Check for all gapped seqs

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d0b0c98..e58dd76 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -49,17 +49,20 @@ public class PairwiseAlignPanel
     double totscore = 0;\r
     int count = ap.av.getSelectionGroup().getSize(false);\r
 \r
-    int acount = 0;\r
     Sequence seq;\r
     for (int i = 1; i < count; i++)\r
     {\r
       for (int j = 0; j < i; j++)\r
       {\r
-        acount++;\r
         AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
                                    ap.av.getSelectionGroup().getSequenceAt(j),\r
                                    "pep");\r
 \r
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)\r
+        {\r
+          continue;\r
+        }\r
+\r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
         as.printAlignment(System.out);\r

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index f52a1d8..ba961ee 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -70,20 +70,25 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         double totscore = 0;\r
         int count = seqs.length;\r
 \r
-        int acount = 0;\r
         Sequence seq;\r
 \r
         for (int i = 1; i < count; i++)\r
         {\r
             for (int j = 0; j < i; j++)\r
             {\r
-                acount++;\r
 \r
                 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
                         seqs[j], seqStrings[j], "pep");\r
 \r
+                if(as.s1str.length()==0 || as.s2str.length()==0)\r
+                {\r
+                  continue;\r
+                }\r
+\r
                 as.calcScoreMatrix();\r
                 as.traceAlignment();\r
+\r
+\r
                 as.printAlignment(System.out);\r
                 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
                 totscore = totscore + scores[i][j];\r
@@ -91,7 +96,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 textarea.append(as.getOutput());\r
                 seq = new Sequence(as.getS1().getName(),\r
                                    as.getAStr1(),\r
-                    as.getS1().getStart(), as.getS1().getEnd()\r
+                                   as.getS1().getStart(),\r
+                                   as.getS1().getEnd()\r
                 );\r
                 sequences.add(seq);\r
 \r