X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=752c6d4335dca76cc37d0b3e04449ca958d94fe9;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=ed21f609d012524c7d29d2f809e0b8a00b6eccc2;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index ed21f60..752c6d4 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,29 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.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.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
@@ -92,12 +100,12 @@ public class SequenceGroup implements AnnotatedCollectionI
* consensus calculation property
*/
private boolean showSequenceLogo = false;
+
/**
* flag indicating if logo should be rendered normalised
*/
private boolean normaliseSequenceLogo;
-
/**
* @return the includeAllConsSymbols
*/
@@ -170,7 +178,9 @@ public class SequenceGroup implements AnnotatedCollectionI
endRes = seqsel.endRes;
cs = seqsel.cs;
if (seqsel.description != null)
+ {
description = new String(seqsel.description);
+ }
hidecols = seqsel.hidecols;
hidereps = seqsel.hidereps;
idColour = seqsel.idColour;
@@ -230,7 +240,9 @@ public class SequenceGroup implements AnnotatedCollectionI
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
@@ -285,11 +297,16 @@ public class SequenceGroup implements AnnotatedCollectionI
return eres;
}
+
+ @Override
public List getSequences()
{
return sequences;
}
- public List getSequences(Map hiddenReps)
+
+ @Override
+ public List getSequences(
+ Map hiddenReps)
{
if (hiddenReps == null)
{
@@ -301,12 +318,12 @@ public class SequenceGroup implements AnnotatedCollectionI
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))
{
SequenceCollectionI hsg = hiddenReps.get(seq);
- for (SequenceI seq2:hsg.getSequences())
+ for (SequenceI seq2 : hsg.getSequences())
{
if (seq2 != seq && !allSequences.contains(seq2))
{
@@ -320,10 +337,11 @@ public class SequenceGroup implements AnnotatedCollectionI
}
}
- public SequenceI[] getSequencesAsArray(Map map)
+ public SequenceI[] getSequencesAsArray(
+ Map map)
{
List tmp = getSequences(map);
- if (tmp==null)
+ if (tmp == null)
{
return null;
}
@@ -465,12 +483,29 @@ public class SequenceGroup implements AnnotatedCollectionI
}
/**
- * 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()
@@ -479,22 +514,17 @@ public class SequenceGroup implements AnnotatedCollectionI
{
return;
}
- if (cs!=null)
- {
- cs.alignmentChanged(this,null);
- }
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);
- cs.alignmentChanged(this,null);
}
if ((conservation != null)
@@ -514,10 +544,13 @@ public class SequenceGroup implements AnnotatedCollectionI
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
@@ -548,7 +581,7 @@ public class SequenceGroup implements AnnotatedCollectionI
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
if (consensus == null)
{
@@ -565,9 +598,10 @@ public class SequenceGroup implements AnnotatedCollectionI
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);
}
/**
@@ -608,20 +642,21 @@ public class SequenceGroup implements AnnotatedCollectionI
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return the first column selected by this group. Runs from 0<=i 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)
{
@@ -948,7 +984,8 @@ public class SequenceGroup implements AnnotatedCollectionI
* (may be null)
* @return new group containing sequences common to this group and alignment
*/
- public SequenceGroup intersect(AlignmentI alignment, Map map)
+ public SequenceGroup intersect(AlignmentI alignment,
+ Map map)
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
@@ -1029,12 +1066,12 @@ public class SequenceGroup implements AnnotatedCollectionI
{
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;
}
@@ -1166,51 +1203,60 @@ public class SequenceGroup implements AnnotatedCollectionI
/**
* set flag indicating if logo should be normalised when rendered
+ *
* @param norm
*/
public void setNormaliseSequenceLogo(boolean norm)
{
- normaliseSequenceLogo=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'
+ // TODO add in other methods like 'getAlignmentAnnotation(String label),
+ // etc'
ArrayList annot = new ArrayList();
- for (SequenceI seq:(Vector)sequences)
+ for (SequenceI seq : sequences)
{
- for (AlignmentAnnotation al: seq.getAnnotation())
+ AlignmentAnnotation[] aa = seq.getAnnotation();
+ if (aa != null)
{
- if (al.groupRef==this)
+ for (AlignmentAnnotation al : aa)
{
- annot.add(al);
+ if (al.groupRef == this)
+ {
+ annot.add(al);
+ }
}
}
}
- if (consensus!=null)
+ if (consensus != null)
{
annot.add(consensus);
}
- if (conservation!=null)
+ 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())
+ ArrayList aa = new ArrayList();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId()==calcId)
+ if (a.getCalcId() == calcId)
{
aa.add(a);
}
@@ -1218,8 +1264,75 @@ public class SequenceGroup implements AnnotatedCollectionI
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;
+ }
}