Overview  Package   Class  Use  Deprecated  Index
Home >> All >> apollo >> dataadapter >> [ synteny overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

apollo.dataadapter.synteny
Class SyntenyAdapterGUI  

java.lang.Object
  AbstractDataAdapterUI
      apollo.dataadapter.CompositeAdapterUI
          apollo.dataadapter.synteny.SyntenyAdapterGUI

---

public class SyntenyAdapterGUI

extends apollo.dataadapter.CompositeAdapterUI

---

Field Summary
protected  DataAdapter	driver
private  javax.swing.JButton	fullPanelButton
protected  IOOperation	op
private  java.util.Properties	props
private  apollo.gui.FullEnsJDBCSyntenyPanel	thePanel

 

Fields inherited from class apollo.dataadapter.CompositeAdapterUI

 

Constructor Summary

SyntenyAdapterGUI(IOOperation op)

 

Method Summary
protected  java.util.List	buildAdapterOrder()           The order of the adapters is given by the synteny style's syntenySpeciesOrder vector.
protected  java.util.Map	buildAdapters()           Read the style file for the synteny adapter to get a list of child adapters to insert here.
void	buildGUI()           Create the tabbed pane.
private  void	doAppropriateFetchesForInputQueryHitAndComparaAdapters(java.lang.Object values, java.lang.String querySpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI, java.lang.String comparaName, SyntenyComparaAdapterGUI comparaAdapterGUI, java.lang.String hitSpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI, apollo.datamodel.CurationSet masterCurationSet)
private  void	doOneSidedFetch(java.lang.Object values, java.lang.String querySpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI, java.lang.String comparaName, SyntenyComparaAdapterGUI comparaAdapterGUI, java.lang.String hitSpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI, apollo.datamodel.CurationSet masterCurationSet)           -Run individual fetch on QUERY species, compile a list of gene stable ids -Run the compara with a "one sided fetch" for dna-aligns -sift the output to see what the "other side" should be -run the individual species fetch for the "other side", as -indicated by the compara analysis.
java.lang.Object	doOperation(java.lang.Object values)           We need to post-process this composite curation set.
private  void	doTwoSidedFetch(java.lang.Object values, java.lang.String querySpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI, java.lang.String comparaName, SyntenyComparaAdapterGUI comparaAdapterGUI, java.lang.String hitSpeciesName, apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI, apollo.datamodel.CurationSet masterCurationSet)           -Run individual species fetches, compile two lists of allowed stable gene ids.
private  void	findDownstreamCurationSets(int startIndex, apollo.datamodel.CurationSet masterCurationSet, java.lang.Object values)           Fill in the curation sets to the "left" of the input index
private  int	findStartAdapterIndex()
private  void	findUpstreamCurationSets(int startIndex, apollo.datamodel.CurationSet masterCurationSet, java.lang.Object values)           Fill in the curation sets to the "right" of the input index
java.util.Properties	getProperties()           Gather properties for each child adapter - prefix each gathered property with the name of the species (so, "myProp" -> "Homo_sapiens:myProp") and then glue all child Properties into one big Properties.
private  boolean	hasRangeInformation(apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI adapterGUI)
private  boolean	hasStableIdInformation(apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI adapterGUI)
void	setDataAdapter(DataAdapter driver)           This sets the SyntenyAdapter as the dataadapter for this GUI.
void	setInput(java.lang.Object input)           This is called specifically by helpers (like the FullEnsJDBCSyntenyPanel) which need to set values directly into the widgets in its children.
void	setProperties(java.util.Properties combinedProperties)            Walk each property we've been handed.

 

Methods inherited from class apollo.dataadapter.CompositeAdapterUI

getAdapterOrder, getAdapters, getSharedData, setAdapterOrder, setAdapters

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

driver

protected DataAdapter driver

---

op

protected IOOperation op

---

props

private java.util.Properties props

---

fullPanelButton

private javax.swing.JButton fullPanelButton

---

thePanel

private apollo.gui.FullEnsJDBCSyntenyPanel thePanel

Constructor Detail

SyntenyAdapterGUI

public SyntenyAdapterGUI(IOOperation op)

Method Detail

setDataAdapter

public void setDataAdapter(DataAdapter driver)

This sets the SyntenyAdapter as the dataadapter for this GUI. We must propagate this relation down to the children, otherwise none of the GUI's in the child adapters will be connected to the child dataadapers.

---

setInput

public void setInput(java.lang.Object input)

This is called specifically by helpers (like the FullEnsJDBCSyntenyPanel) which need to set values directly into the widgets in its children. -- The point is that we get fed something (currently a SyntenyRegion) from the our invoker (currently the SyntenyMenu). We find the adapter gui's relevant to the chromosomes on the region and setInput on them, passing in a HashMap of text-field values relevant to each.

For instance, when given ranges on Human and Mouse, we will set the Human ranges on the Human adapter, the Mouse ranges on the Mouse adapter, and both ranges on the Human/Mouse adapter.

If we get called with anything other than a HashMap, we do nothing.

---

buildGUI

public void buildGUI()

Description copied from class: apollo.dataadapter.CompositeAdapterUI

Create the tabbed pane. Add a new DataAdapter GUI into each tab of the pane.

---

buildAdapters

protected java.util.Map buildAdapters()

Read the style file for the synteny adapter to get a list of child adapters to insert here.

---

getProperties

public java.util.Properties getProperties()

Gather properties for each child adapter - prefix each gathered property with the name of the species (so, "myProp" -> "Homo_sapiens:myProp") and then glue all child Properties into one big Properties. Hand out!

---

setProperties

public void setProperties(java.util.Properties combinedProperties)

Walk each property we've been handed. Strip off the species name at the front of the property, and gather the properties into species-specific groups.

Add to these properties the configuration information in the synteny style file for this species (in particular, we'll throw in the query- and hit-species for the compara-adapters we load into the properties list)

Call setProperties() on each species' adapter, passing in the specific groups we've gathered.

---

buildAdapterOrder

protected java.util.List buildAdapterOrder()

The order of the adapters is given by the synteny style's syntenySpeciesOrder vector.

---

doOperation

public java.lang.Object doOperation(java.lang.Object values)
                             throws org.bdgp.io.DataAdapterException

We need to post-process this composite curation set. Right now, protein homology information is being provided with no "extra" redundant information - namely, the positions of the homologous genes are no longer being stored with the gene pairs, but we have already retrieved these genes in the individual species' curation sets, so we will fill-in the feature pairs' position information with the gene info we already know.

---

findStartAdapterIndex

private int findStartAdapterIndex()
                           throws apollo.dataadapter.DataAdapterException

---

findUpstreamCurationSets

private void findUpstreamCurationSets(int startIndex,
                                      apollo.datamodel.CurationSet masterCurationSet,
                                      java.lang.Object values)
                               throws org.bdgp.io.DataAdapterException

Fill in the curation sets to the "right" of the input index

---

findDownstreamCurationSets

private void findDownstreamCurationSets(int startIndex,
                                        apollo.datamodel.CurationSet masterCurationSet,
                                        java.lang.Object values)
                                 throws org.bdgp.io.DataAdapterException

Fill in the curation sets to the "left" of the input index

---

doAppropriateFetchesForInputQueryHitAndComparaAdapters

private void doAppropriateFetchesForInputQueryHitAndComparaAdapters(java.lang.Object values,
                                                                    java.lang.String querySpeciesName,
                                                                    apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI,
                                                                    java.lang.String comparaName,
                                                                    SyntenyComparaAdapterGUI comparaAdapterGUI,
                                                                    java.lang.String hitSpeciesName,
                                                                    apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI,
                                                                    apollo.datamodel.CurationSet masterCurationSet)
                                                             throws org.bdgp.io.DataAdapterException

---

doTwoSidedFetch

private void doTwoSidedFetch(java.lang.Object values,
                             java.lang.String querySpeciesName,
                             apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI,
                             java.lang.String comparaName,
                             SyntenyComparaAdapterGUI comparaAdapterGUI,
                             java.lang.String hitSpeciesName,
                             apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI,
                             apollo.datamodel.CurationSet masterCurationSet)
                      throws org.bdgp.io.DataAdapterException

-Run individual species fetches, compile two lists of allowed stable gene ids. -Run the compara adapter and get dna-dna aligns for two input ranges -Set the gene stable id info on the compara and get protein aligns. -Fill in protein-align start/end information from the individual species' gene info.

---

doOneSidedFetch

private void doOneSidedFetch(java.lang.Object values,
                             java.lang.String querySpeciesName,
                             apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI querySpeciesAdapterGUI,
                             java.lang.String comparaName,
                             SyntenyComparaAdapterGUI comparaAdapterGUI,
                             java.lang.String hitSpeciesName,
                             apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI hitSpeciesAdapterGUI,
                             apollo.datamodel.CurationSet masterCurationSet)
                      throws org.bdgp.io.DataAdapterException

-Run individual fetch on QUERY species, compile a list of gene stable ids -Run the compara with a "one sided fetch" for dna-aligns -sift the output to see what the "other side" should be -run the individual species fetch for the "other side", as -indicated by the compara analysis. Compile another list of gene stable ids -run the compara for protein-homologies, passing in both lists of gene stable ids.

---

hasRangeInformation

private boolean hasRangeInformation(apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI adapterGUI)

---

hasStableIdInformation

private boolean hasStableIdInformation(apollo.dataadapter.ensj.AnnotationEnsJAdapterGUI adapterGUI)

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> apollo >> dataadapter >> [ synteny overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---