X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=257c8949231bc52150b23f7b99ee6177e85d9718;hb=bdc3ba419ca938fef5eedee9c3078ae1940dcdd4;hp=eda5684502de4e136bc596c68c85e045aa4cba00;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index eda5684..257c894 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,26 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-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;
-import jalview.analysis.*;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
/**
*
@@ -29,7 +37,7 @@ import jalview.analysis.*;
* @author $author$
* @version $Revision$
*/
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
{
SequenceI datasetSequence;
@@ -43,33 +51,42 @@ public class Sequence implements SequenceI
int end;
- Vector pdbIds;
+ 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;
+ Vector annotation;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /**
+ * 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
+ * display name string
* @param sequence
- * string to form a possibly gapped sequence out of
+ * string to form a possibly gapped sequence out of
* @param start
- * first position of non-gap residue in the sequence
+ * first position of non-gap residue in the sequence
* @param end
- * last position of ungapped residues (nearly always only used
- * for display purposes)
+ * last position of ungapped residues (nearly always only used for
+ * display purposes)
*/
public Sequence(String name, String sequence, int start, int end)
{
@@ -104,7 +121,7 @@ public class Sequence implements SequenceI
.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signiature?
+ // Does sequence have the /start-end signature?
if (limitrx.search(name))
{
name = limitrx.left();
@@ -117,7 +134,8 @@ public class Sequence implements SequenceI
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++)
@@ -132,7 +150,10 @@ public class Sequence implements SequenceI
endRes += start - 1;
}
- this.end = endRes;
+ if (end < endRes)
+ {
+ end = endRes;
+ }
}
}
@@ -141,9 +162,9 @@ public class Sequence implements SequenceI
* Creates a new Sequence object.
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param sequence
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public Sequence(String name, String sequence)
{
@@ -156,7 +177,7 @@ public class Sequence implements SequenceI
* reference.
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public Sequence(SequenceI seq)
{
@@ -169,9 +190,9 @@ public class Sequence implements SequenceI
* annotation that is present in the given annotation array.
*
* @param seq
- * the sequence to be copied
+ * the sequence to be copied
* @param alAnnotation
- * an array of annotation including some associated with seq
+ * an array of annotation including some associated with seq
*/
public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
{
@@ -235,7 +256,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param v
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features)
{
@@ -306,34 +327,60 @@ public class Sequence implements SequenceI
}
/**
- * DOCUMENT ME!
+ * 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 DOCUMENT ME!
+ * @return
*/
public SequenceFeature[] getSequenceFeatures()
{
- return sequenceFeatures;
+ 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;
}
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
{
- pdbIds = new Vector();
+ pdbIds = new Vector();
}
- if (!pdbIds.contains(entry))
+ if (pdbIds.contains(entry))
+ {
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+ }
+ else
{
pdbIds.addElement(entry);
}
}
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
+ {
+ oldEntry.setFile(newEntry.getFile());
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param id
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector id)
{
pdbIds = id;
}
@@ -343,7 +390,8 @@ public class Sequence implements SequenceI
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector getPDBId()
{
return pdbIds;
}
@@ -368,7 +416,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setName(String name)
{
@@ -390,7 +438,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setStart(int start)
{
@@ -411,7 +459,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setEnd(int end)
{
@@ -442,7 +490,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSequence(String seq)
{
@@ -473,7 +521,9 @@ public class Sequence implements SequenceI
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)
@@ -492,16 +542,7 @@ public class Sequence implements SequenceI
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)
@@ -533,7 +574,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -553,7 +594,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param desc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDescription(String desc)
{
@@ -570,20 +611,17 @@ public class Sequence implements SequenceI
return this.description;
}
- /**
- * Return the alignment position for a sequence position
- *
- * @param pos
- * lying from start to end
+ /*
+ * (non-Javadoc)
*
- * @return aligned position of residue pos
+ * @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]))
@@ -604,14 +642,7 @@ public class Sequence implements SequenceI
}
}
- /**
- * 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;
@@ -658,11 +689,7 @@ public class Sequence implements SequenceI
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#findPositionMap()
- */
+ @Override
public int[] findPositionMap()
{
int map[] = new int[sequence.length];
@@ -682,11 +709,43 @@ public class Sequence implements SequenceI
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
+ @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;
@@ -695,20 +754,12 @@ public class Sequence implements SequenceI
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);
- }
+ 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)
@@ -719,7 +770,11 @@ public class Sequence implements SequenceI
}
else
{
- int sindex = findIndex(start) - 1;
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
if (sindex == s)
{
// delete characters including start of sequence
@@ -729,7 +784,11 @@ public class Sequence implements SequenceI
else
{
// delete characters after start.
- int eindex = findIndex(end) - 1;
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
if (eindex < j)
{
// delete characters at end of sequence
@@ -761,16 +820,7 @@ public class Sequence implements SequenceI
sequence = tmp;
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- * @param chop
- * DOCUMENT ME!
- */
+ @Override
public void insertCharAt(int i, int length, char c)
{
char[] tmp = new char[sequence.length + length];
@@ -800,26 +850,31 @@ public class Sequence implements SequenceI
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
@@ -830,6 +885,7 @@ public class Sequence implements SequenceI
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
@@ -862,40 +918,43 @@ public class Sequence implements SequenceI
dbrefs = temp;
}
+ @Override
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
+ @Override
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
+ @Override
public AlignmentAnnotation[] getAnnotation()
{
- if (annotation == null)
- {
- return null;
- }
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
- AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
- for (int r = 0; r < ret.length; r++)
- {
- ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
- }
- return ret;
+ @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();
+ this.annotation = new Vector();
+ }
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
}
-
- this.annotation.addElement(annotation);
annotation.setSequenceRef(this);
}
@@ -905,7 +964,9 @@ public class Sequence implements SequenceI
{
this.annotation.removeElement(annotation);
if (this.annotation.size() == 0)
+ {
this.annotation = null;
+ }
}
}
@@ -929,11 +990,7 @@ public class Sequence implements SequenceI
return true;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deriveSequence()
- */
+ @Override
public SequenceI deriveSequence()
{
SequenceI seq = new Sequence(this);
@@ -984,6 +1041,17 @@ public class Sequence implements SequenceI
datasetSequence.setPDBId(getPDBId());
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;
}
@@ -991,8 +1059,9 @@ public class Sequence implements SequenceI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
- * annotations)
+ * @see
+ * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+ * annotations)
*/
public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
{
@@ -1005,16 +1074,14 @@ public class Sequence implements SequenceI
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)
- */
+ @Override
public AlignmentAnnotation[] getAnnotation(String label)
{
if (annotation == null || annotation.size() == 0)
@@ -1047,6 +1114,7 @@ public class Sequence implements SequenceI
return anns;
}
+ @Override
public boolean updatePDBIds()
{
if (datasetSequence != null)
@@ -1100,12 +1168,7 @@ public class Sequence implements SequenceI
return false;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
- * jalview.datamodel.Mapping)
- */
+ @Override
public void transferAnnotation(SequenceI entry, Mapping mp)
{
if (datasetSequence != null)
@@ -1169,4 +1232,55 @@ public class Sequence implements SequenceI
}
}
+ /**
+ * @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;
+ }
+
}