import java.util.HashMap;
import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
import java.util.Vector;
/**
*/
public class SequenceFeature implements FeatureLocationI
{
+ /*
+ * score value if none is set; preferably Float.Nan, but see
+ * JAL-2060 and JAL-2554 for a couple of blockers to that
+ */
+ private static final float NO_SCORE = 0f;
+
private static final String STATUS = "status";
private static final String STRAND = "STRAND";
private static final String LOCATION = "!Location";
/*
+ * 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", ",");
+ }
+
+ /*
* 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 are final to ensure that
- * the integrity of SequenceFeatures data store can't be
- * broken by direct update of these fields
+ * 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
*/
public final String type;
public final String featureGroup;
- public float score;
+ public final float score;
+
+ private final boolean contactFeature;
public String description;
*/
public SequenceFeature(SequenceFeature cpy)
{
- this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup());
-
- score = cpy.score;
- description = cpy.description;
- if (cpy.otherDetails != null)
- {
- try
- {
- otherDetails = (Map<String, Object>) ((HashMap<String, Object>) cpy.otherDetails)
- .clone();
- } catch (Exception e)
- {
- // ignore
- }
- }
- if (cpy.links != null && cpy.links.size() > 0)
- {
- links = new Vector<String>();
- for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
- {
- links.addElement(cpy.links.elementAt(i));
- }
- }
- }
-
- /**
- * Constructor including a Status value
- *
- * @param type
- * @param desc
- * @param status
- * @param begin
- * @param end
- * @param featureGroup
- */
- public SequenceFeature(String type, String desc, String status,
- int begin, int end, String featureGroup)
- {
- this(type, desc, begin, end, featureGroup);
- setStatus(status);
+ this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
+ .getScore());
}
/**
* Constructor
*
- * @param type
- * @param desc
- * @param begin
- * @param end
- * @param featureGroup
+ * @param theType
+ * @param theDesc
+ * @param theBegin
+ * @param theEnd
+ * @param group
*/
- SequenceFeature(String type, String desc, int begin, int end,
- String featureGroup)
+ public SequenceFeature(String theType, String theDesc, int theBegin,
+ int theEnd, String group)
{
- this.type = type;
- this.description = desc;
- this.begin = begin;
- this.end = end;
- this.featureGroup = featureGroup;
+ this(theType, theDesc, theBegin, theEnd, NO_SCORE, group);
}
/**
* Constructor including a score value
*
- * @param type
- * @param desc
- * @param begin
- * @param end
- * @param score
- * @param featureGroup
+ * @param theType
+ * @param theDesc
+ * @param theBegin
+ * @param theEnd
+ * @param theScore
+ * @param group
*/
- public SequenceFeature(String type, String desc, int begin, int end,
- float score, String featureGroup)
+ public SequenceFeature(String theType, String theDesc, int theBegin,
+ int theEnd, float theScore, String group)
{
- this(type, desc, begin, end, featureGroup);
- this.score = score;
+ this.type = theType;
+ this.description = theDesc;
+ this.begin = theBegin;
+ this.end = theEnd;
+ this.featureGroup = group;
+ this.score = theScore;
+
+ /*
+ * for now, only "Disulfide/disulphide bond" is treated as a contact feature
+ */
+ this.contactFeature = "disulfide bond".equalsIgnoreCase(type)
+ || "disulphide bond".equalsIgnoreCase(type);
}
/**
- * A copy constructor that allows the begin and end positions and group to be
- * modified
+ * A copy constructor that allows the value of final fields to be 'modified'
*
* @param sf
+ * @param newType
* @param newBegin
* @param newEnd
* @param newGroup
+ * @param newScore
*/
- public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
- String newGroup)
+ public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+ int newEnd, String newGroup, float newScore)
{
- this(sf.getType(), newBegin, newEnd, newGroup);
+ this(newType, sf.getDescription(), newBegin, newEnd, newScore,
+ newGroup);
+
+ if (sf.otherDetails != null)
+ {
+ otherDetails = new HashMap<String, Object>();
+ 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>();
+ for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
+ {
+ links.addElement(sf.links.elementAt(i));
+ }
+ }
}
/**
- * Constructor that sets the final fields type, begin, end, group
+ * A copy constructor that allows the value of final fields to be 'modified'
*
- * @param theType
- * @param theBegin
- * @param theEnd
- * @param theGroup
+ * @param sf
+ * @param newBegin
+ * @param newEnd
+ * @param newGroup
+ * @param newScore
*/
- private SequenceFeature(String theType, int theBegin, int theEnd,
- String theGroup)
+ public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+ String newGroup, float newScore)
{
- type = theType;
- begin = theBegin;
- end = theEnd;
- featureGroup = theGroup;
+ this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
}
/**
return false;
}
- if (!(type + description + featureGroup + getPhase()).equals(sf.type
- + sf.description + sf.featureGroup + sf.getPhase()))
+ if (!(type + description + featureGroup + getPhase()).equals(
+ sf.type + sf.description + sf.featureGroup + sf.getPhase()))
{
return false;
}
return score;
}
- public void setScore(float value)
- {
- score = value;
- }
-
/**
* Used for getting values which are not in the basic set. eg STRAND, PHASE
* for GFF file
@Override
public boolean isContactFeature()
{
- // TODO abstract one day to a FeatureType class
- if ("disulfide bond".equalsIgnoreCase(type)
- || "disulphide bond".equalsIgnoreCase(type))
- {
- return true;
- }
- return false;
+ return contactFeature;
}
/**
{
return begin == 0 && end == 0;
}
+
+ /**
+ * Answers a formatted text report of feature details
+ *
+ * @return
+ */
+ public String getDetailsReport()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ if (begin == end)
+ {
+ sb.append(String.format("%s %d %s", type, begin, description));
+ }
+ else
+ {
+ sb.append(String.format("%s %d-%d %s", type, begin, end, description));
+ }
+ if (!Float.isNaN(score) && score != 0f)
+ {
+ sb.append(" score=").append(score);
+ }
+ if (featureGroup != null)
+ {
+ sb.append(" (").append(featureGroup).append(")");
+ }
+ sb.append("\n\n");
+
+ if (otherDetails != null)
+ {
+ TreeMap<String, Object> ordered = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ ordered.putAll(otherDetails);
+
+ 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))
+ {
+ /*
+ * split selected INFO data by delimiter over multiple lines
+ */
+ sb.append(key).append("=\n ");
+ String delimiter = INFO_KEYS.get(key);
+ String value = entry.getValue().toString();
+ sb.append(value.replace(delimiter, "\n "));
+ }
+ else
+ {
+ sb.append(key + "=" + entry.getValue().toString() + "\n");
+ }
+ }
+ }
+ String text = sb.toString();
+ return text;
+ }
}
git://source.jalview.org / jalview.git / blobdiff