-package MCview;\r
-\r
-import jalview.gui.*;\r
-import java.io.*;\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-\r
-public class PDBfile extends jalview.io.FileParse {\r
-\r
- public Vector chains = new Vector();\r
-\r
- Vector lineArray = new Vector();\r
-\r
- public PDBfile(String [] lines)\r
- {\r
- for(int i=0; i<lines.length; i++)\r
- lineArray.add(lines[i]);\r
-\r
- noLines = lineArray.size();\r
- parse();\r
- }\r
-\r
- public PDBfile(String inFile, String inType) throws IOException {\r
-\r
- super(inFile,inType);\r
-\r
- String line;\r
- this.lineArray = new Vector();\r
- BufferedReader dataIn;\r
-\r
- if (inType.equals("File"))\r
- dataIn = new BufferedReader(new FileReader( inFile ));\r
-\r
- else\r
- {\r
- URL url = new URL(inFile);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
- }\r
-\r
- while ((line = dataIn.readLine()) != null) {\r
- lineArray.addElement(line);\r
- }\r
- noLines = lineArray.size();\r
-\r
- parse();\r
-\r
-}\r
-\r
-\r
- public void parse() {\r
-\r
- for (int i = 0; i < lineArray.size(); i++) {\r
- StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());\r
- if (str.hasMoreTokens()) {\r
- String inStr = str.nextToken();\r
-\r
- if (inStr.indexOf("ATOM") != -1) {\r
- try {\r
- myAtom tmpatom = new myAtom(str);\r
- if (findChain(tmpatom.chain) != null) {\r
- // System.out.println("Adding to chain " + tmpatom.chain);\r
- findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
- } else {\r
- // System.out.println("Making chain " + tmpatom.chain);\r
- PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
- chains.addElement(tmpchain);\r
- tmpchain.atoms.addElement(tmpatom);\r
- }\r
- } catch(NumberFormatException e) {\r
- System.out.println("Caught" + e);\r
- System.out.println("Atom not added");\r
- }\r
- }\r
- }\r
- }\r
- makeResidueList();\r
- makeCaBondList();\r
- // for (int i=0; i < chains.size() ; i++) {\r
- // String pog = ((PDBChain)chains.elementAt(i)).print();\r
- // System.out.println(pog);\r
- // }\r
- }\r
-\r
- public void makeResidueList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeResidueList();\r
- }\r
- }\r
- public void makeCaBondList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeCaBondList();\r
- }\r
- }\r
-\r
- public PDBChain findChain(String id) {\r
- for (int i=0; i < chains.size(); i++) {\r
- // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);\r
- if (((PDBChain)chains.elementAt(i)).id.equals(id)) {\r
- return (PDBChain)chains.elementAt(i);\r
- }\r
- }\r
- return null;\r
- }\r
-\r
-\r
- public void setChargeColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChargeColours();\r
- }\r
- }\r
-\r
- public void setHydrophobicityColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();\r
- }\r
- }\r
-\r
- public void colourBySequence(DrawableSequence seq) {\r
-//SMJS TODO\r
-// int max = seq.maxchain;\r
-// if (seq.maxchain != -1) {\r
-// ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
-// }\r
- }\r
-\r
- public void setChainColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChainColours();\r
- }\r
- }\r
- public static void main(String[] args) {\r
- try {\r
- PDBfile pdb = new PDBfile("enkp1.pdb","File");\r
- } catch(IOException e) {\r
- System.out.println(e);\r
- System.exit(0);\r
- }\r
- }\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package MCview;
+
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+
+import jalview.datamodel.*;
+import jalview.io.FileParse;
+import jalview.io.RnamlFile;
+import jalview.ws.jws1.Annotate3D;
+
+public class PDBfile extends jalview.io.AlignFile
+{
+ public Vector chains;
+
+ public String id;
+
+ /**
+ * set to true to add chain alignment annotation as visible annotation.
+ */
+ boolean VisibleChainAnnotation = false;
+
+ public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ {
+ super(inFile, inType);
+ }
+
+ public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ {
+ super(source);
+ }
+
+ public String print()
+ {
+ return null;
+ }
+
+ public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ {
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
+
+ chains = new Vector();
+
+ PDBChain tmpchain;
+ String line=null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
+
+ int index = 0;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
+ {
+ if (line.length() > 62)
+ {
+ String tid;
+ if (line.length() > 67)
+ {
+ tid = line.substring(62, 67).trim();
+ }
+ else
+ {
+ tid = line.substring(62).trim();
+ }
+ if (tid.length() > 0)
+ {
+ id = tid;
+ }
+ continue;
+ }
+ }
+ // Were we to do anything with SEQRES - we start it here
+ if (line.indexOf("SEQRES") == 0)
+ {
+ }
+
+ if (line.indexOf("MODEL") == 0)
+ {
+ modelFlag = true;
+ }
+
+ if (line.indexOf("TER") == 0)
+ {
+ terFlag = true;
+ }
+
+ if (modelFlag && line.indexOf("ENDMDL") == 0)
+ {
+ break;
+ }
+ if (line.indexOf("ATOM") == 0
+ || (line.indexOf("HETATM") == 0 && !terFlag))
+ {
+ terFlag = false;
+
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
+ {
+ continue;
+ }
+
+ Atom tmpatom = new Atom(line);
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpchain != null)
+ {
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ else
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
+ }
+ index++;
+ }
+
+ makeResidueList();
+ makeCaBondList();
+
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (int i = 0; i < chains.size(); i++)
+ {
+ SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ if (inFile != null)
+ {
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
+ seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ String path =inFile.getPath();
+ System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D(path);
+ System.out.println(id);
+ //BufferedWriter r = an3d.getReader();
+
+ // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+
+ //String str;
+ // while ((str = in.readLine()) != null) {
+ // System.out.println(str);
+ // System.out.println("toto");
+
+ // }
+ //String type = "File";
+ //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
+ System.out.println("Create rnamfile object");
+ //rnaml.parse("temp");
+ //this.annotations =rnaml.getAnnot();
+
+ }
+
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
+ if (chainannot != null)
+ {
+ for (int ai = 0; ai < chainannot.length; ai++)
+ {
+
+ chainannot[ai].visible = VisibleChainAnnotation;
+ annotations.addElement(chainannot[ai]);
+ }
+ }
+ }
+ } catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");
+ throw new IOException("Out of memory loading PDB File");
+ }
+ catch (NumberFormatException ex)
+ {
+ if (line!=null) {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
+ }
+ }
+
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int p = 0;
+ while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
+ {
+ dataName = dataName.substring(p + 1);
+ }
+ return dataName;
+ }
+
+ public void makeResidueList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
+ }
+ }
+
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ }
+ }
+
+ public PDBChain findChain(String id)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ {
+ return (PDBChain) chains.elementAt(i);
+ }
+ }
+
+ return null;
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
+ }
+ }
+
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ }
+ }
+
+ public void setChainColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ 1.0f / (float) i, .4f, 1.0f));
+ }
+ }
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i<seqs.getLength();i++){
+ if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff