/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
-import java.awt.*;
-
-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
* @author $author$
* @version $Revision$
*/
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
{
String groupName;
boolean displayText = true;
boolean colourText = false;
+
/**
* after Olivier's non-conserved only character display
*/
- boolean showUnconserved = false;
-
+ boolean showNonconserved = false;
+
/**
* group members
*/
- private Vector sequences = new Vector();
+ private List<SequenceI> sequences = new ArrayList<SequenceI>();
+
/**
* representative sequence for this group (if any)
*/
private SequenceI seqrep = null;
+
int width = -1;
/**
- * Colourscheme applied to group if any */
+ * Colourscheme applied to 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;
/**
* consensus calculation property
*/
- private boolean ignoreGapsInConsensus=true;
+ private boolean ignoreGapsInConsensus = true;
+
/**
* consensus calculation property
*/
- private boolean showConsensusProfile=false;
+ private boolean showSequenceLogo = false;
+
+ /**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
/**
* @return the includeAllConsSymbols
*/
- public boolean isIncludeAllConsSymbols()
+ public boolean isShowSequenceLogo()
{
- return showConsensusProfile;
+ return showSequenceLogo;
}
-
/**
* Creates a new SequenceGroup object.
*/
* @param displayText
* @param colourText
* @param start
- * first column of group
+ * first column of group
* @param end
- * last column of group
+ * 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)
{
endRes = end;
recalcConservation();
}
+
/**
* copy constructor
+ *
* @param seqsel
*/
public SequenceGroup(SequenceGroup seqsel)
{
- if (seqsel!=null)
+ if (seqsel != null)
{
- sequences=new Vector();
- Enumeration sq = seqsel.sequences.elements();
- while (sq.hasMoreElements()) {
- sequences.addElement(sq.nextElement());
- };
- if (seqsel.groupName!=null)
+ sequences = new ArrayList<SequenceI>();
+ sequences.addAll(seqsel.sequences);
+ if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
}
colourText = seqsel.colourText;
startRes = seqsel.startRes;
endRes = seqsel.endRes;
- cs =seqsel.cs;
- if (seqsel.description!=null)
+ cs = seqsel.cs;
+ if (seqsel.description != null)
+ {
description = new String(seqsel.description);
+ }
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
idColour = seqsel.idColour;
thresholdTextColour = seqsel.thresholdTextColour;
width = seqsel.width;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
- if (seqsel.conserve!=null)
+ if (seqsel.conserve != null)
{
- recalcConservation(); // safer than
+ recalcConservation(); // safer than
// aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
}
}
}
}
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();
* If sequence ends in gaps, the end residue can be correctly calculated here
*
* @param seq
- * SequenceI
+ * SequenceI
* @return int
*/
public int findEndRes(SequenceI seq)
return eres;
}
- public Vector getSequences(Hashtable hiddenReps)
+ @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, seq2;
- 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))
{
- 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);
}
}
}
}
}
- 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()]);
}
/**
* DOCUMENT ME!
*
* @param col
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param col
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setName(String name)
{
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setConservation(Conservation c)
{
}
/**
- * 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
+ * alignment sequence to be added
* @param recalc
- * true means Group's conservation should be recalculated
+ * true means Group's conservation should be recalculated
*/
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
*/
- private int consPercGaps=25;
+ public void setConsPercGaps(int consPercGaps)
+ {
+ this.consPercGaps = consPercGaps;
+ }
+
/**
* calculate residue conservation for group - but only if necessary.
