X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=39111c3615ba511e49719f4a43e9101a4d380daf;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=ad5837ee7609f08a4f08aac3e65a8d6dae2e24b2;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index ad5837e..39111c3 100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -26,7 +26,9 @@ import jalview.appletgui.FeatureRenderer;
 import jalview.appletgui.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -145,7 +147,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   StructureSelectionManager ssm;
 
   public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
-          String[] chains, AlignmentPanel ap, String protocol)
+          String[] chains, AlignmentPanel ap, DataSourceType protocol)
 
   {
     this.ap = ap;
@@ -159,7 +161,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         pdbentry.setFile("INLINE" + pdb.getId());
       }
@@ -176,7 +178,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     colourBySequence();
 
-    int max = -10;
+    float max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -576,6 +578,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     PDBChain chain;
     if (bysequence && pdb != null)
     {
@@ -603,25 +607,16 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                            sequence[s], pos);
-                  }
+                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
                 pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                            sequence[s], pos);
-                  }
+                  tmp.endCol = sr
+                          .getResidueColour(sequence[s], pos, finder);
                 }
-
               }
             }
           }
@@ -1124,7 +1119,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }