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JAL-4089 use column selection to superpose if 4 or more selected
[jalview.git]
/
src
/
jalview
/
structures
/
models
/
AAStructureBindingModel.java
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
3414e95
..
8436b48
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-20,8
+20,6
@@
*/
package jalview.structures.models;
*/
package jalview.structures.models;
-import java.util.Locale;
-
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
@@
-31,6
+29,7
@@
import java.util.BitSet;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.SwingUtilities;
import java.util.Map;
import javax.swing.SwingUtilities;
@@
-43,6
+42,7
@@
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
@@
-61,6
+61,7
@@
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
@@
-69,9
+70,9
@@
import jalview.util.MessageManager;
/**
*
/**
*
- * A base class to hold common function for 3D structure model binding.
- * Initial version created by refactoring JMol and Chimera binding models, but
- * other structure viewers could in principle be accommodated in future.
+ * A base class to hold common function for 3D structure model binding. Initial
+ * version created by refactoring JMol and Chimera binding models, but other
+ * structure viewers could in principle be accommodated in future.
*
* @author gmcarstairs
*
*
* @author gmcarstairs
*
@@
-91,6
+92,9
@@
public abstract class AAStructureBindingModel
public String chain = "";
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
public boolean isRna;
/*
@@
-167,6
+171,9
@@
public abstract class AAStructureBindingModel
protected boolean colourBySequence = true;
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
private boolean nucleotide;
private boolean finishedInit = false;
@@
-584,7
+591,6
@@
public abstract class AAStructureBindingModel
}
}
}
}
}
}
-
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
@@
-716,7
+722,7
@@
public abstract class AAStructureBindingModel
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
/*
* move on to next pdb file (ignore sequences for other chains
@@
-865,21
+871,39
@@
public abstract class AAStructureBindingModel
{
AlignmentI alignment = view.getAlignment();
HiddenColumns hiddenCols = alignment.getHiddenColumns();
{
AlignmentI alignment = view.getAlignment();
HiddenColumns hiddenCols = alignment.getHiddenColumns();
-
/*
* 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to their PDB structure
*/
/*
* 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to their PDB structure
*/
- BitSet matched = new BitSet();
final int width = alignment.getWidth();
final int width = alignment.getWidth();
- for (int m = 0; m < width; m++)
+ BitSet matched = new BitSet();
+ ColumnSelection cs = view.getAlignViewport().getColumnSelection();
+ // restrict to active column selection, if there is one
+ if (cs != null && cs.hasSelectedColumns()
+ && cs.getSelected().size() >= 4)
{
{
- if (hiddenCols == null || hiddenCols.isVisible(m))
+ for (int s : cs.getSelected())
{
{
- matched.set(m);
+ if (hiddenCols == null)
+ {
+ matched.set(s);
+ }
+ else
+ {
+ matched.set(hiddenCols.visibleToAbsoluteColumn(s));
+ }
+ }
+ }
+ else
+ {
+ for (int m = 0; m < width; m++)
+ {
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
}
}
}
-
AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
@@
-919,6
+943,11
@@
public abstract class AAStructureBindingModel
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
+ AtomSpecType backbone = structures[refStructure].isRna
+ ? AtomSpecType.PHOSPHATE
+ : AtomSpecType.ALPHA;
+ List<AtomSpecModel> models = new ArrayList<AtomSpecModel>();
+ models.add(refAtoms);
/*
* superpose each (other) structure to the reference in turn
*/
/*
* superpose each (other) structure to the reference in turn
*/
@@
-928,20
+957,24
@@
public abstract class AAStructureBindingModel
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
// return this error (Chimera only) to the user
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT)
+ .contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
}
{
error += "; " + reply;
}
}
+ models.add(atomSpec);
}
}
}
}
+ List<StructureCommandI> finalView = commandGenerator
+ .centerViewOn(models);
+ executeCommands(finalView, false, "Centered on Superposition");
}
}
-
return error;
}
return error;
}
@@
-1270,6
+1303,12
@@
public abstract class AAStructureBindingModel
@Override
public void updateColours(Object source)
{
@Override
public void updateColours(Object source)
{
+ if (getViewer() == null)
+ {
+ // can happen if a viewer was not instantiated or cleaned up and is still
+ // registered - mostly during tests
+ return;
+ }
AlignmentViewPanel ap = (AlignmentViewPanel) source;
// ignore events from panels not used to colour this view
if (!getViewer().isUsedForColourBy(ap))
AlignmentViewPanel ap = (AlignmentViewPanel) source;
// ignore events from panels not used to colour this view
if (!getViewer().isUsedForColourBy(ap))