.clicked.connect(self.renormalize) self.bCleanTaxonomy.clicked.connect(self.cleantaxonomy) self.bSubsample.clicked.connect(self.subsample) self.cDebugMode.stateChanged.connect(self.debugmode) # the main list right mouse menu self.bMainList.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) self.bMainList.connect(self.bMainList, QtCore.SIGNAL("customContextMenuRequested(QPoint)"),self.listItemRightClicked) self.show() self.bactdb=False self.cooldb=False try: hs.Debug(6,'Connecting to sequence database') bdbpath=hs.get_data_path('SRBactDB.db','db') hs.Debug(6,'From %s' % bdbpath) self.bactdb=hs.bactdb.dbstart(bdbpath) hs.Debug(6,'Sequence database connected') except: hs.Debug(9,'sequence database file not found') try: hs.Debug(6,'Loading coolseq database') cdbpath=hs.get_data_path('coolseqs.txt','db') hs.Debug(6,'From %s' % cdbpath) self.cooldb=hs.cooldb.loaddb(cdbpath) hs.Debug(6,'coolseq database loaded') except: hs.Debug(9,'CoolDB file not found') # put some experiments: hs.Debug(6,'Loading sample experiment') try: expdat=hs.load('./test_data/bears.clean.new.withtax.biom','./test_data/map.txt') self.addexp(expdat) except: hs.Debug(6,'Sample experiment not found. sorry')
def __init__(self,expdat): super(CleanTaxonomyWindow, self).__init__() uic.loadUi(hs.get_data_path('cleantaxonomy.py','ui'), self) self.cexp=expdat
def __init__(self): super(FilterFastaWindow, self).__init__() uic.loadUi(hs.get_data_path('filterfasta.py','ui'), self) self.bBrowse.clicked.connect(self.browse)