Features added removed from alignment

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 600da64..3209960 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -357,6 +357,12 @@ public class SeqPanel extends JPanel
         return;\r
       }\r
 \r
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+      {\r
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+      }\r
+\r
+\r
         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
                 sequence.getName());\r
 \r
@@ -402,16 +408,29 @@ public class SeqPanel extends JPanel
                 if ( (sf.getBegin() <= sequence.findPosition(res)) &&\r
                     (sf.getEnd() >= sequence.findPosition(res)))\r
                 {\r
-                  if (sbuffer.length() > 6)\r
-                    sbuffer.append("<br>");\r
-\r
-                  sbuffer.append(sf.getType());\r
-                  if (sf.getDescription() != null)\r
-                    sbuffer.append(" " + sf.getDescription());\r
-\r
-                  if (sf.getStatus() != null)\r
+                  if (sf.getType().equals("disulfide bond"))\r
                   {\r
-                    sbuffer.append(" (" + sf.getStatus() + ")");\r
+                    if (sf.getBegin() == sequence.findPosition(res)\r
+                        || sf.getEnd() == sequence.findPosition(res))\r
+                    {\r
+                      if (sbuffer.length() > 6)\r
+                        sbuffer.append("<br>");\r
+                      sbuffer.append("disulfide bond " + sf.getBegin() + ":" +\r
+                                     sf.getEnd());\r
+                    }\r
+                  }\r
+                  else\r
+                  {\r
+                    if (sbuffer.length() > 6)\r
+                      sbuffer.append("<br>");\r
+                    sbuffer.append(sf.getType());\r
+                    if (sf.getDescription() != null)\r
+                      sbuffer.append(" " + sf.getDescription());\r
+\r
+                    if (sf.getStatus() != null)\r
+                    {\r
+                      sbuffer.append(" (" + sf.getStatus() + ")");\r
+                    }\r
                   }\r
                 }\r
 \r
@@ -990,7 +1009,7 @@ public class SeqPanel extends JPanel
 \r
                 try\r
                 {\r
-                    Thread.sleep(75);\r
+                    Thread.sleep(20);\r
                 }\r
                 catch (Exception ex)\r
                 {\r