Check for all gapped seqs

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 464abb0..3c1f5be 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -63,14 +63,14 @@ public class AlignSeq
     int[] seq2;\r
     SequenceI s1;\r
     SequenceI s2;\r
-    String s1str;\r
-    String s2str;\r
+    public String s1str;\r
+    public String s2str;\r
     int maxi;\r
     int maxj;\r
     int[] aseq1;\r
     int[] aseq2;\r
-    public String astr1 = "";\r
-    public String astr2 = "";\r
+    public String astr1="";\r
+    public String astr2="";\r
 \r
     /** DOCUMENT ME!! */\r
     public int seq1start;\r
@@ -96,7 +96,6 @@ public class AlignSeq
     int defInt = 23;\r
     StringBuffer output = new StringBuffer();\r
     String type;\r
-    Runtime rt;\r
 \r
     /**\r
      * Creates a new AlignSeq object.\r
@@ -107,7 +106,6 @@ public class AlignSeq
      */\r
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
-        rt = Runtime.getRuntime();\r
         SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);\r
     }\r
 \r
@@ -124,7 +122,6 @@ public class AlignSeq
                     String string2,\r
                     String type)\r
     {\r
-        rt = Runtime.getRuntime();\r
         SeqInit(s1, string1, s2,  string2,  type);\r
     }\r
 \r
@@ -261,9 +258,18 @@ public class AlignSeq
                         String string2,\r
                         String type)\r
     {\r
+\r
         s1str = extractGaps(jalview.util.Comparison.GapChars, string1);\r
         s2str = extractGaps(jalview.util.Comparison.GapChars, string2);\r
 \r
+        if(s1str.length()==0 || s2str.length()==0)\r
+        {\r
+          System.out.println("ALL GAPS: " +\r
+                             (s1str.length()==0?s1.getName():" ")\r
+                             +(s2str.length()==0?s2.getName():""));\r
+          return;\r
+        }\r
+\r
         this.s1 = s1;\r
         this.s2 = s2;\r
 \r