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JAL-2961 centerViewOn command for structure viewers - called after superposition
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 28 Oct 2022 14:45:22 +0000
(15:45 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 28 Oct 2022 15:29:30 +0000
(16:29 +0100)
src/jalview/ext/jmol/JmolCommands.java
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src/jalview/ext/pymol/PymolCommands.java
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src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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src/jalview/structure/StructureCommandsI.java
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diff --git
a/src/jalview/ext/jmol/JmolCommands.java
b/src/jalview/ext/jmol/JmolCommands.java
index
58b69ef
..
19d64f0
100644
(file)
--- a/
src/jalview/ext/jmol/JmolCommands.java
+++ b/
src/jalview/ext/jmol/JmolCommands.java
@@
-40,7
+40,6
@@
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
-import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
import jalview.util.Platform;
import jalview.util.Comparison;
import jalview.util.Platform;
@@
-207,7
+206,22
@@
public class JmolCommands extends StructureCommandsBase
.append("|");
sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
.append(getCommandSeparator()).append("cartoons");
.append("|");
sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
.append(getCommandSeparator()).append("cartoons");
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("center ");
+ for (AtomSpecModel ranges : residues)
+ {
+ if (sb.length() > 9)
+ {
+ sb.append(" or ");
+ }
+ sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
+ }
return Arrays.asList(new StructureCommand(sb.toString()));
}
return Arrays.asList(new StructureCommand(sb.toString()));
}
diff --git
a/src/jalview/ext/pymol/PymolCommands.java
b/src/jalview/ext/pymol/PymolCommands.java
index
b8b6a98
..
08521a2
100644
(file)
--- a/
src/jalview/ext/pymol/PymolCommands.java
+++ b/
src/jalview/ext/pymol/PymolCommands.java
@@
-363,4
+363,11
@@
public class PymolCommands extends StructureCommandsBase
return CLOSE_PYMOL;
}
return CLOSE_PYMOL;
}
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
}
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
d3dd625
..
829f092
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-20,19
+20,17
@@
*/
package jalview.ext.rbvi.chimera;
*/
package jalview.ext.rbvi.chimera;
-import java.util.Locale;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
import java.util.Map;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
-import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.ColorUtils;
/**
import jalview.util.ColorUtils;
/**
@@
-456,4
+454,11
@@
public class ChimeraCommands extends StructureCommandsBase
return new StructureCommand("list residues attr '" + attName + "'");
}
return new StructureCommand("list residues attr '" + attName + "'");
}
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
}
diff --git
a/src/jalview/structure/StructureCommandsI.java
b/src/jalview/structure/StructureCommandsI.java
index
c8c8070
..
575f256
100644
(file)
--- a/
src/jalview/structure/StructureCommandsI.java
+++ b/
src/jalview/structure/StructureCommandsI.java
@@
-243,4
+243,6
@@
public interface StructureCommandsI
* @return
*/
StructureCommandI getResidueAttributes(String attName);
* @return
*/
StructureCommandI getResidueAttributes(String attName);
+
+ List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues);
}
}