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JAL-3518 more pull up / test coverage of structure command generation
[jalview.git]
/
src
/
jalview
/
ext
/
rbvi
/
chimera
/
ChimeraCommands.java
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
14699ef
..
1b1dd35
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-62,14
+62,6
@@
public class ChimeraCommands extends StructureCommandsBase
private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
@Override
private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
- {
- List<String> colourCommands = buildColourCommands(colourMap);
-
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
-
- @Override
public String getColourCommand(String atomSpec, Color colour)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
public String getColourCommand(String atomSpec, Color colour)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
@@
-83,7
+75,6
@@
public class ChimeraCommands extends StructureCommandsBase
* @param colour
* @return
*/
* @param colour
* @return
*/
- @Override
protected String getColourString(Color colour)
{
return ColorUtils.toTkCode(colour);
protected String getColourString(Color colour)
{
return ColorUtils.toTkCode(colour);
@@
-108,9
+99,7
@@
public class ChimeraCommands extends StructureCommandsBase
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- return commands.toArray(new String[commands.size()]);
+ return setAttributes(featureMap);
}
/**
}
/**
@@
-354,7
+343,7
@@
public class ChimeraCommands extends StructureCommandsBase
* @param featureMap
* @return
*/
* @param featureMap
* @return
*/
- protected List<String> buildSetAttributeCommands(
+ protected String[] setAttributes(
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
@@
-379,13
+368,13
@@
public class ChimeraCommands extends StructureCommandsBase
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- String cmd = getSetAttributeCommand(attributeName, featureValue,
+ String cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
}
atomSpecModel);
commands.add(cmd);
}
}
- return commands;
+ return commands.toArray(new String[commands.size()]);
}
/**
}
/**
@@
-401,7
+390,7
@@
public class ChimeraCommands extends StructureCommandsBase
* @param atomSpecModel
* @return
*/
* @param atomSpecModel
* @return
*/
- protected String getSetAttributeCommand(String attributeName,
+ protected String setAttribute(String attributeName,
String attributeValue,
AtomSpecModel atomSpecModel)
{
String attributeValue,
AtomSpecModel atomSpecModel)
{