-package jalview.datamodel;\r
-\r
-import jalview.analysis.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import MCview.*;\r
-\r
-\r
-public class Sequence implements SequenceI\r
-{\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
- PDBfile pdb;\r
-\r
- public int maxchain = -1;\r
- public int pdbstart;\r
- public int pdbend;\r
- public int seqstart;\r
- public int seqend;\r
-\r
- public Vector sequenceFeatures = new Vector();\r
- public void setSequenceFeatures(Vector v)\r
- {\r
- sequenceFeatures = v;\r
- }\r
-\r
- public Vector getSequenceFeatures()\r
- {return sequenceFeatures; }\r
-\r
- public void setPDBId(String id)\r
- {\r
- pdbId = id;\r
- }\r
- public String getPDBId()\r
- {\r
- return pdbId;\r
- }\r
-\r
- public void setPDBfile(PDBfile pdb)\r
- {\r
- this.pdb = pdb;\r
- int max = -10;\r
- maxchain = -1;\r
-\r
- for (int i=0; i < pdb.chains.size(); i++) {\r
-\r
- System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);\r
- // Now lets compare the sequences to get\r
- // the start and end points.\r
-\r
-\r
- StringTokenizer str = new StringTokenizer(sequence, ".");\r
- String newString = "";\r
-\r
- while (str.hasMoreTokens()) {\r
- newString += str.nextToken();\r
- }\r
- // Align the sequence to the pdb\r
- AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
-\r
- System.out.println("Score = " + as.maxscore);\r
- if (as.maxscore > max) {\r
- System.out.println("New max score");\r
- max = as.maxscore;\r
- maxchain = i;\r
-\r
- pdbstart = as.seq2start;\r
- pdbend = as.seq2end;\r
- seqstart = as.seq1start - 1 ;\r
- seqend = as.seq1end -1;\r
- }\r
-\r
- System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
- System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
- }\r
- }\r
-\r
- public Sequence(String name, String sequence, int start, int end)\r
- {\r
-\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
-\r
- }\r
-\r
- public Sequence(String name,String sequence) {\r
- this(name,sequence,1,sequence.length());\r
- }\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());\r
- }\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
- public String getName() {\r
- return this.name;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
- public int getStart() {\r
- return this.start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
- public int getEnd() {\r
- return this.end;\r
- }\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
- public String getSequence(int start,int end) {\r
- if(end>sequence.length())\r
- end = sequence.length();\r
- return this.sequence.substring(start,end);\r
- }\r
-\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
- return sequence.charAt(i);\r
- } else {\r
- return ' ';\r
- }\r
- }\r
- public void setDescription(String desc) {\r
- this.description = desc;\r
- }\r
- public String getDescription() {\r
- return this.description;\r
- }\r
-\r
- public int findIndex(int pos) {\r
- // returns the alignment position for a residue\r
- int j = start;\r
- int i = 0;\r
-\r
- while (i< sequence.length() && j <= end && j <= pos) {\r
-\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
- j++;\r
-\r
- i++;\r
- }\r
- if (j == end && j < pos)\r
- return end+1;\r
- else\r
- return i;\r
-\r
- }\r
-\r
- public int findPosition(int i) {\r
- // Returns the sequence position for an alignment position\r
- int j = 0;\r
- int pos = start;\r
-\r
- while (j < i && j<sequence.length())\r
- {\r
- char c = sequence.charAt(j);\r
- if (!jalview.util.Comparison.isGap((c)))\r
- pos++;\r
-\r
- j++;\r
- }\r
- return pos;\r
- }\r
- public void deleteCharAt(int i)\r
- {\r
- StringBuffer sbuffer = new StringBuffer(sequence);\r
- sbuffer.deleteCharAt(i);\r
- sequence = sbuffer.toString();\r
- }\r
-\r
- public void deleteChars(int i, int j)\r
- {\r
- StringBuffer sbuffer = new StringBuffer(sequence);\r
- sbuffer.delete(i,j);\r
- sequence = sbuffer.toString();\r
- }\r
-\r
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i,c,true);\r
- }\r
-\r
- public void insertCharAt(int i,char c,boolean chop) {\r
-\r
