FeatureRenderer mixups fixed

[jalview.git] / src / MCview / AppletPDBViewer.java

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 907a6fe..2f8a90f 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -25,15 +25,17 @@ import jalview.appletgui.*;
 import jalview.datamodel.*;\r
 import jalview.schemes.*;\r
 \r
+\r
 public class AppletPDBViewer\r
     extends Frame implements ActionListener, ItemListener\r
 {\r
   AppletPDBCanvas pdbcanvas;\r
-  public AppletPDBViewer(String pdbtext, String type,\r
-                         Sequence seq,\r
-                         SeqCanvas seqcanvas)\r
-  {\r
 \r
+  public AppletPDBViewer(PDBEntry pdbentry,\r
+                         SequenceI[] seq,\r
+                         AlignmentPanel ap,\r
+                         String protocol)\r
+  {\r
     try\r
     {\r
       jbInit();\r
@@ -43,57 +45,50 @@ public class AppletPDBViewer
       ex.printStackTrace();\r
     }\r
 \r
-    pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);\r
+    pdbcanvas = new AppletPDBCanvas(pdbentry, seq, ap, protocol);\r
+\r
 \r
     add(pdbcanvas, BorderLayout.CENTER);\r
 \r
-    StringBuffer title = new StringBuffer(seq.getName() + ":");\r
+    StringBuffer title = new StringBuffer(seq[0].getName()\r
+                                          + ":"\r
+                                          + pdbcanvas.pdbentry.getFile());\r
 \r
     jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);\r
 \r
-    try\r
-    {\r
-      PDBfile pdbfile = new PDBfile(pdbtext, type);\r
-      pdbcanvas.setPDBFile(pdbfile);\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      ex.printStackTrace();\r
-      pdbcanvas.errorLoading = true;\r
-      pdbcanvas.repaint();\r
-    }\r
   }\r
 \r
+\r
+\r
   public void actionPerformed(ActionEvent evt)\r
   {\r
     if (evt.getSource() == mapping)\r
     {\r
-      mapping_actionPerformed();\r
-    }\r
-    else if (evt.getSource() == wire)\r
-    {\r
-      wire_actionPerformed();\r
-    }\r
-    else if (evt.getSource() == depth)\r
-    {\r
-      depth_actionPerformed();\r
-    }\r
-    else if (evt.getSource() == zbuffer)\r
-    {\r
-      zbuffer_actionPerformed();\r
+      jalview.appletgui.CutAndPasteTransfer cap\r
+          = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
+      Frame frame = new Frame();\r
+      frame.add(cap);\r
+      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,\r
+                                       600);\r
+      cap.setText(pdbcanvas.mappingDetails.toString());\r
+\r
     }\r
     else if (evt.getSource() == charge)\r
     {\r
-      charge_actionPerformed();\r
+      pdbcanvas.bysequence = false;\r
+      pdbcanvas.pdb.setChargeColours();\r
     }\r
 \r
     else if (evt.getSource() == chain)\r
     {\r
-      chain_actionPerformed();\r
+      pdbcanvas.bysequence = false;\r
+      pdbcanvas.pdb.setChainColours();\r
     }\r
     else if (evt.getSource() == seqButton)\r
     {\r
-      seqButton_actionPerformed();\r
+      pdbcanvas.bysequence = true;\r
+      pdbcanvas.colourBySequence();\r
+\r
     }\r
     else if (evt.getSource() == zappo)\r
     {\r
@@ -128,26 +123,32 @@ public class AppletPDBViewer
       pdbcanvas.bysequence = false;\r
       new jalview.appletgui.UserDefinedColours(pdbcanvas);\r
     }\r
+\r
+    pdbcanvas.redrawneeded = true;\r
+    pdbcanvas.repaint();\r
+\r
   }\r
 \r
   public void itemStateChanged(ItemEvent evt)\r
   {\r
     if (evt.getSource() == allchains)\r
     {\r
-      allchains_itemStateChanged();\r
+      pdbcanvas.setAllchainsVisible(allchains.getState());\r
     }\r
     else if (evt.getSource() == wire)\r
     {\r
-      wire_actionPerformed();\r
+          pdbcanvas.wire = !pdbcanvas.wire;\r
     }\r
     else if (evt.getSource() == depth)\r
     {\r
-      depth_actionPerformed();\r
+      pdbcanvas.depthcue = !pdbcanvas.depthcue;\r
     }\r
     else if (evt.getSource() == zbuffer)\r
     {\r
-      zbuffer_actionPerformed();\r
+      pdbcanvas.zbuffer = !pdbcanvas.zbuffer;\r
     }\r
+    pdbcanvas.redrawneeded = true;\r
+    pdbcanvas.repaint();\r
   }\r
 \r
   private void jbInit()\r
@@ -238,63 +239,9 @@ public class AppletPDBViewer
   MenuItem buried = new MenuItem();\r
   MenuItem user = new MenuItem();\r
 \r
-  public void charge_actionPerformed()\r
-  {\r
-    pdbcanvas.bysequence = false;\r
-    pdbcanvas.pdb.setChargeColours();\r
-    pdbcanvas.redrawneeded = true;\r
-    pdbcanvas.repaint();\r
-  }\r
-\r
-  public void chain_actionPerformed()\r
-  {\r
-    pdbcanvas.bysequence = false;\r
-    pdbcanvas.pdb.setChainColours();\r
-    pdbcanvas.redrawneeded = true;\r
-    pdbcanvas.repaint();\r
-  }\r
-\r
-  public void zbuffer_actionPerformed()\r
-  {\r
-    pdbcanvas.zbuffer = !pdbcanvas.zbuffer;\r
-    pdbcanvas.redrawneeded = true;\r
-    pdbcanvas.repaint();\r
-  }\r
-\r
-  public void depth_actionPerformed()\r
-  {\r
-    pdbcanvas.depthcue = !pdbcanvas.depthcue;\r
-    pdbcanvas.redrawneeded = true;\r
-    pdbcanvas.repaint();\r
-  }\r
-\r
-  public void wire_actionPerformed()\r
-  {\r
-    pdbcanvas.wire = !pdbcanvas.wire;\r
-    pdbcanvas.redrawneeded = true;\r
-    pdbcanvas.repaint();\r
-  }\r
 \r
-  public void seqButton_actionPerformed()\r
-  {\r
-    pdbcanvas.bysequence = true;\r
-    pdbcanvas.updateSeqColours();\r
-    pdbcanvas.repaint();\r
-  }\r
-\r
-  public void mapping_actionPerformed()\r
-  {\r
-    jalview.appletgui.CutAndPasteTransfer cap\r
-        = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
-    Frame frame = new Frame();\r
-    frame.add(cap);\r
-    jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);\r
-    cap.setText(pdbcanvas.mappingDetails.toString());\r
-  }\r
+//End StructureListener\r
+////////////////////////////\r
 \r
-  public void allchains_itemStateChanged()\r
-  {\r
-    pdbcanvas.setAllchainsVisible(allchains.getState());\r
-  }\r
 \r
 }\r