X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraChain.java;fp=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraChain.java;h=9a29a99dd1adb3e53c582a2277b0b1c97b4aa5ab;hb=bf01811b6e0c8eb15630a73700a602f14908f6a0;hp=92193f2966b260f188af93d57587404685e1fb48;hpb=be2b1727035f39e94c4e5e320ac6011af984bcc6;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
index 92193f2..9a29a99 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
@@ -44,287 +44,329 @@ import java.util.TreeMap;
  * 
  */
 // 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;
+  }
 }