*/
{
return;
}
-
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showConsensusProfile);
+ Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+ endRes + 1, showSequenceLogo);
if (consensus != null)
{
- _updateConsensusRow(cnsns);
+ _updateConsensusRow(cnsns, sequences.size());
}
- if (cs!=null)
+ if (cs != null)
{
cs.setConsensus(cnsns);
-
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
- }
}
- if ((conservation!=null) || (cs!=null && cs.conservationApplied()))
+ if ((conservation != null)
+ || (cs != null && cs.conservationApplied()))
{
Conservation c = new Conservation(groupName,
ResidueProperties.propHash, 3, sequences, startRes,
endRes + 1);
c.calculate();
c.verdict(false, consPercGaps);
- if (conservation!=null)
+ if (conservation != null)
{
_updateConservationRow(c);
}
- if (cs!=null)
- {
- cs.setConservation(c);
-
- if (cs instanceof ClustalxColourScheme)
+ if (cs != null)
{
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
- }
+ if (cs.conservationApplied())
+ {
+ cs.setConservation(c);
+ }
}
}
+ if (cs != null)
+ {
+ cs.alignmentChanged(context != null ? context : this, null);
+ }
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
private void _updateConservationRow(Conservation c)
{
- if (conservation==null)
+ if (conservation == null)
{
getConservation();
}
// update Labels
- conservation.label = "Conservation for "+getName();
- conservation.description = "Conservation for group "+getName()+" less than " + consPercGaps
- + "% gaps";
+ conservation.label = "Conservation for " + getName();
+ conservation.description = "Conservation for group " + getName()
+ + " less than " + consPercGaps + "% gaps";
// preserve width if already set
- int aWidth = (conservation.annotations!=null) ? (endRes<conservation.annotations.length ? conservation.annotations.length : endRes+1) : endRes+1;
+ int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
+ : endRes + 1)
+ : endRes + 1;
conservation.annotations = null;
- conservation.annotations = new Annotation[aWidth]; // should be alignment width
- c.completeAnnotations(conservation,null, startRes, endRes+1);
+ conservation.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+ c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
+
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
- if (consensus==null)
+ if (consensus == null)
{
getConsensus();
}
- consensus.label = "Consensus for "+getName();
+ consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
consensusData = cnsns;
// preserve width if already set
- int aWidth = (consensus.annotations!=null) ? (endRes<consensus.annotations.length ? consensus.annotations.length : endRes+1) : endRes+1;
+ int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
+ : endRes + 1)
+ : endRes + 1;
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
- AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, showConsensusProfile); // TODO: setting container for ignoreGapsInConsensusCalculation);
+ AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+ // container
+ // for
+ // ignoreGapsInConsensusCalculation);
}
/**
- * @param s sequence to either add or remove from group
- * @param recalc flag passed to delete/addSequence to indicate if group properties should be recalculated
+ * @param s
+ * sequence to either add or remove from group
+ * @param recalc
+ * flag passed to delete/addSequence to indicate if group properties
+ * should be recalculated
*/
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();
+ }
}
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return the first column selected by this group. Runs from 0<=i<N_cols
*/
+ @Override
public int getStartRes()
{
return startRes;
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return the groups last selected column. Runs from 0<=i<N_cols
*/
+ @Override
public int getEndRes()
{
return endRes;
}
/**
- * 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)
{
}
/**
- * 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!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDisplayText(boolean state)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDisplayBoxes(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)
- {
- 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)
+ // 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;
}
/**
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setOutlineColour(Color c)
{
/**
*
* returns the sequences in the group ordered by the ordering given by al.
- * this used to return an array with null entries regardless, new behaviour is below.
- * TODO: verify that this does not affect use in applet or application
+ * this used to return an array with null entries regardless, new behaviour is
+ * below. TODO: verify that this does not affect use in applet or application
+ *
* @param al
- * Alignment
- * @return SequenceI[] intersection of sequences in group with al, ordered by al, or null if group does not intersect with al
+ * Alignment
+ * @return SequenceI[] intersection of sequences in group with al, ordered by
+ * al, or null if group does not intersect with al
*/
public SequenceI[] getSequencesInOrder(AlignmentI al)
{
- int sSize = sequences.size();
- int alHeight = al.getHeight();
-
- SequenceI[] seqs = new SequenceI[sSize];
+ return getSequencesInOrder(al, true);
+ }
- int index = 0;
- for (int i = 0; i < alHeight && index < sSize; i++)
+ /**
+ * 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)
+ {
+ synchronized (sequences)
{
- if (sequences.contains(al.getSequenceAt(i)))
+ int sSize = sequences.size();
+ int alHeight = al.getHeight();
+
+ SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+
+ int index = 0;
+ for (int i = 0; i < alHeight && index < sSize; i++)
{
- seqs[index++] = al.getSequenceAt(i);
+ if (sequences.contains(al.getSequenceAt(i)))
+ {
+ seqs[(trim) ? index : i] = al.getSequenceAt(i);
+ index++;
+ }
}
- }
- if (index==0)
- {
- return null;
- }
- if (index<seqs.length)
- {
- SequenceI[] dummy = seqs;
- seqs = new SequenceI[index];
- while (--index>=0)
+ if (index == 0)
+ {
+ return null;
+ }
+ if (!trim)
{
- seqs[index] = dummy[index];
- dummy[index] = null;
+ 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;
}
/**
/**
* @param idColour
- * the idColour to set
+ * the idColour to set
*/
public void setIdColour(Color idColour)
{
}
/**
- * 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)
+ * 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
{
return seqrep != null;
}
+
/**
* visibility of rows or represented rows covered by group
*/
- private boolean hidereps=false;
+ private boolean hidereps = false;
+
/**
- * set visibility of sequences covered by (if no sequence representative is defined)
- * or represented by this group.
+ * set visibility of sequences covered by (if no sequence representative is
+ * defined) or represented by this group.
