*/
package jalview.datamodel;
+import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.Vector;
import jalview.analysis.*;
import jalview.util.*;
}
/**
- * createAlignment
+ * create an alignment from the given array of cigar sequences and gap
+ * character, and marking the given segments as visible in the given
+ * columselection.
*
* @param alseqs
- * SeqCigar[]
* @param gapCharacter
- * char
+ * @param colsel
+ * - columnSelection where hidden regions are marked
+ * @param segments
+ * - visible regions of alignment
* @return SequenceI[]
*/
public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
// System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
}
+ /**
+ * references to entities that this sequence cigar is associated with.
+ */
+ private Hashtable selGroups = null;
+
+ public void setGroupMembership(Object group)
+ {
+ if (selGroups == null)
+ {
+ selGroups = new Hashtable();
+ }
+ selGroups.put(group, new int[0]);
+ }
+
+ /**
+ * Test for and if present remove association to group.
+ *
+ * @param group
+ * @return true if group was associated and it was removed
+ */
+ public boolean removeGroupMembership(Object group)
+ {
+ if (selGroups != null && selGroups.containsKey(group))
+ {
+ selGroups.remove(group);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * forget all associations for this sequence.
+ */
+ public void clearMemberships()
+ {
+ if (selGroups != null)
+ {
+ selGroups.clear();
+ }
+ selGroups = null;
+ }
+
+ /**
+ *
+ * @return null or array of all associated entities
+ */
+ public Object[] getAllMemberships()
+ {
+ if (selGroups == null)
+ {
+ return null;
+ }
+ Object[] mmbs = new Object[selGroups.size()];
+ Enumeration en = selGroups.keys();
+ for (int i = 0; en.hasMoreElements(); i++)
+ {
+ mmbs[i] = en.nextElement();
+ }
+ return mmbs;
+ }
+
+ /**
+ * Test for group membership
+ *
+ * @param sgr
+ * - a selection group or some other object that may be associated
+ * with seqCigar
+ * @return true if sgr is associated with this seqCigar
+ */
+ public boolean isMemberOf(Object sgr)
+ {
+ return (selGroups != null) && selGroups.get(sgr) != null;
+ }
}