*/
package jalview.datamodel;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.datamodel.features.FeatureAttributeType;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureLocationI;
import jalview.datamodel.features.FeatureSources;
import jalview.util.StringUtils;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-import java.util.Vector;
-
/**
* 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 static final String STATUS = "status";
- private static final String STRAND = "STRAND";
+ public static final String STRAND = "STRAND";
- // private key for Phase designed not to conflict with real GFF data
- private static final String PHASE = "!Phase";
+ // key for Phase designed not to conflict with real GFF data
+ public static final String PHASE = "!Phase";
// 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><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?
- }
-
- /*
- * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
- * name1=value1;name2=value2,value3;...etc
- */
- private static final String ATTRIBUTES = "ATTRIBUTES";
-
- /*
* type, begin, end, featureGroup, score and contactFeature are final
* to ensure that the integrity of SequenceFeatures data store
* can't be broken by direct update of these fields
if (sf.otherDetails != null)
{
- otherDetails = new HashMap<String, Object>();
- for (Entry<String, Object> entry : sf.otherDetails.entrySet())
- {
- otherDetails.put(entry.getKey(), entry.getValue());
- }
+ otherDetails = new LinkedHashMap<>();
+ otherDetails.putAll(sf.otherDetails);
}
if (sf.links != null && sf.links.size() > 0)
{
- links = new Vector<String>();
- for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
- {
- links.addElement(sf.links.elementAt(i));
- }
+ links = new Vector<>();
+ links.addAll(sf.links);
}
}
return featureGroup;
}
+ /**
+ * Adds a hyperlink for the feature. This should have the format label|url.
+ *
+ * @param labelLink
+ */
public void addLink(String labelLink)
{
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
+ * 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)
+ public String getValueAsString(String... key)
{
if (otherDetails == null)
{
return null;
}
- Object value = otherDetails.get(key);
+ 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();
}
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ /*
+ * LinkedHashMap preserves insertion order of attributes
+ */
+ otherDetails = new LinkedHashMap<>();
}
otherDetails.put(key, value);
.getAttributeName(key);
}
- FeatureAttributes.getInstance().addAttribute(this.type, key, attDesc,
- value.toString());
+ FeatureAttributes.getInstance().addAttribute(this.type, attDesc, value,
+ key);
}
/*
return (String) getValue(STATUS);
}
- public void setAttributes(String attr)
- {
- setValue(ATTRIBUTES, attr);
- }
-
- public String getAttributes()
- {
- return (String) getValue(ATTRIBUTES);
- }
-
/**
* Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in
* GFF), and 0 for unknown or not (validly) specified
}
/**
- * Answers an html-formatted report of feature details
+ * Answers an html-formatted report of feature details. If parameter
+ * {@code mf} is not null, the feature is a virtual linked feature, and
+ * details included both the original location and the mapped location
+ * (CDS/peptide).
+ *
+ * @param seqName
+ * @param mf
*
* @return
*/
- public String getDetailsReport()
+ public String getDetailsReport(String seqName, MappedFeatures mf)
{
FeatureSourceI metadata = FeatureSources.getInstance()
.getSource(source);
StringBuilder sb = new StringBuilder(128);
sb.append("<br>");
sb.append("<table>");
+ String name = mf == null ? seqName : mf.getLinkedSequenceName();
+ sb.append(String.format(ROW_DATA, "Location", name,
+ begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
+
+ String consequence = "";
+ if (mf != null)
+ {
+ int[] localRange = mf.getMappedPositions(begin, end);
+ int from = localRange[0];
+ int to = localRange[localRange.length - 1];
+ String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
+ sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
+ : from + (isContactFeature() ? ":" : "-") + to));
+ if (mf.isFromCds())
+ {
+ consequence = mf.findProteinVariants(this);
+ }
+ }
sb.append(String.format(ROW_DATA, "Type", type, ""));
- sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end, ""));
String desc = StringUtils.stripHtmlTags(description);
sb.append(String.format(ROW_DATA, "Description", desc, ""));
if (!Float.isNaN(score) && score != 0f)
sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
}
+ if (!consequence.isEmpty())
+ {
+ sb.append(String.format(ROW_DATA, "Consequence",
+ "<i>Translated by Jalview</i>", consequence));
+ }
+
if (otherDetails != null)
{
TreeMap<String, Object> ordered = new TreeMap<>(
for (Entry<String, Object> entry : ordered.entrySet())
{
String key = entry.getKey();
- if (ATTRIBUTES.equals(key))
- {
- 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(String.format(ROW_DATA, key, "", value));
+ 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 :-(
+ {
+ // tried <td title="key"> but it failed to provide a tooltip :-(
String attDesc = null;
if (metadata != null)
{
attDesc = metadata.getAttributeName(key);
}
- String value = entry.getValue().toString();
- if (isValueInteresting(key, value, metadata))
+ String s = entry.getValue().toString();
+ if (isValueInteresting(key, s, metadata))
{
sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, value));
+ : attDesc, s));
}
}
}
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