formatAdapter.formats, remove redundant code

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 920a12d..78c1c24 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -21,8 +21,6 @@ import jalview.datamodel.*;
 \r
 import java.io.*;\r
 import java.util.*;\r
-import java.net.*;\r
-import java.awt.Font;\r
 \r
 public class BLCFile extends AlignFile {\r
 \r

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index d4179b6..0484bdd 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,46 +1,75 @@
 package jalview.io;\r
 \r
 import jalview.datamodel.*;\r
-import java.util.*;\r
+import java.util.Vector;\r
+public class FormatAdapter\r
+{\r
 \r
-public class FormatAdapter {\r
-\r
-  public static String get(String format,Vector seqs) {\r
-\r
-    SequenceI [] s = new SequenceI[seqs.size()];\r
-\r
-    for (int i=0;i<seqs.size(); i++)\r
-      s[i] = (SequenceI)seqs.elementAt(i);\r
+  public static Vector formats = new Vector();\r
+  static{\r
+    formats.addElement("FASTA");\r
+    formats.addElement("MSF");\r
+    formats.addElement("CLUSTAL");\r
+    formats.addElement("BLC");\r
+    formats.addElement("PIR");\r
+    formats.addElement("PFAM");\r
+  }\r
 \r
+  public static SequenceI[] readFile(String inFile, String type, String format)\r
+  {\r
 \r
-    if (FormatProperties.contains(format))\r
+    try\r
     {\r
-      AlignFile afile = FormatFactory.get(format);\r
-      afile.setSeqs(s);\r
-      return afile.print();\r
-    }\r
-    else\r
-       return null;\r
-  }\r
+      AlignFile afile = null;\r
+      if (format.equals("FASTA"))\r
+        afile = new FastaFile(inFile, type);\r
+      else if (format.equals("MSF"))\r
+        afile = new MSFfile(inFile, type);\r
+      else if (format.equals("CLUSTAL"))\r
+        afile = new ClustalFile(inFile, type);\r
+      else if (format.equals("BLC"))\r
+        afile = new BLCFile(inFile, type);\r
+      else if (format.equals("PIR"))\r
+        afile = new PIRFile(inFile, type);\r
+      else if (format.equals("PFAM"))\r
+        afile = new PfamFile(inFile, type);\r
 \r
-  public static SequenceI[] read(String format,String inStr) {\r
-    if (FormatProperties.contains(format)) {\r
-      AlignFile afile = FormatFactory.get(format,inStr);\r
       return afile.getSeqsAsArray();\r
-    } else {\r
-    // Should throw exception\r
-      return null;\r
     }\r
+    catch (Exception e)  {}\r
+\r
+    return null;\r
   }\r
 \r
 \r
-  public static SequenceI[] read(String inFile, String type, String format) {\r
-      try {\r
-        AlignFile afile = FormatFactory.get(format,inFile,type);\r
-        return afile.getSeqsAsArray();\r
-      } catch (Exception e) {    }\r
+  public static String formatSequences(String format, Vector seqs)\r
+  {\r
+    SequenceI [] s = new SequenceI[seqs.size()];\r
+\r
+    for (int i = 0; i < seqs.size(); i++)\r
+      s[i] = (SequenceI) seqs.elementAt(i);\r
+\r
+    try\r
+    {\r
+      AlignFile afile = null;\r
+      if (format.equals("FASTA"))\r
+        afile = new FastaFile();\r
+      else if (format.equals("MSF"))\r
+        afile = new MSFfile();\r
+      else if (format.equals("CLUSTAL"))\r
+        afile = new ClustalFile();\r
+      else if (format.equals("BLC"))\r
+        afile = new BLCFile();\r
+      else if (format.equals("PIR"))\r
+        afile = new PIRFile();\r
+      else if (format.equals("PFAM"))\r
+        afile = new PfamFile();\r
+\r
+      afile.setSeqs(s);\r
+      return afile.print();\r
+    }\r
+    catch (Exception e)  {}\r
 \r
     return null;\r
   }\r
-\r
 }\r

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4337cf6..18e1a6a 100755 (executable)
--- 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)\r
           continue;\r
 \r
-        if(data.indexOf("PILEUP")>-1 || data.indexOf("//")>-1)\r
+        if(data.indexOf("PILEUP")>-1)\r
         {\r
           reply = "MSF";\r
           break;\r

diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index b5fd436..c463c51 100755 (executable)
--- 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) {\r
           // we ignore the returned alignment if we only predicted on a single sequence\r
           String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");\r
-          if (jalview.io.FormatProperties.contains(format))\r
+          if (jalview.io.FormatAdapter.formats.contains(format))\r
           {\r
-            al = new Alignment(jalview.io.FormatAdapter.read(result.getAligfile(),"Paste",format));\r
+            al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));\r
             noMsa = false;\r
             FirstSeq = 0;\r
           }\r