--- /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.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.slf4j.LoggerFactory;
+
+/**
+ * This class provides the implementation for the ChimeraResidue, object
+ *
+ * @author scooter
+ *
+ */
+
+public class ChimeraResidue implements ChimeraStructuralObject, Comparable<ChimeraResidue> {
+
+ /* Constants */
+ public static final int SINGLE_LETTER = 0; // Display residues as a single
+ // letter
+ public static final int THREE_LETTER = 1; // Display residues as three letters
+ public static final int FULL_NAME = 2; // Display full residue names
+
+ private String type; // Residue type
+ private String index; // Residue index
+ private String chainId; // ChainID for this residue
+ private int modelNumber; // model number for this residue
+ private int subModelNumber; // sub-model number for this residue
+ protected int residueNumber;
+ protected String insertionCode;
+ private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
+ private Object userData; // user data to associate with this residue
+ // public static HashMap<String, String> aaNames = null; // a map of amino acid
+ // names
+ private static int displayType = THREE_LETTER; // the current display type
+ private boolean selected = false; // the selection state
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber) {
+ this(type, index, modelNumber, 0);
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue
+ *
+ * @param type
+ * the residue type
+ * @param index
+ * the index of the residue
+ * @param modelNumber
+ * the model number this residue is part of
+ * @param subModelNumber
+ * the sub-model number this residue is part of
+ */
+ public ChimeraResidue(String type, String index, int modelNumber, int subModelNumber) {
+ this.type = type;
+ this.index = index;
+ this.modelNumber = modelNumber;
+ this.subModelNumber = subModelNumber;
+ splitInsertionCode(this.index);
+ // if (aaNames == null) {
+ // initNames();
+ // }
+ }
+
+ /**
+ * Constructor to create a new ChimeraResidue from an input line
+ *
+ * @param chimeraInputLine
+ * a Chimera residue description
+ */
+ // invoked when listing (selected) residues: listr spec #0; lists level residue
+ // Line: residue id #0:37.A type MET
+ public ChimeraResidue(String chimeraInputLine) {
+ // initNames();
+ String[] split1 = chimeraInputLine.split(":");
+
+ // First half has model number -- get the number
+ int numberOffset = split1[0].indexOf('#');
+ String model = split1[0].substring(numberOffset + 1);
+ int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
+ try {
+ this.subModelNumber = 0;
+ if (decimalOffset > 0) {
+ this.subModelNumber = Integer.parseInt(model.substring(decimalOffset + 1));
+ this.modelNumber = Integer.parseInt(model.substring(0, decimalOffset));
+ } else {
+ this.modelNumber = Integer.parseInt(model);
+ }
+ } catch (Exception e) {
+ LoggerFactory.getLogger(ChimeraResidue.class)
+ .error("Unexpected return from Chimera: " + model);
+ this.modelNumber = -1;
+ }
+
+ // Second half has residue info: index & type
+ String[] rTokens = split1[1].split(" ");
+ this.type = rTokens[2];
+
+ String[] iTokens = rTokens[0].split("\\.");
+ if (iTokens.length > 0) {
+ this.index = iTokens[0];
+
+ // Careful, might or might not have a chainID
+ if (iTokens.length > 1)
+ this.chainId = iTokens[1];
+ else
+ this.chainId = "_";
+ } else
+ this.index = rTokens[0];
+
+ splitInsertionCode(this.index);
+ }
+
+ /**
+ * Set the selected state for this residue
+ *
+ * @param selected
+ * the selection state to set
+ */
+ public void setSelected(boolean selected) {
+ this.selected = selected;
+ }
+
+ /**
+ * Return the selected state of this residue
+ *
+ * @return the selected state
+ */
+ public boolean isSelected() {
+ return selected;
+ }
+
+ /**
+ * Return an array made up of this residue (required for ChimeraStructuralObject interface
+ *
+ * @return a List with this residue as its sole member
+ */
+ public List<ChimeraStructuralObject> getChildren() {
+ List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
+ v.add(this);
+ return v;
+ }
+
+ /**
+ * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
+ * where <i>residue_name</i> could be either the single letter, three letter, or full name
+ * representation of the amino acid.
+ *
+ * @return the string representation
+ */
+ public String displayName() {
+ return toString();
+ }
+
+ /**
+ * Return the string representation of this residue as follows: "<i>residue_name</i> <i>index</i>"
+ * where <i>residue_name</i> could be either the single letter, three letter, or full name
+ * representation of the amino acid.
