- */
-package jalview.io;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-public class JPredFile
- extends AlignFile
-{
- Vector ids;
- Vector conf;
- Hashtable Scores; // Hash of names and score vectors
-
- public JPredFile(String inStr)
- {
- super(inStr);
- }
-
- public void initData()
- {
-
- super.initData();
- Scores = new Hashtable();
- }
-
- public JPredFile(String inFile, String type)
- throws IOException
- {
-
- super(inFile, type);
- }
-
- /**
- * parse a JPred concise file into a sequence-alignment like object.
- */
-
- public void parse()
- throws IOException
- {
-
- String line;
-
- noSeqs = 0;
- Vector seq_entries = new Vector();
- Vector ids = new Vector();
-
- while ( (line = nextLine()) != null)
- {
- // Concise format allows no comments or non comma-formatted data
- StringTokenizer str = new StringTokenizer(line, ":");
- String id = "";
- String seq = "";
- if (str.hasMoreTokens())
- {
- id = str.nextToken();
- String seqsym = str.nextToken();
- StringTokenizer symbols = new StringTokenizer(seqsym, ",");
- // decide if we have more than just alphanumeric symbols
- int numSymbols = symbols.countTokens();
- if (seq.length() != (2 * numSymbols))
- {
- // Set of scalars for some property
- if (Scores.containsKey(id))
- {
- int i = 1;
- while (Scores.containsKey(id + "_" + i))
- {
- i++;
- }
- id = id + "_" + i;
- }
- Vector scores = new Vector(numSymbols);
- // Typecheck from first entry
- int i = 0;
- String ascore = symbols.nextToken();
- try
- {
- // store elements as floats...
- do
- {
- Float score = new Float(ascore);
- scores.set(i, (Object) score);
- ascore = symbols.nextToken();
- }
- while (++i < numSymbols);
- }
- catch (Exception e)
- {
- // or just keep them as strings
- for (int j = 0; j < i; j++)
- {
- scores.set(j,
- (Object)
- ( (Float) scores.get(j)).toString());
- }
- do
- {
- scores.set(i, ascore);
- ascore = symbols.nextToken();
- }
- while (++i < numSymbols);
- }
- Scores.put(id, scores);
- }
- else
- {
- if (id.equals("jnetconf"))
- {
- id = "Prediction Confidence";
- this.conf = new Vector(numSymbols);
- for (int i = 0; i < numSymbols; i++)
- {
- conf.set(i, (Object) symbols.nextToken());
- }
- }
- else
- {
- // Sequence or a prediction string (rendered as sequence)
-
- StringBuffer newseq = new StringBuffer();
- for (int i = 0; i < numSymbols; i++)
- {
- newseq.append(symbols.nextToken());
- }
- if (id.indexOf(";") > -1)
- {
- seq_entries.addElement(newseq);
- ids.addElement(id.substring(id.indexOf(";")));
- noSeqs++;
- }
- else
- {
- if (id.equals("JNETPRED"))
- {
- id = "Predicted Secondary Structure";
- }
- seq_entries.addElement(newseq);
- ids.addElement(id);
- }
- }
- }
-
- }
- }
-
- if (noSeqs < 1)
- {
- throw new IOException("JpredFile Parser: No sequence in the prediction!");
- }
- maxLength = seq_entries.elementAt(0).toString().length();
- for (int i = 0; i < ids.size(); i++)
- {
- // Add all sequence like objects
-
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seq_entries.elementAt(i).toString(), 1,
- seq_entries.elementAt(i).toString().length());
- if (!isValidProteinSequence(newSeq.getSequence()))
- {
- throw new IOException("JPredConcise: Not a valid protein sequence - ("
- + ids.elementAt(i).toString() + ")");
- }
-
- if (maxLength != seq_entries.elementAt(i).toString().length())
- {
- throw new IOException("JPredConcise: Entry (" +
- ids.elementAt(i).toString()
- + ") has an unexpected number of columns");
- }
- seqs.addElement(newSeq);
-
- }
- }
-
- /**
- * print
- *
- * @return String
- */
-
- public String print()
- {
- return "Not Supported";
- }
-}
+ */\r
+package jalview.io;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.util.*;\r
+\r
+import java.io.*;\r
+\r
+import java.util.*;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class JPredFile extends AlignFile\r
+{\r
+ Vector ids;\r
+ Vector conf;\r
+ Hashtable Scores; // Hash of names and score vectors\r
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector\r
+ private int QuerySeqPosition;\r
+\r
+ /**\r
+ * Creates a new JPredFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public JPredFile(String inStr)\r
+ {\r
+ super(inStr);\r
+ }\r
+\r
+ /**\r
+ * Creates a new JPredFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public JPredFile(String inFile, String type) throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param QuerySeqPosition DOCUMENT ME!\r
+ */\r
+ public void setQuerySeqPosition(int QuerySeqPosition)\r
+ {\r
+ this.QuerySeqPosition = QuerySeqPosition;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getQuerySeqPosition()\r
+ {\r
+ return QuerySeqPosition;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Hashtable getScores()\r
+ {\r
+ return Scores;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Hashtable getSymscores()\r
+ {\r
+ return Symscores;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void initData()\r
+ {\r
+ super.initData();\r
