X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d64e133777ce29d50430e6b889888dd5e16b3569;hb=34e29960cefd8e743de8734ca0ea2778bab12a40;hp=691a1f1f3d1602659932bfc13097c5f77ac6a4c9;hpb=df36af4b025b8435e31ae060a939e9c855e03506;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 691a1f1..d4290a3 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,229 +1,1454 @@
-package jalview.datamodel;
-
-import jalview.analysis.*;
-import java.awt.*;
-import java.util.*;
-import MCview.*;
-
-
-public class Sequence implements SequenceI
-{
- protected String name;
- protected String sequence;
- protected String description;
- protected int start;
- protected int end;
- protected String displayId;
- protected Color color = Color.white;
- String pdbId;
- PDBfile pdb;
-
- public int maxchain = -1;
- public int pdbstart;
- public int pdbend;
- public int seqstart;
- public int seqend;
-
- public Vector sequenceFeatures = new Vector();
- public void setSequenceFeatures(Vector v)
- {
- sequenceFeatures = v;
- }
-
- public Vector getSequenceFeatures()
- {return sequenceFeatures; }
-
- public void setPDBId(String id)
- {
- pdbId = id;
- }
- public String getPDBId()
- {
- return pdbId;
- }
-
- public void setPDBfile(PDBfile pdb)
- {
- this.pdb = pdb;
- int max = -10;
- maxchain = -1;
-
- for (int i=0; i < pdb.chains.size(); i++) {
-
- System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);
- // Now lets compare the sequences to get
- // the start and end points.
-
-
- StringTokenizer str = new StringTokenizer(sequence, ".");
- String newString = "";
-
- while (str.hasMoreTokens()) {
- newString += str.nextToken();
- }
- // Align the sequence to the pdb
- AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- as.printAlignment();
-
- System.out.println("Score = " + as.maxscore);
- if (as.maxscore > max) {
- System.out.println("New max score");
- max = as.maxscore;
- maxchain = i;
-
- pdbstart = as.seq2start;
- pdbend = as.seq2end;
- seqstart = as.seq1start - 1 ;
- seqend = as.seq1end -1;
- }
-
- System.out.println("PDB start/end " + pdbstart + " " + pdbend);
- System.out.println("SEQ start/end " + seqstart + " " + seqend);
- }
- }
-
- public Sequence(String name, String sequence, int start, int end)
- {
-
- this.name = name;
- this.sequence = sequence;
- this.start = start;
- this.end = end;
-
- setDisplayId();
-
- }
-
- public Sequence(String name,String sequence) {
- this(name,sequence,1,sequence.length());
- }
- public Sequence(SequenceI seq) {
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
- }
- public String getDisplayId() {
- return displayId;
- }
- public void setDisplayId() {
- displayId = name + "/" + start + "-" + end;
- }
- public void setName(String name) {
- this.name = name;
- setDisplayId();
- }
- public String getName() {
- return this.name;
- }
- public void setStart(int start) {
- this.start = start;
- setDisplayId();
- }
- public int getStart() {
- return this.start;
- }
- public void setEnd(int end) {
- this.end = end;
- setDisplayId();
- }
- public int getEnd() {
- return this.end;
- }
- public int getLength() {
- return this.sequence.length();
- }
- public void setSequence(String seq) {
- this.sequence = seq;
- }
- public String getSequence() {
- return this.sequence;
- }
- public String getSequence(int start,int end) {
- if(end>sequence.length())
- end = sequence.length();
- return this.sequence.substring(start,end);
- }
-
- public char getCharAt(int i) {
- if (i < sequence.length()) {
- return sequence.charAt(i);
- } else {
- return ' ';
- }
- }
- public void setDescription(String desc) {
- this.description = desc;
- }
- public String getDescription() {
- return this.description;
- }
-
- 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) {
-
- char c = sequence.charAt(i);
-
- if (!jalview.util.Comparison.isGap((c)))
- j++;
-
- i++;
- }
- if (j == end && j < pos)
- return end+1;
- else
- return i;
-
- }
-
- public int findPosition(int i) {
- // Returns the sequence position for an alignment position
- int j = 0;
- int pos = start;
-
- while (j < i && j.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+/**
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence extends ASequence implements SequenceI
+{
+ SequenceI datasetSequence;
+
+ String name;
+
+ private char[] sequence;
+
+ String description;
+
+ int start;
+
+ int end;
+
+ Vector pdbIds;
+
+ String vamsasId;
+
+ DBRefEntry[] dbrefs;
+
+ RNA rna;
+
+ /**
+ * This annotation is displayed below the alignment but the positions are tied
+ * to the residues of this sequence
+ *
+ * TODO: change to List<>
+ */
+ Vector annotation;
+
+ /**
+ * The index of the sequence in a MSA
+ */
+ int index = -1;
+
+ /** array of sequence 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)
+ {
+ initSeqAndName(name, sequence.toCharArray(), start, end);
+ }
+
+ public Sequence(String name, char[] sequence, int start, int end)
+ {
+ initSeqAndName(name, sequence, start, end);
+ }
+
+ /**
+ * Stage 1 constructor - assign name, sequence, and set start and end fields.
