/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
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
+/**
+ * @author JimP
+ *
+ */
+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;
+
+ public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
}
- /** 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)
{
- if (i < sequences.size())
+ if (i>-1 && i < sequences.size())
{
return (SequenceI) sequences.elementAt(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)
}
/**
- * DOCUMENT ME!
+ * remove any annotation that references gp
+ *
+ * @param gp
+ * (if null, removes all group associated annotation)
*/
+ private void removeAnnotationForGroup(SequenceGroup gp)
+ {
+ if (annotations == null || annotations.length == 0)
+ {
+ return;
+ }
+ // remove annotation very quickly
+ AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ int i, p, k;
+ if (gp == null)
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef != null)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ else
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef == gp)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ if (p > 0)
+ {
+ // clear out the group associated annotation.
+ for (i = 0; i < p; i++)
+ {
+ unhookAnnotation(todelete[i]);
+ todelete[i] = null;
+ }
+ t = new AlignmentAnnotation[k];
+ for (i = 0; i < k; i++)
+ {
+ t[i] = tokeep[i];
+ }
+ annotations = t;
+ }
+ }
+
public void deleteAllGroups()
{
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
groups.removeAllElements();
}
{
if (groups.contains(g))
{
+ removeAnnotationForGroup(g);
groups.removeElement(g);
}
}
/** */
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();
}
- /** */
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
public int findIndex(SequenceI s)
{
int i = 0;
return -1;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ public int findIndex(SearchResults results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
+
/**
* 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()
return gapCharacter;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
*/
public boolean isAligned()
{
- int width = getWidth();
+ return isAligned(false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ public boolean isAligned(boolean includeHidden)
+ {
+ int width = getWidth();
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
+ includeHidden = true; // no hidden sequences to check against.
+ }
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() != width)
+ if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
{
- return false;
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
+ }
}
}
return true;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
*/
public boolean deleteAnnotation(AlignmentAnnotation aa)
{
+ return deleteAnnotation(aa, true);
+ }
+
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
int aSize = 1;
if (annotations != null)
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)
- aa.sequenceRef.removeAlignmentAnnotation(aa);
+ if (unhook) {
+ unhookAnnotation(aa);
+ }
}
return swap;
}
/**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
+ * remove any object references associated with this annotation
+ *
+ * @param aa
+ */
+ private void unhookAnnotation(AlignmentAnnotation aa)
+ {
+ if (aa.sequenceRef != null)
+ {
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+ }
+ if (aa.groupRef != null)
+ {
+ // probably need to do more here in the future (post 2.5.0)
+ aa.groupRef = null;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
*/
public void addAnnotation(AlignmentAnnotation aa)
{
+ addAnnotation(aa, -1);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation, int)
+ */
+ public void addAnnotation(AlignmentAnnotation aa, int pos)
+ {
+ if(aa.getRNAStruc()!= null){
+ hasRNAStructure=true;
+ }
+
int aSize = 1;
if (annotations != null)
{
}
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
- temp[aSize - 1] = aa;
-
int i = 0;
-
+ if (pos == -1 || pos >= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
if (aSize > 1)
{
- for (i = 0; i < (aSize - 1); i++)
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
{
- temp[i] = annotations[i];
+ if (p == pos)
+ {
+ p++;
+ }
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
return false;
}
}
+
+ public boolean hasRNAStructure(){
+ //TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
public void setDataset(Alignment data)
{
}
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)
return modified;
}
+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed
+ */
+ public boolean justify(boolean right)
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+ int ends[] = new int[sequences.size() * 2];
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ // This should really be a sequence method
+ ends[i * 2] = current.findIndex(current.getStart());
+ ends[i * 2 + 1] = current.findIndex(current.getStart()
+ + current.getLength());
+ boolean hitres = false;
+ for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+ {
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
+ {
+ maxLength = j - ends[i * 2];
+ }
+ }
+ }
+ }
+ }
+
+ maxLength++;
+ // now edit the flanking gaps to justify to either left or right
+ int cLength, extent, diff;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+
+ cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+ diff = maxLength - cLength; // number of gaps to indent
+ extent = current.getLength();
+ if (right)
+ {
+ // right justify
+ if (extent > ends[i * 2 + 1])
+ {
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
+ modified = true;
+ }
+ if (ends[i * 2] > diff)
+ {
+ current.deleteChars(0, ends[i * 2] - diff);
+ modified = true;
+ }
+ else
+ {
+ if (ends[i * 2] < diff)
+ {
+ current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ else
+ {
+ // left justify
+ if (ends[i * 2] > 0)
+ {
+ current.deleteChars(0, ends[i * 2]);
+ modified = true;
+ ends[i * 2 + 1] -= ends[i * 2];
+ extent -= ends[i * 2];
+ }
+ if (extent > maxLength)
+ {
+ current.deleteChars(maxLength + 1, extent);
+ modified = true;
+ }
+ else
+ {
+ if (extent < maxLength)
+ {
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ }
+ return modified;
+ }
+
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
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)
- * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+
+ 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)
- * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ /*
+ * (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)
- * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.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--;
}
}
return removed;
}
+
+ public void append(AlignmentI toappend)
+ {
+ // TODO test this method for a future 2.5 release
+ // currently tested for use in jalview.gui.SequenceFetcher
+ boolean samegap = toappend.getGapCharacter() == getGapCharacter();
+ char oldc = toappend.getGapCharacter();
+ boolean hashidden = toappend.getHiddenSequences() != null
+ && toappend.getHiddenSequences().hiddenSequences != null;
+ // get all sequences including any hidden ones
+ Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+ .getFullAlignment().getSequences() : toappend.getSequences();
+ if (sqs != null)
+ {
+ Enumeration sq = sqs.elements();
+ while (sq.hasMoreElements())
+ {
+ SequenceI addedsq = (SequenceI) sq.nextElement();
+ if (!samegap)
+ {
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
+ {
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
+ }
+ }
+ addSequence(addedsq);
+ }
+ }
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
+ {
+ addAnnotation(alan[a]);
+ }
+ AlignedCodonFrame[] acod = toappend.getCodonFrames();
+ for (int a = 0; acod != null && a < acod.length; a++)
+ {
+ this.addCodonFrame(acod[a]);
+ }
+ Vector sg = toappend.getGroups();
+ if (sg != null)
+ {
+ Enumeration el = sg.elements();
+ while (el.hasMoreElements())
+ {
+ addGroup((SequenceGroup) el.nextElement());
+ }
+ }
+ if (toappend.getHiddenSequences() != null)
+ {
+ HiddenSequences hs = toappend.getHiddenSequences();
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new HiddenSequences(this);
+ }
+ if (hs.hiddenSequences != null)
+ {
+ for (int s = 0; s < hs.hiddenSequences.length; s++)
+ {
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s] != null)
+ {
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+ }
+ }
+ }
+ }
+ if (toappend.getProperties() != null)
+ {
+ // we really can't do very much here - just try to concatenate strings
+ // where property collisions occur.
+ Enumeration key = toappend.getProperties().keys();
+ while (key.hasMoreElements())
+ {
+ Object k = key.nextElement();
+ Object ourval = this.getProperty(k);
+ Object toapprop = toappend.getProperty(k);
+ if (ourval != null)
+ {
+ if (ourval.getClass().equals(toapprop.getClass())
+ && !ourval.equals(toapprop))
+ {
+ if (ourval instanceof String)
+ {
+ // append strings
+ this.setProperty(k, ((String) ourval) + "; "
+ + ((String) toapprop));
+ }
+ else
+ {
+ if (ourval instanceof Vector)
+ {
+ // append vectors
+ Enumeration theirv = ((Vector) toapprop).elements();
+ while (theirv.hasMoreElements())
+ {
+ ((Vector) ourval).addElement(theirv);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ // just add new property directly
+ setProperty(k, toapprop);
+ }
+
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff