X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=0944c3465bad8d23900a57ceac74543f0d1d1649;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=fbcf3031ddccae71e49a0c607afd8569656734db;hpb=b1cf67d148cd9cca4a12d245b6dad85a0a7376c7;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index fbcf303..0944c34 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,29 +1,37 @@
/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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 .
+ * 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.Enumeration;
+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
@@ -31,7 +39,7 @@ import jalview.schemes.*;
* @author $author$
* @version $Revision$
*/
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
{
String groupName;
@@ -46,23 +54,27 @@ public class SequenceGroup
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 Vector sequences = new Vector();
+
/**
* 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;
int startRes = 0;
@@ -82,11 +94,17 @@ public class SequenceGroup
/**
* consensus calculation property
*/
- private boolean ignoreGapsInConsensus=true;
+ private boolean ignoreGapsInConsensus = true;
+
/**
* consensus calculation property
*/
- private boolean showSequenceLogo=false;
+ private boolean showSequenceLogo = false;
+
+ /**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
/**
* @return the includeAllConsSymbols
@@ -96,7 +114,6 @@ public class SequenceGroup
return showSequenceLogo;
}
-
/**
* Creates a new SequenceGroup object.
*/
@@ -115,9 +132,9 @@ public class SequenceGroup
* @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,
ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
@@ -133,20 +150,24 @@ public class SequenceGroup
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 Vector();
+ Enumeration sq = seqsel.sequences.elements();
+ while (sq.hasMoreElements())
+ {
+ sequences.addElement(sq.nextElement());
+ }
+ ;
+ if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
}
@@ -155,9 +176,11 @@ public class SequenceGroup
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;
@@ -168,9 +191,9 @@ public class SequenceGroup
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(); // ??
}
}
@@ -217,10 +240,12 @@ public class SequenceGroup
}
}
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();
@@ -248,7 +273,7 @@ public class SequenceGroup
* If sequence ends in gaps, the end residue can be correctly calculated here
*
* @param seq
- * SequenceI
+ * SequenceI
* @return int
*/
public int findEndRes(SequenceI seq)
@@ -273,7 +298,15 @@ 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)
{
@@ -282,17 +315,16 @@ public class SequenceGroup
else
{
Vector allSequences = new Vector();
- SequenceI seq, seq2;
+ SequenceI seq;
for (int i = 0; i < sequences.size(); i++)
{
- seq = (SequenceI) sequences.elementAt(i);
+ seq = 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);
@@ -305,27 +337,22 @@ 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()]);
}
/**
* DOCUMENT ME!
*
* @param col
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -359,7 +386,7 @@ public class SequenceGroup
* DOCUMENT ME!
*
* @param col
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -398,7 +425,7 @@ public class SequenceGroup
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setName(String name)
{
@@ -425,7 +452,7 @@ public class SequenceGroup
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setConservation(Conservation c)
{
@@ -433,12 +460,14 @@ 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
+ * 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)
{
@@ -454,10 +483,28 @@ public class SequenceGroup
}
/**
- * 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.
*/
@@ -467,45 +514,43 @@ public class SequenceGroup
{
return;
}
-
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, showSequenceLogo);
+ 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
@@ -516,41 +561,55 @@ public class SequenceGroup
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 0)
{
- width = ((SequenceI) sequences.elementAt(0)).getLength();
+ width = sequences.elementAt(0).getLength();
}
for (int i = 1; i < sequences.size(); i++)
{
- SequenceI seq = (SequenceI) sequences.elementAt(i);
+ SequenceI seq = sequences.elementAt(i);
if (seq.getLength() > width)
{
@@ -740,7 +799,7 @@ public class SequenceGroup
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setOutlineColour(Color c)
{
@@ -760,36 +819,57 @@ public class SequenceGroup
/**
*
* 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)
{
+ 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)
+ if (index == 0)
{
return null;
}
- if (index=0)
+ while (--index >= 0)
{
seqs[index] = dummy[index];
dummy[index] = null;
@@ -808,7 +888,7 @@ public class SequenceGroup
/**
* @param idColour
- * the idColour to set
+ * the idColour to set
*/
public void setIdColour(Color idColour)
{
@@ -824,14 +904,17 @@ public class SequenceGroup
}
/**
- * 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
@@ -840,39 +923,48 @@ public class SequenceGroup
{
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
@@ -881,58 +973,79 @@ public class SequenceGroup
{
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 map)
{
SequenceGroup sgroup = new SequenceGroup(this);
- SequenceI[] insect=getSequencesInOrder(alignment);
+ SequenceI[] insect = getSequencesInOrder(alignment);
sgroup.sequences = new Vector();
- for (int s=0;insect!=null && s annot = new ArrayList();
+ 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()
+ {
+ 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;
}
+}