/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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
* 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.*;
+import java.util.List;
import java.awt.*;
* @author $author$
* @version $Revision$
*/
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
{
String groupName;
/**
* group members
*/
- private Vector sequences = new Vector();
+ private Vector<SequenceI> sequences = new Vector<SequenceI>();
/**
* representative sequence for this group (if any)
private boolean showSequenceLogo = false;
/**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
+
+ /**
* @return the includeAllConsSymbols
*/
public boolean isShowSequenceLogo()
if (seqsel != null)
{
sequences = new Vector();
- Enumeration sq = seqsel.sequences.elements();
+ Enumeration<SequenceI> sq = seqsel.sequences.elements();
while (sq.hasMoreElements())
{
sequences.addElement(sq.nextElement());
if (!found)
continue;
}
- AlignmentAnnotation newannot = new AlignmentAnnotation(seq
- .getAnnotation()[a]);
+ AlignmentAnnotation newannot = new AlignmentAnnotation(
+ seq.getAnnotation()[a]);
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
return eres;
}
- public Vector getSequences(Hashtable hiddenReps)
+ public List<SequenceI> getSequences()
+ {
+ return sequences;
+ }
+
+ public List<SequenceI> getSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
if (hiddenReps == null)
{
else
{
Vector allSequences = new Vector();
- SequenceI seq, seq2;
+ SequenceI seq;
for (int i = 0; i < sequences.size(); i++)
{
seq = (SequenceI) sequences.elementAt(i);
allSequences.addElement(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);
}
}
- public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+ public SequenceI[] getSequencesAsArray(
+ Map<SequenceI, SequenceCollectionI> map)
{
- Vector tmp = getSequences(hiddenReps);
+ List<SequenceI> 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()]);
}
/**
}
/**
- * 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
{
return;
}
-
+ if (cs != null)
+ {
+ cs.alignmentChanged(this, null);
+ }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
if (cs != null)
{
cs.setConsensus(cnsns);
-
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
- }
+ cs.alignmentChanged(this, null);
}
if ((conservation != null)
}
if (cs != null)
{
- cs.setConservation(c);
-
- if (cs instanceof ClustalxColourScheme)
+ if (cs.conservationApplied())
{
- ((ClustalxColourScheme) cs)
- .resetClustalX(sequences, getWidth());
+ cs.setConservation(c);
+ cs.alignmentChanged(this, null);
}
}
}
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return the first column selected by this group. Runs from 0<=i<N_cols
*/
public int getStartRes()
{
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return the groups last selected column. Runs from 0<=i<N_cols
*/
public int getEndRes()
{
}
/**
- * DOCUMENT ME!
+ * Set the first column selected by this group. Runs from 0<=i<N_cols
*
* @param i
- * DOCUMENT ME!
*/
public void setStartRes(int i)
{
}
/**
- * DOCUMENT ME!
+ * Set the groups last selected column. Runs from 0<=i<N_cols
*
* @param i
- * DOCUMENT ME!
*/
public void setEndRes(int i)
{
*/
public SequenceI[] getSequencesInOrder(AlignmentI al)
{
+ 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
+ *
+ * @param al
+ * @param trim
+ * @return null or array
+ */
+ public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
+ {
int sSize = sequences.size();
int alHeight = al.getHeight();
- SequenceI[] seqs = new SequenceI[sSize];
+ 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)))
{
- seqs[index++] = 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;
*
* @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<SequenceI, SequenceCollectionI> map)
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
sgroup.sequences = new Vector();
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]);
}
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
*/
{
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
}
}
- SequenceI sq = new Sequence("Group" + getName() + " Consensus", seqs
- .toString());
+ SequenceI sq = new Sequence("Group" + getName() + " Consensus",
+ seqs.toString());
sq.setDescription("Percentage Identity Consensus "
+ ((ignoreGapsInConsensus) ? " without gaps" : ""));
return sq;
{
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<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+ for (SequenceI seq : (Vector<SequenceI>) sequences)
+ {
+ for (AlignmentAnnotation al : seq.getAnnotation())
+ {
+ 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<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId)
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ public void clear()
+ {
+ sequences.clear();
+ }
}
git://source.jalview.org / jalview.git / blobdiff