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Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0
[jalview.git]
/
src
/
jalview
/
analysis
/
Grouping.java
diff --git
a/src/jalview/analysis/Grouping.java
b/src/jalview/analysis/Grouping.java
index
165a3df
..
def5d5a
100644
(file)
--- a/
src/jalview/analysis/Grouping.java
+++ b/
src/jalview/analysis/Grouping.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.
*
@@
-91,8
+91,8
@@
public class Grouping
i = 0;
for (String key : gps.keySet())
{
i = 0;
for (String key : gps.keySet())
{
- SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
- + key, null, true, true, false, 0, width - 1);
+ SequenceGroup group = new SequenceGroup(gps.get(key),
+ "Subseq: " + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
}
groups[i++] = group;
}
@@
-178,8
+178,8
@@
public class Grouping
i = 0;
for (String key : gps.keySet())
{
i = 0;
for (String key : gps.keySet())
{
- SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
- + key, null, true, true, false, 0, width - 1);
+ SequenceGroup group = new SequenceGroup(gps.get(key),
+ "Subseq: " + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
}
groups[i++] = group;
}
@@
-269,7
+269,7
@@
public class Grouping
* seqs.length) { for (int i = 0; i < seqs.length; i++) { if (!hasScore[i])
* { scores[i] = (max + i); } else { int nf=(feats[i]==null) ? 0
* :((SequenceFeature[]) feats[i]).length;
* seqs.length) { for (int i = 0; i < seqs.length; i++) { if (!hasScore[i])
* { scores[i] = (max + i); } else { int nf=(feats[i]==null) ? 0
* :((SequenceFeature[]) feats[i]).length;
- * System.err.println("Sorting on Score: seq "+seqs[i].getName()+
+ * jalview.bin.Console.errPrintln("Sorting on Score: seq "+seqs[i].getName()+
* " Feats: "+nf+" Score : "+scores[i]); } } }
*
* jalview.util.QuickSort.sort(scores, seqs); } else if
* " Feats: "+nf+" Score : "+scores[i]); } } }
*
* jalview.util.QuickSort.sort(scores, seqs); } else if
@@
-280,7
+280,7
@@
public class Grouping
* (int i=0;i<seqs.length; i++) { double nf; scores[i] =
* (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[])
* feats[i]).length));
* (int i=0;i<seqs.length; i++) { double nf; scores[i] =
* (0.05+fr*i)+(nf=((feats[i]==null) ? 0.0 :1.0*((SequenceFeature[])
* feats[i]).length));
- * System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+ * jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
* " Feats: "+nf+" Score : "+scores[i]); }
* jalview.util.QuickSort.sort(scores, seqs); } else { if
* (method==FEATURE_LABEL) { throw new Error("Not yet implemented."); } } if
* " Feats: "+nf+" Score : "+scores[i]); }
* jalview.util.QuickSort.sort(scores, seqs); } else { if
* (method==FEATURE_LABEL) { throw new Error("Not yet implemented."); } } if