/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
-import java.awt.*;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
/**
- * DOCUMENT ME!
- *
+ *
+ * Implements the SequenceI interface for a char[] based sequence object.
+ *
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
- SequenceI datasetSequence;
- String name;
- private String sequence;
- String description;
- int start;
- int end;
- Color color = Color.white;
- 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;
-
- /** DOCUMENT ME!! */
- public SequenceFeature [] sequenceFeatures;
-
- /** This array holds hidden sequences
- * of which this sequence is the representitive member of a group
- */
- SequenceGroup hiddenSequences;
-
- /**
- * Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- public Sequence(String name, String 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()
- {
- // 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;
- char ch;
- for (int j = 0; j < sequence.length(); j++)
- {
- ch = sequence.charAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- endRes++;
- }
- }
- if (endRes > 0)
- {
- endRes += start - 1;
- }
+ SequenceI datasetSequence;
- this.end = endRes;
- }
+ String name;
- }
+ private char[] sequence;
+
+ String description;
+
+ int start;
+
+ int end;
+
+ Vector<PDBEntry> pdbIds;
+
+ String vamsasId;
- /**
- * Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
- */
- public Sequence(String name, String sequence)
+ 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<AlignmentAnnotation> 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)
{
- this(name, sequence, 1, -1);
+ System.err
+ .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ name = "";
}
-
- /**
- * Creates a new Sequence object.
- *
- * @param seq DOCUMENT ME!
- */
- public Sequence(SequenceI seq)
+ // Does sequence have the /start-end signature?
+ if (limitrx.search(name))
{
- this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+ name = limitrx.left();
+ endrx.search(limitrx.stringMatched());
+ setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
+ endrx.matchedFrom() - 1)));
+ setEnd(Integer.parseInt(endrx.stringMatched()));
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature [] features)
+ 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
{
- sequenceFeatures = features;
+ 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;
+ }
}
- public synchronized void addSequenceFeature(SequenceFeature sf)
+ }
+
+ /**
+ * 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)
+ {
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {
+ initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+ seq.getEnd());
+ description = seq.getDescription();
+ if (seq.getSequenceFeatures() != null)
{
- if(sequenceFeatures==null)
+ SequenceFeature[] sf = seq.getSequenceFeatures();
+ for (int i = 0; i < sf.length; i++)
{
- sequenceFeatures = new SequenceFeature[0];
+ addSequenceFeature(new SequenceFeature(sf[i]));
}
-
- for(int i=0; i<sequenceFeatures.length; i++)
+ }
+ setDatasetSequence(seq.getDatasetSequence());
+ if (datasetSequence == null && seq.getDBRef() != null)
+ {
+ // only copy DBRefs if we really are a dataset sequence
+ DBRefEntry[] dbr = seq.getDBRef();
+ for (int i = 0; i < dbr.length; i++)
{
- if(sequenceFeatures[i].equals(sf))
+ addDBRef(new DBRefEntry(dbr[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)
{
- return;
+ // only copy the given annotation
+ AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+ addAlignmentAnnotation(newann);
}
}
-
- SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
- temp[sequenceFeatures.length] = sf;
-
- sequenceFeatures = temp;
}
+ if (seq.getAllPDBEntries() != null)
+ {
+ Vector ids = seq.getAllPDBEntries();
+ 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;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature [] getSequenceFeatures()
+ public synchronized void addSequenceFeature(SequenceFeature sf)
+ {
+ if (sequenceFeatures == null)
{
- return sequenceFeatures;
+ sequenceFeatures = new SequenceFeature[0];
}
- public void addPDBId(PDBEntry entry)
+ for (int i = 0; i < sequenceFeatures.length; i++)
{
- if(pdbIds == null)
- pdbIds = new Vector();
+ if (sequenceFeatures[i].equals(sf))
+ {
+ return;
+ }
+ }
- pdbIds.addElement(entry);
+ 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;
}
- /**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
- */
- public void setPDBId(Vector id)
+ int index = 0;
+ for (index = 0; index < sequenceFeatures.length; index++)
{
- pdbIds = id;
+ if (sequenceFeatures[index].equals(sf))
+ {
+ break;
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId()
+ if (index == sequenceFeatures.length)
{
- return pdbIds;
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDisplayId(boolean jvsuffix)
+ int sfLength = sequenceFeatures.length;
+ if (sfLength < 2)
+ {
+ sequenceFeatures = null;
+ }
+ else
{
- StringBuffer result = new StringBuffer(name);
- if (jvsuffix)
+ SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
+ System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+ if (index < sfLength)
{
- result.append("/" + start + "-" + end);
+ System.arraycopy(sequenceFeatures, index + 1, temp, index,
+ sequenceFeatures.length - index - 1);
}
- return result.toString();
+ sequenceFeatures = temp;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name)
+ /**
+ * 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
+ */
+ 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)
{
- this.name = name;
- this.parseId();
+ seq = seq.getDatasetSequence();
+ features = ((Sequence) seq).sequenceFeatures;
}
+ return features;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName()
+ public void addPDBId(PDBEntry entry)
+ {
+ if (pdbIds == null)
{
- return this.name;
+ pdbIds = new Vector<PDBEntry>();
}
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- */
- public void setStart(int start)
+ if (pdbIds.contains(entry))
