import jalview.analysis.WUSSParseException;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Map.Entry;
/**
*/
public boolean autoCalculated = false;
+ /**
+ * unique ID for this annotation, used to match up the same annotation row
+ * shown in multiple views and alignments
+ */
public String annotationId;
+ /**
+ * the sequence this annotation is associated with (or null)
+ */
public SequenceI sequenceRef;
- /** DOCUMENT ME!! */
+ /** label shown in dropdown menus and in the annotation label area */
public String label;
- /** DOCUMENT ME!! */
+ /** longer description text shown as a tooltip */
public String description;
- /** DOCUMENT ME!! */
+ /** Array of annotations placed in the current coordinate system */
public Annotation[] annotations;
public ArrayList<SimpleBP> bps = null;
public SequenceFeature[] _rnasecstr = null;
/**
- * position of annotation resulting in invalid WUSS parsing or -1
+ * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+ * there was no RNA structure in this annotation
*/
- private long invalidrnastruc = -1;
+ private long invalidrnastruc = -2;
/**
* Updates the _rnasecstr field Determines the positions that base pair and
isrna = true;
showAllColLabels = true;
scaleColLabel = true;
+ _markRnaHelices();
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
}
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
+
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
+ }
+ /**
+ * map of positions in the associated annotation
+ */
public java.util.Hashtable<Integer, Annotation> sequenceMapping;
/** DOCUMENT ME!! */
@Override
public char charAt(int index)
{
- String dc;
return ((index + offset < 0) || (index + offset) >= max
- || annotations[index + offset] == null || (dc = annotations[index
- + offset].displayCharacter.trim()).length() < 1) ? '.' : dc
- .charAt(0);
+ || annotations[index + offset] == null || (annotations[index
+ + offset].secondaryStructure < ' ') ? ' '
+ : annotations[index + offset].secondaryStructure);
}
public String toString()
for (int i = offset; i < mx; i++)
{
- String dc;
- string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
- .trim()).length() < 1) ? '.' : dc.charAt(0);
+ string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' '
+ : annotations[i].secondaryStructure;
}
return new String(string);
}
this.scaleColLabel = annotation.scaleColLabel;
this.showAllColLabels = annotation.showAllColLabels;
this.calcId = annotation.calcId;
+ if (annotation.properties!=null)
+ {
+ properties = new HashMap<String,String>();
+ for (Map.Entry<String, String> val:annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
{
threshold = new GraphLine(annotation.threshold);
}
+ Annotation[] ann = annotation.annotations;
if (annotation.annotations != null)
{
- Annotation[] ann = annotation.annotations;
this.annotations = new Annotation[ann.length];
for (int i = 0; i < ann.length; i++)
{
}
}
}
- ;
- if (annotation.sequenceRef != null)
+ }
+ if (annotation.sequenceRef != null)
+ {
+ this.sequenceRef = annotation.sequenceRef;
+ if (annotation.sequenceMapping != null)
{
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
+ Integer p = null;
+ sequenceMapping = new Hashtable();
+ Enumeration pos = annotation.sequenceMapping.keys();
+ while (pos.hasMoreElements())
{
- Integer p = null;
- sequenceMapping = new Hashtable();
- Enumeration pos = annotation.sequenceMapping.keys();
- while (pos.hasMoreElements())
+ // could optimise this!
+ p = (Integer) pos.nextElement();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
{
- // could optimise this!
- p = (Integer) pos.nextElement();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
for (int i = 0; i < ann.length; i++)
{
if (ann[i] == a)
}
}
}
- else
- {
- this.sequenceMapping = null;
- }
+ }
+ else
+ {
+ this.sequenceMapping = null;
}
}
// TODO: check if we need to do this: JAL-952
protected String calcId = "";
/**
+ * properties associated with the calcId
+ */
+ protected Map<String, String> properties = new HashMap<String, String>();
+
+ /**
* base colour for line graphs. If null, will be set automatically by
* searching the alignment annotation
*/
// trim positions
}
}
+ }
+ /**
+ * like liftOver but more general.
+ *
+ * Takes an array of int pairs that will be used to update the internal
+ * sequenceMapping and so shuffle the annotated positions
+ *
+ * @param newref
+ * - new sequence reference for the annotation row - if null,
+ * sequenceRef is left unchanged
+ * @param mapping
+ * array of ints containing corresponding positions
+ * @param from
+ * - column for current coordinate system (-1 for index+1)
+ * @param to
+ * - column for destination coordinate system (-1 for index+1)
+ * @param idxoffset
+ * - offset added to index when referencing either coordinate system
+ * @note no checks are made as to whether from and/or to are sensible
+ * @note caller should add the remapped annotation to newref if they have not
+ * already
+ */
+ public void remap(SequenceI newref, int[][] mapping, int from, int to,
+ int idxoffset)
+ {
+ if (mapping != null)
+ {
+ Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+ int index = -1;
+ for (int mp[] : mapping)
+ {
+ if (index++ < 0)
+ {
+ continue;
+ }
+ Annotation ann = null;
+ if (from == -1)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
+ }
+ else
+ {
+ if (mp != null && mp.length > from)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(mp[from]));
+ }
+ }
+ if (ann != null)
+ {
+ if (to == -1)
+ {
+ remap.put(Integer.valueOf(idxoffset + index), ann);
+ }
+ else
+ {
+ if (to > -1 && to < mp.length)
+ {
+ remap.put(Integer.valueOf(mp[to]), ann);
+ }
+ }
+ }
+ }
+ sequenceMapping = remap;
+ old.clear();
+ if (newref != null)
+ {
+ sequenceRef = newref;
+ }
+ adjustForAlignment();
+ }
+ }
+
+ public String getProperty(String property)
+ {
+ if (properties == null)
+ {
+ return null;
+ }
+ return properties.get(property);
+ }
+
+ public void setProperty(String property, String value)
+ {
+ if (properties==null)
+ {
+ properties = new HashMap<String,String>();
+ }
+ properties.put(property, value);
+ }
+
+ public boolean hasProperties()
+ {
+ return properties != null && properties.size() > 0;
+ }
+
+ public Collection<String> getProperties()
+ {
+ if (properties == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+ return properties.keySet();
}
}
git://source.jalview.org / jalview.git / blobdiff