X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=71d8c11b633b4986a9222cf0a298ba009413b186;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=1937a8f0aaba0f3eed94408ab8678ad78fe190a8;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1937a8f..71d8c11 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -16,149 +16,150 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import jalview.datamodel.*;
+
 import java.io.*;
+
 import java.net.*;
+
 import java.util.*;
 
 
 public class PDBfile extends jalview.io.FileParse {
+    public Vector chains = new Vector();
+    Vector lineArray = new Vector();
 
-  public Vector chains = new Vector();
+    public PDBfile(String[] lines) {
+        for (int i = 0; i < lines.length; i++)
+            lineArray.addElement(lines[i]);
 
-  Vector lineArray = new Vector();
-
-  public PDBfile(String [] lines)
-  {
-    for(int i=0; i<lines.length; i++)
-      lineArray.addElement(lines[i]);
+        noLines = lineArray.size();
+        parse();
+    }
 
-    noLines = lineArray.size();
-    parse();
-  }
+    public PDBfile(String inFile, String inType) throws IOException {
+        super(inFile, inType);
 
-  public PDBfile(String inFile, String inType) throws IOException {
+        String line;
+        this.lineArray = new Vector();
 
-    super(inFile,inType);
+        BufferedReader dataIn;
 
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
+        if (inType.equals("File")) {
+            dataIn = new BufferedReader(new FileReader(inFile));
+        }
+        else {
+            URL url = new URL(inFile);
+            this.fileSize = 0;
+            dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+        }
 
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
+        while ((line = dataIn.readLine()) != null) {
+            lineArray.addElement(line);
+        }
 
-    else
-    {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
+        noLines = lineArray.size();
 
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
+        parse();
     }
-    noLines = lineArray.size();
 
-    parse();
+    public void parse() {
+        for (int i = 0; i < lineArray.size(); i++) {
+            StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)
+                                                               .toString());
+
+            if (str.hasMoreTokens()) {
+                String inStr = str.nextToken();
+
+                if (inStr.indexOf("ATOM") != -1) {
+                    try {
+                        myAtom tmpatom = new myAtom(str);
+
+                        if (findChain(tmpatom.chain) != null) {
+                            //   System.out.println("Adding to chain " + tmpatom.chain);
+                            findChain(tmpatom.chain).atoms.addElement(tmpatom);
+                        } else {
+                            //  System.out.println("Making chain " + tmpatom.chain);
+                            PDBChain tmpchain = new PDBChain(tmpatom.chain);
+                            chains.addElement(tmpchain);
+                            tmpchain.atoms.addElement(tmpatom);
+                        }
+                    } catch (NumberFormatException e) {
+                        System.err.println("Caught" + e);
+                        System.err.println("Record not added to PDB model:" +
+                            lineArray.elementAt(i).toString());
+                    }
+                }
+            }
+        }
 
-}
+        makeResidueList();
+        makeCaBondList();
 
+        //    for (int i=0; i < chains.size() ; i++) {
+        //  String pog = ((PDBChain)chains.elementAt(i)).print();
+        //  System.out.println(pog);
+        // }
+    }
 
-  public void parse() {
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-           //   System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-            //  System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.err.println("Caught" +  e);
-            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());
-          }
+    public void makeResidueList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeResidueList();
         }
-      }
-    }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  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++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      if (((PDBChain)chains.elementAt(i)).id.equals(id)) {
-        return (PDBChain)chains.elementAt(i);
-      }
+
+    public void makeCaBondList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeCaBondList();
+        }
     }
-    return null;
-  }
 
+    public PDBChain findChain(String id) {
+        for (int i = 0; i < chains.size(); i++) {
+            // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
+            if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
+                return (PDBChain) chains.elementAt(i);
+            }
+        }
 
-  public void setChargeColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChargeColours();
+        return null;
     }
-  }
 
-  public void setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
-    }
-  }
-
-  public void colourBySequence(Sequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
+    public void setChargeColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChargeColours();
+        }
     }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      e.printStackTrace();
-      System.exit(0);
+
+    public void setHydrophobicityColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
+        }
     }
-  }
-}
 
+    public void colourBySequence(Sequence seq) {
+        //SMJS TODO
+        //    int max = seq.maxchain;
+        //    if (seq.maxchain != -1) {
+        //      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
+        //    }
+    }
 
+    public void setChainColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChainColours();
+        }
+    }
 
+    public static void main(String[] args) {
+        try {
+            PDBfile pdb = new PDBfile("enkp1.pdb", "File");
+        } catch (IOException e) {
+            System.out.println(e);
+            e.printStackTrace();
+            System.exit(0);
+        }
+    }
+}