/**
* Overrides the protected Object.clone() method exposing it as public. It performs a 2 tier copy,
* that is, it does a memcopy of the instance and then sets all the non-primitive data fields to
* clones of themselves.
*
* @return -A minimum 2 deep copy of this object.
*/
public Object clone() {
GeneExpressionQuery myClone = null;
myClone = (GeneExpressionQuery) super.clone();
if (allGenesCrit != null) {
myClone.allGenesCrit = (AllGenesCriteria) allGenesCrit.clone();
}
if (arrayPlatformCriteria != null) {
myClone.arrayPlatformCriteria = (ArrayPlatformCriteria) arrayPlatformCriteria.clone();
}
if (cloneOrProbeIDCriteria != null) {
myClone.cloneOrProbeIDCriteria = (CloneOrProbeIDCriteria) cloneOrProbeIDCriteria.clone();
}
if (foldChgCrit != null) {
myClone.foldChgCrit = (FoldChangeCriteria) foldChgCrit.clone();
}
if (geneIDCrit != null) {
myClone.geneIDCrit = (GeneIDCriteria) geneIDCrit.clone();
}
if (geneOntologyCriteria != null) {
myClone.geneOntologyCriteria = (GeneOntologyCriteria) geneOntologyCriteria.clone();
}
if (pathwayCriteria != null) {
myClone.pathwayCriteria = (PathwayCriteria) pathwayCriteria.clone();
}
if (regionCrit != null) {
myClone.regionCrit = (RegionCriteria) regionCrit.clone();
}
return myClone;
}
public String toString() {
ResourceBundle labels = null;
String OutStr = "<B>Gene Expression Query</B>";
OutStr += "<BR><B class='otherBold'>Query Name: </b>" + this.getQueryName();
try {
labels = ResourceBundle.getBundle(RembrandtConstants.APPLICATION_RESOURCES, Locale.US);
FoldChangeCriteria thisFoldChangeCrit = this.getFoldChgCrit();
if ((thisFoldChangeCrit != null) && !thisFoldChangeCrit.isEmpty() && labels != null) {
String thisCriteria = thisFoldChangeCrit.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
Collection foldChangeObjects = thisFoldChangeCrit.getFoldChangeObjects();
for (Iterator iter = foldChangeObjects.iterator(); iter.hasNext(); ) {
DomainElement de = (DomainElement) iter.next();
String thisDomainElement = de.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(
thisDomainElement.substring(thisDomainElement.lastIndexOf(".") + 1))
+ ": "
+ de.getValue();
}
} else {
logger.debug("Fold Change Criteria is empty or Application Resources file is missing");
}
AllGenesCriteria thisAllGenesCrit = this.getAllGenesCrit();
if (thisAllGenesCrit != null && !thisAllGenesCrit.isEmpty()) {
OutStr += "<br /><b class='otherbold'>Gene</b><br /> All Genes";
} else logger.debug("This is not an All Genes Query");
GeneIDCriteria thisGeneIDCrit = this.getGeneIDCrit();
if ((thisGeneIDCrit != null) && !thisGeneIDCrit.isEmpty() && labels != null) {
String thisCriteria = thisGeneIDCrit.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
Collection geneIDObjects = thisGeneIDCrit.getGeneIdentifiers();
int count = 0;
for (Iterator iter = geneIDObjects.iterator(); iter.hasNext() && count < 5; ) {
count++;
DomainElement de = (DomainElement) iter.next();
String thisDomainElement = de.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(
thisDomainElement.substring(thisDomainElement.lastIndexOf(".") + 1))
+ ": "
+ de.getValue();
}
if (geneIDObjects != null && geneIDObjects.size() > 5) {
OutStr += "<BR> ...";
}
} else logger.debug("Gene ID Criteria is empty or Application Resources file is missing");
SampleCriteria thisSampleIDCrit = this.getSampleIDCrit();
if ((thisSampleIDCrit != null) && !thisSampleIDCrit.isEmpty() && labels != null) {
String thisCriteria = thisSampleIDCrit.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
Collection sampleIDObjects = thisSampleIDCrit.getSampleIDs();
int count = 0;
if (sampleIDObjects != null) {
for (Iterator iter = sampleIDObjects.iterator(); iter.hasNext() && count < 5; ) {
count++;
DomainElement de = (DomainElement) iter.next();
String thisDomainElement = de.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(
thisDomainElement.substring(thisDomainElement.lastIndexOf(".") + 1))
