X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0652fb5fa0951b268c3a6a5720c2dc6afdf8bc97;hb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;hp=eda5684502de4e136bc596c68c85e045aa4cba00;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index eda5684..0652fb5 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,26 +1,33 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 jalview.analysis.AlignSeq;
+
+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;
/**
*
@@ -49,27 +56,36 @@ public class Sequence implements SequenceI
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
*/
- Vector annotation;
+ int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** 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)
{
@@ -117,7 +133,8 @@ 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 +149,10 @@ public class Sequence implements SequenceI
endRes += start - 1;
}
- this.end = endRes;
+ if (end < endRes)
+ {
+ end = endRes;
+ }
}
}
@@ -141,9 +161,9 @@ 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 +176,7 @@ public class Sequence implements SequenceI
* reference.
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public Sequence(SequenceI seq)
{
@@ -169,9 +189,9 @@ 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 +255,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param v
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSequenceFeatures(SequenceFeature[] features)
{
@@ -331,7 +351,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param id
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setPDBId(Vector id)
{
@@ -368,7 +388,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setName(String name)
{
@@ -390,7 +410,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setStart(int start)
{
@@ -411,7 +431,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setEnd(int end)
{
@@ -442,7 +462,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSequence(String seq)
{
@@ -473,7 +493,9 @@ 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 +514,7 @@ 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 +546,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -553,7 +566,7 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param desc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDescription(String desc)
{
@@ -570,20 +583,17 @@ 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 +614,7 @@ 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;
@@ -701,6 +704,7 @@ public class Sequence implements SequenceI
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
+ j = sequence.length;
}
else
{
@@ -709,6 +713,9 @@ public class Sequence implements SequenceI
System.arraycopy(sequence, j, tmp, i, sequence.length - j);
}
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)
@@ -765,11 +772,11 @@ public class Sequence implements SequenceI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param chop
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void insertCharAt(int i, int length, char c)
{
@@ -872,30 +879,40 @@ public class Sequence implements SequenceI
return datasetSequence;
}
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation()
{
- if (annotation == null)
- {
- return null;
- }
-
- AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
- for (int r = 0; r < ret.length; r++)
- {
- ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
- }
+ return annotation == null ? null : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
+ }
- return ret;
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
+ @Override
+ public boolean hasAnnotation(AlignmentAnnotation ann)
+ {
+ return annotation == null ? false : annotation.contains(ann);
}
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
{
this.annotation = new Vector();
}
-
- this.annotation.addElement(annotation);
+ if (!this.annotation.contains(annotation))
+ {
+ this.annotation.addElement(annotation);
+ }
annotation.setSequenceRef(this);
}
@@ -905,7 +922,9 @@ public class Sequence implements SequenceI
{
this.annotation.removeElement(annotation);
if (this.annotation.size() == 0)
+ {
this.annotation = null;
+ }
}
}
@@ -984,6 +1003,17 @@ 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 +1021,9 @@ 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)
{
@@ -1005,7 +1036,9 @@ public class Sequence implements SequenceI
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] != null)
+ {
addAlignmentAnnotation(annotations[i]);
+ }
}
}
}
@@ -1103,8 +1136,9 @@ public class Sequence implements SequenceI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
- * jalview.datamodel.Mapping)
+ * @see
+ * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
+ * jalview.datamodel.Mapping)
*/
public void transferAnnotation(SequenceI entry, Mapping mp)
{
@@ -1169,4 +1203,60 @@ 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;
+ }
+
+ /**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source) and label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ */
+ @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;
+ }
+
}