import jalview.analysis.*;
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
*/
-public class Alignment
- implements AlignmentI
+public class Alignment implements AlignmentI
{
protected Alignment dataset;
+
protected Vector sequences;
+
protected Vector groups = new Vector();
+
protected char gapCharacter = '-';
+
protected int type = NUCLEOTIDE;
+
public static final int PROTEIN = 0;
+
public static final int NUCLEOTIDE = 1;
/** DOCUMENT ME!! */
}
- /** Make an alignment from an array of Sequences.
- *
+ /**
+ * Make an alignment from an array of Sequences.
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
/**
* Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
+ *
+ * @param seqs
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
- SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
- new ColumnSelection(), null);
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+ gapCharacter, new ColumnSelection(), null);
initAlignment(seqs);
}
/**
- * Make a new alignment from an CigarArray
- * JBPNote - can only do this when compactAlignment does not contain hidden regions.
- * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
- * @param compactAlignment CigarArray
+ * Make a new alignment from an CigarArray JBPNote - can only do this when
+ * compactAlignment does not contain hidden regions. JBPNote - must also check
+ * that compactAlignment resolves to a set of SeqCigars - or construct them
+ * appropriately.
+ *
+ * @param compactAlignment
+ * CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getSequences()
public SequenceI[] getSequencesArray()
{
- if (sequences==null)
+ if (sequences == null)
return null;
SequenceI[] reply = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceI getSequenceAt(int i)
return null;
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void addSequence(SequenceI snew)
snew = adding;
}
}
- if (sequences==null) {
- initAlignment(new SequenceI[] { snew });
- } else {
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[]
+ { snew });
+ }
+ else
+ {
sequences.addElement(snew);
}
- if (hiddenSequences!=null)
+ if (hiddenSequences != null)
hiddenSequences.adjustHeightSequenceAdded();
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void setSequenceAt(int i, SequenceI snew)
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getGroups()
public void finalize()
{
- if(getDataset()!=null)
+ if (getDataset() != null)
getDataset().removeAlignmentRef();
dataset = null;
}
/**
- * decrement the alignmentRefs counter by one and call finalize if it goes to zero.
+ * decrement the alignmentRefs counter by one and call finalize if it goes to
+ * zero.
*/
private void removeAlignmentRef()
{
- if (--alignmentRefs==0)
+ if (--alignmentRefs == 0)
{
finalize();
}
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
public void deleteSequence(SequenceI s)
{
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
*/
public void deleteSequence(int i)
{
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceGroup[] findAllGroups(SequenceI s)
/** */
public SequenceI findName(String name)
{
- return findName(name,false);
+ return findName(name, false);
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
}
-
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, boolean)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
*/
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
-
+
int i = 0;
- SequenceI sq=null;
- String sqname=null;
- if (startAfter!=null)
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
{
// try to find the sequence in the alignment
- boolean matched=false;
- while (i<sequences.size())
+ boolean matched = false;
+ while (i < sequences.size())
{
- if (getSequenceAt(i++)==startAfter)
+ if (getSequenceAt(i++) == startAfter)
{
matched = true;
break;
}
if (!matched)
{
- i=0;
+ i = 0;
}
}
while (i < sequences.size())
sq = getSequenceAt(i);
sqname = sq.getName();
if (sqname.equals(token) // exact match
- || (b && // allow imperfect matches - case varies
+ || (b && // allow imperfect matches - case varies
(sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
return null;
}
+
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getHeight()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWidth()
/**
* DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gc)
{
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString()
- .replace('.', gc)
- .replace('-', gc)
- .replace(' ', gc)
- );
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
+ '-', gc).replace(' ', gc));
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean isAligned()
return true;
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
*/
public boolean deleteAnnotation(AlignmentAnnotation aa)
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
- boolean swap=false;
+ boolean swap = false;
int tIndex = 0;
for (int i = 0; i < aSize; i++)
{
if (annotations[i] == aa)
{
- swap=true;
+ swap = true;
continue;
}
- if (tIndex<temp.length)
+ if (tIndex < temp.length)
temp[tIndex++] = annotations[i];
}
if (swap)
{
annotations = temp;
- if(aa.sequenceRef!=null)
+ if (aa.sequenceRef != null)
aa.sequenceRef.removeAlignmentAnnotation(aa);
}
return swap;
/**
* DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
+ *
+ * @param aa
+ * DOCUMENT ME!
*/
public void addAnnotation(AlignmentAnnotation aa)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
}
dataset.addAlignmentRef();
}
+
/**
* reference count for number of alignments referencing this one.
*/
- int alignmentRefs=0;
+ int alignmentRefs = 0;
+
/**
* increase reference count to this alignment.
*/
{
boolean modified = false;
- //Remove excess gaps from the end of alignment
+ // Remove excess gaps from the end of alignment
int maxLength = -1;
SequenceI current;
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
{
- if (j > maxLength && !jalview.util.Comparison.isGap(
- current.getCharAt(j)))
+ if (j > maxLength
+ && !jalview.util.Comparison.isGap(current.getCharAt(j)))
{
maxLength = j;
break;
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size();
- i++)
+ for (int i = 0; i < sequences.size(); i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
if (cLength < maxLength)
{
- current.insertCharAt(cLength,
- maxLength - cLength, gapCharacter);
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
modified = true;
}
else if (current.getLength() > maxLength)
SeqCigar alseqs[] = new SeqCigar[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
- alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
+ alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
}
CigarArray cal = new CigarArray(alseqs);
cal.addOperation(CigarArray.M, getWidth());
public void setProperty(Object key, Object value)
{
- if(alignmentProperties==null)
+ if (alignmentProperties == null)
alignmentProperties = new Hashtable();
- alignmentProperties.put(key,value);
+ alignmentProperties.put(key, value);
}
public Object getProperty(Object key)
{
- if(alignmentProperties!=null)
+ if (alignmentProperties != null)
return alignmentProperties.get(key);
else
return null;
{
return alignmentProperties;
}
- AlignedCodonFrame[] codonFrameList=null;
- /* (non-Javadoc)
+
+ AlignedCodonFrame[] codonFrameList = null;
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
*/
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons==null)
+ if (codons == null)
return;
- if (codonFrameList==null)
+ if (codonFrameList == null)
{
- codonFrameList = new AlignedCodonFrame[] { codons };
+ codonFrameList = new AlignedCodonFrame[]
+ { codons };
return;
}
- AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
t[codonFrameList.length] = codons;
codonFrameList = t;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
public AlignedCodonFrame getCodonFrame(int index)
return codonFrameList[index];
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
- if (seq==null || codonFrameList==null)
+ if (seq == null || codonFrameList == null)
return null;
- Vector cframes=new Vector();
- for (int f=0;f<codonFrameList.length; f++)
+ Vector cframes = new Vector();
+ for (int f = 0; f < codonFrameList.length; f++)
{
if (codonFrameList[f].involvesSequence(seq))
cframes.addElement(codonFrameList[f]);
}
- if (cframes.size()==0)
+ if (cframes.size() == 0)
return null;
AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
cframes.copyInto(cfr);
return cfr;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
public AlignedCodonFrame[] getCodonFrames()
return codonFrameList;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
*/
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
- if (codons==null || codonFrameList==null)
+ if (codons == null || codonFrameList == null)
return false;
- boolean removed=false;
- int i=0,iSize=codonFrameList.length;
- while (i<iSize)
+ boolean removed = false;
+ int i = 0, iSize = codonFrameList.length;
+ while (i < iSize)
{
- if (codonFrameList[i]==codons)
+ if (codonFrameList[i] == codons)
{
- removed=true;
- if (i+1<iSize)
+ removed = true;
+ if (i + 1 < iSize)
{
- System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+ System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+ - i - 1);
}
iSize--;
}
git://source.jalview.org / jalview.git / blobdiff