Modifications for Applet PDB

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 2bc934f..b1d8805 100755 (executable)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -421,7 +421,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {\r
         for (int ii = 0; ii < pdb.chains.size(); ii++)\r
         {\r
-          ( (PDBChain) pdb.chains.elementAt(ii)).colourBySequence(sr, fr);\r
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );\r
         }\r
       }\r
 \r
@@ -430,6 +430,50 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 \r
     }\r
 \r
+    // This method has been taken out of PDBChain to allow\r
+    // Applet and Application specific sequence renderers to be used\r
+    void colourBySequence(PDBChain chain)\r
+    {\r
+      for (int i = 0; i < chain.bonds.size(); i++)\r
+      {\r
+        Bond tmp = (Bond) chain.bonds.elementAt(i);\r
+\r
+        if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
+            (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))\r
+        {\r
+          int pos = chain.seqstart +\r
+              (tmp.at1.resNumber - chain.pdbstart - chain.offset);\r
+\r
+          int index = sequence.findIndex(pos);\r
+\r
+          tmp.startCol = sr.findSequenceColour(tmp.startCol, sequence, index);\r
+\r
+          tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
+\r
+        }\r
+        else\r
+        {\r
+          tmp.startCol = Color.gray;\r
+        }\r
+\r
+        if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
+            (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))\r
+        {\r
+          int pos = chain.seqstart +\r
+              (tmp.at2.resNumber - chain.pdbstart - chain.offset);\r
+          int index = sequence.findIndex(pos);\r
+\r
+          tmp.endCol = sr.findSequenceColour(tmp.endCol, sequence, index);\r
+          tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);\r
+        }\r
+        else\r
+        {\r
+          tmp.endCol = Color.gray;\r
+        }\r
+      }\r
+    }\r
+\r
+\r
     public void drawScene(Graphics g) {\r
         // Sort the bonds by z coord\r
         Vector bonds = new Vector();\r

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 166e537..208ecd0 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -143,8 +143,8 @@ public class PDBChain {
         }\r
 \r
         sequence = new Sequence("PDB_seq", seq, 1, seq.length());\r
-      //  System.out.println("PDB Sequence is :\nSequence = " + seq);\r
-      //  System.out.println("No of residues = " + residues.size());\r
+     //   System.out.println("PDB Sequence is :\nSequence = " + seq);\r
+     //   System.out.println("No of residues = " + residues.size());\r
     }\r
 \r
     public void setChargeColours() {\r
@@ -229,47 +229,7 @@ public class PDBChain {
         }\r
     }\r
 \r
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,\r
-                                 jalview.gui.FeatureRenderer fr)\r
-    {\r
 \r
-        for (int i = 0; i < bonds.size(); i++)\r
-        {\r
-            Bond tmp = (Bond) bonds.elementAt(i);\r
-\r
-                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&\r
-                        (tmp.at1.resNumber <= ((offset + pdbend) - 1)))\r
-                    {\r
-                    int pos = seqstart +\r
-                        (tmp.at1.resNumber - pdbstart - offset);\r
-\r
-\r
-                    int index = sequence.findIndex(pos);\r
-\r
-                    tmp.startCol = sr.findSequenceColour(Color.gray, sequence,  index);\r
-\r
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
-\r
-                } else\r
-                {\r
-                    tmp.startCol = Color.gray;\r
-                }\r
-\r
-                if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&\r
-                        (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {\r
-                    int pos = seqstart +\r
-                        (tmp.at2.resNumber - pdbstart - offset);\r
-                    int index = sequence.findIndex(pos);\r
-\r
-                   tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);\r
-                   tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);\r
-                }\r
-                else\r
-                {\r
-                    tmp.endCol = Color.gray;\r
-                }\r
-        }\r
-    }\r
 \r
     public void setChainColours() {\r
         for (int i = 0; i < bonds.size(); i++) {\r

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8cbe37d..f9d842f 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -48,6 +48,10 @@ public class PDBfile extends jalview.io.FileParse {
         if (inType.equals("File")) {\r
             dataIn = new BufferedReader(new FileReader(inFile));\r
         }\r
+        else if(inType.equals("Paste"))\r
+        {\r
+            dataIn = new BufferedReader(new StringReader(inFile));\r
+        }\r
         else {\r
             URL url = new URL(inFile);\r
             this.fileSize = 0;\r
@@ -79,7 +83,6 @@ public class PDBfile extends jalview.io.FileParse {
                             //   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
@@ -132,10 +135,11 @@ public class PDBfile extends jalview.io.FileParse {
         }\r
     }\r
 \r
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,\r
-                                 jalview.gui.FeatureRenderer fr) {\r
+    public void colourBySequence()//jalview.gui.SequenceRenderer sr,\r
+                                // jalview.gui.FeatureRenderer fr)\r
+                                {\r
             for (int i = 0; i < chains.size(); i++) {\r
-              ((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);\r
+              //((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);\r
             }\r
     }\r
 \r