*
*/
// TODO: [Optional] Implement toAttr() method
-public class ChimeraChain implements ChimeraStructuralObject {
+public class ChimeraChain implements ChimeraStructuralObject
+{
- /**
- * The model/subModel number this chain is a part of
- */
- private int modelNumber;
- private int subModelNumber;
+ /**
+ * The model/subModel number this chain is a part of
+ */
+ private int modelNumber;
- /**
- * A pointer to the model this chain is a part of
- */
- private ChimeraModel chimeraModel;
+ private int subModelNumber;
- /**
- * The chainID (from the PDB record)
- */
- private String chainId;
+ /**
+ * A pointer to the model this chain is a part of
+ */
+ private ChimeraModel chimeraModel;
- /**
- * The residues that are part of this chain
- */
- private TreeMap<String, ChimeraResidue> residueMap;
+ /**
+ * The chainID (from the PDB record)
+ */
+ private String chainId;
- /**
- * userData to associate with this chain
- */
- private Object userData;
+ /**
+ * The residues that are part of this chain
+ */
+ private TreeMap<String, ChimeraResidue> residueMap;
- /**
- * Flag to indicate the selection state
- */
- private boolean selected = false;
+ /**
+ * userData to associate with this chain
+ */
+ private Object userData;
- /**
- * Constructor to create a new ChimeraChain
- *
- * @param model
- * the model number this chain is part of
- * @param subModel
- * the subModel number this chain is part of
- * @param chainId
- * the chain ID for this chain
- */
- public ChimeraChain(int model, int subModel, String chainId) {
- this.modelNumber = model;
- this.subModelNumber = subModel;
- this.chainId = chainId;
- residueMap = new TreeMap<String, ChimeraResidue>();
- }
+ /**
+ * Flag to indicate the selection state
+ */
+ private boolean selected = false;
- /**
- * set the selected state of this chain
- *
- * @param selected
- * a boolean to set the selected state to
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
+ /**
+ * Constructor to create a new ChimeraChain
+ *
+ * @param model
+ * the model number this chain is part of
+ * @param subModel
+ * the subModel number this chain is part of
+ * @param chainId
+ * the chain ID for this chain
+ */
+ public ChimeraChain(int model, int subModel, String chainId)
+ {
+ this.modelNumber = model;
+ this.subModelNumber = subModel;
+ this.chainId = chainId;
+ residueMap = new TreeMap<String, ChimeraResidue>();
+ }
- /**
- * return the selected state of this chain
- *
- * @return the selected state
- */
- public boolean isSelected() {
- return selected;
- }
+ /**
+ * set the selected state of this chain
+ *
+ * @param selected
+ * a boolean to set the selected state to
+ */
+ public void setSelected(boolean selected)
+ {
+ this.selected = selected;
+ }
- public boolean hasSelectedChildren() {
- if (selected) {
- return true;
- } else {
- for (ChimeraResidue residue : getResidues()) {
- if (residue.isSelected())
- return true;
- }
- }
- return false;
- }
+ /**
+ * return the selected state of this chain
+ *
+ * @return the selected state
+ */
+ public boolean isSelected()
+ {
+ return selected;
+ }
- /**
- * Return the list of selected residues
- *
- * @return all selected residues
- */
- public List<ChimeraResidue> getSelectedResidues() {
- List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
- if (selected) {
- residueList.addAll(getResidues());
- } else {
- for (ChimeraResidue residue : getResidues()) {
- if (residue.isSelected())
- residueList.add(residue);
- }
- }
- return residueList;
- }
+ public boolean hasSelectedChildren()
+ {
+ if (selected)
+ {
+ return true;
+ }
+ else
+ {
+ for (ChimeraResidue residue : getResidues())
+ {
+ if (residue.isSelected())
+ return true;
+ }
+ }
+ return false;
+ }
- /**
- * Add a residue to the chain.
- *
- * @param residue
- * the ChimeraResidue to add to the chain.
