X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0267f45b5fdba865e0be04dedc7e4b137f336b1f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=1c33ab1462ac7cbe663fda0cb1dd24046c980f8c;hpb=6a91de2e48559da8034762a7d77a143435362029;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 1c33ab1..0267f45 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,63 +1,91 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
+import jalview.analysis.AlignSeq;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
-import jalview.analysis.*;
+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
- implements SequenceI
+public class Sequence implements SequenceI
{
SequenceI datasetSequence;
+
String name;
- private char [] sequence;
+
+ 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;
+ RNA rna;
- /** array of seuqence features - may not be null for a valid sequence object */
- public SequenceFeature[] sequenceFeatures;
+ /**
+ * 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)
+ *
+ * @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)
{
@@ -69,7 +97,7 @@ public class Sequence
checkValidRange();
}
- public Sequence(String name, char [] sequence, int start, int end)
+ public Sequence(String name, char[] sequence, int start, int end)
{
this.name = name;
this.sequence = sequence;
@@ -80,15 +108,16 @@ public class Sequence
}
com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
- "[0-9]{1,}$");
+ "[/][0-9]{1,}[-][0-9]{1,}$");
+
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
void parseId()
{
- if (name==null)
+ if (name == null)
{
- System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err
+ .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
// Does sequence have the /start-end signiature?
@@ -97,19 +126,20 @@ public class Sequence
name = limitrx.left();
endrx.search(limitrx.stringMatched());
setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
- endrx.matchedFrom() - 1)));
+ endrx.matchedFrom() - 1)));
setEnd(Integer.parseInt(endrx.stringMatched()));
}
}
void checkValidRange()
{
- if (end < 1)
+ // 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] ))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
endRes++;
}
@@ -119,16 +149,21 @@ public class Sequence
endRes += start - 1;
}
- this.end = endRes;
+ if (end < endRes)
+ {
+ end = endRes;
+ }
}
}
/**
* Creates a new Sequence object.
- *
- * @param name DOCUMENT ME!
- * @param sequence DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ * @param sequence
+ * DOCUMENT ME!
*/
public Sequence(String name, String sequence)
{
@@ -136,53 +171,63 @@ public class Sequence
}
/**
- * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
- * but inherits any existing dataset sequence reference.
- * @param seq DOCUMENT ME!
+ * 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
+ * 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());
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
description = seq.getDescription();
- if (seq.getSequenceFeatures()!=null) {
+ if (seq.getSequenceFeatures() != null)
+ {
SequenceFeature[] sf = seq.getSequenceFeatures();
- for (int i=0; i= sequence.length)
{
return new char[0];
@@ -458,26 +508,20 @@ public class Sequence
end = sequence.length;
}
- char [] reply = new char[end-start];
- System.arraycopy(sequence, start, reply, 0, end-start);
+ 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
- */
+ @Override
public SequenceI getSubSequence(int start, int end)
{
if (start < 0)
{
start = 0;
}
- char [] seq = getSequence(start, end);
+ char[] seq = getSequence(start, end);
if (seq.length == 0)
{
return null;
@@ -487,22 +531,23 @@ public class Sequence
// JBPNote - this is an incomplete copy.
SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
nseq.setDescription(description);
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
- nseq.setDatasetSequence(datasetSequence);
+ nseq.setDatasetSequence(datasetSequence);
}
else
{
- nseq.setDatasetSequence(this);
+ nseq.setDatasetSequence(this);
}
return nseq;
}
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public char getCharAt(int i)
@@ -519,8 +564,9 @@ public class Sequence
/**
* DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
*/
public void setDescription(String desc)
{
@@ -529,7 +575,7 @@ public class Sequence
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getDescription()
@@ -537,20 +583,18 @@ public class Sequence
return this.description;
}
- /**
- * Return the alignment position for a sequence position
- *
- * @param pos lying from start to end
- *
- * @return aligned position of residue pos
+ /*
+ * (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;
-
- while ( (i < sequence.length) && (j <= end) && (j <= pos))
+ // 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]))
{
@@ -560,7 +604,7 @@ public class Sequence
i++;
}
- if ( (j == end) && (j < pos))
+ if ((j == end) && (j < pos))
{
return end + 1;
}
@@ -570,21 +614,15 @@ public class Sequence
}
}
- /**
- * 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
- */
+ @Override
public int findPosition(int i)
{
int j = 0;
int pos = start;
int seqlen = sequence.length;
- while ( (j < i) && (j < seqlen))
+ while ((j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap( sequence[j] ))
+ if (!jalview.util.Comparison.isGap(sequence[j]))
{
pos++;
}
@@ -596,14 +634,16 @@ public class Sequence
}
/**
- * 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
+ * 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));
+ 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;
@@ -621,31 +661,89 @@ public class Sequence
return map;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
+ @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;
+ int newstart = start, newend = end;
if (i >= sequence.length)
{
return;
}
- char [] tmp;
+ char[] tmp;
if (j >= sequence.length)
{
tmp = new char[i];
- System.arraycopy(sequence,0,tmp,0,i);
+ System.arraycopy(sequence, 0, tmp, 0, i);
+ j = sequence.length;
}
else
{
- tmp = new char[sequence.length-j+i];
- System.arraycopy(sequence,0,tmp,0,i);
- System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+ 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;
+ boolean createNewDs = false;
+ // TODO: take a look at the new dataset creation validation method below -
+ // this could become time comsuming for large sequences - consider making it
+ // more efficient
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@ -653,26 +751,33 @@ public class Sequence
if (createNewDs)
{
newend--;
- } else {
- int sindex = findIndex(start)-1;
- if (sindex==s)
+ }
+ else
{
- // 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= sequence.length)
{
@@ -709,51 +807,61 @@ public class Sequence
i = sequence.length;
}
else
- {
+ {
System.arraycopy(sequence, 0, tmp, 0, i);
- }
-
+ }
int index = i;
while (length > 0)
{
- tmp[ index++ ] = c;
+ tmp[index++] = c;
length--;
}
if (i < sequence.length)
{
- System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+ 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 setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
+ @Override
public DBRefEntry[] getDBRef()
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRef();
+ }
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
@@ -763,13 +871,13 @@ public class Sequence
int i, iSize = dbrefs.length;
- for(i=0; i0)
+ if (newpdb.size() > 0)
{
Enumeration en = newpdb.elements();
while (en.hasMoreElements())
@@ -1003,6 +1144,117 @@ public class Sequence
return false;
}
-}
+ @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.getPDBId() != null)
+ {
+ Enumeration e = entry.getPDBId().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);
+ }
+ }
+ }
+
+ /**
+ * @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;
+ }
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ 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;
+ }
+
+}