X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=63728ae816fe12b96a448fde9e38f7febb4aa25a;hb=56e5bdc625697d50d7d3f422616f0f1b40ca2828;hp=71d8c11b633b4986a9222cf0a298ba009413b186;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 71d8c11..63728ae 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -18,24 +18,24 @@
 */
 package MCview;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 
 import java.net.*;
 
 import java.util.*;
+import java.awt.Color;
+import jalview.io.AppletFormatAdapter;
 
 
 public class PDBfile extends jalview.io.FileParse {
     public Vector chains = new Vector();
     Vector lineArray = new Vector();
+    public String id;
 
     public PDBfile(String[] lines) {
         for (int i = 0; i < lines.length; i++)
             lineArray.addElement(lines[i]);
 
-        noLines = lineArray.size();
         parse();
     }
 
@@ -47,12 +47,24 @@ public class PDBfile extends jalview.io.FileParse {
 
         BufferedReader dataIn;
 
-        if (inType.equals("File")) {
+
+        if (inType.equals(AppletFormatAdapter.FILE)) {
             dataIn = new BufferedReader(new FileReader(inFile));
         }
-        else {
+        else if(inType.equals(AppletFormatAdapter.PASTE))
+        {
+            dataIn = new BufferedReader(new StringReader(inFile));
+        }
+        else if (inType.equalsIgnoreCase(AppletFormatAdapter.CLASSLOADER))
+        {
+          java.io.InputStream is = getClass().getResourceAsStream("/" +
+              inFile);
+
+          dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        }
+        else
+        {
             URL url = new URL(inFile);
-            this.fileSize = 0;
             dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
         }
 
@@ -60,48 +72,72 @@ public class PDBfile extends jalview.io.FileParse {
             lineArray.addElement(line);
         }
 
-        noLines = lineArray.size();
 
         parse();
+        lineArray = null;
     }
 
-    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 parse()
+    {
+        PDBChain tmpchain;
+        String line;
+        boolean modelFlag = false;
+        boolean terFlag = false;
+
+
+        for (int i = 0; i < lineArray.size(); i++)
+        {
+
+           line = lineArray.elementAt(i).toString();
+
+
+           if (line.indexOf("HEADER") == 0)
+           {
+             id = line.substring(62, 67).trim();
+             continue;
+           }
+
+           if(line.indexOf("MODEL")==0)
+             modelFlag = true;
 
-        makeResidueList();
-        makeCaBondList();
+           if(line.indexOf("TER")==0)
+             terFlag = true;
 
-        //    for (int i=0; i < chains.size() ; i++) {
-        //  String pog = ((PDBChain)chains.elementAt(i)).print();
-        //  System.out.println(pog);
-        // }
+           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);
+              }
+
+          }
+        }
+
+       makeResidueList();
+       makeCaBondList();
     }
 
     public void makeResidueList() {
@@ -118,7 +154,6 @@ 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 +168,19 @@ 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)
+                );
         }
     }
 }