X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=b4cb3b17024087dd717c678610991f0f2648a3fb;hb=a94284081155efc1183fac5d8254826db542a933;hp=5d0841e72afd4cfc60b6e62336094e354cc10fc5;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 5d0841e..b4cb3b1 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
@@ -470,12 +472,29 @@ 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()
@@ -484,10 +503,6 @@ public class SequenceGroup implements AnnotatedCollectionI
{
return;
}
- if (cs != null)
- {
- cs.alignmentChanged(this, null);
- }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -499,7 +514,6 @@ public class SequenceGroup implements AnnotatedCollectionI
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this, null);
}
if ((conservation != null)
@@ -519,10 +533,13 @@ 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
@@ -570,9 +587,10 @@ public class SequenceGroup implements AnnotatedCollectionI
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);
}
/**
@@ -1195,11 +1213,15 @@ public class SequenceGroup implements AnnotatedCollectionI
ArrayList annot = new ArrayList();
for (SequenceI seq : (Vector) 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);
+ }
}
}
}
@@ -1232,4 +1254,27 @@ public class SequenceGroup implements AnnotatedCollectionI
{
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;
+ }
}