X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=3c1f5be415798a68fac10bb3c087d20f1c591cca;hb=b242374a54c1288647de25dcf02163da168044a0;hp=2fd17737892ddbaf6fd867838e7aa4923ea4e88b;hpb=70426041e78c134bb4052983ac6897933ae5f702;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 2fd1773..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;
@@ -96,8 +96,6 @@ public class AlignSeq
     int defInt = 23;
     StringBuffer output = new StringBuffer();
     String type;
-    Runtime rt;
-
 
     /**
      * Creates a new AlignSeq object.
@@ -108,8 +106,23 @@ public class AlignSeq
      */
     public AlignSeq(SequenceI s1, SequenceI s2, String type)
     {
-        rt = Runtime.getRuntime();
-        SeqInit(s1, s2, type);
+        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);
+    }
+
+    /**
+     * Creates a new AlignSeq object.
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public AlignSeq(SequenceI s1,
+                    String string1,
+                    SequenceI s2,
+                    String string2,
+                    String type)
+    {
+        SeqInit(s1, string1, s2,  string2,  type);
     }
 
     /**
@@ -239,10 +252,23 @@ public class AlignSeq
      * @param s2 DOCUMENT ME!
      * @param type DOCUMENT ME!
      */
-    public void SeqInit(SequenceI s1, SequenceI s2, String type)
+    public void SeqInit(SequenceI s1,
+                        String string1,
+                        SequenceI s2,
+                        String string2,
+                        String type)
     {
-        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());
-        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());
+
+        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;
@@ -424,11 +450,11 @@ public class AlignSeq
         output.append("Length of alignment = " + (aseq1.length - count) + "\n");
         output.append("Sequence ");
         output.append(new Format("%" + maxid + "s").form(s1.getName()));
-        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +
+        output.append(" :  " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +
             s1str.length() + ")\n");
         output .append("Sequence ");
         output.append(new Format("%" + maxid + "s").form(s2.getName()));
-        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
+        output.append(" :  " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +
             s2str.length() + ")\n\n");
 
         for (int j = 0; j < nochunks; j++)
@@ -500,7 +526,7 @@ public class AlignSeq
         output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
 
         try{
-          os.println(output.toString());
+          os.print(output.toString());
         }catch(Exception ex){}
     }