- SequenceI [] sequences;
- int start;
- int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
- int maxLength = 0; // used by quality calcs
- boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
- Hashtable [] total;
-
- /** Stores calculated quality values */
- public Vector quality;
-
- /** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
- String consString = "";
- Sequence consSequence;
- Hashtable propHash;
- int threshold;
- String name = "";
- int[][] cons2;
-
- /**
- * Creates a new Conservation object.
- *
- * @param name Name of conservation
- * @param propHash DOCUMENT ME!
- * @param threshold to count the residues in residueHash(). commonly used value is 3
- * @param sequences sequences to be used in calculation
- * @param start start residue position
- * @param end end residue position
- */
- public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
+ SequenceI[] sequences;
+ int start;
+ int end;
+ Vector seqNums; // vector of int vectors where first is sequence checksum
+ int maxLength = 0; // used by quality calcs
+ boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
+ Hashtable[] total;
+
+ /** Stores calculated quality values */
+ public Vector quality;
+
+ /** Stores maximum and minimum values of quality values */
+ public Double[] qualityRange = new Double[2];
+ String consString = "";
+ Sequence consSequence;
+ Hashtable propHash;
+ int threshold;
+ String name = "";
+ int[][] cons2;
+
+ /**
+ * Creates a new Conservation object.
+ *
+ * @param name Name of conservation
+ * @param propHash DOCUMENT ME!
+ * @param threshold to count the residues in residueHash(). commonly used value is 3
+ * @param sequences sequences to be used in calculation
+ * @param start start residue position
+ * @param end end residue position
+ */
+ public Conservation(String name, Hashtable propHash, int threshold,
+ Vector sequences, int start, int end)
+ {
+
+ this.name = name;
+ this.propHash = propHash;
+ this.threshold = threshold;
+ this.start = start;
+ this.end = end;
+
+ maxLength = end - start + 1; // default width includes bounds of calculation
+
+ int s, sSize = sequences.size();
+ SequenceI[] sarray = new SequenceI[sSize];
+ this.sequences = sarray;
+
+ for (s = 0; s < sSize; s++)