From 621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Jul 2006 10:40:23 +0000
Subject: [PATCH] Check for all gapped seqs

---
 src/jalview/analysis/AlignSeq.java            |   20 +++++++++++++-------
 src/jalview/appletgui/PairwiseAlignPanel.java |    7 +++++--
 src/jalview/gui/PairwiseAlignPanel.java       |   12 +++++++++---
 3 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 464abb0..3c1f5be 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -63,14 +63,14 @@ public class AlignSeq
     int[] seq2;
     SequenceI s1;
     SequenceI s2;
-    String s1str;
-    String s2str;
+    public String s1str;
+    public String s2str;
     int maxi;
     int maxj;
     int[] aseq1;
     int[] aseq2;
-    public String astr1 = "";
-    public String astr2 = "";
+    public String astr1="";
+    public String astr2="";
 
     /** DOCUMENT ME!! */
     public int seq1start;
@@ -96,7 +96,6 @@ public class AlignSeq
     int defInt = 23;
     StringBuffer output = new StringBuffer();
     String type;
-    Runtime rt;
 
     /**
      * Creates a new AlignSeq object.
@@ -107,7 +106,6 @@ public class AlignSeq
      */
     public AlignSeq(SequenceI s1, SequenceI s2, String type)
     {
-        rt = Runtime.getRuntime();
         SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);
     }
 
@@ -124,7 +122,6 @@ public class AlignSeq
                     String string2,
                     String type)
     {
-        rt = Runtime.getRuntime();
         SeqInit(s1, string1, s2,  string2,  type);
     }
 
@@ -261,9 +258,18 @@ public class AlignSeq
                         String string2,
                         String type)
     {
+
         s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
         s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
 
+        if(s1str.length()==0 || s2str.length()==0)
+        {
+          System.out.println("ALL GAPS: " +
+                             (s1str.length()==0?s1.getName():" ")
+                             +(s2str.length()==0?s2.getName():""));
+          return;
+        }
+
         this.s1 = s1;
         this.s2 = s2;
 
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d0b0c98..e58dd76 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -49,17 +49,20 @@ public class PairwiseAlignPanel
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize(false);
 
-    int acount = 0;
     Sequence seq;
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
       {
-        acount++;
         AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
                                    ap.av.getSelectionGroup().getSequenceAt(j),
                                    "pep");
 
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)
+        {
+          continue;
+        }
+
         as.calcScoreMatrix();
         as.traceAlignment();
         as.printAlignment(System.out);
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index f52a1d8..ba961ee 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -70,20 +70,25 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         double totscore = 0;
         int count = seqs.length;
 
-        int acount = 0;
         Sequence seq;
 
         for (int i = 1; i < count; i++)
         {
             for (int j = 0; j < i; j++)
             {
-                acount++;
 
                 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
                         seqs[j], seqStrings[j], "pep");
 
+                if(as.s1str.length()==0 || as.s2str.length()==0)
+                {
+                  continue;
+                }
+
                 as.calcScoreMatrix();
                 as.traceAlignment();
+
+
                 as.printAlignment(System.out);
                 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
                 totscore = totscore + scores[i][j];
@@ -91,7 +96,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 textarea.append(as.getOutput());
                 seq = new Sequence(as.getS1().getName(),
                                    as.getAStr1(),
-                    as.getS1().getStart(), as.getS1().getEnd()
+                                   as.getS1().getStart(),
+                                   as.getS1().getEnd()
                 );
                 sequences.add(seq);
 
-- 
1.7.10.2