*/
package jalview.datamodel;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Set;
import java.util.Vector;
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
{
int i = 0;
- if (jalview.util.Comparison.isNucleotide(seqs))
+ if (Comparison.isNucleotide(seqs))
{
type = NUCLEOTIDE;
}
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ * @see AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
public SequenceGroup findGroup(SequenceI s)
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+ * AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ * @see AlignmentI#findName(java.lang.String, boolean)
*/
@Override
public SequenceI findName(String token, boolean b)
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * @see AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
@Override
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ * @see AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
@Override
public int findIndex(SequenceI s)
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ * AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
public int findIndex(SearchResults results)
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#isAligned()
+ * @see AlignmentI#isAligned()
*/
@Override
public boolean isAligned()
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ * @see AlignmentI#isAligned(boolean)
*/
@Override
public boolean isAligned(boolean includeHidden)
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * @seeAlignmentI#deleteAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@Override
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * @seeAlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@Override
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * @seeAlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
@Override
for (int j = current.getLength(); j > maxLength; j--)
{
if (j > maxLength
- && !jalview.util.Comparison.isGap(current.getCharAt(j)))
+ && !Comparison.isGap(current.getCharAt(j)))
{
maxLength = j;
break;
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
- if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ if (!Comparison.isGap(current.getCharAt(j)))
{
if (!hitres)
{
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
@Override
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ * AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
@Override
public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
/**
* Sets the codon frame mappings (replacing any existing mappings).
*
- * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ * @see AlignmentI#setCodonFrames()
*/
@Override
public void setCodonFrames(Set<AlignedCodonFrame> acfs)
* Returns the set of codon frame mappings. Any changes to the returned set
* will affect the alignment.
*
- * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ * @see AlignmentI#getCodonFrames()
*/
@Override
public Set<AlignedCodonFrame> getCodonFrames()
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * @seeAlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
@Override