From b5dceeaf4112cd63aa1642dd8851b3ec19a7c81e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 3 May 2005 12:46:13 +0000
Subject: [PATCH] formatAdapter.formats, remove redundant code

---
 src/jalview/io/BLCFile.java       |    2 -
 src/jalview/io/FormatAdapter.java |   87 ++++++++++++++++++++++++-------------
 src/jalview/io/IdentifyFile.java  |    2 +-
 src/jalview/io/JPredClient.java   |    4 +-
 4 files changed, 61 insertions(+), 34 deletions(-)

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 920a12d..78c1c24 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -21,8 +21,6 @@ import jalview.datamodel.*;
 
 import java.io.*;
 import java.util.*;
-import java.net.*;
-import java.awt.Font;
 
 public class BLCFile extends AlignFile {
 
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index d4179b6..0484bdd 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,46 +1,75 @@
 package jalview.io;
 
 import jalview.datamodel.*;
-import java.util.*;
+import java.util.Vector;
+public class FormatAdapter
+{
 
-public class FormatAdapter {
-
-  public static String get(String format,Vector seqs) {
-
-    SequenceI [] s = new SequenceI[seqs.size()];
-
-    for (int i=0;i<seqs.size(); i++)
-      s[i] = (SequenceI)seqs.elementAt(i);
+  public static Vector formats = new Vector();
+  static{
+    formats.addElement("FASTA");
+    formats.addElement("MSF");
+    formats.addElement("CLUSTAL");
+    formats.addElement("BLC");
+    formats.addElement("PIR");
+    formats.addElement("PFAM");
+  }
 
+  public static SequenceI[] readFile(String inFile, String type, String format)
+  {
 
-    if (FormatProperties.contains(format))
+    try
     {
-      AlignFile afile = FormatFactory.get(format);
-      afile.setSeqs(s);
-      return afile.print();
-    }
-    else
-       return null;
-  }
+      AlignFile afile = null;
+      if (format.equals("FASTA"))
+        afile = new FastaFile(inFile, type);
+      else if (format.equals("MSF"))
+        afile = new MSFfile(inFile, type);
+      else if (format.equals("CLUSTAL"))
+        afile = new ClustalFile(inFile, type);
+      else if (format.equals("BLC"))
+        afile = new BLCFile(inFile, type);
+      else if (format.equals("PIR"))
+        afile = new PIRFile(inFile, type);
+      else if (format.equals("PFAM"))
+        afile = new PfamFile(inFile, type);
 
-  public static SequenceI[] read(String format,String inStr) {
-    if (FormatProperties.contains(format)) {
-      AlignFile afile = FormatFactory.get(format,inStr);
       return afile.getSeqsAsArray();
-    } else {
-    // Should throw exception
-      return null;
     }
+    catch (Exception e)  {}
+
+    return null;
   }
 
 
-  public static SequenceI[] read(String inFile, String type, String format) {
-      try {
-        AlignFile afile = FormatFactory.get(format,inFile,type);
-        return afile.getSeqsAsArray();
-      } catch (Exception e) {    }
+  public static String formatSequences(String format, Vector seqs)
+  {
+    SequenceI [] s = new SequenceI[seqs.size()];
+
+    for (int i = 0; i < seqs.size(); i++)
+      s[i] = (SequenceI) seqs.elementAt(i);
+
+    try
+    {
+      AlignFile afile = null;
+      if (format.equals("FASTA"))
+        afile = new FastaFile();
+      else if (format.equals("MSF"))
+        afile = new MSFfile();
+      else if (format.equals("CLUSTAL"))
+        afile = new ClustalFile();
+      else if (format.equals("BLC"))
+        afile = new BLCFile();
+      else if (format.equals("PIR"))
+        afile = new PIRFile();
+      else if (format.equals("PFAM"))
+        afile = new PfamFile();
+
+      afile.setSeqs(s);
+      return afile.print();
+    }
+    catch (Exception e)  {}
 
     return null;
   }
-
 }
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4337cf6..18e1a6a 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -41,7 +41,7 @@ public class IdentifyFile
         if(data.indexOf("#")==0 || data.length()<1)
           continue;
 
-        if(data.indexOf("PILEUP")>-1 || data.indexOf("//")>-1)
+        if(data.indexOf("PILEUP")>-1)
         {
           reply = "MSF";
           break;
diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index b5fd436..c463c51 100755
--- a/src/jalview/io/JPredClient.java
+++ b/src/jalview/io/JPredClient.java
@@ -198,9 +198,9 @@ public class JPredClient
         if (this.msa!=null && result.getAligfile()!=null) {
           // we ignore the returned alignment if we only predicted on a single sequence
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");
-          if (jalview.io.FormatProperties.contains(format))
+          if (jalview.io.FormatAdapter.formats.contains(format))
           {
-            al = new Alignment(jalview.io.FormatAdapter.read(result.getAligfile(),"Paste",format));
+            al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));
             noMsa = false;
             FirstSeq = 0;
           }
-- 
1.7.10.2