Stockholm parser

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e59c191..2901969 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,81 +20,100 @@ package jalview.io;
 \r
 import jalview.datamodel.*;\r
 \r
-import java.util.Vector;\r
 \r
-\r
-public class FormatAdapter {\r
-    public static Vector formats = new Vector();\r
-\r
-    static {\r
-        formats.addElement("FASTA");\r
-        formats.addElement("MSF");\r
-        formats.addElement("PileUp");\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
-        try {\r
-            AlignFile afile = null;\r
-\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("PileUp")) {\r
-                afile = new PileUpfile(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
-\r
-            return afile.getSeqsAsArray();\r
-        } catch (Exception e) {\r
-            System.err.println("Failed to read alignment using the '" + format +\r
-                "' reader.");\r
-            e.printStackTrace();\r
-        }\r
-\r
-        return null;\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FormatAdapter extends AppletFormatAdapter\r
+{\r
+\r
+    public String formatSequences(String format,\r
+                                  SequenceI [] seqs,\r
+                                  String [] omitHiddenColumns)\r
+    {\r
+      if(omitHiddenColumns!=null)\r
+      {\r
+        SequenceI [] tmp = new SequenceI[seqs.length];\r
+        for(int i=0; i<seqs.length; i++)\r
+          tmp [i] = new Sequence(\r
+              seqs[i].getName(), omitHiddenColumns[i],\r
+              seqs[i].getStart(), seqs[i].getEnd());\r
+\r
+        seqs = tmp;\r
+      }\r
+\r
+      return formatSequences(format, seqs);\r
     }\r
 \r
-    public static String formatSequences(String format, Vector seqs) {\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
+     * DOCUMENT ME!\r
+     *\r
+     * @param format DOCUMENT ME!\r
+     * @param seqs DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String formatSequences(String format,\r
+                                  SequenceI [] seqs)\r
+    {\r
+\r
+        try\r
+        {\r
             AlignFile afile = null;\r
 \r
-            if (format.equals("FASTA")) {\r
+            if (format.equalsIgnoreCase("FASTA"))\r
+            {\r
                 afile = new FastaFile();\r
-            } else if (format.equals("MSF")) {\r
-                afile = new MSFfile();\r
-            } else if (format.equals("PileUp")) {\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("MSF"))\r
+            {\r
+              afile = new MSFfile();\r
+              afile.addJVSuffix(\r
+                  jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("PileUp"))\r
+            {\r
                 afile = new PileUpfile();\r
-            } else if (format.equals("CLUSTAL")) {\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("CLUSTAL"))\r
+            {\r
                 afile = new ClustalFile();\r
-            } else if (format.equals("BLC")) {\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("BLC"))\r
+            {\r
                 afile = new BLCFile();\r
-            } else if (format.equals("PIR")) {\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("PIR"))\r
+            {\r
                 afile = new PIRFile();\r
-            } else if (format.equals("PFAM")) {\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
+            }\r
+            else if (format.equalsIgnoreCase("PFAM"))\r
+            {\r
                 afile = new PfamFile();\r
+                afile.addJVSuffix(\r
+                    jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
             }\r
 \r
-            afile.setSeqs(s);\r
+            afile.setSeqs(seqs);\r
 \r
             return afile.print();\r
-        } catch (Exception e) {\r
+        }\r
+        catch (Exception e)\r
+        {\r
             System.err.println("Failed to write alignment as a '" + format +\r
                 "' file\n");\r
             e.printStackTrace();\r