- String tmp = new String(sequence);\r
-\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);\r
- } else {\r
- sequence = tmp + String.valueOf(c);\r
- }\r
-\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\r
- }\r
-\r
-}\r
+/*
+* 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
+*/
+package jalview.datamodel;
+
+
+import java.util.*;
+
+import jalview.analysis.*;
+
+/**
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence
+ implements SequenceI
+{
+ SequenceI datasetSequence;
+ String name;
+ private char [] sequence;
+ String description;
+ int start;
+ int end;
+ Vector pdbIds;
+ String vamsasId;
+ DBRefEntry[] dbrefs;
+
+ /** This annotation is displayed below the alignment but the
+ * positions are tied to the residues of this sequence */
+ Vector annotation;
+
+ /** array of seuqence features - may not be null for a valid sequence object */
+ public SequenceFeature[] sequenceFeatures;
+
+
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name display name string
+ * @param sequence string to form a possibly gapped sequence out of
+ * @param start first position of non-gap residue in the sequence
+ * @param end last position of ungapped residues (nearly always only used for display purposes)
+ */
+ public Sequence(String name, String sequence, int start, int end)
+ {
+ this.name = name;
+ this.sequence = sequence.toCharArray();
+ this.start = start;
+ this.end = end;
+ parseId();
+ checkValidRange();
+ }
+
+ public Sequence(String name, char [] sequence, int start, int end)
+ {
+ this.name = name;
+ this.sequence = sequence;
+ this.start = start;
+ this.end = end;
+ parseId();
+ checkValidRange();
+ }
+
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+ "[0-9]{1,}$");
+
+ void parseId()
+ {
+ if (name==null)
+ {
+ System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ name = "";
+ }
+ // Does sequence have the /start-end signiature?
+ if (limitrx.search(name))
+ {
+ name = limitrx.left();
+ endrx.search(limitrx.stringMatched());
+ setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
+ endrx.matchedFrom() - 1)));
+ setEnd(Integer.parseInt(endrx.stringMatched()));
+ }
+ }
+
+ void checkValidRange()
+ {
+ if (end < 1)
+ {
+ int endRes = 0;
+ for (int j = 0; j < sequence.length; j++)
+ {
+ if (!jalview.util.Comparison.isGap( sequence[j] ))
+ {
+ endRes++;
+ }
+ }
+ if (endRes > 0)
+ {
+ endRes += start - 1;
+ }
+
+ this.end = endRes;
+ }
+
+ }
+
+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name DOCUMENT ME!
+ * @param sequence DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence)
+ {
+ this(name, sequence, 1, -1);
+ }
+
+ /**
+ * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
+ * but inherits any existing dataset sequence reference.
+ * @param seq DOCUMENT ME!
+ */
+ public Sequence(SequenceI seq)
+ {
+ this(seq, seq.getAnnotation());
+ }
+ /**
+ * Create a new sequence object with new features, DBRefEntries, and PDBIds
+ * but inherits any existing dataset sequence reference, and duplicate of
+ * any annotation that is present in the given annotation array.
+ * @param seq the sequence to be copied
+ * @param alAnnotation an array of annotation including some associated with seq
+ */
+ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+ {
+ this(seq.getName(),
+ seq.getSequence(),
+ seq.getStart(),
+ seq.getEnd());
+ description = seq.getDescription();
+ if (seq.getSequenceFeatures()!=null) {
+ SequenceFeature[] sf = seq.getSequenceFeatures();
+ for (int i=0; i<sf.length; i++) {
+ addSequenceFeature(new SequenceFeature(sf[i]));
+ }
+ }
+ if (seq.getDBRef()!=null) {
+ DBRefEntry[] dbr = seq.getDBRef();
+ for (int i=0; i<dbr.length; i++) {
+ addDBRef(new DBRefEntry(dbr[i]));
+ }
+ }
+ setDatasetSequence(seq.getDatasetSequence());
+ if (seq.getAnnotation()!=null) {
+ AlignmentAnnotation[] sqann = seq.getAnnotation();
+ for (int i=0;i<sqann.length; i++)
+ {
+ if (sqann[i]==null)
+ {
+ continue;
+ }
+ boolean found = (alAnnotation==null);
+ if (!found)
+ {
+ for (int apos = 0; !found && apos<alAnnotation.length; apos++)
+ {
+ found = (alAnnotation[apos] == sqann[i]);
+ }
+ }
+ if (found)
+ {
+ // only copy the given annotation
+ AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+ addAlignmentAnnotation(newann);
+ }
+ }
+ }
+ if (seq.getPDBId()!=null) {
+ Vector ids = seq.getPDBId();
+ Enumeration e = ids.elements();
+ while (e.hasMoreElements()) {
+ this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void setSequenceFeatures(SequenceFeature[] features)
+ {
+ sequenceFeatures = features;
+ }
+
+ public synchronized void addSequenceFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures == null)
+ {
+ sequenceFeatures = new SequenceFeature[0];
+ }
+
+ for (int i = 0; i < sequenceFeatures.length; i++)
+ {
+ if (sequenceFeatures[i].equals(sf))
+ {
+ return;
+ }
+ }
+
+ SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+ temp[sequenceFeatures.length] = sf;
+
+ sequenceFeatures = temp;
+ }
+
+ public void deleteFeature(SequenceFeature sf)
+ {
+ if(sequenceFeatures==null)
+ {
+ return;
+ }
+
+ int index=0;
+ for (index = 0; index < sequenceFeatures.length; index++)
+ {
+ if (sequenceFeatures[index].equals(sf))
+ {
+ break;
+ }
+ }
+
+
+ if(index==sequenceFeatures.length)
+ {
+ return;
+ }
+
+ int sfLength = sequenceFeatures.length;
+ if(sfLength<2)
+ {
+ sequenceFeatures = null;
+ }
+ else
+ {
+ SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+ if(index<sfLength)
+ {
+ System.arraycopy(sequenceFeatures,
+ index + 1,
+ temp,
+ index, sequenceFeatures.length - index -1);
+ }
+
+ sequenceFeatures = temp;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature[] getSequenceFeatures()
+ {
+ return sequenceFeatures;
+ }
+
+ public void addPDBId(PDBEntry entry)
+ {
+ if (pdbIds == null)
+ {
+ pdbIds = new Vector();
+ }
+
+ pdbIds.addElement(entry);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public void setPDBId(Vector id)
+ {
+ pdbIds = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getPDBId()
+ {
+ return pdbIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayId(boolean jvsuffix)
+ {
+ StringBuffer result = new StringBuffer(name);
+ if (jvsuffix)
+ {
+ result.append("/" + start + "-" + end);
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setName(String name)
+ {
+ this.name = name;
+ this.parseId();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getName()
+ {
+ return this.name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ */
+ public void setStart(int start)
+ {
+ this.start = start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStart()
+ {
+ return this.start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param end DOCUMENT ME!
+ */
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEnd()
+ {
+ return this.end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getLength()
+ {
+ return this.sequence.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setSequence(String seq)
+ {
+ this.sequence = seq.toCharArray();
+ checkValidRange();
+ }
+
+
+ public String getSequenceAsString()
+ {
+ return new String(sequence);
+ }
+
+ public String getSequenceAsString(int start, int end)
+ {
+ return new String(getSequence(start, end));
+ }
+
+
+ public char [] getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char [] getSequence(int start, int end)
+ {
+ if (start<0)
+ start=0;
+ // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+ if (start >= sequence.length)
+ {
+ return new char[0];
+ }
+
+ if (end >= sequence.length)
+ {
+ end = sequence.length;
+ }
+
+ char [] reply = new char[end-start];
+ System.arraycopy(sequence, start, reply, 0, end-start);
+
+ return reply;
+ }
+
+
+ /**
+ * make a new Sequence object from start to end (including gaps) over this seqeunce
+ * @param start int
+ * @param end int
+ * @return SequenceI
+ */
+ public SequenceI getSubSequence(int start, int end)
+ {
+ if (start < 0)
+ {
+ start = 0;
+ }
+ char [] seq = getSequence(start, end);
+ if (seq.length == 0)
+ {
+ return null;
+ }
+ int nstart = findPosition(start);
+ int nend = findPosition(end) - 1;
+ // JBPNote - this is an incomplete copy.
+ SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
+ nseq.setDescription(description);
+ if (datasetSequence!=null)
+ {
+ nseq.setDatasetSequence(datasetSequence);
+ }
+ else
+ {
+ nseq.setDatasetSequence(this);
+ }
+ return nseq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getCharAt(int i)
+ {
+ if (i < sequence.length)
+ {
+ return sequence[i];
+ }
+ else
+ {
+ return ' ';
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void setDescription(String desc)
+ {
+ this.description = desc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return this.description;
+ }
+
+ /**
+ * Return the alignment position for a sequence position
+ *
+ * @param pos lying from start to end
+ *
+ * @return aligned position of residue pos
+ */
+ public int findIndex(int pos)
+ {
+ // returns the alignment position for a residue
+ int j = start;
+ int i = 0;
+
+ while ( (i < sequence.length) && (j <= end) && (j <= pos))
+ {
+ if (!jalview.util.Comparison.isGap(sequence[i]))
+ {
+ j++;
+ }
+
+ i++;
+ }
+
+ if ( (j == end) && (j < pos))
+ {
+ return end + 1;
+ }
+ else
+ {
+ return i;
+ }
+ }
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i column index in alignment (from 1)
+ *
+ * @return residue number for residue (left of and) nearest ith column
+ */
+ public int findPosition(int i)
+ {
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ( (j < i) && (j < seqlen))
+ {
+ if (!jalview.util.Comparison.isGap( sequence[j] ))
+ {
+ pos++;
+ }
+
+ j++;
+ }
+
+ return pos;
+ }
+
+ /**
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+ */
+ public int[] gapMap()
+ {
+ String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
+ GapChars, new String(sequence));
+ int[] map = new int[seq.length()];
+ int j = 0;
+ int p = 0;
+
+ while (j < sequence.length)
+ {
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ map[p++] = j;
+ }
+
+ j++;
+ }
+
+ return map;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#deleteChars(int, int)
+ */
+ public void deleteChars(int i, int j)
+ {
+ int newstart=start,newend=end;
+ if (i >= sequence.length)
+ {
+ return;
+ }
+
+ char [] tmp;
+
+ if (j >= sequence.length)
+ {
+ tmp = new char[i];
+ System.arraycopy(sequence,0,tmp,0,i);
+ }
+ else
+ {
+ tmp = new char[sequence.length-j+i];
+ System.arraycopy(sequence,0,tmp,0,i);
+ System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+ }
+ boolean createNewDs=false;
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+ if (createNewDs)
+ {
+ newend--;
+ } else {
+ int sindex = findIndex(start)-1;
+ if (sindex==s)
+ {
+ // delete characters including start of sequence
+ newstart = findPosition(j);
+ break; // don't need to search for any more residue characters.
+ } else {
+ // delete characters after start.
+ int eindex = findIndex(end)-1;
+ if (eindex<j)
+ {
+ // delete characters at end of sequence
+ newend = findPosition(i-1);
+ break; // don't need to search for any more residue characters.
+ } else {
+ createNewDs=true;
+ newend--; // decrease end position by one for the deleted residue and search further
+ }
+ }
+ }
+ }
+ }
+ // deletion occured in the middle of the sequence
+ if (createNewDs && this.datasetSequence != null)
+ {
+ // construct a new sequence
+ Sequence ds = new Sequence(datasetSequence);
+ // TODO: remove any non-inheritable properties ?
+ // TODO: create a sequence mapping (since there is a relation here ?)
+ ds.deleteChars(i, j);
+ datasetSequence = ds;
+ }
+ start = newstart;
+ end = newend;
+ sequence = tmp;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ * @param chop DOCUMENT ME!
+ */
+ public void insertCharAt(int i, int length, char c)
+ {
+ char [] tmp = new char[sequence.length+length];
+
+ if (i >= sequence.length)
+ {
+ System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+ i = sequence.length;
+ }
+ else
+ {
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ }
+
+
+ int index = i;
+ while (length > 0)
+ {
+ tmp[ index++ ] = c;
+ length--;
+ }
+
+ if (i < sequence.length)
+ {
+ System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+ }
+
+ sequence = tmp;
+ }
+
+ public void insertCharAt(int i, char c)
+ {
+ insertCharAt(i, 1, c);
+ }
+
+ public String getVamsasId()
+ {
+ return vamsasId;
+ }
+
+ public void setVamsasId(String id)
+ {
+ vamsasId = id;
+ }
+
+ public void setDBRef(DBRefEntry[] dbref)
+ {
+ dbrefs = dbref;
+ }
+
+ public DBRefEntry[] getDBRef()
+ {
+ return dbrefs;
+ }
+
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (dbrefs == null)
+ {
+ dbrefs = new DBRefEntry[0];
+ }
+
+ int i, iSize = dbrefs.length;
+
+ for(i=0; i<iSize; i++)
+ {
+ if(dbrefs[i].equalRef(entry))
+ {
+ if (entry.getMap()!=null)
+ {
+ if (dbrefs[i].getMap()==null)
+ {
+ // overwrite with 'superior' entry that contains a mapping.
+ dbrefs[i] = entry;
+ }
+ }
+ return;
+ }
+ }
+
+ DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, iSize);
+ temp[temp.length - 1] = entry;
+
+ dbrefs = temp;
+ }
+
+ public void setDatasetSequence(SequenceI seq)
+ {
+ datasetSequence = seq;
+ }
+
+ public SequenceI getDatasetSequence()
+ {
+ return datasetSequence;
+ }
+
+ public AlignmentAnnotation[] getAnnotation()
+ {
+ if (annotation == null)
+ {
+ return null;
+ }
+
+ AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
+ for (int r = 0; r < ret.length; r++)
+ {
+ ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+ }
+
+ return ret;
+ }
+
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if (this.annotation == null)
+ {
+ this.annotation = new Vector();
+ }
+
+ this.annotation.addElement(annotation);
+ annotation.setSequenceRef(this);
+ }
+
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if(this.annotation!=null)
+ {
+ this.annotation.removeElement(annotation);
+ if(this.annotation.size()==0)
+ this.annotation = null;
+ }
+ }
+
+
+ /**
+ * test if this is a valid candidate for another
+ * sequence's dataset sequence.
+ *
+ */
+ private boolean isValidDatasetSequence()
+ {
+ if (datasetSequence!=null)
+ {
+ return false;
+ }
+ for (int i=0;i<sequence.length; i++)
+ {
+ if (jalview.util.Comparison.isGap(sequence[i]))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#deriveSequence()
+ */
+ public SequenceI deriveSequence()
+ {
+ SequenceI seq=new Sequence(this);
+ if (datasetSequence != null)
+ {
+ // duplicate current sequence with same dataset
+ seq.setDatasetSequence(datasetSequence);
+ }
+ else
+ {
+ if (isValidDatasetSequence())
+ {
+ // Use this as dataset sequence
+ seq.setDatasetSequence(this);
+ } else {
+ // Create a new, valid dataset sequence
+ SequenceI ds = seq;
+ ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
+ setDatasetSequence(ds);
+ ds.setSequenceFeatures(getSequenceFeatures());
+ seq = this; // and return this sequence as the derived sequence.
+ }
+ }
+ return seq;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#createDatasetSequence()
+ */
+ public SequenceI createDatasetSequence()
+ {
+ if (datasetSequence==null)
+ {
+ datasetSequence = new Sequence(getName(),
+ AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ getSequenceAsString()),
+ getStart(),
+ getEnd());
+ datasetSequence.setSequenceFeatures(getSequenceFeatures());
+ datasetSequence.setDescription(getDescription());
+ setSequenceFeatures(null);
+ // move database references onto dataset sequence
+ datasetSequence.setDBRef(getDBRef());
+ setDBRef(null);
+ }
+ return datasetSequence;
+ }
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] annotations)
+ */
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
+ {
+ if (annotation!=null) {
+ annotation.removeAllElements();
+ }
+ if (annotations!=null) {
+ for (int i=0; i<annotations.length; i++)
+ {
+ if (annotations[i]!=null)
+ addAlignmentAnnotation(annotations[i]);
+ }
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+ */
+ public AlignmentAnnotation[] getAnnotation(String label)
+ {
+ if (annotation==null || annotation.size()==0)
+ {
+ return null;
+ }
+
+ Vector subset = new Vector();
+ Enumeration e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+ if (ann.label!=null && ann.label.equals(label))
+ {
+ subset.addElement(ann);
+ }
+ }
+ if (subset.size()==0)
+ {
+ return null;
+ }
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+ int i=0;
+ e = subset.elements();
+ while (e.hasMoreElements())
+ {
+ anns[i++] = (AlignmentAnnotation) e.nextElement();
+ }
+ subset.removeAllElements();
+ return anns;
+ }
+
+}
+
+
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