/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * 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.*;
+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
/**
* group members
*/
- private Vector<SequenceI> sequences = new Vector<SequenceI>();
+ private List<SequenceI> sequences = new ArrayList<SequenceI>();
/**
* representative sequence for this group (if any)
*/
public ColourSchemeI cs;
+ // start column (base 0)
int startRes = 0;
+ // end column (base 0)
int endRes = 0;
public Color outlineColour = Color.black;
* @param end
* last column of group
*/
- public SequenceGroup(Vector sequences, String groupName,
+ public SequenceGroup(List<SequenceI> sequences, String groupName,
ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
boolean colourText, int start, int end)
{
{
if (seqsel != null)
{
- sequences = new Vector();
- Enumeration<SequenceI> sq = seqsel.sequences.elements();
- while (sq.hasMoreElements())
- {
- sequences.addElement(sq.nextElement());
- }
- ;
+ sequences = new ArrayList<SequenceI>();
+ sequences.addAll(seqsel.sequences);
if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
endRes = seqsel.endRes;
cs = seqsel.cs;
if (seqsel.description != null)
+ {
description = new String(seqsel.description);
+ }
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
idColour = seqsel.idColour;
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
return eres;
}
+ @Override
public List<SequenceI> getSequences()
{
return sequences;
}
+ @Override
public List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
if (hiddenReps == null)
{
+ // TODO: need a synchronizedCollection here ?
return sequences;
}
else
{
- Vector allSequences = new Vector();
- SequenceI seq;
- for (int i = 0; i < sequences.size(); i++)
+ List<SequenceI> allSequences = new ArrayList<SequenceI>();
+ for (SequenceI seq : sequences)
{
- seq = (SequenceI) sequences.elementAt(i);
- allSequences.addElement(seq);
+ allSequences.add(seq);
if (hiddenReps.containsKey(seq))
{
SequenceCollectionI hsg = hiddenReps.get(seq);
{
if (seq2 != seq && !allSequences.contains(seq2))
{
- allSequences.addElement(seq2);
+ allSequences.add(seq2);
}
}
}
*/
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 (percent) for performing a conservation calculation
+ * Max Gaps Threshold (percent) for performing a conservation calculation
*/
private int consPercGaps = 25;
/**
* set Max Gaps Threshold (percent) for performing a conservation calculation
- * @param consPercGaps
+ *
+ * @param consPercGaps
*/
public void setConsPercGaps(int consPercGaps)
{
{
return;
}
- if (cs != null)
- {
- cs.alignmentChanged(this, null);
- }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this, null);
}
if ((conservation != null)
if (cs.conservationApplied())
{
cs.setConservation(c);
- cs.alignmentChanged(this, null);
}
}
}
+ if (cs != null)
+ {
+ cs.alignmentChanged(context != null ? context : this, null);
+ }
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
- // for
- // ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+ // container
+ // for
+ // ignoreGapsInConsensusCalculation);
}
/**
*/
public void addOrRemove(SequenceI s, boolean recalc)
{
- if (sequences.contains(s))
- {
- deleteSequence(s, recalc);
- }
- else
+ synchronized (sequences)
{
- addSequence(s, recalc);
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ 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();
+ }
}
}
*
* @return the first column selected by this group. Runs from 0<=i<N_cols
*/
+ @Override
public int getStartRes()
{
return startRes;
*
* @return the groups last selected column. Runs from 0<=i<N_cols
*/
+ @Override
public int getEndRes()
{
return endRes;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return number of sequences in group
*/
public int getSize()
{
}
/**
- * DOCUMENT ME!
- *
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return the ith sequence
*/
public SequenceI getSequenceAt(int i)
{
- return (SequenceI) sequences.elementAt(i);
+ return sequences.get(i);
}
/**
- * DOCUMENT ME!
- *
* @param state
- * DOCUMENT ME!
+ * colourText
*/
public void setColourText(boolean state)
{
}
/**
- * DOCUMENT ME!
+ * computes the width of current set of sequences and returns it
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
- // MC This needs to get reset when characters are inserted and deleted
- if (sequences.size() > 0)
+ synchronized (sequences)
{
- width = ((SequenceI) sequences.elementAt(0)).getLength();
- }
-
- for (int i = 1; i < sequences.size(); i++)
- {
- SequenceI seq = (SequenceI) sequences.elementAt(i);
-
- if (seq.getLength() > width)
+ // MC This needs to get reset when characters are inserted and deleted
+ boolean first = true;
+ for (SequenceI seq : sequences)
{
- width = seq.getLength();
+ if (first || seq.getLength() > width)
+ {
+ width = seq.getLength();
+ first = false;
+ }
}
+ return width;
}
-
- return width;
}
/**
*/
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;
}
/**
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
- sgroup.sequences = new Vector();
+ sgroup.sequences = new ArrayList<SequenceI>();
for (int s = 0; insect != null && s < insect.length; 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;
}
// TODO add in other methods like 'getAlignmentAnnotation(String label),
// etc'
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
- for (SequenceI seq : (Vector<SequenceI>) sequences)
+ synchronized (sequences)
{
- for (AlignmentAnnotation al : seq.getAnnotation())
+ for (SequenceI seq : sequences)
{
- if (al.groupRef == this)
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
{
- annot.add(al);
+ for (AlignmentAnnotation al : aa)
+ {
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
+ }
}
}
- }
- if (consensus != null)
- {
- annot.add(consensus);
- }
- if (conservation != null)
- {
- annot.add(conservation);
+ if (consensus != null)
+ {
+ annot.add(consensus);
+ }
+ if (conservation != null)
+ {
+ annot.add(conservation);
+ }
}
return annot.toArray(new AlignmentAnnotation[0]);
}
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<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ 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;
+ }
+
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
public void clear()
{
- sequences.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;
}
}
git://source.jalview.org / jalview.git / blobdiff