- */
- public void addResidue(ChimeraResidue residue) {
- String index = residue.getIndex();
- // Put it in our map so that we can return it in order
- residueMap.put(index, residue);
- }
+ /**
+ * Return the list of selected residues
+ *
+ * @return all selected residues
+ */
+ public List<ChimeraResidue> getSelectedResidues()
+ {
+ List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
+ if (selected)
+ {
+ residueList.addAll(getResidues());
+ }
+ else
+ {
+ for (ChimeraResidue residue : getResidues())
+ {
+ if (residue.isSelected())
+ residueList.add(residue);
+ }
+ }
+ return residueList;
+ }
- /**
- * Return the list of residues in this chain in pdb residue order
- *
- * @return a Collection of residues in residue order
- */
- public Collection<ChimeraResidue> getResidues() {
- return residueMap.values();
- }
+ /**
+ * Add a residue to the chain.
+ *
+ * @param residue
+ * the ChimeraResidue to add to the chain.
+ */
+ public void addResidue(ChimeraResidue residue)
+ {
+ String index = residue.getIndex();
+ // Put it in our map so that we can return it in order
+ residueMap.put(index, residue);
+ }
- /**
- * Return the list of residues in this chain as a list
- *
- * @return List of residues
- */
- public List<ChimeraStructuralObject> getChildren() {
- return new ArrayList<ChimeraStructuralObject>(residueMap.values());
- }
+ /**
+ * Return the list of residues in this chain in pdb residue order
+ *
+ * @return a Collection of residues in residue order
+ */
+ public Collection<ChimeraResidue> getResidues()
+ {
+ return residueMap.values();
+ }
- /**
- * Get a specific residue
- *
- * @param residueIndex
- * String representation of the residue index
- * @return the ChimeraResidue represented by the residueIndex
- */
- public ChimeraResidue getResidue(String index) {
- // Integer index = new Integer(residueIndex);
- if (residueMap.containsKey(index))
- return residueMap.get(index);
- return null;
- }
+ /**
+ * Return the list of residues in this chain as a list
+ *
+ * @return List of residues
+ */
+ public List<ChimeraStructuralObject> getChildren()
+ {
+ return new ArrayList<ChimeraStructuralObject>(residueMap.values());
+ }
- /**
- * Get a list of residues as a residue range
- *
- * @param residueRange
- * String representation of the residue range
- * @return the List of ChimeraResidues represented by the range
- */
- public List<ChimeraResidue> getResidueRange(String residueRange) {
- String[] range = residueRange.split("-", 2);
- if (range[1] == null || range[1].length() == 0) {
- range[1] = range[0];
- }
- List<ChimeraResidue> resultRange = new ArrayList<ChimeraResidue>();
- int start = Integer.parseInt(range[0]);
- int end = Integer.parseInt(range[1]);
- for (int i = start; i <= end; i++) {
- String index = String.valueOf(i);
- if (residueMap.containsKey(index))
- resultRange.add(residueMap.get(index));
- }
- return resultRange;
- }
+ /**
+ * Get a specific residue
+ *
+ * @param residueIndex
+ * String representation of the residue index
+ * @return the ChimeraResidue represented by the residueIndex
+ */
+ public ChimeraResidue getResidue(String index)
+ {
+ // Integer index = new Integer(residueIndex);
+ if (residueMap.containsKey(index))
+ return residueMap.get(index);
+ return null;
+ }
- /**
- * Get the ID for this chain
- *
- * @return String value of the chainId
- */
- public String getChainId() {
- return chainId;
- }
+ /**
+ * Get a list of residues as a residue range
+ *
+ * @param residueRange
+ * String representation of the residue range
+ * @return the List of ChimeraResidues represented by the range
+ */
+ public List<ChimeraResidue> getResidueRange(String residueRange)
+ {
+ String[] range = residueRange.split("-", 2);
+ if (range[1] == null || range[1].length() == 0)
+ {
+ range[1] = range[0];
+ }
+ List<ChimeraResidue> resultRange = new ArrayList<ChimeraResidue>();
+ int start = Integer.parseInt(range[0]);
+ int end = Integer.parseInt(range[1]);
+ for (int i = start; i <= end; i++)
+ {
+ String index = String.valueOf(i);
+ if (residueMap.containsKey(index))
+ resultRange.add(residueMap.get(index));
+ }
+ return resultRange;
+ }
- /**
- * Get the model number for this chain
- *
- * @return the model number
- */
- public int getModelNumber() {
- return modelNumber;
- }
+ /**
+ * Get the ID for this chain
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId()
+ {
+ return chainId;
+ }
- /**
- * Get the sub-model number for this chain
- *
- * @return the sub-model number
- */
- public int getSubModelNumber() {