{
- this.start = start;
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStart()
+ else
{
- return this.start;
+ pdbIds.addElement(entry);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
- */
- public void setEnd(int end)
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
{
- this.end = end;
+ oldEntry.setFile(newEntry.getFile());
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setPDBId(Vector<PDBEntry> id)
+ {
+ pdbIds = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Vector<PDBEntry> getAllPDBEntries()
+ {
+ return pdbIds;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayId(boolean jvsuffix)
+ {
+ StringBuffer result = new StringBuffer(name);
+ if (jvsuffix)
{
- return this.end;
+ result.append("/" + start + "-" + end);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getLength()
+ 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;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#getSequence(int, int)
+ */
+ public char[] getSequence(int start, int end)
+ {
+ if (start < 0)
{
- return this.sequence.length();
+ start = 0;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setSequence(String seq)
+ // JBPNote - left to user to pad the result here (TODO:Decide on this
+ // policy)
+ if (start >= sequence.length)
{
- this.sequence = seq;
- checkValidRange();
+ return new char[0];
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence()
+ if (end >= sequence.length)
{
- return this.sequence;
+ end = sequence.length;
}
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence(int start, int end)
- {
- // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
- if (start >= sequence.length())
- {
- return "";
- }
+ char[] reply = new char[end - start];
+ System.arraycopy(sequence, start, reply, 0, end - start);
- if (end >= sequence.length())
- {
- end = sequence.length();
- }
+ return reply;
+ }
- return this.sequence.substring(start, end);
- }
- /**
- * 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;
- String seq = getSequence(start, end);
- if (seq=="")
- 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.setDatasetSequence(getDatasetSequence());
- return nseq;
- }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i)
- {
- if (i < sequence.length())
- {
- return sequence.charAt(i);
- }
- else
- {
- return ' ';
- }
+ @Override
+ public SequenceI getSubSequence(int start, int end)
+ {
+ if (start < 0)
+ {
+ start = 0;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
- */
- public void setDescription(String desc)
+ char[] seq = getSequence(start, end);
+ if (seq.length == 0)
{
- this.description = desc;
+ return null;
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription()
+ 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
{
- return this.description;
+ nseq.setDatasetSequence(this);
}
+ return nseq;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int findIndex(int pos)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getCharAt(int i)
+ {
+ if (i < sequence.length)
+ {
+ return sequence[i];
+ }
+ else
{
- // returns the alignment position for a residue
- int j = start;
- int i = 0;
+ return ' ';
+ }
+ }
- while ((i < sequence.length()) && (j <= end) && (j <= pos))
- {
- if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
- {
- j++;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
+ */
+ public void setDescription(String desc)
+ {
+ this.description = desc;
+ }
- i++;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription()
+ {
+ return this.description;
+ }
- if ((j == end) && (j < pos))
- {
- return end + 1;
- }
- else
- {
- return i;
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.SequenceI#findIndex(int)
+ */
+ 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++;
}
- /**
- * 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)
+ if ((j == end) && (j < pos))
{
- int j = 0;
- int pos = start;
- int seqlen=sequence.length();
- while ((j < i) && (j < seqlen))
- {
- if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
- {
- pos++;
- }
+ return end + 1;
+ }
+ else
+ {
+ return i;
+ }
+ }
- j++;
- }
+ @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++;
+ }
- return pos;
+ j++;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int[] gapMap()
- {
- // Returns an int array giving the position of each residue in the sequence in the alignment
- String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
- int[] map = new int[seq.length()];
- int j = 0;
- int p = 0;
+ return pos;
+ }
- while (j < sequence.length())
- {
- if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
- {
- map[p++] = j;
- }
+ /**
+ * 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;
- j++;
- }
+ while (j < sequence.length)
+ {
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ map[p++] = j;
+ }
- return map;
+ j++;
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i)
+ 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))
{
- if (i >= sequence.length())
- {
- return;
- }
+ map[j] = pos;
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ pos++;
+ }
- sequence = sequence.substring(0, i) + sequence.substring(i + 1);
+ j++;
}
+ return map;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void deleteChars(int i, int j)
+ @Override
+ public List<int[]> getInsertions()
+ {
+ ArrayList<int[]> map = new ArrayList<int[]>();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
{
- if (i >= sequence.length())
- {
- return;
- }
-
- if (j >= sequence.length())
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
{
- sequence = sequence.substring(0, i);
+ lastj = j;
}
- else
+ }
+ else
+ {
+ if (lastj != -1)
{
- sequence = sequence.substring(0, i) + sequence.substring(j);
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
}
+ }
+ j++;
}
+ if (lastj != -1)
+ {
+ map.add(new int[] { lastj, j - 1 });
+ lastj = -1;
+ }
+ return map;
+ }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- * @param chop DOCUMENT ME!
- */
- public void insertCharAt(int i, char c)
+ @Override
+ public void deleteChars(int i, int j)
+ {
+ int newstart = start, newend = end;
+ if (i >= sequence.length || i < 0)
{
- String tmp = new String(sequence);
+ return;
+ }
- if (i < sequence.length())
+ 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)
{
- sequence = tmp.substring(0, i) + String.valueOf(c) +
- tmp.substring(i);
+ newend--;
}
else
{
- // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
- char[] ch = new char[(1 + i) - sequence.length()];
-
- for (int j = 0, k = ch.length; j < k; j++)
- ch[j] = c;
-
- sequence = tmp + String.valueOf(ch);
+ 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
+ }
+ }
}
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c)
+ // deletion occured in the middle of the sequence
+ if (createNewDs && this.datasetSequence != null)
{
- this.color = c;
+ // 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!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor()
- {
- return color;
- }
+ @Override
+ public void insertCharAt(int i, int length, char c)
+ {
+ char[] tmp = new char[sequence.length + length];
- public String getVamsasId()
+ if (i >= sequence.length)
{
- return vamsasId;
+ System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+ i = sequence.length;
}
-
- public void setVamsasId(String id)
+ else
{
- vamsasId = id;
+ System.arraycopy(sequence, 0, tmp, 0, i);
}
- public void setDBRef(DBRefEntry [] dbref)
+ int index = i;
+ while (length > 0)
{
- dbrefs = dbref;
+ tmp[index++] = c;
+ length--;
}
- public DBRefEntry [] getDBRef()
+ if (i < sequence.length)
{
- return dbrefs;
+ System.arraycopy(sequence, i, tmp, index, sequence.length - i);
}
- public void addDBRef(DBRefEntry entry)
- {
- if(dbrefs == null)
- dbrefs = new DBRefEntry[0];
+ sequence = tmp;
+ }
- DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
- System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+ @Override
+ public void insertCharAt(int i, char c)
+ {
+ insertCharAt(i, 1, c);
+ }
- temp[temp.length-1] = entry;
+ @Override
+ public String getVamsasId()
+ {
+ return vamsasId;
+ }
- dbrefs = temp;
- }
+ @Override
+ public void setVamsasId(String id)
+ {
+ vamsasId = id;
+ }
- public void setDatasetSequence(SequenceI seq)
+ @Override
+ public void setDBRef(DBRefEntry[] dbref)
+ {
+ dbrefs = dbref;
+ }
+
+ @Override
+ public DBRefEntry[] getDBRef()
+ {
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
{
- datasetSequence = seq;
+ return datasetSequence.getDBRef();
}
+ return dbrefs;
+ }
- public SequenceI getDatasetSequence()
+ @Override
+ public void addDBRef(DBRefEntry entry)
+ {
+ if (dbrefs == null)
{
- return datasetSequence;
+ dbrefs = new DBRefEntry[0];
}
- public AlignmentAnnotation [] getAnnotation()
+ int i, iSize = dbrefs.length;
+
+ for (i = 0; i < iSize; i++)
{
- if(annotation==null)
- return null;
+ 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;
+ }
+ }
- AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
- for(int r = 0; r<ret.length; r++)
- ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+ DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, iSize);
+ temp[temp.length - 1] = entry;
- return ret;
- }
+ dbrefs = temp;
+ }
- public void addAlignmentAnnotation(AlignmentAnnotation annotation)
- {
- if(this.annotation==null)
- this.annotation = new Vector();
+ @Override
+ public void setDatasetSequence(SequenceI seq)
+ {
+ datasetSequence = seq;
+ }
- this.annotation.addElement( annotation );
- }
+ @Override
+ public SequenceI getDatasetSequence()
+ {
+ return datasetSequence;
+ }
- public SequenceGroup getHiddenSequences()
+ @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)
{
- return hiddenSequences;
+ this.annotation = new Vector<AlignmentAnnotation>();
}
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
+ }
+ annotation.setSequenceRef(this);
+ }
- public void addHiddenSequence(SequenceI seq)
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ if (this.annotation != null)
{
- if(hiddenSequences==null)
+ this.annotation.removeElement(annotation);
+ if (this.annotation.size() == 0)
{
- hiddenSequences = new SequenceGroup();
+ this.annotation = null;
}
- hiddenSequences.addSequence(seq, false);
}
+ }
- public void showHiddenSequence(SequenceI seq)
+ /**
+ * test if this is a valid candidate for another sequence's dataset sequence.
+ *
+ */
+ private boolean isValidDatasetSequence()
+ {
+ if (datasetSequence != null)
{
- hiddenSequences.deleteSequence(seq, false);
- if (hiddenSequences.getSize(false) < 1)
+ return false;
+ }
+ for (int i = 0; i < sequence.length; i++)
+ {
+ if (jalview.util.Comparison.isGap(sequence[i]))
{
- hiddenSequences = null;
+ return false;
}
}
+ return true;
+ }
- public void changeCase(boolean toUpper, int start, int end)
+ @Override
+ public SequenceI deriveSequence()
+ {
+ SequenceI seq = new Sequence(this);
+ if (datasetSequence != null)
{
- StringBuffer newSeq = new StringBuffer();
+ // 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;
+ }
- if(end>sequence.length())
- end = sequence.length();
+ /*
+ * (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);
+ datasetSequence.setPDBId(getAllPDBEntries());
+ setPDBId(null);
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ 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;
+ }
- if (start > 0)
+ /*
+ * (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++)
{
- newSeq.append(sequence.substring(0, start));
+ if (annotations[i] != null)
+ {
+ addAlignmentAnnotation(annotations[i]);
+ }
}
+ }
+ }
- if (toUpper)
- newSeq.append(sequence.substring(start, end).toUpperCase());
- else
- newSeq.append(sequence.substring(start, end).toLowerCase());
+ @Override
+ public AlignmentAnnotation[] getAnnotation(String label)
+ {
+ if (annotation == null || annotation.size() == 0)
+ {
+ return null;
+ }
- if (end < sequence.length())
- newSeq.append(sequence.substring(end));
+ 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;
+ }
- sequence = newSeq.toString();
+ @Override
+ public boolean updatePDBIds()
+ {
+ if (datasetSequence != null)
+ {
+ // TODO: could merge DBRefs
+ return datasetSequence.updatePDBIds();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return false;
+ }
+ Vector newpdb = new Vector();
+ for (int i = 0; i < dbrefs.length; i++)
+ {
+ if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+ {
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setId(dbrefs[i].getAccessionId());
+ if (pdbIds == null || pdbIds.size() == 0)
+ {
+ newpdb.addElement(pdbe);
+ }
+ else
+ {
+ Enumeration en = pdbIds.elements();
+ boolean matched = false;
+ while (!matched && en.hasMoreElements())
+ {
+ PDBEntry anentry = (PDBEntry) en.nextElement();
+ if (anentry.getId().equals(pdbe.getId()))
+ {
+ matched = true;
+ }
+ }
+ if (!matched)
+ {
+ newpdb.addElement(pdbe);
+ }
+ }
+ }
}
+ if (newpdb.size() > 0)
+ {
+ Enumeration en = newpdb.elements();
+ while (en.hasMoreElements())
+ {
+ addPDBId((PDBEntry) en.nextElement());
+ }
+ return true;
+ }
+ return false;
+ }
- public void toggleCase(int start, int end)
+ @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)
{
- StringBuffer newSeq = new StringBuffer();
- if(end>sequence.length())
- end = sequence.length();
+ 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]);
+ }
+ }
+ }
+ }
- if (start > 0)
- {
- newSeq.append(sequence.substring(0, start));
- }
+ // 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.getDBRef();
+ 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);
+ }
+ }
+ }
- char nextChar;
- for(int c=start; c<end; c++)
- {
- nextChar = sequence.charAt(c);
- if(Character.isLetter(nextChar))
- {
- if(Character.isUpperCase(nextChar))
- nextChar = Character.toLowerCase(nextChar);
- else
- nextChar = Character.toUpperCase(nextChar);
- }
+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ 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)
+ */
+ public void setIndex(int value)
+ {
+ index = value;
+ }
- newSeq.append(nextChar);
- }
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
- if (end < sequence.length())
- newSeq.append(sequence.substring(end));
+ public RNA getRNA()
+ {
+ return rna;
+ }
- sequence = newSeq.toString();
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ 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;
+ }
+
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
- public SequenceI getSubSequence(int start)
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
{
- int e=getLength();
- if (start>=e)
+ if (getDatasetSequence() == null
+ || getDatasetSequence().getAllPDBEntries() == null)
+ {
return null;
- return getSubSequence(start, getLength());
+ }
+ List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff