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package proteinstructure; |
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import java.io.*; |
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import java.util.*; |
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import edu.uci.ics.jung.graph.util.EdgeType; |
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|
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/** |
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* A RIG loaded from a Casp contact prediction file. |
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* @author stehr |
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* @data 2007-12-19 |
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*/ |
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public class CaspRRFileRIGraph extends RIGraph { |
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private static final long serialVersionUID = 1L; |
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|
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/** |
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* Constructs a RIGraph object based on a Casp contact prediction file. |
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* @param fileName the contact prediction file |
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* @throws IOException |
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* @throws GraphFileFormatError |
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*/ |
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public CaspRRFileRIGraph (String fileName) throws IOException, GraphFileFormatError{ |
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super(); |
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// we set the sequence to blank when we read from file as we don't have the full sequence |
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// if sequence is present in RR file then is read from there |
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this.sequence=""; |
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this.contactType=ProtStructGraph.NO_CONTACT_TYPE; |
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this.distCutoff=ProtStructGraph.NO_CUTOFF; |
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// we initialise pdbCode, chainCode and pdbChainCode to corresponding constants (empty strings at the moment) since file doesn't specify then |
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this.pdbCode=Pdb.NO_PDB_CODE; |
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this.chainCode=Pdb.NO_CHAIN_CODE; |
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this.pdbChainCode=Pdb.NO_PDB_CHAIN_CODE; |
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|
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readFromCaspRRFile(fileName); |
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|
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} |
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private void readFromCaspRRFile(String fileName) throws FileNotFoundException, IOException, GraphFileFormatError { |
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CaspRRFileData rrData = new CaspRRFileData(); |
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File inFile = new File(fileName); |
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if(!CaspRRFileData.isValidCaspRRFile(inFile)) throw new GraphFileFormatError(fileName + " is not a valid casp contact prediction file."); |
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rrData.readFromFile(new File(fileName)); |
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|
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// convert meta data |
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this.sequence = rrData.getSequence(); |
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this.contactType = CaspRRFileData.DEFAULT_CONT_TYPE; // i.e. Cb |
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this.groupNum = rrData.groupNum; |
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this.targetNum = rrData.targetNum; |
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this.caspModelNum = rrData.modelNum; |
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|
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// add vertices |
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serials2nodes = new TreeMap<Integer,RIGNode>(); |
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if (sequence == null || sequence.equals("")) throw new GraphFileFormatError("No sequence found in " + fileName); |
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this.fullLength = sequence.length(); |
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for (int i=0;i<sequence.length();i++){ |
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String letter = String.valueOf(sequence.charAt(i)); |
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RIGNode node = new RIGNode(i+1,AAinfo.oneletter2threeletter(letter)); |
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serials2nodes.put(i+1, node); |
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this.addVertex(node); |
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} |
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|
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// set distCutoff |
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CaspRRFileData.RRContact firstContact = rrData.getContacts().get(0); |
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this.distCutoff = firstContact.maxDist; |
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|
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// add edges |
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for(CaspRRFileData.RRContact cont:rrData.getContacts()) { |
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if(cont.minDist != 0) throw new GraphFileFormatError("Non-zero minimum distance value in " + fileName + "."); |
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if(this.distCutoff != cont.maxDist) throw new GraphFileFormatError("Distance cutoffs in " + fileName + " are not equal."); |
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this.addEdge(new RIGEdge(cont.weight), serials2nodes.get(cont.i), serials2nodes.get(cont.j), EdgeType.UNDIRECTED); |
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} |
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} |
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|
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} |
