X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=752c6d4335dca76cc37d0b3e04449ca958d94fe9;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=3b9e26a8361004ae02153ae76fa3ef2b7b922377;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 3b9e26a..752c6d4 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -6,25 +6,32 @@
*
* 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
@@ -171,7 +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;
@@ -231,7 +240,9 @@ public class SequenceGroup implements AnnotatedCollectionI
}
}
if (!found)
+ {
continue;
+ }
}
AlignmentAnnotation newannot = new AlignmentAnnotation(
seq.getAnnotation()[a]);
@@ -287,11 +298,13 @@ public class SequenceGroup implements AnnotatedCollectionI
return eres;
}
+ @Override
public List getSequences()
{
return sequences;
}
+ @Override
public List getSequences(
Map hiddenReps)
{
@@ -305,7 +318,7 @@ 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 +483,7 @@ 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 +497,8 @@ 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 +549,7 @@ 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 +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, nseq); // TODO: setting container
- // for
- // ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+ // container
+ // for
+ // ignoreGapsInConsensusCalculation);
}
/**
@@ -631,6 +646,7 @@ 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)
{
@@ -1207,7 +1225,7 @@ 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)
{
AlignmentAnnotation[] aa = seq.getAnnotation();
if (aa != null)
@@ -1246,20 +1264,70 @@ 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;
+ this.context = context;
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AnnotatedCollectionI#getContext()
*/
@Override