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JAL-98 ProfileI interface for Profile
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
c0e36b1
..
2870a2c
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 2.9.0b2)
- * Copyright (C) 2015 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.
*
@@
-26,10
+26,8
@@
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
import java.util.ArrayList;
import java.awt.Color;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
/**
* Collects a set contiguous ranges on a set of sequences
/**
* Collects a set contiguous ranges on a set of sequences
@@
-45,8
+43,6
@@
public class SequenceGroup implements AnnotatedCollectionI
Conservation conserve;
Conservation conserve;
- Vector aaFrequency;
-
boolean displayBoxes = true;
boolean displayText = true;
boolean displayBoxes = true;
boolean displayText = true;
@@
-531,7
+527,7
@@
public class SequenceGroup implements AnnotatedCollectionI
boolean upd = false;
try
{
boolean upd = false;
try
{
- Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+ ProfileI[] cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
if (consensus != null)
{
endRes + 1, showSequenceLogo);
if (consensus != null)
{
@@
-603,9
+599,9
@@
public class SequenceGroup implements AnnotatedCollectionI
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
- public Hashtable[] consensusData = null;
+ public ProfileI[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+ private void _updateConsensusRow(ProfileI[] cnsns, long nseq)
{
if (consensus == null)
{
{
if (consensus == null)
{