* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
+
import java.util.*;
import java.awt.*;
/**
* Construct score matrix for sequences with standard DNA or PEPTIDE matrix
- * @param s1 - sequence 1
- * @param string1 - string to use for s1
- * @param s2 - sequence 2
- * @param string2 - string to use for s2
+ *
+ * @param s1
+ * - sequence 1
+ * @param string1
+ * - string to use for s1
+ * @param s2
+ * - sequence 2
+ * @param string2
+ * - string to use for s2
* @param type
* DNA or PEPTIDE
*/
/**
* Construct score matrix for sequences with custom substitution matrix
- * @param s1 - sequence 1
- * @param string1 - string to use for s1
- * @param s2 - sequence 2
- * @param string2 - string to use for s2
- * @param scoreMatrix - substitution matrix to use for alignment
+ *
+ * @param s1
+ * - sequence 1
+ * @param string1
+ * - string to use for s1
+ * @param s2
+ * - sequence 2
+ * @param string2
+ * - string to use for s2
+ * @param scoreMatrix
+ * - substitution matrix to use for alignment
*/
public void SeqInit(SequenceI s1, String string1, SequenceI s2,
String string2, ScoreMatrix scoreMatrix)
* construct score matrix for string1 and string2 (after removing any existing
* gaps
*
- * @param string1
+ * @param string1
* @param string2
*/
private void SeqInit(String string1, String string2)
{
lastmatch = true;
// extend mapping interval.
- if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
+ if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
{
as1.add(Integer.valueOf(alignpos));
as2.add(Integer.valueOf(pdbpos));