public static GridPanel getSamplePairsByAnalysisPanel(
List<FileGroup> analysisFileGroupList,
Map<FileGroup, Sample> fileGroupHpa2SampleMap,
Map<FileGroup, Sample> fileGroupMsp1SampleMap) {
GridPanel panel = new GridPanel();
panel.setTitle("Sample Pairs");
panel.setResizable(true);
panel.setMaximizable(true);
panel.setOrder(1);
GridContent content = new GridContent();
content.addDataFields(new GridDataField("Analysis", "String")); // dataIndex, datatype
content.addDataFields(
new GridDataField("Hpa2/Beta-GT Sample", "String")); // dataIndex, datatype
content.addDataFields(new GridDataField("Msp1 Sample", "String")); // dataIndex, datatype
content.addColumn(
new GridColumn("Analysis", "Analysis", 500, 0)); // header,dataIndex width=250; flex=0
content.addColumn(
new GridColumn(
"Hpa2/Beta-GT Sample",
"Hpa2/Beta-GT Sample",
250,
0)); // header,dataIndex width=250; flex=0
content.addColumn(
new GridColumn("Msp1 Sample", "Msp1 Sample", 1)); // header,dataIndex width=250; flex=0
// create rows with information
for (FileGroup fileGroup : analysisFileGroupList) {
if (fileGroupHpa2SampleMap.isEmpty()) {
logger.debug("fileGroupHpa2SampleMap is empty ");
}
List<String> row = new ArrayList<String>();
row.add(fileGroup.getDescription());
Sample hpa2Sample = fileGroupHpa2SampleMap.get(fileGroup);
String hpa2SampleName = "Unexpected Error";
if (hpa2Sample != null) {
hpa2SampleName = hpa2Sample.getName();
} else {
logger.debug("hpa2Sample is null");
}
Sample msp1Sample = fileGroupMsp1SampleMap.get(fileGroup);
String msp1SampleName = "Standard Reference";
if (msp1Sample != null && msp1Sample.getId().intValue() > 0) {
msp1SampleName = msp1Sample.getName();
}
logger.debug("hpa2SampleName = " + hpa2SampleName);
logger.debug("msp1SampleName = " + msp1SampleName);
row.add(hpa2SampleName);
row.add(msp1SampleName);
content.addDataRow(row);
}
panel.setContent(content);
return panel;
}
@Override
public String getTypeOfHelpLibrary(Sample sample) {
try {
return (String)
MetaHelper.getMetaValue(
HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, sample.getSampleMeta());
} catch (MetadataException e) {
}
// not found
return null;
}
@Override
public String getTypeOfHelpLibraryRequestedForMacromolecule(Sample sample) {
try {
return (String)
MetaHelper.getMetaValue(
HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, sample.getSampleMeta());
} catch (MetadataException e) {
}
// not found
return null;
}
@Override
public boolean isBetaGTMspI(Sample s) {
String enzymeString;
try {
if (s.getParentId() != null) {
// if it has a parent sample, which means it's a facility library, use its parent sample to
// check for library type
s = sampleService.getSampleById(s.getParentId());
}
if (!s.getSampleType().getIName().equalsIgnoreCase("dna")) { // not dna, so must be library
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, s.getSampleMeta());
} else { // genomic DNA
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, s.getSampleMeta());
}
if (enzymeString.equals("beta-GT-MspI")) {
return true;
}
} catch (MetadataException e) {
// not found
logger.debug(
"Restriction Enzyme Meta (and libraryToCreate meta) not found for Sample id = "
+ s.getId());
}
return false;
}
public static GridPanel getLibrariesAndHcountFilesUsedByAnalysisPanel(
List<FileGroup> analysisFileGroupList,
Map<FileGroup, List<Sample>> fileGroupLibrariesUsedMap,
Map<FileGroup, List<FileHandle>> fileGroupHcountFilesUsedMap) {
GridPanel panel = new GridPanel();
panel.setTitle("Libraries & Hcount Files Used");
panel.setResizable(true);
panel.setMaximizable(true);
panel.setOrder(1);
GridContent content = new GridContent();
content.addDataFields(new GridDataField("Analysis", "String")); // dataIndex, datatype
content.addDataFields(new GridDataField("Libraries Used", "String")); // dataIndex, datatype
content.addDataFields(new GridDataField("Hcount Files Used", "String")); // dataIndex, datatype
content.addColumn(
new GridColumn("Analysis", "Analysis", 500, 0)); // header,dataIndex width=500; flex=0
content.addColumn(
new GridColumn(
"Libraries Used", "Libraries Used", 150, 0)); // header,dataIndex width=300; flex=0
content.addColumn(
new GridColumn("Hcount Files Used", "Hcount Files Used", 1)); // header,dataIndex flex=1
// create rows with information
for (FileGroup fileGroup : analysisFileGroupList) {
List<String> row = new ArrayList<String>();
row.add(fileGroup.getDescription());
List<Sample> libraries = fileGroupLibrariesUsedMap.get(fileGroup);
if (libraries.isEmpty()) {
row.add("Error");
} else {
StringBuilder libraryNamesAsStringBuilder = new StringBuilder();
for (Sample library : libraries) {
if (libraryNamesAsStringBuilder.length() > 0) {
libraryNamesAsStringBuilder.append("<br />");
}
libraryNamesAsStringBuilder.append(library.getName());
}
row.add(new String(libraryNamesAsStringBuilder));
}
List<FileHandle> bamFiles = fileGroupHcountFilesUsedMap.get(fileGroup);
if (bamFiles.isEmpty()) {
row.add("Error");
} else {
StringBuilder fileNamesAsStringBuilder = new StringBuilder();
for (FileHandle fh : bamFiles) {
if (fileNamesAsStringBuilder.length() > 0) {
fileNamesAsStringBuilder.append("<br />");
}
fileNamesAsStringBuilder.append(fh.getFileName());
}
row.add(new String(fileNamesAsStringBuilder));
}
content.addDataRow(row);
}
panel.setContent(content);
return panel;
}