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patch for JAL-1853 - use given gap character to reconstruct alignment
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
c6b9cbd
..
3439248
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,11
+20,6
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
@@
-32,6
+27,11
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+
/**
* Collects a set contiguous ranges on a set of sequences
*
/**
* Collects a set contiguous ranges on a set of sequences
*
@@
-76,8
+76,10
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public ColourSchemeI cs;
*/
public ColourSchemeI cs;
+ // start column (base 0)
int startRes = 0;
int startRes = 0;
+ // end column (base 0)
int endRes = 0;
public Color outlineColour = Color.black;
int endRes = 0;
public Color outlineColour = Color.black;
@@
-1295,6
+1297,9
@@
public class SequenceGroup implements AnnotatedCollectionI
return false;
}
return false;
}
+ /**
+ * Remove all sequences from the group (leaving other properties unchanged).
+ */
public void clear()
{
synchronized (sequences)
public void clear()
{
synchronized (sequences)