X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=01d3d8d626f1eb53767631146123f43687d57bdd;hb=f21eb611044169a07a7d4c6e2f69dd772fa7c872;hp=271374ff0dc2380c4e8165642514fe6605e0f96d;hpb=b1c9b42f08c639868c2509dffacdf29f299c5f0d;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 271374f..01d3d8d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,30 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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
+ * 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 .
+ *
+ * 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 java.util.*;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
/**
* @author JimP
- *
+ *
*/
public class Alignment implements AlignmentI
{
@@ -77,7 +87,7 @@ public class Alignment implements AlignmentI
/**
* Make an alignment from an array of Sequences.
- *
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
@@ -87,7 +97,7 @@ public class Alignment implements AlignmentI
/**
* Make a new alignment from an array of SeqCigars
- *
+ *
* @param seqs
* SeqCigar[]
*/
@@ -103,19 +113,19 @@ public class Alignment implements AlignmentI
* compactAlignment does not contain hidden regions. JBPNote - must also check
* that compactAlignment resolves to a set of SeqCigars - or construct them
* appropriately.
- *
+ *
* @param compactAlignment
* CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error("Alignment(CigarArray) not yet implemented");
+ throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -137,7 +147,9 @@ public class Alignment implements AlignmentI
public SequenceI[] getSequencesArray()
{
if (sequences == null)
+ {
return null;
+ }
synchronized (sequences)
{
return sequences.toArray(new SequenceI[sequences.size()]);
@@ -146,10 +158,10 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param i
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -167,7 +179,7 @@ public class Alignment implements AlignmentI
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
@Override
@@ -201,12 +213,14 @@ public class Alignment implements AlignmentI
}
}
if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
+ }
}
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
@Override
@@ -222,7 +236,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -235,7 +249,9 @@ public class Alignment implements AlignmentI
public void finalize()
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
dataset = null;
sequences = null;
@@ -258,7 +274,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param s
* DOCUMENT ME!
*/
@@ -270,7 +286,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param i
* DOCUMENT ME!
*/
@@ -289,7 +305,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
@@ -312,7 +328,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
@@ -370,7 +386,7 @@ public class Alignment implements AlignmentI
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
@@ -378,7 +394,7 @@ public class Alignment implements AlignmentI
/**
* remove any annotation that references gp
- *
+ *
* @param gp
* (if null, removes all group associated annotation)
*/
@@ -445,6 +461,10 @@ public class Alignment implements AlignmentI
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
groups.clear();
}
}
@@ -459,6 +479,7 @@ public class Alignment implements AlignmentI
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
@@ -472,7 +493,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
@Override
@@ -483,7 +504,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
@@ -555,7 +576,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
@Override
@@ -578,7 +599,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@@ -600,7 +621,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -611,7 +632,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -632,7 +653,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @param gc
* DOCUMENT ME!
*/
@@ -652,7 +673,7 @@ public class Alignment implements AlignmentI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
@@ -663,7 +684,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#isAligned()
*/
@Override
@@ -674,7 +695,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
@Override
@@ -701,7 +722,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@@ -739,7 +760,9 @@ public class Alignment implements AlignmentI
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
@@ -755,7 +778,7 @@ public class Alignment implements AlignmentI
/**
* remove any object references associated with this annotation
- *
+ *
* @param aa
*/
private void unhookAnnotation(AlignmentAnnotation aa)
@@ -773,7 +796,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@@ -785,7 +808,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
@@ -935,6 +958,27 @@ public class Alignment implements AlignmentI
else if (dataset == null && data != null)
{
dataset = data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
}
dataset.addAlignmentRef();
}
@@ -1005,7 +1049,7 @@ public class Alignment implements AlignmentI
/**
* Justify the sequences to the left or right by deleting and inserting gaps
* before the initial residue or after the terminal residue
- *
+ *
* @param right
* true if alignment padded to right, false to justify to left
* @return true if alignment was changed
@@ -1135,7 +1179,9 @@ public class Alignment implements AlignmentI
public void setProperty(Object key, Object value)
{
if (alignmentProperties == null)
+ {
alignmentProperties = new Hashtable();
+ }
alignmentProperties.put(key, value);
}
@@ -1144,9 +1190,13 @@ public class Alignment implements AlignmentI
public Object getProperty(Object key)
{
if (alignmentProperties != null)
+ {
return alignmentProperties.get(key);
+ }
else
+ {
return null;
+ }
}
@Override
@@ -1159,7 +1209,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
@@ -1168,7 +1218,9 @@ public class Alignment implements AlignmentI
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
+ {
return;
+ }
if (codonFrameList == null)
{
codonFrameList = new AlignedCodonFrame[]
@@ -1183,7 +1235,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
@Override
@@ -1194,7 +1246,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
@@ -1202,15 +1254,21 @@ public class Alignment implements AlignmentI
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
+ {
return null;
+ }
Vector cframes = new Vector();
for (int f = 0; f < codonFrameList.length; f++)
{
if (codonFrameList[f].involvesSequence(seq))
+ {
cframes.addElement(codonFrameList[f]);
+ }
}
if (cframes.size() == 0)
+ {
return null;
+ }
AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
cframes.copyInto(cfr);
return cfr;
@@ -1218,7 +1276,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
@Override
@@ -1229,7 +1287,7 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
@@ -1237,7 +1295,9 @@ public class Alignment implements AlignmentI
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
+ {
return false;
+ }
boolean removed = false;
int i = 0, iSize = codonFrameList.length;
while (i < iSize)
@@ -1381,17 +1441,21 @@ public class Alignment implements AlignmentI
@Override
public AlignmentAnnotation findOrCreateAnnotation(String name,
- String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
{
- assert(name!=null);
- for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ assert (name != null);
+ if (annotations != null)
{
- if (annot.autoCalculated == autoCalc
- && (name.equals(annot.label))
- && (calcId==null || annot.getCalcId().equals(calcId))
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
{
- return annot;
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef
+ && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
}
}
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
@@ -1425,6 +1489,27 @@ public class Alignment implements AlignmentI
return aa;
}
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ */
+ @Override
+ public Iterable findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
@Override
public void moveSelectedSequencesByOne(SequenceGroup sg,
Map map, boolean up)
@@ -1476,4 +1561,70 @@ public class Alignment implements AlignmentI
}
}
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+
+ private SequenceI seqrep=null;
+
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
}