From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 18:35:31 +0000 (+0000)
Subject: Modifications for Applet PDB
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0083bf4d00fcc93d81890dafd5ba8ba413705533;p=jalview.git

Modifications for Applet PDB
---

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 2bc934f..b1d8805 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -421,7 +421,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
         {
-          ( (PDBChain) pdb.chains.elementAt(ii)).colourBySequence(sr, fr);
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );
         }
       }
 
@@ -430,6 +430,50 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     }
 
+    // This method has been taken out of PDBChain to allow
+    // Applet and Application specific sequence renderers to be used
+    void colourBySequence(PDBChain chain)
+    {
+      for (int i = 0; i < chain.bonds.size(); i++)
+      {
+        Bond tmp = (Bond) chain.bonds.elementAt(i);
+
+        if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+            (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
+        {
+          int pos = chain.seqstart +
+              (tmp.at1.resNumber - chain.pdbstart - chain.offset);
+
+          int index = sequence.findIndex(pos);
+
+          tmp.startCol = sr.findSequenceColour(tmp.startCol, sequence, index);
+
+          tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+
+        }
+        else
+        {
+          tmp.startCol = Color.gray;
+        }
+
+        if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+            (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
+        {
+          int pos = chain.seqstart +
+              (tmp.at2.resNumber - chain.pdbstart - chain.offset);
+          int index = sequence.findIndex(pos);
+
+          tmp.endCol = sr.findSequenceColour(tmp.endCol, sequence, index);
+          tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
+        }
+        else
+        {
+          tmp.endCol = Color.gray;
+        }
+      }
+    }
+
+
     public void drawScene(Graphics g) {
         // Sort the bonds by z coord
         Vector bonds = new Vector();
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 166e537..208ecd0 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -143,8 +143,8 @@ public class PDBChain {
         }
 
         sequence = new Sequence("PDB_seq", seq, 1, seq.length());
-      //  System.out.println("PDB Sequence is :\nSequence = " + seq);
-      //  System.out.println("No of residues = " + residues.size());
+     //   System.out.println("PDB Sequence is :\nSequence = " + seq);
+     //   System.out.println("No of residues = " + residues.size());
     }
 
     public void setChargeColours() {
@@ -229,47 +229,7 @@ public class PDBChain {
         }
     }
 
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,
-                                 jalview.gui.FeatureRenderer fr)
-    {
 
-        for (int i = 0; i < bonds.size(); i++)
-        {
-            Bond tmp = (Bond) bonds.elementAt(i);
-
-                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
-                        (tmp.at1.resNumber <= ((offset + pdbend) - 1)))
-                    {
-                    int pos = seqstart +
-                        (tmp.at1.resNumber - pdbstart - offset);
-
-
-                    int index = sequence.findIndex(pos);
-
-                    tmp.startCol = sr.findSequenceColour(Color.gray, sequence,  index);
-
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
-
-                } else
-                {
-                    tmp.startCol = Color.gray;
-                }
-
-                if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&
-                        (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
-                    int pos = seqstart +
-                        (tmp.at2.resNumber - pdbstart - offset);
-                    int index = sequence.findIndex(pos);
-
-                   tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);
-                   tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);
-                }
-                else
-                {
-                    tmp.endCol = Color.gray;
-                }
-        }
-    }
 
     public void setChainColours() {
         for (int i = 0; i < bonds.size(); i++) {
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8cbe37d..f9d842f 100755
--- 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")) {
             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;
@@ -79,7 +83,6 @@ public class PDBfile extends jalview.io.FileParse {
                             //   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);
@@ -132,10 +135,11 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,
-                                 jalview.gui.FeatureRenderer fr) {
+    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);
+              //((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
             }
     }