Applet changes

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index f0b7514..93d4c92 100755 (executable)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -75,6 +75,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     Vector highlightRes;\r
     boolean pdbAction = false;\r
     Bond highlightBond1, highlightBond2;\r
+    boolean errorLoading = false;\r
 \r
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)\r
     {\r
@@ -179,8 +180,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         setupBonds();\r
 \r
         scale = findScale();\r
-\r
-        updateSeqColours();\r
     }\r
 \r
 \r
@@ -352,13 +351,23 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     public void paint(Graphics g)\r
     {\r
 \r
-      if(visiblebonds==null)\r
+      if(errorLoading)\r
       {\r
+        g.setColor(Color.white);\r
+        g.fillRect(0,0,getSize().width, getSize().height);\r
         g.setColor(Color.black);\r
         g.setFont(new Font("Verdana", Font.BOLD, 14));\r
-        g.drawString("Error Parsing Pasted PDB data!!", 50, getSize().height/2);\r
+        g.drawString("Error loading PDB data!!", 50, getSize().height/2);\r
         return;\r
       }\r
+      else if(visiblebonds==null)\r
+      {\r
+        g.setColor(Color.black);\r
+        g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+        g.drawString("Fetching PDB data...", 50, getSize().height/2);\r
+        return;\r
+      }\r
+\r
 \r
 \r
         //Only create the image at the beginning -\r
@@ -377,7 +386,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
          }catch(Exception ex)\r
          {\r
            ex.printStackTrace();\r
-           System.out.println(getSize());\r
          }\r
         }\r
 \r

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 8598c8d..c3063a8 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -16,7 +16,7 @@ public class AppletPDBViewer extends Frame
       AppletPDBCanvas pdbcanvas;\r
 \r
 \r
-      public AppletPDBViewer(String pdbtext,\r
+      public AppletPDBViewer(String pdbtext,String type,\r
                        Sequence seq,\r
                        SeqCanvas seqcanvas)\r
       {\r
@@ -40,9 +40,13 @@ public class AppletPDBViewer extends Frame
         jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);\r
 \r
         try{\r
-        PDBfile pdbfile = new PDBfile(pdbtext, "Paste");\r
+        PDBfile pdbfile = new PDBfile(pdbtext, type);\r
         pdbcanvas.setPDBFile(pdbfile);\r
-        }catch(Exception ex){ex.printStackTrace();}\r
+        }\r
+        catch(Exception ex){\r
+          pdbcanvas.errorLoading = true;\r
+          pdbcanvas.repaint();\r
+        }\r
       }\r
 \r
 \r

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index e3f36f7..5f162b0 100755 (executable)
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -55,12 +55,6 @@ public class Bond {
         this.endCol = bond.endCol;\r
     }\r
 \r
-    public void print() {\r
-        System.out.println("Start " + start[0] + " " + start[1] + " " +\r
-            start[2]);\r
-        System.out.println("End   " + end[0] + " " + end[1] + " " + end[2]);\r
-    }\r
-\r
     public float length() {\r
         float len = ((end[0] - start[0]) * (end[0] - start[0])) +\r
             ((end[1] - start[1]) * (end[1] - start[1])) +\r

diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 2effba6..66c3798 100755 (executable)
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -34,15 +34,6 @@ public class MCMatrix {
         matrix[i][j] = value;\r
     }\r
 \r
-    public void print() {\r
-        System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +\r
-            matrix[0][2]);\r
-        System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +\r
-            matrix[1][2]);\r
-        System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +\r
-            matrix[2][2]);\r
-    }\r
-\r
     public void rotatex(float degrees) {\r
         mycos = (float) (Math.cos(degrees * myconst));\r
         mysin = (float) (Math.sin(degrees * myconst));\r

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 1fade31..5f23a26 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -105,6 +105,8 @@ public class PDBChain {
                     makeBond(at1, at2);\r
                 }\r
             }\r
+            else\r
+              System.out.println("not found "+i);\r
         }\r
     }\r
 \r

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index b3e4e28..d7b7c97 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -67,6 +67,7 @@ public class PDBfile extends jalview.io.FileParse {
         noLines = lineArray.size();\r
 \r
         parse();\r
+        lineArray = null;\r
     }\r
 \r
     public void parse()\r
@@ -76,11 +77,13 @@ public class PDBfile extends jalview.io.FileParse {
         boolean modelFlag = false;\r
         boolean terFlag = false;\r
 \r
+\r
         for (int i = 0; i < lineArray.size(); i++)\r
         {\r
 \r
            line = lineArray.elementAt(i).toString();\r
 \r
+\r
            if (line.indexOf("HEADER") == 0)\r
            {\r
              id = line.substring(62, 67).trim();\r
@@ -96,39 +99,38 @@ public class PDBfile extends jalview.io.FileParse {
            if(modelFlag && line.indexOf("ENDMDL")==0)\r
              break;\r
 \r
-           if (line.indexOf("ATOM")==0\r
-               || (line.indexOf("HETATM")==0 && !terFlag) )\r
+           if (    line.indexOf("ATOM")==0\r
+               || (line.indexOf("HETATM")==0 && !terFlag)\r
+             )\r
             {\r
               terFlag = false;\r
 \r
-                    try {\r
-                        Atom tmpatom = new Atom(line);\r
-\r
-                        //Jalview is only interested in CA bonds????\r
-                        if(!tmpatom.name.equals("CA"))\r
-                          continue;\r
-\r
-                        tmpchain = findChain(tmpatom.chain);\r
-                        if ( tmpchain != null)\r
-                        {\r
-                          tmpchain.atoms.addElement(tmpatom);\r
-                        }\r
-                        else\r
-                        {\r
-                            tmpchain = new PDBChain(tmpatom.chain);\r
-                            chains.addElement(tmpchain);\r
-                            tmpchain.atoms.addElement(tmpatom);\r
-                        }\r
-                    } catch (NumberFormatException e) {\r
-                        System.err.println("Caught" + e);\r
-                        System.err.println("Record not added to PDB model:" +\r
-                            lineArray.elementAt(i).toString());\r
-                    }\r
-                }\r
+\r
+              //Jalview is only interested in CA bonds????\r
+              if (!line.substring(12, 15).trim().equals("CA"))\r
+              {\r
+                continue;\r
+              }\r
+\r
+              Atom tmpatom = new Atom(line);\r
+\r
+              tmpchain = findChain(tmpatom.chain);\r
+              if (tmpchain != null)\r
+              {\r
+                tmpchain.atoms.addElement(tmpatom);\r
+              }\r
+              else\r
+              {\r
+                tmpchain = new PDBChain(tmpatom.chain);\r
+                chains.addElement(tmpchain);\r
+                tmpchain.atoms.addElement(tmpatom);\r
+              }\r
+\r
+          }\r
         }\r
 \r
-        makeResidueList();\r
-        makeCaBondList();\r
+       makeResidueList();\r
+       makeCaBondList();\r
     }\r
 \r
     public void makeResidueList() {\r