X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=b4cb3b17024087dd717c678610991f0f2648a3fb;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=3b9e26a8361004ae02153ae76fa3ef2b7b922377;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 3b9e26a..b4cb3b1 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -6,14 +6,16 @@
*
* 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;
@@ -470,7 +472,7 @@ public class SequenceGroup implements AnnotatedCollectionI
}
/**
- * Max Gaps Threshold (percent) for performing a conservation calculation
+ * Max Gaps Threshold (percent) for performing a conservation calculation
*/
private int consPercGaps = 25;
@@ -484,7 +486,8 @@ public class SequenceGroup implements AnnotatedCollectionI
/**
* set Max Gaps Threshold (percent) for performing a conservation calculation
- * @param consPercGaps
+ *
+ * @param consPercGaps
*/
public void setConsPercGaps(int consPercGaps)
{
@@ -535,7 +538,7 @@ public class SequenceGroup implements AnnotatedCollectionI
}
if (cs != null)
{
- cs.alignmentChanged(context!=null ? context : this, null);
+ cs.alignmentChanged(context != null ? context : this, null);
}
} catch (java.lang.OutOfMemoryError err)
{
@@ -584,9 +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);
}
/**
@@ -1250,16 +1254,22 @@ 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;
+ this.context = context;
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AnnotatedCollectionI#getContext()
*/
@Override