X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=c4fe563123894da879ff4dc1bb45d7585ff0e898;hb=75d17bc3d8444203906499e651df6a69f6c2f518;hp=8cbe37d3d439824889373b77c521f5f91e749d08;hpb=65bf1cd0ea1526762e829059bf6ae0901db9731d;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8cbe37d..c4fe563 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -23,11 +23,13 @@ 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();
+    String id;
 
     public PDBfile(String[] lines) {
         for (int i = 0; i < lines.length; i++)
@@ -48,6 +50,10 @@ public class PDBfile extends jalview.io.FileParse {
         if (inType.equals("File")) {
             dataIn = new BufferedReader(new FileReader(inFile));
         }
+        else if(inType.equals("Paste"))
+        {
+            dataIn = new BufferedReader(new StringReader(inFile));
+        }
         else {
             URL url = new URL(inFile);
             this.fileSize = 0;
@@ -63,24 +69,45 @@ public class PDBfile extends jalview.io.FileParse {
         parse();
     }
 
-    public void parse() {
-        for (int i = 0; i < lineArray.size(); i++) {
-            StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)
-                                                               .toString());
+    public void parse()
+    {
+        PDBChain tmpchain;
+        String line;
+        boolean modelFlag = 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 (str.hasMoreTokens()) {
-                String inStr = str.nextToken();
+           if(line.indexOf("MODEL")==0)
+             modelFlag = true;
 
-                if (inStr.indexOf("ATOM") != -1) {
+           if(modelFlag && line.indexOf("ENDMDL")==0)
+             break;
+
+           if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
+            {
                     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);
+                        Atom tmpatom = new Atom(line);
+
+                        //Jalview is only interested in CA bonds????
+                        if(!tmpatom.name.equals("CA"))
+                          continue;
+
+                        tmpchain = findChain(tmpatom.chain);
+                        if ( tmpchain != null)
+                        {
+                          tmpchain.atoms.addElement(tmpatom);
+                        }
+                        else
+                        {
+                            tmpchain = new PDBChain(tmpatom.chain);
                             chains.addElement(tmpchain);
                             tmpchain.atoms.addElement(tmpatom);
                         }
@@ -90,7 +117,6 @@ public class PDBfile extends jalview.io.FileParse {
                             lineArray.elementAt(i).toString());
                     }
                 }
-            }
         }
 
         makeResidueList();
@@ -111,7 +137,6 @@ 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);
             }
@@ -132,16 +157,13 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,
-                                 jalview.gui.FeatureRenderer fr) {
-            for (int i = 0; i < chains.size(); i++) {
-              ((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
-            }
-    }
-
-    public void setChainColours() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChainColours();
+    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)
+                );
         }
     }
 }