+ Scores = new Hashtable();\r
+ ids = null;\r
+ conf = null;\r
+ }\r
+\r
+ /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */\r
+ public void parse() throws IOException\r
+ {\r
+ // JBPNote log.System.out.println("all read in ");\r
+ String line;\r
+ QuerySeqPosition = -1;\r
+ noSeqs = 0;\r
+\r
+ Vector seq_entries = new Vector();\r
+ Vector ids = new Vector();\r
+ Hashtable Symscores = new Hashtable();\r
+\r
+ while ((line = nextLine()) != null)\r
+ {\r
+ // Concise format allows no comments or non comma-formatted data\r
+ StringTokenizer str = new StringTokenizer(line, ":");\r
+ String id = "";\r
+\r
+ if (!str.hasMoreTokens())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ id = str.nextToken();\r
+\r
+ String seqsym = str.nextToken();\r
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");\r
+\r
+ // decide if we have more than just alphanumeric symbols\r
+ int numSymbols = symbols.countTokens();\r
+\r
+ if (numSymbols == 0)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (seqsym.length() != (2 * numSymbols))\r
+ {\r
+ // Set of scalars for some property\r
+ if (Scores.containsKey(id))\r
+ {\r
+ int i = 1;\r
+\r
+ while (Scores.containsKey(id + "_" + i))\r
+ {\r
+ i++;\r
+ }\r
+\r
+ id = id + "_" + i;\r
+ }\r
+\r
+ Vector scores = new Vector();\r
+\r
+ // Typecheck from first entry\r
+ int i = 0;\r
+ String ascore = "dead";\r
+\r
+ try\r
+ {\r
+ // store elements as floats...\r
+ while (symbols.hasMoreTokens())\r
+ {\r
+ ascore = symbols.nextToken();\r
+\r
+ Float score = new Float(ascore);\r
+ scores.addElement((Object) score);\r
+ }\r
+\r
+ Scores.put(id, scores);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ // or just keep them as strings\r
+ i = scores.size();\r
+\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ scores.set(j,\r
+ (Object) ((Float) scores.get(j)).toString());\r
+ }\r
+\r
+ scores.addElement((Object) ascore);\r
+\r
+ while (symbols.hasMoreTokens())\r
+ {\r
+ ascore = symbols.nextToken();\r
+ scores.addElement((Object) ascore);\r
+ }\r
+\r
+ Scores.put(id, scores);\r
+ }\r
+ }\r
+ else if (id.equals("jnetconf"))\r
+ {\r
+ // log.debug System.out.println("here");\r
+ id = "Prediction Confidence";\r
+ this.conf = new Vector(numSymbols);\r
+\r
+ for (int i = 0; i < numSymbols; i++)\r
+ {\r
+ conf.set(i, (Object) symbols.nextToken());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // Sequence or a prediction string (rendered as sequence)\r
+ StringBuffer newseq = new StringBuffer();\r
+\r
+ for (int i = 0; i < numSymbols; i++)\r
+ {\r
+ newseq.append(symbols.nextToken());\r
+ }\r
+\r
+ if (id.indexOf(";") > -1)\r
+ {\r
+ seq_entries.addElement(newseq);\r
+\r
+ int i = 1;\r
+ String name = id.substring(id.indexOf(";") + 1);\r
+\r
+ while (ids.lastIndexOf(name) > -1)\r
+ {\r
+ name = id.substring(id.indexOf(";") + 1) + "_" + 1;\r
+ }\r
+\r
+ ids.addElement(name);\r
+\r
+ noSeqs++;\r
+ }\r
+ else\r
+ {\r
+ if (id.equals("JNETPRED"))\r
+ {\r
+ id = "Predicted Secondary Structure";\r
+ }\r
+\r
+ seq_entries.addElement(newseq.toString());\r
+ ids.addElement(id);\r
+ Symscores.put((Object) id,\r
+ (Object) new Integer(ids.size() - 1));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (noSeqs < 1)\r
+ {\r
+ throw new IOException(\r
+ "JpredFile Parser: No sequence in the prediction!");\r
+ }\r
+\r
+ maxLength = seq_entries.elementAt(0).toString().length();\r
+\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ // Add all sequence like objects\r
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seq_entries.elementAt(i).toString(), 1,\r
+ seq_entries.elementAt(i).toString().length());\r
+\r
+ if (!Symscores.containsKey(ids.elementAt(i)) &&\r
+ !isValidProteinSequence(newSeq.getSequence()))\r
+ {\r
+ throw new IOException(\r
+ "JPredConcise: Not a valid protein sequence - (" +\r
+ ids.elementAt(i).toString() + ")");\r
+ }\r
+\r
+ if (maxLength != seq_entries.elementAt(i).toString().length())\r
+ {\r
+ throw new IOException("JPredConcise: Entry (" +\r
+ ids.elementAt(i).toString() +\r
+ ") has an unexpected number of columns");\r
+ }\r
+\r
+ if (newSeq.getName().startsWith("QUERY") &&\r
+ (QuerySeqPosition == -1))\r
+ {\r
+ QuerySeqPosition = seqs.size();\r
+ }\r
+\r
+ seqs.addElement(newSeq);\r
+ }\r
+ }\r
+\r
+ /**
+ * print
+ *
+ * @return String
+ */\r
+ public String print()\r
+ {\r
+ return "Not Supported";\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param args DOCUMENT ME!\r
+ */\r
+ public static void main(String[] args)\r
+ {\r
+ try\r
+ {\r
+ JPredFile blc = new JPredFile(args[0], "File");\r
+\r
+ for (int i = 0; i < blc.seqs.size(); i++)\r
+ {\r
+ System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +\r
+ "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +\r
+ "\n");\r
+ }\r
+ }\r
+ catch (java.io.IOException e)\r
+ {\r
+ System.err.println("Exception " + e);\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+}\r
+\r
+\r