+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structure;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
-
import java.awt.Color;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import jalview.bin.Console;
+
/**
* A base class holding methods useful to all classes that implement commands
* for structure viewers
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
private static final String CMD_SEPARATOR = ";";
/**
*
* @return
*/
- protected static String getCommandSeparator()
+ protected String getCommandSeparator()
{
return CMD_SEPARATOR;
}
- @Override
- public String[] setAttributesForFeatures(StructureSelectionManager ssm,
- String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
- {
- // default does nothing, override where this is implemented
- return null;
- }
-
/**
* Returns the lowest model number used by the structure viewer
*
}
/**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
+ * Helper method to add one contiguous range to the AtomSpec model for the
+ * given value (creating the model if necessary). As used by Jalview,
+ * {@code value} is
* <ul>
* <li>a colour, when building a 'colour structure by sequence' command</li>
* <li>a feature value, when building a 'set Chimera attributes from features'
* @param chain
*/
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
- Object value,
- int model, int startPos, int endPos, String chain)
+ Object value, String model, int startPos, int endPos,
+ String chain)
{
/*
* Get/initialize map of data for the colour
atomSpec = new AtomSpecModel();
map.put(value, atomSpec);
}
-
+
atomSpec.addRange(model, startPos, endPos, chain);
}
/**
+ * Makes a structure viewer attribute name for a Jalview feature type by
+ * prefixing it with "jv_", and replacing any non-alphanumeric characters with
+ * an underscore
+ *
+ * @param featureType
+ * @return
+ */
+ protected String makeAttributeName(String featureType)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
+ {
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
+ }
+ String attName = NAMESPACE_PREFIX + sb.toString();
+ return attName;
+ }
+
+ /**
* Traverse the map of colours/models/chains/positions to construct a list of
* 'color' commands (one per distinct colour used). The format of each command
* is specific to the structure viewer.
+ * <p>
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
*
* @param colourMap
* @return
*/
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+ public List<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> colourMap)
{
- /*
- * This version concatenates all commands into a single String (semi-colon
- * delimited). If length limit issues arise, refactor to return one color
- * command per colour.
- */
- List<String> commands = new ArrayList<>();
- StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ List<StructureCommandI> commands = new ArrayList<>();
+ StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+ boolean first = true;
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
- if (!firstColour)
+ final AtomSpecModel colourData = colourMap.get(colour);
+ StructureCommandI command = getColourCommand(colourData, colour);
+ if (!first)
{
- sb.append(getCommandSeparator()).append(" ");
+ sb.append(getCommandSeparator());
}
- firstColour = false;
- final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(getColourCommand(colourData, colour));
+ first = false;
+ sb.append(command.getCommand());
}
- commands.add(sb.toString());
- return commands.toArray(new String[commands.size()]);
+ commands.add(new StructureCommand(sb.toString()));
+ return commands;
}
/**
* @param colour
* @return
*/
- protected String getColourCommand(AtomSpecModel atomSpecModel, Color colour)
+ protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
+ Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
- return getColourCommand(atomSpec, colour);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
+ return colourResidues(atomSpec, colour);
}
/**
* @param colour
* @return
*/
- protected abstract String getColourCommand(String atomSpec, Color colour);
+ protected abstract StructureCommandI colourResidues(String atomSpec,
+ Color colour);
@Override
- public String colourByResidues(Map<String, Color> colours)
+ public List<StructureCommandI> colourByResidues(
+ Map<String, Color> colours)
{
- StringBuilder cmd = new StringBuilder(12 * colours.size());
-
+ List<StructureCommandI> commands = new ArrayList<>();
for (Entry<String, Color> entry : colours.entrySet())
{
- String residue = entry.getKey();
- String atomSpec = getResidueSpec(residue);
- cmd.append(getColourCommand(atomSpec, entry.getValue()));
- cmd.append(getCommandSeparator());
+ commands.add(colourResidue(entry.getKey(), entry.getValue()));
}
- return cmd.toString();
+ return commands;
+ }
+
+ private StructureCommandI colourResidue(String resName, Color col)
+ {
+ String atomSpec = getResidueSpec(resName);
+ return colourResidues(atomSpec, col);
}
/**
* @return
*/
protected abstract String getResidueSpec(String residue);
+
+ @Override
+ public List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI restoreSession(String filePath)
+ {
+ return loadFile(filePath);
+ }
}
git://source.jalview.org / jalview.git / blobdiff