- return subModelNumber;
- }
+ /**
+ * Get the model number for this chain
+ *
+ * @return the model number
+ */
+ public int getModelNumber()
+ {
+ return modelNumber;
+ }
- /**
- * Return a string representation of this chain as follows: Chain <i>chainId</i>
- * (<i>residue_count</i> residues)
- *
- * @return String representation of chain
- */
- public String displayName() {
- if (chainId.equals("_")) {
- return ("Chain (no ID) (" + getResidueCount() + " residues)");
- } else {
- return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
- }
- }
+ /**
+ * Get the sub-model number for this chain
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber()
+ {
+ return subModelNumber;
+ }
- /**
- * Return a string representation of this chain as follows: Node xxx [Model yyyy Chain
- * <i>chainId</i>]
- *
- * @return String representation of chain
- */
- public String toString() {
- String displayName = chimeraModel.getModelName();
- if (displayName.length() > 14)
- displayName = displayName.substring(0, 13) + "...";
- if (chainId.equals("_")) {
- return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
- } else {
- return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
- }
- }
+ /**
+ * Return a string representation of this chain as follows: Chain
+ * <i>chainId</i> (<i>residue_count</i> residues)
+ *
+ * @return String representation of chain
+ */
+ public String displayName()
+ {
+ if (chainId.equals("_"))
+ {
+ return ("Chain (no ID) (" + getResidueCount() + " residues)");
+ }
+ else
+ {
+ return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
+ }
+ }
- /**
- * Return the Chimera specification for this chain
- *
- * @return Chimera specification
- */
- public String toSpec() {
- if (chainId.equals("_")) {
- return ("#" + modelNumber + "." + subModelNumber + ":.");
- } else {
- return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
- }
- }
+ /**
+ * Return a string representation of this chain as follows: Node xxx [Model
+ * yyyy Chain <i>chainId</i>]
+ *
+ * @return String representation of chain
+ */
+ public String toString()
+ {
+ String displayName = chimeraModel.getModelName();
+ if (displayName.length() > 14)
+ displayName = displayName.substring(0, 13) + "...";
+ if (chainId.equals("_"))
+ {
+ return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
+ }
+ else
+ {
+ return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
+ }
+ }
- /**
- * Return the number of residues in this chain
- *
- * @return integer number of residues
- */
- public int getResidueCount() {
- return residueMap.size();
- }
+ /**
+ * Return the Chimera specification for this chain
+ *
+ * @return Chimera specification
+ */
+ public String toSpec()
+ {
+ if (chainId.equals("_"))
+ {
+ return ("#" + modelNumber + "." + subModelNumber + ":.");
+ }
+ else
+ {
+ return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
+ }
+ }
- /**
- * Set the ChimeraModel for this chain
- *
- * @param model
- * ChimeraModel to associate with this chain
- */
- public void setChimeraModel(ChimeraModel model) {
- this.chimeraModel = model;
- }
+ /**
+ * Return the number of residues in this chain
+ *
+ * @return integer number of residues
+ */
+ public int getResidueCount()
+ {
+ return residueMap.size();
+ }
- /**
- * Get the ChimeraModel for this chain
- *
- * @return ChimeraModel associated with this chain
- */
- public ChimeraModel getChimeraModel() {
- return chimeraModel;
- }
+ /**
+ * Set the ChimeraModel for this chain
+ *
+ * @param model
+ * ChimeraModel to associate with this chain
+ */
+ public void setChimeraModel(ChimeraModel model)
+ {
+ this.chimeraModel = model;
+ }
- /**
- * Get the user data for this Chain
- *
- * @return user data
- */
- public Object getUserData() {
- return userData;
- }
+ /**
+ * Get the ChimeraModel for this chain
+ *
+ * @return ChimeraModel associated with this chain
+ */
+ public ChimeraModel getChimeraModel()
+ {
+ return chimeraModel;
+ }
- /**
- * Set the user data for this Chain
- *
- * @param data
- * the user data to associate with this chain
- */
- public void setUserData(Object data) {
- this.userData = data;
- }
+ /**
+ * Get the user data for this Chain
+ *
+ * @return user data
+ */
+ public Object getUserData()
+ {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this Chain
+ *
+ * @param data
+ * the user data to associate with this chain
+ */
+ public void setUserData(Object data)
+ {
+ this.userData = data;
+ }
}
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