+ ": "
+ de.getValue();
}
}
if (sampleIDObjects != null && sampleIDObjects.size() > 5) {
OutStr += "<BR> ...";
}
if (thisSampleIDCrit.getExcludeResections() != null
&& thisSampleIDCrit.getExcludeResections() == true) {
OutStr += "<BR>Exclude Re-Resection Sets";
}
} else logger.debug("Sample ID Criteria is empty or Application Resources file is missing");
RegionCriteria thisRegionCrit = this.getRegionCrit();
if ((thisRegionCrit != null) && !thisRegionCrit.isEmpty() && labels != null) {
String thisCriteria = thisRegionCrit.getClass().getName();
logger.debug("thisCriteria is :" + thisCriteria);
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
DomainElement cytoBandDE = thisRegionCrit.getCytoband();
DomainElement cytoBandEndDE = thisRegionCrit.getEndCytoband();
DomainElement chromosomeDE = thisRegionCrit.getChromNumber();
DomainElement chrStartDE = thisRegionCrit.getStart();
DomainElement chrEndDE = thisRegionCrit.getEnd();
if (chromosomeDE != null) {
String chromosomeDEStr = chromosomeDE.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(
chromosomeDEStr.substring(chromosomeDEStr.lastIndexOf(".") + 1))
+ ": "
+ chromosomeDE.getValue();
if (cytoBandDE != null && cytoBandEndDE != null) {
String cytoBandStr = cytoBandDE.getClass().getName();
String cytoBandEndStr = cytoBandEndDE.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(cytoBandStr.substring(cytoBandStr.lastIndexOf(".") + 1))
+ ": "
+ cytoBandDE.getValue();
OutStr += " to " + cytoBandEndDE.getValue();
} else if (cytoBandDE != null && cytoBandEndDE == null) {
String cytoBandStr = cytoBandDE.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(cytoBandStr.substring(cytoBandStr.lastIndexOf(".") + 1))
+ ": "
+ cytoBandDE.getValue();
} else {
if (chrStartDE != null && chrEndDE != null) {
String chrStartDEStr = chrStartDE.getClass().getName();
String chrEndDEStr = chrEndDE.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(
chrStartDEStr.substring(
chrStartDEStr.lastIndexOf(".") + 1, chrStartDEStr.lastIndexOf("$")))
+ "(kb)";
OutStr +=
"<BR> "
+ labels.getString(
chrStartDEStr.substring(chrStartDEStr.lastIndexOf(".") + 1))
+ ": "
+ chrStartDE.getValue();
OutStr +=
"<BR> "
+ labels.getString(chrEndDEStr.substring(chrEndDEStr.lastIndexOf(".") + 1))
+ ": "
+ chrEndDE.getValue();
}
}
}
} else {
logger.debug("Region Criteria is empty or Application Resources file is missing");
}
// starting DiseaseOrGradeCriteria
DiseaseOrGradeCriteria thisDiseaseCrit = this.getDiseaseOrGradeCriteria();
if ((thisDiseaseCrit != null) && !thisDiseaseCrit.isEmpty() && labels != null) {
Collection diseaseColl = thisDiseaseCrit.getDiseases();
String thisCriteria = thisDiseaseCrit.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B><BR>";
Iterator iter = diseaseColl.iterator();
while (iter.hasNext()) {
DiseaseNameDE diseaseDE = (DiseaseNameDE) iter.next();
OutStr += " " + ((String) diseaseDE.getValue()) + "<BR> ";
}
} else {
logger.debug("Disease Criteria is empty or Application Resources file is missing");
} // end of DiseaseOrGradeCriteria
// starting cloneorProbeCriteria
CloneOrProbeIDCriteria thisCloneOrProbeCriteria = this.getCloneOrProbeIDCriteria();
if ((thisCloneOrProbeCriteria != null)
&& !thisCloneOrProbeCriteria.isEmpty()
&& labels != null) {
String thisCriteria = thisCloneOrProbeCriteria.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
Collection cloneColl = thisCloneOrProbeCriteria.getIdentifiers();
Iterator iter = cloneColl.iterator();
int count = 0;
while (iter.hasNext() && count < 5) {
count++;
CloneIdentifierDE cloneIdentifierDE = (CloneIdentifierDE) iter.next();
String cloneStr = cloneIdentifierDE.getClass().getName();
OutStr +=
"<BR> "
+ labels.getString(cloneStr.substring(cloneStr.lastIndexOf(".") + 1))
+ ": "
+ cloneIdentifierDE.getValue()
+ "";
}
if (cloneColl != null && cloneColl.size() > 5) {
