*/
package jalview.datamodel;
+import jalview.datamodel.features.FeatureAttributeType;
import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
import jalview.util.StringUtils;
import java.util.HashMap;
// private key for ENA location designed not to conflict with real GFF data
private static final String LOCATION = "!Location";
- private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td></tr>";
+ private static final String ROW_DATA = "<tr><td width=\"10%%\">%s</td><td width=\"50%%\">%s</td><td width=\"40%%\">%s</td></tr>";
/*
* map of otherDetails special keys, and their value fields' delimiter
public Vector<String> links;
+ /*
+ * the identifier (if known) for the FeatureSource held in FeatureSources,
+ * as a provider of metadata about feature attributes
+ */
+ private String source;
+
/**
* Constructs a duplicate feature. Note: Uses makes a shallow copy of the
* otherDetails map, so the new and original SequenceFeature may reference the
*/
public String getDetailsReport()
{
+ FeatureSourceI metadata = FeatureSources.getInstance()
+ .getSource(source);
+
StringBuilder sb = new StringBuilder(128);
sb.append("<br>");
sb.append("<table>");
- sb.append(String.format(ROW_DATA, "Type", type));
+ sb.append(String.format(ROW_DATA, "Type", type, ""));
sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end));
+ : begin + (isContactFeature() ? ":" : "-") + end, ""));
String desc = StringUtils.stripHtmlTags(description);
- sb.append(String.format(ROW_DATA, "Description", desc));
+ sb.append(String.format(ROW_DATA, "Description", desc, ""));
if (!Float.isNaN(score) && score != 0f)
{
- sb.append(String.format(ROW_DATA, "Score", score));
+ sb.append(String.format(ROW_DATA, "Score", score, ""));
}
if (featureGroup != null)
{
- sb.append(String.format(ROW_DATA, "Group", featureGroup));
+ sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
}
if (otherDetails != null)
String[] values = entry.getValue().toString().split(delimiter);
for (String value : values)
{
- sb.append("<tr><td>").append(key).append("</td><td>")
- .append(value)
- .append("</td></tr>");
+ sb.append(String.format(ROW_DATA, key, "", value));
}
}
else
{ // tried <td title="key"> but it failed to provide a tooltip :-(
- sb.append("<tr><td>").append(key).append("</td><td>");
- sb.append(entry.getValue().toString()).append("</td></tr>");
+ String attDesc = null;
+ if (metadata != null)
+ {
+ attDesc = metadata.getAttributeName(key);
+ }
+ String value = entry.getValue().toString();
+ if (isValueInteresting(key, value, metadata))
+ {
+ sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+ : attDesc, value));
+ }
}
}
}
String text = sb.toString();
return text;
}
+
+ /**
+ * Answers true if we judge the value is worth displaying, by some heuristic
+ * rules, else false
+ *
+ * @param key
+ * @param value
+ * @param metadata
+ * @return
+ */
+ boolean isValueInteresting(String key, String value,
+ FeatureSourceI metadata)
+ {
+ /*
+ * currently suppressing zero values as well as null or empty
+ */
+ if (value == null || "".equals(value) || ".".equals(value)
+ || "0".equals(value))
+ {
+ return false;
+ }
+
+ if (metadata == null)
+ {
+ return true;
+ }
+
+ FeatureAttributeType attributeType = metadata.getAttributeType(key);
+ if (attributeType == FeatureAttributeType.Float
+ || attributeType.equals(FeatureAttributeType.Integer))
+ {
+ try
+ {
+ float fval = Float.valueOf(value);
+ if (fval == 0f)
+ {
+ return false;
+ }
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+
+ return true; // default to interesting
+ }
+
+ /**
+ * Sets the feature source identifier
+ *
+ * @param theSource
+ */
+ public void setSource(String theSource)
+ {
+ source = theSource;
+ }
}
--- /dev/null
+package jalview.datamodel.features;
+
+/**
+ * A class to model the datatype of feature attributes.
+ *
+ * @author gmcarstairs
+ *
+ */
+public enum FeatureAttributeType
+{
+ String, Integer, Float, Character, Flag;
+}
--- /dev/null
+package jalview.datamodel.features;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A class to model one source of feature data, including metadata about
+ * attributes of features
+ *
+ * @author gmcarstairs
+ *
+ */
+public class FeatureSource implements FeatureSourceI
+{
+ private String name;
+
+ private Map<String, String> attributeNames;
+
+ private Map<String, FeatureAttributeType> attributeTypes;
+
+ /**
+ * Constructor
+ *
+ * @param theName
+ */
+ public FeatureSource(String theName)
+ {
+ this.name = theName;
+ attributeNames = new HashMap<>();
+ attributeTypes = new HashMap<>();
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String getAttributeName(String attributeId)
+ {
+ return attributeNames.get(attributeId);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public FeatureAttributeType getAttributeType(String attributeId)
+ {
+ return attributeTypes.get(attributeId);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void setAttributeName(String id, String attName)
+ {
+ attributeNames.put(id, attName);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void setAttributeType(String id, FeatureAttributeType type)
+ {
+ attributeTypes.put(id, type);
+ }
+
+}
--- /dev/null
+package jalview.datamodel.features;
+
+public interface FeatureSourceI
+{
+ /**
+ * Answers a name for the feature source (not necessarily unique)
+ *
+ * @return
+ */
+ String getName();
+
+ /**
+ * Answers the 'long name' of an attribute given its id (short name or
+ * abbreviation), or null if not known
+ *
+ * @param attributeId
+ * @return
+ */
+ String getAttributeName(String attributeId);
+
+ /**
+ * Sets the 'long name' of an attribute given its id (short name or
+ * abbreviation).