+ * start and end are updated values from name2 if it ends with /start-end
+ *
+ * @param name2
+ * @param sequence2
+ * @param start2
+ * @param end2
+ */
+ protected void initSeqAndName(String name2, char[] sequence2, int start2,
+ int end2)
+ {
+ this.name = name2;
+ this.sequence = sequence2;
+ this.start = start2;
+ this.end = end2;
+ 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 signature?
+ 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()
+ {
+ // Note: JAL-774 :
+ // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+ {
+ 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;
+ }
+
+ if (end < endRes)
+ {
+ 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 AlignmentAnnotations but inherits
+ * any existing dataset sequence reference. If non exists, everything is
+ * copied.
+ *
+ * @param seq
+ * if seq is a dataset sequence, behaves like a plain old copy
+ * constructor
+ */
+ 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)
+ {
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ /**
+ * does the heavy lifting when cloning a dataset sequence, or coping data from
+ * dataset to a new derived sequence.
+ *
+ * @param seq
+ * - source of attributes.
+ * @param alAnnotation
+ * - alignment annotation present on seq that should be copied onto
+ * this sequence
+ */
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ {
+ char[] oseq = seq.getSequence();
+ initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+ seq.getStart(),
+ seq.getEnd());
+ }
+ description = seq.getDescription();
+ if (seq != datasetSequence)
+ {
+ setDatasetSequence(seq.getDatasetSequence());
+ }
+ if (datasetSequence == null && seq.getDBRefs() != null)
+ {
+ // only copy DBRefs and seqfeatures if we really are a dataset sequence
+ DBRefEntry[] dbr = seq.getDBRefs();
+ for (int i = 0; i < dbr.length; i++)
+ {
+ addDBRef(new DBRefEntry(dbr[i]));
+ }
+ if (seq.getSequenceFeatures() != null)
+ {
+ SequenceFeature[] sf = seq.getSequenceFeatures();
+ for (int i = 0; i < sf.length; i++)
+ {
+ addSequenceFeature(new SequenceFeature(sf[i]));
+ }
+ }
+ }
+ 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.getAllPDBEntries() != null)
+ {
+ Vector ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
+ {
+ this.addPDBId(new PDBEntry(pdb));
+ }
+ }
+ }
+
+
+ @Override
+ public void setSequenceFeatures(SequenceFeature[] features)
+ {
+ if (datasetSequence == null)
+ {
+ sequenceFeatures = features;
+ }
+ else
+ {
+ if (datasetSequence.getSequenceFeatures() != features
+ && datasetSequence.getSequenceFeatures() != null
+ && datasetSequence.getSequenceFeatures().length > 0)
+ {
+ new Exception(
+ "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+ .printStackTrace();
+ }
+ datasetSequence.setSequenceFeatures(features);
+ }
+ }
+
+ @Override
+ public synchronized void addSequenceFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures==null && datasetSequence != null)
+ {
+ datasetSequence.addSequenceFeature(sf);
+ return;
+ }
+ 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;
+ }
+
+ @Override
+ public void deleteFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures == null)
+ {
+ if (datasetSequence!=null) {
+ datasetSequence.deleteFeature(sf);
+ }
+ 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;
+ }
+ }
+
+ /**
+ * Returns the sequence features (if any), looking first on the sequence, then
+ * on its dataset sequence, and so on until a non-null value is found (or
+ * none). This supports retrieval of sequence features stored on the sequence
+ * (as in the applet) or on the dataset sequence (as in the Desktop version).
