X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=17348c2cf08763271f3bf1fc3300e8293f209fbb;hb=341e759bcdf94d50e58217f55a87f25a44eeef54;hp=521bdbedb7cfa4ce33834eac54440785b1cb2880;hpb=279af6f3b1803de7a1e467b83a7205df18e70d48;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 521bdbe..17348c2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,30 +1,37 @@
/*
- * 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;
-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
@@ -287,11 +294,13 @@ public class SequenceGroup implements AnnotatedCollectionI
return eres;
}
+ @Override
public List getSequences()
{
return sequences;
}
+ @Override
public List getSequences(
Map hiddenReps)
{
@@ -305,7 +314,7 @@ 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))
{
@@ -470,7 +479,7 @@ 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 +493,8 @@ public class SequenceGroup implements AnnotatedCollectionI
/**
* set Max Gaps Threshold (percent) for performing a conservation calculation
- * @param consPercGaps
+ *
+ * @param consPercGaps
*/
public void setConsPercGaps(int consPercGaps)
{
@@ -500,10 +510,6 @@ public class SequenceGroup implements AnnotatedCollectionI
{
return;
}
- if (cs != null)
- {
- cs.alignmentChanged(this, null);
- }
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -515,7 +521,6 @@ public class SequenceGroup implements AnnotatedCollectionI
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this, null);
}
if ((conservation != null)
@@ -535,10 +540,13 @@ 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
@@ -586,9 +594,10 @@ 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);
}
/**
@@ -633,6 +642,7 @@ public class SequenceGroup implements AnnotatedCollectionI
*
* @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)
{
@@ -1209,13 +1221,17 @@ public class SequenceGroup implements AnnotatedCollectionI
// 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);
+ }
}
}
}
@@ -1244,8 +1260,52 @@ public class SequenceGroup implements AnnotatedCollectionI
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;
+ }
}