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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
analysis
/
Grouping.java
diff --git
a/src/jalview/analysis/Grouping.java
b/src/jalview/analysis/Grouping.java
index
ddf483b
..
def5d5a
100644
(file)
--- a/
src/jalview/analysis/Grouping.java
+++ b/
src/jalview/analysis/Grouping.java
@@
-25,7
+25,6
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@
-92,8
+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;
}
@@
-128,6
+127,11
@@
public class Grouping
}
}
}
}
}
}
+
+ /*
+ * get selected columns (in the order they were selected);
+ * note this could include right-to-left ranges
+ */
int[] spos = new int[cs.getSelected().size()];
int width = -1;
int i = 0;
int[] spos = new int[cs.getSelected().size()];
int width = -1;
int i = 0;
@@
-136,11
+140,6
@@
public class Grouping
spos[i++] = pos.intValue();
}
spos[i++] = pos.intValue();
}
- /*
- * ensure column selection is in ascending order
- */
- Arrays.sort(spos);
-
for (i = 0; i < sequences.length; i++)
{
int slen = sequences[i].getLength();
for (i = 0; i < sequences.length; i++)
{
int slen = sequences[i].getLength();
@@
-179,8
+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;
}
@@
-270,7
+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
@@
-281,7
+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