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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
300c950
..
98510e3
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-125,8
+125,7
@@
public class Alignment implements AlignmentI
/**
* Make a new alignment from an array of SeqCigars
*
/**
* Make a new alignment from an array of SeqCigars
*
- * @param seqs
- * SeqCigar[]
+ * @param alseqs
*/
public Alignment(SeqCigar[] alseqs)
{
*/
public Alignment(SeqCigar[] alseqs)
{
@@
-399,6
+398,10
@@
public class Alignment implements AlignmentI
return null;
}
return null;
}
+ private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+ private ArrayList<SequenceGroup> temp = new ArrayList<>();
+
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
@@
-408,11
+411,15
@@
public class Alignment implements AlignmentI
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- ArrayList<SequenceGroup> temp = new ArrayList<>();
synchronized (groups)
{
int gSize = groups.size();
synchronized (groups)
{
int gSize = groups.size();
+ if (gSize == 0)
+ {
+ return noGroups;
+ }
+ temp.clear();
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
@@
-719,6
+726,17
@@
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!
*
@@
-1179,7
+1197,8
@@
public class Alignment implements AlignmentI
int maxLength = -1;
SequenceI current;
int maxLength = -1;
SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ int nseq = sequences.size();
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
@@
-1196,7
+1215,7
@@
public class Alignment implements AlignmentI
maxLength++;
int cLength;
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size(); i++)
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
{
current = getSequenceAt(i);
cLength = current.getLength();
@@
-1895,9
+1914,12
@@
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
@@
-2012,4
+2034,17
@@
public class Alignment implements AlignmentI
}
}
}
}
+ @Override
+ public void resetColors()
+ {
+ for (int i = getHeight(); --i >= 0;)
+ {
+ sequences.get(i).resetColors();
+ }
+ // if (dataset != null)
+ // {
+ // dataset.resetColors();
+ // }
+ }
+
}
}