+ *
* @param visibility
*/
public void setHidereps(boolean visibility)
{
hidereps = visibility;
}
+
/**
*
- * @return true if sequences represented (or covered) by this group should be hidden
+ * @return true if sequences represented (or covered) by this group should be
+ * hidden
*/
public boolean isHidereps()
{
return hidereps;
}
+
/**
* visibility of columns intersecting this group
*/
- private boolean hidecols=false;
+ private boolean hidecols = false;
+
/**
* set intended visibility of columns covered by this group
+ *
* @param visibility
*/
public void setHideCols(boolean visibility)
{
hidecols = visibility;
}
+
/**
*
* @return true if columns covered by group should be hidden
{
return hidecols;
}
+
/**
- * create a new sequence group from the intersection of this group
- * with an alignment Hashtable of hidden representatives
+ * create a new sequence group from the intersection of this group with an
+ * alignment Hashtable of hidden representatives
*
- * @param alignment (may not be null)
- * @param hashtable (may be null)
+ * @param alignment
+ * (may not be null)
+ * @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]))
- {
- sgroup.sequences.addElement(insect[s]); }
+ SequenceI[] insect = getSequencesInOrder(alignment);
+ sgroup.sequences = new ArrayList<SequenceI>();
+ for (int s = 0; insect != null && s < insect.length; s++)
+ {
+ if (map == null || map.containsKey(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;
}
/**
* @return the showUnconserved
*/
- public boolean getShowunconserved()
+ public boolean getShowNonconserved()
{
- return showUnconserved;
+ return showNonconserved;
}
/**
- * @param showUnconserved the showUnconserved to set
+ * @param showNonconserved
+ * the showUnconserved to set
*/
- public void setShowunconserved(boolean displayNonconserved)
+ public void setShowNonconserved(boolean displayNonconserved)
{
- this.showUnconserved = displayNonconserved;
+ this.showNonconserved = displayNonconserved;
}
- AlignmentAnnotation consensus=null,conservation=null;
+
+ AlignmentAnnotation consensus = null, conservation = null;
/**
* flag indicating if consensus histogram should be rendered
*/
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 null;
}
- if (consensus==null)
+ if (consensus == null)
{
- consensus = new AlignmentAnnotation("","",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ 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.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
*/
- public AlignmentAnnotation getConservationRow() {
- if (conservation == null) {
- conservation = new AlignmentAnnotation("","", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ public AlignmentAnnotation getConservationRow()
+ {
+ if (conservation == null)
+ {
+ conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 11f, AlignmentAnnotation.BAR_GRAPH);
+ }
+
conservation.hasText = true;
conservation.autoCalculated = true;
conservation.groupRef = this;
- }
- conservation.label = "Conservation for "+getName();
- conservation.description = "Conservation for group "+getName()+" less than " + consPercGaps
- + "% gaps";
+ conservation.label = "Conservation for " + getName();
+ conservation.description = "Conservation for group " + getName()
+ + " less than " + consPercGaps + "% gaps";
return conservation;
}
*
* @return true if annotation rows have been instantiated for this group
*/
- public boolean hasAnnotationRows()
- {
- return consensus!=null || conservation!=null;
- }
+ public boolean hasAnnotationRows()
+ {
+ return consensus != null || conservation != null;
+ }
public SequenceI getConsensusSeq()
{
}
}
- 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 sq;
}
public void setIgnoreGapsConsensus(boolean state)
{
- if (this.ignoreGapsInConsensus!=state && consensus!=null)
+ if (this.ignoreGapsInConsensus != state && consensus != null)
{
ignoreGapsInConsensus = state;
recalcConservation();
}
ignoreGapsInConsensus = state;
}
+
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensus;
}
+
/**
- * @param includeAllConsSymbols the includeAllConsSymbols to set
+ * @param showSequenceLogo
+ * indicates if a sequence logo is shown for consensus annotation
*/
- public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
+ public void setshowSequenceLogo(boolean showSequenceLogo)
{
- if (this.showConsensusProfile!=includeAllConsSymbols && consensus!=null) {
- this.showConsensusProfile = includeAllConsSymbols;
+ // TODO: decouple calculation from settings update
+ if (this.showSequenceLogo != showSequenceLogo && consensus != null)
+ {
+ this.showSequenceLogo = showSequenceLogo;
recalcConservation();
}
- this.showConsensusProfile = includeAllConsSymbols;
+ this.showSequenceLogo = showSequenceLogo;
}
-
/**
*
- * @param showConsHist flag indicating if the consensus histogram for this group should be rendered
+ * @param showConsHist
+ * flag indicating if the consensus histogram for this group should
+ * be rendered
*/
public void setShowConsensusHistogram(boolean showConsHist)
{
-
- if (showConsensusHistogram!=showConsHist && consensus!=null) {
+
+ if (showConsensusHistogram != showConsHist && consensus != null)
+ {
this.showConsensusHistogram = showConsHist;
recalcConservation();
}
this.showConsensusHistogram = showConsHist;
}
+
/**
* @return the showConsensusHistogram
*/
{
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>();
+ 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<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ 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<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()
+ {
+ 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