git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2446 merged to spike branch
[jalview.git]
/
src
/
jalview
/
ext
/
varna
/
VarnaCommands.java
diff --git
a/src/jalview/ext/varna/VarnaCommands.java
b/src/jalview/ext/varna/VarnaCommands.java
index
75afcbd
..
d65f1d5
100644
(file)
--- a/
src/jalview/ext/varna/VarnaCommands.java
+++ b/
src/jalview/ext/varna/VarnaCommands.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.
*
@@
-20,10
+20,10
@@
*/
package jalview.ext.varna;
*/
package jalview.ext.varna;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
@@
-47,7
+47,8
@@
public class VarnaCommands
*/
public static String[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
*/
public static String[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ SequenceI[][] sequence, SequenceRenderer sr,
+ FeatureColourFinder finder,
AlignmentI alignment)
{
ArrayList<String> str = new ArrayList<String>();
AlignmentI alignment)
{
ArrayList<String> str = new ArrayList<String>();
@@
-58,7
+59,9
@@
public class VarnaCommands
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
if (mapping == null || mapping.length < 1)
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
if (mapping == null || mapping.length < 1)
+ {
continue;
continue;
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
@@
-79,14
+82,15
@@
public class VarnaCommands
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
continue;
+ }
lastPos = pos;
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"