+ *
+ * @param id
+ * @param name
+ */
+ void setAttributeName(String id, String name);
+
+ /**
+ * Answers the datatype of the attribute with given id, or null if not known
+ *
+ * @param attributeId
+ * @return
+ */
+ FeatureAttributeType getAttributeType(String attributeId);
+
+ /**
+ * Sets the datatype of the attribute with given id
+ *
+ * @param id
+ * @param type
+ */
+ void setAttributeType(String id, FeatureAttributeType type);
+}
--- /dev/null
+package jalview.datamodel.features;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class FeatureSources
+{
+ private static FeatureSources instance = new FeatureSources();
+
+ private Map<String, FeatureSourceI> sources;
+
+ /**
+ * Answers the singelton instance of this class
+ *
+ * @return
+ */
+ public static FeatureSources getInstance()
+ {
+ return instance;
+ }
+
+ private FeatureSources()
+ {
+ sources = new HashMap<>();
+ }
+
+ /**
+ * Answers the FeatureSource with the given unique identifier, or null if not
+ * known
+ *
+ * @param sourceId
+ * @return
+ */
+ public FeatureSourceI getSource(String sourceId)
+ {
+ return sources.get(sourceId);
+ }
+
+ /**
+ * Adds the given source under the given key. This will replace any existing
+ * source with the same id, it is the caller's responsibility to ensure keys
+ * are unique if necessary.
+ *
+ * @param sourceId
+ * @param source
+ */
+ public void addSource(String sourceId, FeatureSource source)
+ {
+ sources.put(sourceId, source);
+ }
+}
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
+import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureSource;
+import jalview.datamodel.features.FeatureSources;
import jalview.ext.ensembl.EnsemblMap;
import jalview.ext.htsjdk.VCFReader;
import jalview.io.gff.Gff3Helper;
private int csqAlleleNumberFieldIndex = -1;
private int csqFeatureFieldIndex = -1;
+ /*
+ * a unique identifier under which to save metadata about feature
+ * attributes (selected INFO field data)
+ */
+ private String sourceId;
+
/**
* Constructor given an alignment context
*
reader = new VCFReader(filePath);
header = reader.getFileHeader();
- VCFHeaderLine ref = header
- .getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+
+ sourceId = filePath;
+
+ saveMetadata(sourceId);
/*
* get offset of CSQ ALLELE_NUM and Feature if declared
*/
locateCsqFields();
+ VCFHeaderLine ref = header
+ .getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
String vcfAssembly = ref.getValue();
int varCount = 0;
}
/**
+ * Reads metadata (such as INFO field descriptions and datatypes) and saves
+ * them for future reference
+ *
+ * @param sourceId
+ */
+ void saveMetadata(String sourceId)
+ {
+ FeatureSource metadata = new FeatureSource(sourceId);
+
+ for (VCFInfoHeaderLine info : header.getInfoHeaderLines())
+ {
+ String attributeId = info.getID();
+ String desc = info.getDescription();
+ VCFHeaderLineType type = info.getType();
+ FeatureAttributeType attType = null;
+ switch (type)
+ {
+ case Character:
+ attType = FeatureAttributeType.Character;
+ break;
+ case Flag:
+ attType = FeatureAttributeType.Flag;
+ break;
+ case Float:
+ attType = FeatureAttributeType.Float;
+ break;
+ case Integer:
+ attType = FeatureAttributeType.Integer;
+ break;
+ case String:
+ attType = FeatureAttributeType.String;
+ break;
+ }
+ metadata.setAttributeName(attributeId, desc);
+ metadata.setAttributeType(attributeId, attType);
+ }
+
+ FeatureSources.getInstance().addSource(sourceId, metadata);
+ }
+
+ /**
* Records the position of selected fields defined in the CSQ INFO header (if
* there is one). CSQ fields are declared in the CSQ INFO Description e.g.
* <p>
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
featureEnd, score, FEATURE_GROUP_VCF);
+ sf.setSource(sourceId);
sf.setValue(Gff3Helper.ALLELES, alleles);
git://source.jalview.org / jalview.git / commitdiff