--- /dev/null
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package ext.edu.ucsf.rbvi.strucviz2;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.TreeMap;
+
+/**
+ * This class provides the implementation for the ChimeraChain object
+ *
+ * @author scooter
+ *
+ */
+// TODO: [Optional] Implement toAttr() method
+public class ChimeraChain implements ChimeraStructuralObject {
+
+ /**
+ * The model/subModel number this chain is a part of
+ */
+ private int modelNumber;
+ private int subModelNumber;
+
+ /**
+ * A pointer to the model this chain is a part of
+ */
+ private ChimeraModel chimeraModel;
+
+ /**
+ * The chainID (from the PDB record)
+ */
+ private String chainId;
+
+ /**
+ * The residues that are part of this chain
+ */
+ private TreeMap<String, ChimeraResidue> residueMap;
+
+ /**
+ * userData to associate with this chain
+ */
+ private Object userData;
+
+ /**
+ * Flag to indicate the selection state
+ */
+ private boolean selected = false;
+
+ /**
+ * 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>();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * return the selected state of this chain
+ *
+ * @return the selected state
+ */
+ public boolean isSelected() {
+ return selected;
+ }
+
+ public boolean hasSelectedChildren() {
+ if (selected) {
+ return true;
+ } else {
+ for (ChimeraResidue residue : getResidues()) {
+ if (residue.isSelected())
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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 in pdb residue order
+ *
+ * @return a Collection of residues in residue order
+ */
+ public Collection<ChimeraResidue> getResidues() {
+ return residueMap.values();
+ }
+
+ /**
+ * 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 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 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 ID for this chain
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId() {
+ return chainId;
+ }
+
+ /**
+ * Get the model number for this chain
+ *
+ * @return the model number
+ */
+ public int getModelNumber() {
+ return modelNumber;
+ }
+
+ /**
+ * 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: 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 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 Chimera specification for this chain
+ *
+ * @return Chimera specification
+ */
+ public String toSpec() {
+ if (chainId.equals("_")) {
+ return ("#" + modelNumber + "." + subModelNumber + ":.");
+ } else {
+ return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
+ }
+ }
+
+ /**
+ * Return the number of residues in this chain
+ *
+ * @return integer number of residues
+ */
+ public int getResidueCount() {
+ return residueMap.size();
+ }
+
+ /**
+ * Set the ChimeraModel for this chain
+ *
+ * @param model
+ * ChimeraModel to associate with this chain
+ */
+ public void setChimeraModel(ChimeraModel model) {
+ this.chimeraModel = model;
+ }
+
+ /**
+ * Get the ChimeraModel for this chain
+ *
+ * @return ChimeraModel associated with this chain
+ */
+ public ChimeraModel getChimeraModel() {
+ return chimeraModel;
+ }
+
+ /**
+ * 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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