X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=3153e3c87101cf4e34817c59037110dcd9b1c622;hb=2794d58ed2b048de8cad254bea750f69d859240d;hp=71d8c11b633b4986a9222cf0a298ba009413b186;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 71d8c11..3153e3c 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,86 +22,107 @@ import jalview.datamodel.*;
 
 import java.io.*;
 
-import java.net.*;
-
 import java.util.*;
+import java.awt.Color;
 
 
-public class PDBfile extends jalview.io.FileParse {
-    public Vector chains = new Vector();
-    Vector lineArray = new Vector();
+public class PDBfile extends jalview.io.AlignFile {
+    public Vector chains;
+    public String id;
 
-    public PDBfile(String[] lines) {
-        for (int i = 0; i < lines.length; i++)
-            lineArray.addElement(lines[i]);
+    public PDBfile(String inFile, String inType) throws IOException
+    {
+        super(inFile, inType);
+    }
 
-        noLines = lineArray.size();
-        parse();
+    public String print()
+    {
+      return null;
     }
 
-    public PDBfile(String inFile, String inType) throws IOException {
-        super(inFile, inType);
+    public void parse() throws IOException
+    {
+        chains = new Vector();
 
+        PDBChain tmpchain;
         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()));
-        }
-
-        while ((line = dataIn.readLine()) != null) {
-            lineArray.addElement(line);
-        }
-
-        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());
-                    }
-                }
-            }
+        boolean modelFlag = false;
+        boolean terFlag = false;
+
+
+        int index = 0;
+        while((line = nextLine())!=null)
+        {
+           if (line.indexOf("HEADER") == 0)
+           {
+             id = line.substring(62, 67).trim();
+             continue;
+           }
+
+           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????
+              if (!line.substring(12, 15).trim().equals("CA"))
+              {
+                continue;
+              }
+
+              Atom tmpatom = new Atom(line);
+              tmpchain = findChain(tmpatom.chain);
+              if (tmpchain != null)
+              {
+                tmpchain.atoms.addElement(tmpatom);
+              }
+              else
+              {
+                tmpchain = new PDBChain(tmpatom.chain);
+                chains.addElement(tmpchain);
+                tmpchain.atoms.addElement(tmpatom);
+              }
+          }
+          index ++;
         }
 
-        makeResidueList();
-        makeCaBondList();
-
-        //    for (int i=0; i < chains.size() ; i++) {
-        //  String pog = ((PDBChain)chains.elementAt(i)).print();
-        //  System.out.println(pog);
-        // }
+       makeResidueList();
+       makeCaBondList();
+
+       if(id==null)
+       {
+         id = inFile.getName();
+       }
+       for (int i = 0; i < chains.size(); i++)
+       {
+         SequenceI seq = ( (PDBChain) chains.elementAt(i)).
+             sequence;
+         seq.setName(id + "|" + seq.getName());
+         Sequence dataset = new Sequence(seq.
+             getName(),
+             seq.getSequence().toString(), seq.getStart(), seq.getEnd());
+
+         PDBEntry entry = new PDBEntry();
+         entry.setId(id);
+         if(inFile!=null)
+           entry.setFile(inFile.getAbsolutePath());
+
+         seq.setDatasetSequence(dataset);
+         dataset.addPDBId(entry);
+
+         getSeqs().addElement(seq);
+       }
     }
 
     public void makeResidueList() {
@@ -118,7 +139,6 @@ public class PDBfile extends jalview.io.FileParse {
 
     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);
             }
@@ -133,33 +153,19 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    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() {
+    public void setColours(jalview.schemes.ColourSchemeI cs) {
         for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChainColours();
+            ((PDBChain) chains.elementAt(i)).setChainColours(cs);
         }
     }
 
-    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 setChainColours()
+    {
+       for (int i = 0; i < chains.size(); i++)
+       {
+            ((PDBChain) chains.elementAt(i)).setChainColours(
+                     Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
+                );
         }
     }
 }