+ *
+ * @return
+ */
+ @Override
+ public SequenceFeature[] getSequenceFeatures()
+ {
+ SequenceFeature[] features = sequenceFeatures;
+
+ SequenceI seq = this;
+ int count = 0; // failsafe against loop in sequence.datasetsequence...
+ while (features == null && seq.getDatasetSequence() != null
+ && count++ < 10)
+ {
+ seq = seq.getDatasetSequence();
+ features = ((Sequence) seq).sequenceFeatures;
+ }
+ return features;
+ }
+
+ @Override
+ public boolean addPDBId(PDBEntry entry)
+ {
+ if (pdbIds == null)
+ {
+ pdbIds = new Vector();
+ pdbIds.add(entry);
+ return true;
+ }
+
+ for (PDBEntry pdbe : pdbIds)
+ {
+ if (pdbe.updateFrom(entry))
+ {
+ return false;
+ }
+ }
+ pdbIds.addElement(entry);
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setPDBId(Vector id)
+ {
+ pdbIds = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Vector getAllPDBEntries()
+ {
+ return pdbIds == null ? new Vector() : pdbIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ 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!
+ */
+ @Override
+ public void setName(String name)
+ {
+ this.name = name;
+ this.parseId();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public String getName()
+ {
+ return this.name;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param start
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setStart(int start)
+ {
+ this.start = start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getStart()
+ {
+ return this.start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param end
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setEnd(int end)
+ {
+ this.end = end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getEnd()
+ {
+ return this.end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getLength()
+ {
+ return this.sequence.length;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setSequence(String seq)
+ {
+ this.sequence = seq.toCharArray();
+ checkValidRange();
+ }
+
+ @Override
+ public String getSequenceAsString()
+ {
+ return new String(sequence);
+ }
+
+ @Override
+ public String getSequenceAsString(int start, int end)
+ {
+ return new String(getSequence(start, end));
+ }
+
+ @Override
+ public char[] getSequence()
+ {
+ return sequence;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#getSequence(int, int)
+ */
+ @Override
+ 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;
+ }
+
+ @Override
+ 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;
+ }
+
+ /**
+ * Returns the character of the aligned sequence at the given position (base
+ * zero), or space if the position is not within the sequence's bounds
+ *
+ * @return
+ */
+ @Override
+ public char getCharAt(int i)
+ {
+ if (i >= 0 && i < sequence.length)
+ {
+ return sequence[i];
+ }
+ else
+ {
+ return ' ';
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setDescription(String desc)
+ {
+ this.description = desc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public String getDescription()
+ {
+ return this.description;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#findIndex(int)
+ */
+ @Override
+ public int findIndex(int pos)
+ {
+ // returns the alignment position for a residue
+ int j = start;
+ int i = 0;
+ // Rely on end being at least as long as the length of the sequence.
+ 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;
+ }
+ }
+
+ @Override
+ 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
+ */
+ @Override
+ 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;
+ }
+
+ @Override
+ public int[] findPositionMap()
+ {
+ int map[] = new int[sequence.length];
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ map[j] = pos;
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ pos++;
+ }
+
+ j++;
+ }
+ return map;
+ }
+
+ @Override
+ public List getInsertions()
+ {
+ ArrayList map = new ArrayList();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ }
+ j++;
+ }
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ return map;
+ }
+
+ @Override
+ public void deleteChars(int i, int j)
+ {
+ int newstart = start, newend = end;
+ if (i >= sequence.length || i < 0)
+ {
+ return;
+ }
+
+ char[] tmp = StringUtils.deleteChars(sequence, i, j);
+ boolean createNewDs = false;
+ // TODO: take a (second look) at the dataset creation validation method for
+ // the very large sequence case
+ int eindex = -1, sindex = -1;
+ boolean ecalc = false, scalc = false;
+ for (int s = i; s < j; s++)
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ {
+ if (createNewDs)
+ {
+ newend--;
+ }
+ else
+ {
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
+ 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.
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
+ 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;
+ }
+
+ @Override
+ 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;
+ }
+
+ @Override
+ public void insertCharAt(int i, char c)
+ {
+ insertCharAt(i, 1, c);
+ }
+
+ @Override
+ public String getVamsasId()
+ {
+ return vamsasId;
+ }
+
+ @Override
+ public void setVamsasId(String id)
+ {
+ vamsasId = id;
+ }
+
+ @Override
+ public void setDBRefs(DBRefEntry[] dbref)
+ {
+ dbrefs = dbref;
+ }
+
+ @Override
+ public DBRefEntry[] getDBRefs()
+ {
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRefs();
+ }
+ return dbrefs;
+ }
+
+ @Override
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (datasetSequence != null)
+ {
+ datasetSequence.addDBRef(entry);
+ return;
+ }
+
+ if (dbrefs == null)
+ {
+ dbrefs = new DBRefEntry[0];
+ }
+
+ for (DBRefEntryI dbr : dbrefs)
+ {
+ if (dbr.updateFrom(entry))
+ {
+ /*
+ * found a dbref that either matched, or could be
+ * updated from, the new entry - no need to add it
+ */
+ return;
+ }
+ }
+
+ /*
+ * extend the array to make room for one more
+ */
+ // TODO use an ArrayList instead
+ int j = dbrefs.length;
+ DBRefEntry[] temp = new DBRefEntry[j + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, j);
+ temp[temp.length - 1] = entry;
+
+ dbrefs = temp;
+ }
+
+ @Override
+ public void setDatasetSequence(SequenceI seq)
+ {
+ // TODO check for circular reference before setting?
+ datasetSequence = seq;
+ }
+
+ @Override
+ public SequenceI getDatasetSequence()
+ {
+ return datasetSequence;
+ }
+
+ @Override
+ public AlignmentAnnotation[] getAnnotation()
+ {
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
+
+ @Override
+ public boolean hasAnnotation(AlignmentAnnotation ann)
+ {
+ return annotation == null ? false : annotation.contains(ann);
+ }
+
+ @Override
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if (this.annotation == null)
+ {
+ this.annotation = new Vector();
+ }
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
+ }
+ annotation.setSequenceRef(this);
+ }
+
+ @Override
+ 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;
+ }
+
+ @Override
+ public SequenceI deriveSequence()
+ {
+ Sequence seq=null;
+ if (datasetSequence == null)
+ {
+ if (isValidDatasetSequence())
+ {
+ // Use this as dataset sequence
+ seq = new Sequence(getName(), "", 1, -1);
+ seq.setDatasetSequence(this);
+ seq.initSeqFrom(this, getAnnotation());
+ return seq;
+ }
+ else
+ {
+ // Create a new, valid dataset sequence
+ createDatasetSequence();
+ }
+ }
+ return new Sequence(this);
+ }
+
+ private boolean _isNa;
+
+ private long _seqhash = 0;
+
+ @Override
+ public boolean isProtein()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.isProtein();
+ }
+ if (_seqhash != sequence.hashCode())
+ {
+ _seqhash = sequence.hashCode();
+ _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+ }
+ return !_isNa;
+ };
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#createDatasetSequence()
+ */
+ @Override
+ public SequenceI createDatasetSequence()
+ {
+ if (datasetSequence == null)
+ {
+ Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, getSequenceAsString()),
+ getStart(), getEnd());
+
+ datasetSequence = dsseq;
+
+ dsseq.setDescription(description);
+ // move features and database references onto dataset sequence
+ dsseq.sequenceFeatures = sequenceFeatures;
+ sequenceFeatures=null;
+ dsseq.dbrefs = dbrefs;
+ dbrefs=null;
+ // TODO: search and replace any references to this sequence with
+ // references to the dataset sequence in Mappings on dbref
+ dsseq.pdbIds = pdbIds;
+ pdbIds = null;
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ // annotation is cloned rather than moved, to preserve what's currently
+ // on the alignment
+ for (AlignmentAnnotation aa : annotation)
+ {
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(_aa);
+ }
+ }
+ }
+ return datasetSequence;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+ * annotations)
+ */
+ @Override
+ 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]);
+ }
+ }
+ }
+ }
+
+ @Override
+ 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;
+ }
+
+ @Override
+ public boolean updatePDBIds()
+ {
+ if (datasetSequence != null)
+ {
+ // TODO: could merge DBRefs
+ return datasetSequence.updatePDBIds();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return false;
+ }
+ boolean added = false;
+ for (DBRefEntry dbr : dbrefs)
+ {
+ if (DBRefSource.PDB.equals(dbr.getSource()))
+ {
+ /*
+ * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+ * PDB id is not already present in a 'matching' PDBEntry
+ * Constructor parses out a chain code if appended to the accession id
+ * (a fudge used to 'store' the chain code in the DBRef)
+ */
+ PDBEntry pdbe = new PDBEntry(dbr);
+ added |= addPDBId(pdbe);
+ }
+ }
+ return added;
+ }
+
+ @Override
+ public void transferAnnotation(SequenceI entry, Mapping mp)
+ {
+ if (datasetSequence != null)
+ {
+ datasetSequence.transferAnnotation(entry, mp);
+ return;
+ }
+ if (entry.getDatasetSequence() != null)
+ {
+ transferAnnotation(entry.getDatasetSequence(), mp);
+ return;
+ }
+ // transfer any new features from entry onto sequence
+ if (entry.getSequenceFeatures() != null)
+ {
+
+ SequenceFeature[] sfs = entry.getSequenceFeatures();
+ for (int si = 0; si < sfs.length; si++)
+ {
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
+ : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
+ if (sf != null && sf.length > 0)
+ {
+ for (int sfi = 0; sfi < sf.length; sfi++)
+ {
+ addSequenceFeature(sf[sfi]);
+ }
+ }
+ }
+ }
+
+ // transfer PDB entries
+ if (entry.getAllPDBEntries() != null)
+ {
+ Enumeration e = entry.getAllPDBEntries().elements();
+ while (e.hasMoreElements())
+ {
+ PDBEntry pdb = (PDBEntry) e.nextElement();
+ addPDBId(pdb);
+ }
+ }
+ // transfer database references
+ DBRefEntry[] entryRefs = entry.getDBRefs();
+ if (entryRefs != null)
+ {
+ for (int r = 0; r < entryRefs.length; r++)
+ {
+ DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+ if (newref.getMap() != null && mp != null)
+ {
+ // remap ref using our local mapping
+ }
+ // we also assume all version string setting is done by dbSourceProxy
+ /*
+ * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
+ * newref.setSource(dbSource); }
+ */
+ addDBRef(newref);
+ }
+ }
+ }
+
+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ @Override
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ @Override
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ @Override
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ @Override
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List result = new ArrayList();
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (ann.calcId != null && ann.calcId.equals(calcId)
+ && ann.label != null && ann.label.equals(label))
+ {
+ result.add(ann);
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() != null)
+ {
+ return getDatasetSequence().getPDBEntry(pdbIdStr);
+ }
+ if (pdbIds == null)
+ {
+ return null;
+ }
+ List entries = getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
+
+ @Override
+ public List getPrimaryDBRefs()
+ {
+ if (datasetSequence!=null)
+ {
+ return datasetSequence.getPrimaryDBRefs();
+ }
+ if (dbrefs==null || dbrefs.length==0)
+ {
+ return Collections.emptyList();
+ }
+ synchronized (dbrefs)
+ {
+ List primaries = new ArrayList();
+ DBRefEntry[] tmp = new DBRefEntry[1];
+ for (DBRefEntry ref : dbrefs)
+ {
+ if (!ref.isPrimaryCandidate())
+ {
+ continue;
+ }
+ if (ref.hasMap())
+ {
+ MapList mp = ref.getMap().getMap();
+ if (mp.getFromLowest() > start || mp.getFromHighest() < end)
+ {
+ // map only involves a subsequence, so cannot be primary
+ continue;
+ }
+ }
+ // whilst it looks like it is a primary ref, we also sanity check type
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
+ DBRefUtils.getCanonicalName(ref.getSource())))
+ {
+ // PDB dbrefs imply there should be a PDBEntry associated
+ // TODO: tighten PDB dbrefs
+ // formally imply Jalview has actually downloaded and
+ // parsed the pdb file. That means there should be a cached file
+ // handle on the PDBEntry, and a real mapping between sequence and
+ // extracted sequence from PDB file
+ PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+ if (pdbentry != null && pdbentry.getFile() != null)
+ {
+ primaries.add(ref);
+ }
+ continue;
+ }
+ // check standard protein or dna sources
+ tmp[0] = ref;
+ DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+ if (res != null && res[0] == tmp[0])
+ {
+ primaries.add(ref);
+ continue;
+ }
+ }
+ return primaries;
+ }
+ }
+
+}