\r
import java.io.*;\r
\r
-import java.net.*;\r
-\r
import java.util.*;\r
+import java.awt.Color;\r
\r
\r
-public class PDBfile extends jalview.io.FileParse {\r
- public Vector chains = new Vector();\r
- Vector lineArray = new Vector();\r
+public class PDBfile extends jalview.io.AlignFile {\r
+ public Vector chains;\r
+ public String id;\r
\r
- public PDBfile(String[] lines) {\r
- for (int i = 0; i < lines.length; i++)\r
- lineArray.addElement(lines[i]);\r
+ public PDBfile(String inFile, String inType) throws IOException\r
+ {\r
+ super(inFile, inType);\r
+ }\r
\r
- noLines = lineArray.size();\r
- parse();\r
+ public String print()\r
+ {\r
+ return null;\r
}\r
\r
- public PDBfile(String inFile, String inType) throws IOException {\r
- super(inFile, inType);\r
+ public void parse() throws IOException\r
+ {\r
+ chains = new Vector();\r
\r
+ PDBChain tmpchain;\r
String line;\r
- this.lineArray = new Vector();\r
-\r
- BufferedReader dataIn;\r
-\r
- if (inType.equals("File")) {\r
- dataIn = new BufferedReader(new FileReader(inFile));\r
- }\r
- else {\r
- URL url = new URL(inFile);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ boolean modelFlag = false;\r
+ boolean terFlag = false;\r
+\r
+\r
+ int index = 0;\r
+ while((line = nextLine())!=null)\r
+ {\r
+ if (line.indexOf("HEADER") == 0)\r
+ {\r
+ id = line.substring(62, 67).trim();\r
+ continue;\r
+ }\r
+\r
+ if(line.indexOf("MODEL")==0)\r
+ modelFlag = true;\r
+\r
+ if(line.indexOf("TER")==0)\r
+ terFlag = true;\r
+\r
+ if(modelFlag && line.indexOf("ENDMDL")==0)\r
+ break;\r
+\r
+ if ( line.indexOf("ATOM")==0\r
+ || (line.indexOf("HETATM")==0 && !terFlag)\r
+ )\r
+ {\r
+ terFlag = false;\r
+\r
+\r
+ //Jalview is only interested in CA bonds????\r
+ if (!line.substring(12, 15).trim().equals("CA"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ Atom tmpatom = new Atom(line);\r
+ tmpchain = findChain(tmpatom.chain);\r
+ if (tmpchain != null)\r
+ {\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ else\r
+ {\r
+ tmpchain = new PDBChain(tmpatom.chain);\r
+ chains.addElement(tmpchain);\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ }\r
+ index ++;\r
}\r
\r
- while ((line = dataIn.readLine()) != null) {\r
- lineArray.addElement(line);\r
- }\r
-\r
- noLines = lineArray.size();\r
-\r
- parse();\r
- }\r
-\r
- public void parse() {\r
- for (int i = 0; i < lineArray.size(); i++) {\r
- StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)\r
- .toString());\r
-\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
-\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.err.println("Caught" + e);\r
- System.err.println("Record not added to PDB model:" +\r
- lineArray.elementAt(i).toString());\r
- }\r
- }\r
- }\r
- }\r
-\r
- makeResidueList();\r
- makeCaBondList();\r
-\r
- // for (int i=0; i < chains.size() ; i++) {\r
- // String pog = ((PDBChain)chains.elementAt(i)).print();\r
- // System.out.println(pog);\r
- // }\r
+ makeResidueList();\r
+ makeCaBondList();\r
+\r
+ if(id==null)\r
+ {\r
+ id = inFile.getName();\r
+ }\r
+ for (int i = 0; i < chains.size(); i++)\r
+ {\r
+ SequenceI seq = ( (PDBChain) chains.elementAt(i)).\r
+ sequence;\r
+ seq.setName(id + "|" + seq.getName());\r
+ Sequence dataset = new Sequence(seq.\r
+ getName(),\r
+ seq.getSequence().toString(), seq.getStart(), seq.getEnd());\r
+\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id);\r
+ if(inFile!=null)\r
+ entry.setFile(inFile.getAbsolutePath());\r
+\r
+ seq.setDatasetSequence(dataset);\r
+ dataset.addPDBId(entry);\r
+\r
+ getSeqs().addElement(seq);\r
+ }\r
}\r
\r
public void makeResidueList() {\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
}\r
\r
- public void setHydrophobicityColours() {\r
+ public void setColours(jalview.schemes.ColourSchemeI cs) {\r
for (int i = 0; i < chains.size(); i++) {\r
- ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();\r
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);\r
}\r
}\r
\r
- public void colourBySequence(Sequence 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
+ public void setChainColours()\r
+ {\r
+ for (int i = 0; i < chains.size(); i++)\r
+ {\r
+ ((PDBChain) chains.elementAt(i)).setChainColours(\r
+ Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)\r
+ );\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff