Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 0dd58ad..08bca8c 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -26,7 +26,9 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
 import jalview.gui.SequenceRenderer;
+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;
@@ -141,7 +143,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   String errorMessage;
 
   void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol)
+          AlignmentPanel ap, DataSourceType protocol)
   {
     this.ap = ap;
     this.pdbentry = pdbentry;
@@ -153,7 +155,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol.equals(jalview.io.DataSourceType.PASTE))
       {
         pdbentry.setFile("INLINE" + pdb.getId());
       }
@@ -545,6 +547,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
     PDBChain chain;
     if (bysequence && pdb != null)
     {
@@ -572,23 +575,15 @@ public class PDBCanvas extends JPanel 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);
                 }
 
               }