*/
package jalview.datamodel;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
import jalview.util.StringUtils;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
+import intervalstore.api.IntervalI;
+
/**
* A class that models a single contiguous feature on a sequence. If flag
* 'contactFeature' is true, the start and end positions are interpreted instead
// 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>";
-
- /*
- * map of otherDetails special keys, and their value fields' delimiter
- */
- private static final Map<String, String> INFO_KEYS = new HashMap<>();
-
- static
- {
- INFO_KEYS.put("CSQ", ",");
- // todo capture second level metadata (CSQ FORMAT)
- // and delimiter "|" so as to report in a table within a table?
- }
+ private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
/*
* ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
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
this(newType, sf.getDescription(), newBegin, newEnd, newScore,
newGroup);
+ this.source = sf.source;
+
if (sf.otherDetails != null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
for (Entry<String, Object> entry : sf.otherDetails.entrySet())
{
otherDetails.put(entry.getKey(), entry.getValue());
}
if (sf.links != null && sf.links.size() > 0)
{
- links = new Vector<String>();
+ links = new Vector<>();
for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
{
links.addElement(sf.links.elementAt(i));
@Override
public boolean equals(Object o)
{
- return equals(o, false);
+ return (o != null && (o instanceof SequenceFeature)
+ && equalsInterval((SequenceFeature) o));
}
/**
+ * Having determined that this is in fact a SequenceFeature, now check it for
+ * equivalence. Overridden in CrossRef; used by IntervalStore (possibly).
+ */
+ @Override
+ public boolean equalsInterval(IntervalI sf)
+ {
+ return sf != null && equals((SequenceFeature) sf, false);
+ }
+ /**
* Overloaded method allows the equality test to optionally ignore the
* 'Parent' attribute of a feature. This supports avoiding adding many
* superficially duplicate 'exon' or CDS features to genomic or protein
* @param ignoreParent
* @return
*/
- public boolean equals(Object o, boolean ignoreParent)
+ public boolean equals(SequenceFeature sf, boolean ignoreParent)
{
- if (o == null || !(o instanceof SequenceFeature))
- {
- return false;
- }
-
- SequenceFeature sf = (SequenceFeature) o;
- boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
- : score == sf.score;
- if (begin != sf.begin || end != sf.end || !sameScore)
- {
- return false;
- }
-
- if (getStrand() != sf.getStrand())
- {
- return false;
- }
-
- if (!(type + description + featureGroup + getPhase()).equals(
- sf.type + sf.description + sf.featureGroup + sf.getPhase()))
- {
- return false;
- }
- if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
- {
- return false;
- }
- if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
- {
- return false;
- }
- if (!ignoreParent)
- {
- if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
- {
- return false;
- }
- }
- return true;
+ return (begin == sf.begin && end == sf.end
+ && getStrand() == sf.getStrand()
+ && (Float.isNaN(score) ? Float.isNaN(sf.score)
+ : score == sf.score)
+ && (type + description + featureGroup + getPhase())
+ .equals(sf.type + sf.description + sf.featureGroup
+ + sf.getPhase())
+ && equalAttribute(getValue("ID"), sf.getValue("ID"))
+ && equalAttribute(getValue("Name"), sf.getValue("Name"))
+ && (ignoreParent || equalAttribute(getValue("Parent"),
+ sf.getValue("Parent"))));
}
/**
{
if (links == null)
{
- links = new Vector<String>();
+ links = new Vector<>();
}
if (!links.contains(labelLink))
}
/**
+ * Answers the value of the specified attribute as string, or null if no such
+ * value. If more than one attribute name is provided, tries to resolve as keys
+ * to nested maps. For example, if attribute "CSQ" holds a map of key-value
+ * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
+ * in that map.
+ *
+ * @param key
+ * @return
+ */
+ public String getValueAsString(String... key)
+ {
+ if (otherDetails == null)
+ {
+ return null;
+ }
+ Object value = otherDetails.get(key[0]);
+ if (key.length > 1 && value instanceof Map<?, ?>)
+ {
+ value = ((Map) value).get(key[1]);
+ }
+ return value == null ? null : value.toString();
+ }
+
+ /**
* Returns a property value for the given key if known, else the specified
* default value
*
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
}
otherDetails.put(key, value);
+ recordAttribute(key, value);
}
}
+ /**
+ * Notifies the addition of a feature attribute. This lets us keep track of
+ * which attributes are present on each feature type, and also the range of
+ * numerical-valued attributes.
+ *
+ * @param key
+ * @param value
+ */
+ protected void recordAttribute(String key, Object value)
+ {
+ String attDesc = null;
+ if (source != null)
+ {
+ attDesc = FeatureSources.getInstance().getSource(source)
+ .getAttributeName(key);
+ }
+
+ FeatureAttributes.getInstance().addAttribute(this.type, attDesc, value,
+ key);
+ }
+
/*
* The following methods are added to maintain the castor Uniprot mapping file
* for the moment.
*/
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)
{
continue; // to avoid double reporting
}
- if (INFO_KEYS.containsKey(key))
+
+ Object value = entry.getValue();
+ if (value instanceof Map<?, ?>)
{
/*
- * split selected INFO data by delimiter over multiple lines
+ * expand values in a Map attribute across separate lines
+ * copy to a TreeMap for alphabetical ordering
*/
- String delimiter = INFO_KEYS.get(key);
- String[] values = entry.getValue().toString().split(delimiter);
- for (String value : values)
+ Map<String, Object> values = (Map<String, Object>) value;
+ SortedMap<String, Object> sm = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ sm.putAll(values);
+ for (Entry<?, ?> e : sm.entrySet())
{
- sb.append("<tr><td>").append(key).append("</td><td>")
- .append(value)
- .append("</td></tr>");
+ sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
+ .getValue().toString()));
}
}
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>");
+ {
+ // tried <td title="key"> but it failed to provide a tooltip :-(
+ String attDesc = null;
+ if (metadata != null)
+ {
+ attDesc = metadata.getAttributeName(key);
+ }
+ String s = entry.getValue().toString();
+ if (isValueInteresting(key, s, metadata))
+ {
+ sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+ : attDesc, s));
+ }
}
}
}
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 attType = metadata.getAttributeType(key);
+ if (attType != null
+ && (attType == FeatureAttributeType.Float || attType
+ .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;
+ }
+
+
+}
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getEnd() - b.getEnd();
+ }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getBegin() - b.getBegin();
+ }
}
git://source.jalview.org / jalview.git / blobdiff