set icon false if raising windows

[jalview.git] / src / jalview / datamodel / HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index e244dd7..9d9fa81 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -35,7 +35,6 @@ public class HiddenSequences
   {\r
     if(hiddenSequences==null)\r
     {\r
-      System.out.println("H is null");\r
       return 0;\r
     }\r
     int count = 0;\r
@@ -74,10 +73,13 @@ public class HiddenSequences
 \r
     for (int i = 0; i < hiddenSequences.length; i++)\r
     {\r
+      if(hiddenSequences[i]==null)\r
+        continue;\r
+\r
       if (i > deletionIndex)\r
         tmp[i-1] = hiddenSequences[i];\r
       else\r
-        tmp[i] = hiddenSequences[i];\r
+       tmp[i] = hiddenSequences[i];\r
     }\r
 \r
    hiddenSequences = tmp;\r
@@ -112,7 +114,7 @@ public class HiddenSequences
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);\r
 \r
     if(hiddenSequences[alignmentIndex]!=null)\r
-    System.out.println("ERROR!!!!!!!!!!!");\r
+      System.out.println("ERROR!!!!!!!!!!!");\r
 \r
     hiddenSequences[alignmentIndex] = sequence;\r
 \r
@@ -159,12 +161,18 @@ public class HiddenSequences
 \r
       if(seq!=null)\r
       {\r
-        revealedSeqs.addElement(seq);\r
-        alignment.getSequences().insertElementAt(seq, alignmentIndex);\r
-        if(repSequence!=null)\r
-        {\r
-          repSequence.showHiddenSequence(seq);\r
-        }\r
+        if(seq.getLength()>0)\r
+         {\r
+           revealedSeqs.addElement(seq);\r
+           alignment.getSequences().insertElementAt(seq, alignmentIndex);\r
+         }\r
+         else\r
+           System.out.println(seq.getName()+" has been deleted whilst hidden");\r
+\r
+         if (repSequence != null)\r
+         {\r
+           repSequence.showHiddenSequence(seq);\r
+         }\r
       }\r
 \r
     }\r
@@ -182,7 +190,7 @@ public class HiddenSequences
     int index = 0;\r
     int hiddenSeqs = 0;\r
     if(hiddenSequences.length<=alignmentIndex)\r
-      System.out.println(alignmentIndex+" "+hiddenSequences.length);\r
+      alignmentIndex = hiddenSequences.length-1;\r
 \r
     while(index <= alignmentIndex)\r
     {\r