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Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
90bdcae
..
a6f2bf4
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-54,11
+54,7
@@
public class Alignment implements AlignmentI
protected char gapCharacter = '-';
protected char gapCharacter = '-';
- protected int type = NUCLEOTIDE;
-
- public static final int PROTEIN = 0;
-
- public static final int NUCLEOTIDE = 1;
+ private boolean nucleotide = true;
public boolean hasRNAStructure = false;
public boolean hasRNAStructure = false;
@@
-76,14
+72,7
@@
public class Alignment implements AlignmentI
hiddenSequences = new HiddenSequences(this);
codonFrameList = new ArrayList<AlignedCodonFrame>();
hiddenSequences = new HiddenSequences(this);
codonFrameList = new ArrayList<AlignedCodonFrame>();
- if (Comparison.isNucleotide(seqs))
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
+ nucleotide = Comparison.isNucleotide(seqs);
sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
@@
-218,7
+207,9
@@
public class Alignment implements AlignmentI
}
/**
}
/**
- * Adds a sequence to the alignment. Recalculates maxLength and size.
+ * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+ * this currently does not recalculate whether or not the alignment is
+ * nucleotide, so mixed alignments may have undefined behaviour.
*
* @param snew
*/
*
* @param snew
*/
@@
-978,29
+969,9
@@
public class Alignment implements AlignmentI
}
@Override
}
@Override
- public void setNucleotide(boolean b)
- {
- if (b)
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
- }
-
- @Override
public boolean isNucleotide()
{
public boolean isNucleotide()
{
- if (type == NUCLEOTIDE)
- {
- return true;
- }
- else
- {
- return false;
- }
+ return nucleotide;
}
@Override
}
@Override
@@
-1591,7
+1562,6
@@
public class Alignment implements AlignmentI
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
- assert (name != null);
if (annotations != null)
{
for (AlignmentAnnotation annot : getAlignmentAnnotation())
if (annotations != null)
{
for (AlignmentAnnotation annot : getAlignmentAnnotation())
@@
-1623,14
+1593,18
@@
public class Alignment implements AlignmentI
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a : getAlignmentAnnotation())
+ List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
{
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a.getCalcId()
- .equals(calcId)))
+ for (AlignmentAnnotation a : alignmentAnnotation)
{
{
- aa.add(a);
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a
+ .getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
}
}
return aa;
}
}
return aa;