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Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
93ad332
..
5ad8be1
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-21,7
+21,6
@@
package jalview.datamodel;
import jalview.analysis.AlignmentUtils;
package jalview.datamodel;
import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.io.FastaFile;
import jalview.util.Comparison;
import jalview.util.LinkedIdentityHashSet;
import jalview.io.FastaFile;
import jalview.util.Comparison;
import jalview.util.LinkedIdentityHashSet;
@@
-47,7
+46,7
@@
import java.util.Vector;
* @author JimP
*
*/
* @author JimP
*
*/
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
{
private Alignment dataset;
{
private Alignment dataset;
@@
-302,15
+301,20
@@
public class Alignment implements AlignmentI
}
@Override
}
@Override
- public void finalize() throws Throwable
+ public void close()
{
if (getDataset() != null)
{
{
if (getDataset() != null)
{
- getDataset().removeAlignmentRef();
+ try
+ {
+ getDataset().removeAlignmentRef();
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
}
nullReferences();
}
nullReferences();
- super.finalize();
}
/**
}
/**
@@
-717,6
+721,17
@@
public class Alignment implements AlignmentI
return maxLength;
}
return maxLength;
}
+ @Override
+ public int getVisibleWidth()
+ {
+ int w = getWidth();
+ if (hiddenCols != null)
+ {
+ w -= hiddenCols.getSize();
+ }
+ return w;
+ }
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-1130,7
+1145,7
@@
public class Alignment implements AlignmentI
// verify all mappings are in dataset
for (AlignedCodonFrame cf : codonFrameList)
{
// verify all mappings are in dataset
for (AlignedCodonFrame cf : codonFrameList)
{
- for (SequenceToSequenceMapping ssm : cf.getMappings())
+ for (SequenceMapping ssm : cf.getMappings())
{
if (!seqs.contains(ssm.getFromSeq()))
{
{
if (!seqs.contains(ssm.getFromSeq()))
{
@@
-1893,9
+1908,12
@@
public class Alignment implements AlignmentI
}
@Override
}
@Override
- public void setHiddenColumns(HiddenColumns cols)
+ public boolean setHiddenColumns(HiddenColumns cols)
{
{
+ boolean changed = cols == null ? hiddenCols != null
+ : !cols.equals(hiddenCols);
hiddenCols = cols;
hiddenCols = cols;
+ return changed;
}
@Override
}
@Override