From 128c1c559ce7749ba5a39d30e6108f5ce8f4b99e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 27 May 2005 09:31:14 +0000
Subject: [PATCH] Response to bug mantis?id=8187 - some quick hacks to read
 and write david's MSF file with '~' as a gap character.

---
 src/jalview/io/FormatAdapter.java |    5 +++++
 src/jalview/io/IdentifyFile.java  |    6 ++++++
 src/jalview/io/MSFfile.java       |   13 ++++++++-----
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dba0c61..3e5e250 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -9,6 +9,7 @@ public class FormatAdapter
   static{
     formats.addElement("FASTA");
     formats.addElement("MSF");
+    formats.addElement("PileUp");
     formats.addElement("CLUSTAL");
     formats.addElement("BLC");
     formats.addElement("PIR");
@@ -25,6 +26,8 @@ public class FormatAdapter
         afile = new FastaFile(inFile, type);
       else if (format.equals("MSF"))
         afile = new MSFfile(inFile, type);
+      else if (format.equals("PileUp"))
+              afile = new PileUpfile(inFile, type);
       else if (format.equals("CLUSTAL"))
         afile = new ClustalFile(inFile, type);
       else if (format.equals("BLC"))
@@ -59,6 +62,8 @@ public class FormatAdapter
         afile = new FastaFile();
       else if (format.equals("MSF"))
         afile = new MSFfile();
+      else if (format.equals("PileUp"))
+        afile = new PileUpfile();
       else if (format.equals("CLUSTAL"))
         afile = new ClustalFile();
       else if (format.equals("BLC"))
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 55d771b..eebde9b 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -43,6 +43,12 @@ public class IdentifyFile
 
         if(data.indexOf("PILEUP")>-1)
         {
+          reply = "PileUp";
+          break;
+        }
+        if((data.indexOf("!!")>-1)
+           && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT ")))
+        {
           reply = "MSF";
           break;
         }
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 9495f82..3c18432 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -19,8 +19,10 @@ public class MSFfile extends AlignFile {
     super(inFile,type);
   }
 
-  public void parse() {
+  private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~","-");
+  private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex("["+jalview.util.Comparison.GapChars+"]","\\~");
 
+  public void parse() {
     int       i       = 0;
     boolean   seqFlag = false;
     String    key     = new String();
@@ -106,7 +108,8 @@ public class MSFfile extends AlignFile {
             }
           }
         }
-
+        // Replace ~ with a sensible gap character
+        seq = gapre.replaceAll(seq);
         Sequence newSeq = new Sequence(head,seq,start,end);
 
         seqs.addElement(newSeq);
@@ -195,15 +198,15 @@ public class MSFfile extends AlignFile {
           int end = start + 10;
 
           if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
-            out.append(s[j].getSequence().substring(start,end));
+            out.append(re2gap.replaceAll(s[j].getSequence().substring(start,end)));
             if (k < 4) {
-              out.append(" ");
+              // out.append(" ");
             } else {
               out.append("\n");
             }
           } else {
             if (start < s[j].getSequence().length()) {
-              out.append(s[j].getSequence().substring(start));
+              out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));
               out.append("\n");
             } else {
               if (k == 0) {
-- 
1.7.10.2