OutStr += "<BR> ...";
}
} else {
logger.debug("Clone or Probe Criteria is empty or Application Resources file is missing.");
} // end of cloneorProbeCriteria
// starting of GeneOntologyCriteria
GeneOntologyCriteria thisGeneOntologyCriteria = this.getGeneOntologyCriteria();
if ((thisGeneOntologyCriteria != null)
&& !thisGeneOntologyCriteria.isEmpty()
&& labels != null) {
Collection goColl = thisGeneOntologyCriteria.getGOIdentifiers();
Iterator iter = goColl.iterator();
while (iter.hasNext()) {
GeneOntologyDE geneOntologyDE = (GeneOntologyDE) iter.next();
String goStr = geneOntologyDE.getClass().getName();
OutStr +=
"<BR>"
+ labels.getString(goStr.substring(goStr.lastIndexOf(".") + 1))
+ ": "
+ geneOntologyDE.getValue()
+ "";
}
} else {
logger.debug("GeneOntolgoy Criteria is empty or Application Resources file is missing.");
} // end of GeneOntologyCriteria
// starting PathwayCriteria
PathwayCriteria thisPathwayCriteria = this.getPathwayCriteria();
if ((thisPathwayCriteria != null) && !thisPathwayCriteria.isEmpty() && labels != null) {
String thisCriteria = thisPathwayCriteria.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria.lastIndexOf(".") + 1))
+ "</B>";
Collection pathwayColl = thisPathwayCriteria.getPathwayNames();
Iterator iter = pathwayColl.iterator();
while (iter.hasNext()) {
PathwayDE pathwayDE = (PathwayDE) iter.next();
String pathwayStr = pathwayDE.getClass().getName();
OutStr += "<BR> " + pathwayDE.getValue();
}
} else {
logger.debug("PathwayCriteria is empty or Application Resources file is missing");
}
/*
* TODO: Prashant Can you please fix this commented code. I have
* changed the PathwayCriteria class definition So the below code
* needs to be readjusted
*/
/*
* // start of pathway criteria PathwayCriteria thisPathwayCriteria =
* this.getPathwayCriteria(); if(!thisPathwayCriteria.isEmpty() &&
* labels != null){ PathwayDE pathwayDE =
* thisPathwayCriteria.getPathwayNames(); String pathwayStr =
* pathwayDE.getClass().getName(); OutStr += " <BR>
* "+labels.getString(pathwayStr.substring(pathwayStr.lastIndexOf(".")+1))+":
* "+pathwayDE.getValue()+""; } else{ logger.debug("PathwayCriteria
* is empty or Application Resources file is missing."); } // end of
* PathwayCriteria
*/
// start of ArrayPlatformCriteria
ArrayPlatformCriteria thisArrayPlatformCriteria = this.getArrayPlatformCriteria();
if ((thisArrayPlatformCriteria != null)
&& !thisArrayPlatformCriteria.isEmpty()
&& labels != null) {
ArrayPlatformDE arrayPlatformDE = thisArrayPlatformCriteria.getPlatform();
String arrayPlatformStr = arrayPlatformDE.getClass().getName();
OutStr +=
"<BR><B class='otherBold'>"
+ labels.getString(
arrayPlatformStr.substring(arrayPlatformStr.lastIndexOf(".") + 1))
+ "</B>";
OutStr += "<BR> " + arrayPlatformDE.getValue() + " ";
} else {
logger.debug("ArrayPlatformCriteria is empty or Application Resources file is missing.");
} // end of PathwayCriteria
// start institution Criteria
/* InstitutionCriteria thisInstitutionCriteria = this.getInstitutionCriteria();
if ((thisInstitutionCriteria != null)&& !thisInstitutionCriteria.isEmpty() && labels != null) {
Collection institutionColl = thisInstitutionCriteria.getInstitutions();
String thisCriteria = thisInstitutionCriteria.getClass().getName();
OutStr += "<BR><B class='otherBold'>"
+ labels.getString(thisCriteria.substring(thisCriteria
.lastIndexOf(".") + 1)) + "</B><BR>";
Iterator iter = institutionColl.iterator();
while (iter.hasNext()) {
InstitutionDE institutionDE= (InstitutionDE) iter.next();
OutStr += "" + ((String) institutionDE.getInstituteName())
+ "<BR>";
}
}
else {
logger.debug("institution Criteria is empty or Application Resources file is missing.");
}// end of institution Criteria
*/
} // end of try
catch (Exception ie) {
logger.error("Error in ResourceBundle - ");
logger.error(ie);
ie.printStackTrace();
}
OutStr += "<BR><BR>";
return OutStr;
}