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JAL-2757 fix PDB also; suppress stack trace and compiler warnings
[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
e665982
..
dad8511
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-21,12
+21,14
@@
package jalview.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
package jalview.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
@@
-59,16
+61,16
@@
public class ChimeraCommands
* @param sequence
* @param sr
* @param fr
* @param sequence
* @param sr
* @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
* @return
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
{
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, fr, viewport);
+ sequence, sr, viewPanel);
List<String> colourCommands = buildColourCommands(colourMap);
List<String> colourCommands = buildColourCommands(colourMap);
@@
-186,10
+188,13
@@
public class ChimeraCommands
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
{
- ColumnSelection cs = viewport.getColumnSelection();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
@@
-228,14
+233,13
@@
public class ChimeraCommands
continue;
}
continue;
}
- Color colour = sr.getResidueColour(seq, r, fr);
+ Color colour = sr.getResidueColour(seq, r, finder);
/*
* darker colour for hidden regions
*/
if (!cs.isVisible(r))
{
/*
* darker colour for hidden regions
*/
if (!cs.isVisible(r))
{
- // colour = ColorUtils.darkerThan(colour);
colour = Color.GRAY;
}
colour = Color.GRAY;
}
@@
-265,8
+269,8
@@
public class ChimeraCommands
// final colour range
if (lastColour != null)
{
// final colour range
if (lastColour != null)
{
- addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
- lastChain);
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
// break;
}
}
// break;
}
@@
-310,16
+314,15
@@
public class ChimeraCommands
* @param ssm
* @param files
* @param seqs
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, fr, alignment);
+ ssm, files, seqs, viewPanel);
List<String> commands = buildSetAttributeCommands(featureMap);
List<String> commands = buildSetAttributeCommands(featureMap);
@@
-339,22
+342,28
@@
public class ChimeraCommands
* @param ssm
* @param files
* @param seqs
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ return theMap;
+ }
+
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
{
return theMap;
}
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
{
return theMap;
}
+ AlignmentI alignment = viewPanel.getAlignment();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@
-402,12
+411,8
@@
public class ChimeraCommands
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs == null)
- {
- return;
- }
-
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
@@
-418,7
+423,7
@@
public class ChimeraCommands
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
- if (isFromViewer || !visibleFeatures.contains(type))
+ if (isFromViewer)
{
continue;
}
{
continue;
}
@@
-445,8
+450,8
@@
public class ChimeraCommands
}
for (int[] range : mappedRanges)
{
}
for (int[] range : mappedRanges)
{
- addColourRange(featureValues, value, modelNumber, range[0], range[1],
- mapping.getChain());
+ addColourRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
}
}
}
@@
-508,9
+513,11
@@
public class ChimeraCommands
* to an underscore.
*
* @param featureType
* to an underscore.
*
* @param featureType
- * @return <pre>
- * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
- * </pre>
+ * @return
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
*/
protected static String makeAttributeName(String featureType)
{
*/
protected static String makeAttributeName(String featureType)
{