X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=dec4fa433dac9c8d4562233b568650944049b414;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=f045555ad991e3090f470465343fddcce6cd02ad;hpb=cf8e95cb72c90c73963816ca71856ba1ab7e1d99;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index f045555..dec4fa4 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,28 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- *
+ * 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 java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
-import jalview.analysis.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* Collects a set contiguous ranges on a set of sequences
@@ -30,7 +38,7 @@ import jalview.schemes.*;
* @author $author$
* @version $Revision$
*/
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
{
String groupName;
@@ -54,7 +62,7 @@ public class SequenceGroup
/**
* group members
*/
- private Vector sequences = new Vector();
+ private List sequences = new ArrayList();
/**
* representative sequence for this group (if any)
@@ -93,6 +101,11 @@ public class SequenceGroup
private boolean showSequenceLogo = false;
/**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
+
+ /**
* @return the includeAllConsSymbols
*/
public boolean isShowSequenceLogo()
@@ -122,7 +135,7 @@ public class SequenceGroup
* @param end
* last column of group
*/
- public SequenceGroup(Vector sequences, String groupName,
+ public SequenceGroup(List sequences, String groupName,
ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
boolean colourText, int start, int end)
{
@@ -146,13 +159,8 @@ public class SequenceGroup
{
if (seqsel != null)
{
- sequences = new Vector();
- Enumeration sq = seqsel.sequences.elements();
- while (sq.hasMoreElements())
- {
- sequences.addElement(sq.nextElement());
- }
- ;
+ sequences = new ArrayList();
+ sequences.addAll(seqsel.sequences);
if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
@@ -164,7 +172,9 @@ public class SequenceGroup
endRes = seqsel.endRes;
cs = seqsel.cs;
if (seqsel.description != null)
+ {
description = new String(seqsel.description);
+ }
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
idColour = seqsel.idColour;
@@ -224,7 +234,9 @@ public class SequenceGroup
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
@@ -280,29 +292,35 @@ public class SequenceGroup
return eres;
}
- public Vector getSequences(Hashtable hiddenReps)
+ @Override
+ public List getSequences()
+ {
+ return sequences;
+ }
+
+ @Override
+ public List getSequences(
+ Map hiddenReps)
{
if (hiddenReps == null)
{
+ // TODO: need a synchronizedCollection here ?
return sequences;
}
else
{
- Vector allSequences = new Vector();
- SequenceI seq, seq2;
- for (int i = 0; i < sequences.size(); i++)
+ List allSequences = new ArrayList();
+ for (SequenceI seq : sequences)
{
- seq = (SequenceI) sequences.elementAt(i);
- allSequences.addElement(seq);
+ allSequences.add(seq);
if (hiddenReps.containsKey(seq))
{
- SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
- for (int h = 0; h < hsg.getSize(); h++)
+ SequenceCollectionI hsg = hiddenReps.get(seq);
+ for (SequenceI seq2 : hsg.getSequences())
{
- seq2 = hsg.getSequenceAt(h);
if (seq2 != seq && !allSequences.contains(seq2))
{
- allSequences.addElement(seq2);
+ allSequences.add(seq2);
}
}
}
@@ -312,20 +330,15 @@ public class SequenceGroup
}
}
- public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+ public SequenceI[] getSequencesAsArray(
+ Map map)
{
- Vector tmp = getSequences(hiddenReps);
+ List tmp = getSequences(map);
if (tmp == null)
{
return null;
}
- SequenceI[] result = new SequenceI[tmp.size()];
- for (int i = 0; i < result.length; i++)
- {
- result[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return result;
+ return tmp.toArray(new SequenceI[tmp.size()]);
}
/**
@@ -440,7 +453,9 @@ public class SequenceGroup
}
/**
- * Add s to this sequence group
+ * Add s to this sequence group. If aligment sequence is already contained in
+ * group, it will not be added again, but recalculation may happen if the flag
+ * is set.
*
* @param s
* alignment sequence to be added
@@ -449,24 +464,44 @@ public class SequenceGroup
*/
public void addSequence(SequenceI s, boolean recalc)
{
- if (s != null && !sequences.contains(s))
+ synchronized (sequences)
{
- sequences.addElement(s);
- }
+ if (s != null && !sequences.contains(s))
+ {
+ sequences.add(s);
+ }
- if (recalc)
- {
- recalcConservation();
+ if (recalc)
+ {
+ recalcConservation();
+ }
}
}
/**
- * Max Gaps Threshold for performing a conservation calculation TODO: make
- * this a configurable property - or global to an alignment view
+ * Max Gaps Threshold (percent) for performing a conservation calculation
*/
private int consPercGaps = 25;
/**
+ * @return Max Gaps Threshold for performing a conservation calculation
+ */
+ public int getConsPercGaps()
+ {
+ return consPercGaps;
+ }
+
+ /**
+ * set Max Gaps Threshold (percent) for performing a conservation calculation
+ *
+ * @param consPercGaps
+ */
+ public void setConsPercGaps(int consPercGaps)
+ {
+ this.consPercGaps = consPercGaps;
+ }
+
+ /**
* calculate residue conservation for group - but only if necessary.
*/
public void recalcConservation()
@@ -475,23 +510,17 @@ public class SequenceGroup
{
return;
}
-
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
if (consensus != null)
{
- _updateConsensusRow(cnsns);
+ _updateConsensusRow(cnsns, sequences.size());
}
if (cs != null)
{
cs.setConsensus(cnsns);
-
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
- }
}
if ((conservation != null)
@@ -508,15 +537,16 @@ public class SequenceGroup
}
if (cs != null)
{
- cs.setConservation(c);
-
- if (cs instanceof ClustalxColourScheme)
+ if (cs.conservationApplied())
{
- ((ClustalxColourScheme) cs)
- .resetClustalX(sequences, getWidth());
+ cs.setConservation(c);
}
}
}
+ if (cs != null)
+ {
+ cs.alignmentChanged(context != null ? context : this, null);
+ }
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
@@ -547,7 +577,7 @@ public class SequenceGroup
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
if (consensus == null)
{
@@ -564,9 +594,10 @@ public class SequenceGroup
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
- // for
- // ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+ // container
+ // for
+ // ignoreGapsInConsensusCalculation);
}
/**
@@ -578,6 +609,8 @@ public class SequenceGroup
*/
public void addOrRemove(SequenceI s, boolean recalc)
{
+ synchronized (sequences)
+ {
if (sequences.contains(s))
{
deleteSequence(s, recalc);
@@ -585,42 +618,47 @@ public class SequenceGroup
else
{
addSequence(s, recalc);
+ }
}
}
/**
- * DOCUMENT ME!
+ * remove
*
* @param s
- * DOCUMENT ME!
+ * to be removed
* @param recalc
- * DOCUMENT ME!
+ * true means recalculate conservation
*/
public void deleteSequence(SequenceI s, boolean recalc)
{
- sequences.removeElement(s);
-
- if (recalc)
+ synchronized (sequences)
{
- recalcConservation();
+ sequences.remove(s);
+
+ if (recalc)
+ {
+ recalcConservation();
+ }
}
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return the first column selected by this group. Runs from 0<=i 0)
- {
- width = ((SequenceI) sequences.elementAt(0)).getLength();
- }
-
- for (int i = 1; i < sequences.size(); i++)
+ synchronized (sequences)
{
- SequenceI seq = (SequenceI) sequences.elementAt(i);
-
- if (seq.getLength() > width)
- {
- width = seq.getLength();
+ // MC This needs to get reset when characters are inserted and deleted
+ boolean first=true;
+ for (SequenceI seq:sequences) {
+ if (first || seq.getLength() > width)
+ {
+ width = seq.getLength();
+ first = false;
+ }
}
+ return width;
}
-
- return width;
}
/**
@@ -794,48 +821,54 @@ public class SequenceGroup
{
return getSequencesInOrder(al, true);
}
+
/**
- * return an array representing the intersection of the group with al, optionally returning an array the size of al.getHeight()
- * where nulls mark the non-intersected sequences
+ * return an array representing the intersection of the group with al,
+ * optionally returning an array the size of al.getHeight() where nulls mark
+ * the non-intersected sequences
+ *
* @param al
* @param trim
* @return null or array
*/
public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
{
- int sSize = sequences.size();
- int alHeight = al.getHeight();
+ synchronized (sequences)
+ {
+ int sSize = sequences.size();
+ int alHeight = al.getHeight();
- SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+ SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
- int index = 0;
- for (int i = 0; i < alHeight && index < sSize; i++)
- {
- if (sequences.contains(al.getSequenceAt(i)))
+ int index = 0;
+ for (int i = 0; i < alHeight && index < sSize; i++)
{
- seqs[(trim) ? index : i] = al.getSequenceAt(i);
- index++;
+ if (sequences.contains(al.getSequenceAt(i)))
+ {
+ seqs[(trim) ? index : i] = al.getSequenceAt(i);
+ index++;
+ }
}
- }
- if (index == 0)
- {
- return null;
- }
- if (!trim)
- {
- return seqs;
- }
- if (index < seqs.length)
- {
- SequenceI[] dummy = seqs;
- seqs = new SequenceI[index];
- while (--index >= 0)
+ if (index == 0)
{
- seqs[index] = dummy[index];
- dummy[index] = null;
+ return null;
+ }
+ if (!trim)
+ {
+ return seqs;
+ }
+ if (index < seqs.length)
+ {
+ SequenceI[] dummy = seqs;
+ seqs = new SequenceI[index];
+ while (--index >= 0)
+ {
+ seqs[index] = dummy[index];
+ dummy[index] = null;
+ }
}
+ return seqs;
}
- return seqs;
}
/**
@@ -940,31 +973,23 @@ public class SequenceGroup
*
* @param alignment
* (may not be null)
- * @param hashtable
+ * @param map
* (may be null)
* @return new group containing sequences common to this group and alignment
*/
- public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
+ public SequenceGroup intersect(AlignmentI alignment,
+ Map map)
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
- sgroup.sequences = new Vector();
+ sgroup.sequences = new ArrayList();
for (int s = 0; insect != null && s < insect.length; s++)
{
- if (hashtable == null || hashtable.containsKey(insect[s]))
+ if (map == null || map.containsKey(insect[s]))
{
- sgroup.sequences.addElement(insect[s]);
+ sgroup.sequences.add(insect[s]);
}
}
- // Enumeration en =getSequences(hashtable).elements();
- // while (en.hasMoreElements())
- // {
- // SequenceI elem = (SequenceI) en.nextElement();
- // if (alignment.getSequences().contains(elem))
- // {
- // sgroup.addSequence(elem, false);
- // }
- // }
return sgroup;
}
@@ -993,6 +1018,20 @@ public class SequenceGroup
private boolean showConsensusHistogram;
/**
+ * set this alignmentAnnotation object as the one used to render consensus
+ * annotation
+ *
+ * @param aan
+ */
+ public void setConsensus(AlignmentAnnotation aan)
+ {
+ if (consensus == null)
+ {
+ consensus = aan;
+ }
+ }
+
+ /**
*
* @return automatically calculated consensus row
*/
@@ -1011,16 +1050,30 @@ public class SequenceGroup
{
consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+ consensus.groupRef = this;
+ consensus.label = "Consensus for " + getName();
+ consensus.description = "Percent Identity";
}
- consensus.hasText = true;
- consensus.autoCalculated = true;
- consensus.groupRef = this;
- consensus.label = "Consensus for " + getName();
- consensus.description = "Percent Identity";
return consensus;
}
/**
+ * set this alignmentAnnotation object as the one used to render consensus
+ * annotation
+ *
+ * @param aan
+ */
+ public void setConservationRow(AlignmentAnnotation aan)
+ {
+ if (conservation == null)
+ {
+ conservation = aan;
+ }
+ }
+
+ /**
* get the conservation annotation row for this group
*
* @return autoCalculated annotation row
@@ -1131,4 +1184,145 @@ public class SequenceGroup
{
return showConsensusHistogram;
}
+
+ /**
+ * set flag indicating if logo should be normalised when rendered
+ *
+ * @param norm
+ */
+ public void setNormaliseSequenceLogo(boolean norm)
+ {
+ normaliseSequenceLogo = norm;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ @Override
+ /**
+ * returns a new array with all annotation involving this group
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ // TODO add in other methods like 'getAlignmentAnnotation(String label),
+ // etc'
+ ArrayList annot = new ArrayList();
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
+ {
+ for (AlignmentAnnotation al : aa)
+ {
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
+ }
+ }
+ }
+ if (consensus != null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation != null)
+ {
+ annot.add(conservation);
+ }
+ }
+ return annot.toArray(new AlignmentAnnotation[0]);
+ }
+
+ @Override
+ public Iterable findAnnotation(String calcId)
+ {
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ /**
+ * Returns a list of annotations that match the specified sequenceRef, calcId
+ * and label, ignoring null values.
+ *
+ * @return list of AlignmentAnnotation objects
+ */
+ @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;
+ }
+
+ /**
+ * Answer true if any annotation matches the calcId passed in (if not null).
+ *
+ * @param calcId
+ * @return
+ */
+ public boolean hasAnnotation(String calcId)
+ {
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public void clear()
+ {
+ synchronized (sequences)
+ {
+ sequences.clear();
+ }
+ }
+
+ private AnnotatedCollectionI context;
+
+ /**
+ * set the alignment or group context for this group
+ *
+ * @param context
+ */
+ public void setContext(AnnotatedCollectionI context)
+ {
+ this.context = context;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return context;
+ }
}