X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=401ad01c22b7a9377201b65858544131c46d60bc;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=60ad85c7a30678cb1e9faa98edadf007d5df0660;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 60ad85c..401ad01 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -69,8 +69,8 @@ public class AlignSeq
     int maxj;
     int[] aseq1;
     int[] aseq2;
-    String astr1 = "";
-    String astr2 = "";
+    public String astr1 = "";
+    public String astr2 = "";
 
     /** DOCUMENT ME!! */
     public int seq1start;
@@ -94,7 +94,7 @@ public class AlignSeq
     int[][] lookup = ResidueProperties.getBLOSUM62();
     String[] intToStr = pep;
     int defInt = 23;
-    String output = "";
+    StringBuffer output = new StringBuffer();
     String type;
     Runtime rt;
 
@@ -169,7 +169,7 @@ public class AlignSeq
      */
     public String getOutput()
     {
-        return output;
+        return output.toString();
     }
 
     /**
@@ -263,7 +263,7 @@ public class AlignSeq
         }
         else
         {
-            output = output + ("Wrong type = dna or pep only");
+            output.append("Wrong type = dna or pep only");
             System.exit(0);
         }
 
@@ -406,7 +406,7 @@ public class AlignSeq
     /**
      * DOCUMENT ME!
      */
-    public void printAlignment()
+    public void printAlignment(java.io.PrintStream os)
     {
         // Find the biggest id length for formatting purposes
         int maxid = s1.getName().length();
@@ -420,39 +420,33 @@ public class AlignSeq
         int nochunks = ((aseq1.length - count) / len) + 1;
         pid = 0;
 
-        output = output + ("Score = " + score[maxi][maxj] + "\n");
-        output = output +
-            ("Length of alignment = " + (aseq1.length - count) + "\n");
-        output = output + ("Sequence ");
-        output = output + (new Format("%" + maxid + "s").form(s1.getName()));
-        output = output +
-            (" :  " + seq1start + " - " + seq1end + " (Sequence length = " +
+        output.append("Score = " + score[maxi][maxj] + "\n");
+        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 = " +
             s1str.length() + ")\n");
-        output = output + ("Sequence ");
-        output = output + (new Format("%" + maxid + "s").form(s2.getName()));
-        output = output +
-            (" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
+        output .append("Sequence ");
+        output.append(new Format("%" + maxid + "s").form(s2.getName()));
+        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
             s2str.length() + ")\n\n");
 
         for (int j = 0; j < nochunks; j++)
         {
             // Print the first aligned sequence
-            output = output +
-                (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
+            output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
 
             for (int i = 0; i < len; i++)
             {
                 if ((count + i + (j * len)) < aseq1.length)
                 {
-                    output = output +
-                        (new Format("%s").form(intToStr[aseq1[count + i +
+                    output.append(new Format("%s").form(intToStr[aseq1[count + i +
                             (j * len)]]));
                 }
             }
 
-            output = output + ("\n");
-            output = output +
-                (new Format("%" + (maxid) + "s").form(" ") + " ");
+            output.append("\n");
+            output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
 
             // Print out the matching chars
             for (int i = 0; i < len; i++)
@@ -464,7 +458,7 @@ public class AlignSeq
                             !intToStr[aseq1[count + i + (j * len)]].equals("-"))
                     {
                         pid++;
-                        output = output + ("|");
+                        output.append("|");
                     }
                     else if (type.equals("pep"))
                     {
@@ -472,40 +466,42 @@ public class AlignSeq
                                     intToStr[aseq1[count + i + (j * len)]],
                                     intToStr[aseq2[count + i + (j * len)]]) > 0)
                         {
-                            output = output + (".");
+                            output.append(".");
                         }
                         else
                         {
-                            output = output + (" ");
+                            output.append(" ");
                         }
                     }
                     else
                     {
-                        output = output + (" ");
+                        output.append(" ");
                     }
                 }
             }
 
             // Now print the second aligned sequence
-            output = output + ("\n");
-            output = output +
-                (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
+            output = output.append("\n");
+            output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
 
             for (int i = 0; i < len; i++)
             {
                 if ((count + i + (j * len)) < aseq1.length)
                 {
-                    output = output +
-                        (new Format("%s").form(intToStr[aseq2[count + i +
+                    output .append(new Format("%s").form(intToStr[aseq2[count + i +
                             (j * len)]]));
                 }
             }
 
-            output = output + ("\n\n");
+            output = output .append("\n\n");
         }
 
         pid = pid / (float) (aseq1.length - count) * 100;
-        output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
+        output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
+
+        try{
+          os.print(output.toString());
+        }catch(Exception ex){}
     }
 
     /**
@@ -659,14 +655,14 @@ public class AlignSeq
     public static String extractGaps(String gapChar, String seq)
     {
         StringTokenizer str = new StringTokenizer(seq, gapChar);
-        String newString = "";
+        StringBuffer newString = new StringBuffer();
 
         while (str.hasMoreTokens())
         {
-            newString = newString + str.nextToken();
+            newString.append( str.nextToken() );
         }
 
-        return newString;
+        return newString.toString();
     }
 
     /**