+ *
+ * @return the string representation
+ */
+ public String toString() {
+ if (displayType == FULL_NAME) {
+ return (ChimUtils.toFullName(type) + " " + index);
+ } else if (displayType == SINGLE_LETTER) {
+ return (ChimUtils.toSingleLetter(type) + " " + index);
+ } else if (displayType == THREE_LETTER) {
+ return (ChimUtils.toThreeLetter(type) + " " + index);
+ } else {
+ return (type + " " + index);
+ }
+ }
+
+ /**
+ * Return the Chimera specification for this Residue
+ *
+ * @return Chimera specification
+ */
+ public String toSpec() {
+ if (!chainId.equals("_"))
+ return ("#" + modelNumber + ":" + index + "." + chainId);
+ else
+ return ("#" + modelNumber + ":" + index + ".");
+ }
+
+ /**
+ * Get the index of this residue
+ *
+ * @return residue index
+ */
+ public String getIndex() {
+ return this.index;
+ }
+
+ /**
+ * Get the chainID for this residue
+ *
+ * @return String value of the chainId
+ */
+ public String getChainId() {
+ return this.chainId;
+ }
+
+ /**
+ * Get the type for this residue
+ *
+ * @return residue type
+ */
+ public String getType() {
+ return this.type;
+ }
+
+ /**
+ * Get the model number for this residue
+ *
+ * @return the model number
+ */
+ public int getModelNumber() {
+ return this.modelNumber;
+ }
+
+ /**
+ * Get the sub-model number for this residue
+ *
+ * @return the sub-model number
+ */
+ public int getSubModelNumber() {
+ return this.subModelNumber;
+ }
+
+ /**
+ * Get the model this residue is part of
+ *
+ * @return the ChimeraModel
+ */
+ public ChimeraModel getChimeraModel() {
+ return this.chimeraModel;
+ }
+
+ /**
+ * Set the model this residue is part of
+ *
+ * @param chimeraModel
+ * the ChimeraModel this model is part of
+ */
+ public void setChimeraModel(ChimeraModel chimeraModel) {
+ this.chimeraModel = chimeraModel;
+ }
+
+ /**
+ * Get the user data for this residue
+ *
+ * @return user data
+ */
+ public Object getUserData() {
+ return userData;
+ }
+
+ /**
+ * Set the user data for this Residue
+ *
+ * @param data
+ * the user data to associate with this residue
+ */
+ public void setUserData(Object data) {
+ this.userData = data;
+ }
+
+ public int compareTo(ChimeraResidue c2) {
+ if (residueNumber < c2.residueNumber)
+ return -1;
+ else if (residueNumber == c2.residueNumber) {
+ if (insertionCode == null && c2.insertionCode == null)
+ return 0;
+ else if (insertionCode == null)
+ return -1;
+ else if (c2.insertionCode == null)
+ return 1;
+ return (insertionCode.compareTo(c2.insertionCode));
+ }
+ return 1;
+ }
+
+ public void splitInsertionCode(String residue) {
+ // OK, split the index into number and insertion code
+ Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
+ Matcher m = p.matcher(residue);
+ if (m.matches()) {
+ this.residueNumber = Integer.parseInt(m.group(1));
+ if (m.groupCount() > 1)
+ this.insertionCode = m.group(2);
+ else
+ this.insertionCode = null;
+ }
+ }
+
+ /**********************************************
+ * Static routines
+ *********************************************/
+
+ /**
+ * Initialize the residue names
+ */
+ // private static void initNames() {
+ // // Create our residue name table
+ // aaNames = new HashMap<String, String>();
+ // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+ // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+ // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+ // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+ // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+ // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+ // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+ // aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+ // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+ // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+ // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+ // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
+ // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
+ // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
+ // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
+ // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
+ // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
+ // aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+ // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+ // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+ // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+ // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+ // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+ // aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+ // }
+
+ /**
+ * Set the display type.
+ *
+ * @param type
+ * the display type
+ */
+ public static void setDisplayType(int type) {
+ displayType = type;
+ }
+
+ public static int getDisplayType() {
+ return displayType;
+ }
+
+ public boolean hasSelectedChildren() {
+ return false;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff