-/**
- * PredFile.java
- * JalviewX / Vamsas Project
- * JPred.seq.concise reader
- */
-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
- Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
- 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();
- Hashtable Symscores = new Hashtable();
- 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())
- {
- continue;
- }
-
- 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 (numSymbols==0) {
- continue;
- }
-
- if (seqsym.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();
- // Typecheck from first entry
- int i = 0;
- String ascore="dead";
- try
- {
- // store elements as floats...
- while (symbols.hasMoreTokens()) {
- ascore = symbols.nextToken();
- Float score = new Float(ascore);
- scores.addElement( (Object) score);
- }
- Scores.put(id, scores);
- }
- catch (Exception e)
- {
- // or just keep them as strings
- i = scores.size();
- for (int j = 0; j < i; j++)
- {
- scores.set(j,
- (Object) ( (Float) scores.get(j)).toString());
- }
- scores.addElement((Object) ascore);
- while (symbols.hasMoreTokens()) {
- {
- ascore = symbols.nextToken();
- scores.addElement( (Object) ascore);
- }
- }
- 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);
- int i=1;
- String name = id.substring(id.indexOf(";")+1);
- while (ids.lastIndexOf(name)>-1) {
- name = id.substring(id.indexOf(";")+1)+"_"+1;
- }
- ids.addElement(name);
- noSeqs++;
- }
- else
- {
- if (id.equals("JNETPRED")) {
- id = "Predicted Secondary Structure";
- }
- seq_entries.addElement( newseq.toString() );
- ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
- }
- }
- }
-
-
- 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 (!Symscores.containsKey(ids.elementAt(i))
- && !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";
- }
-
- public static void main(String[] args)
- {
- try
- {
- JPredFile blc = new JPredFile(args[0], "File");
- for (int i = 0; i < blc.seqs.size(); i++)
- {
- System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName()
- + "\n" +
- ( (Sequence) blc.seqs.elementAt(i)).getSequence()
- + "\n");
- }
- }
- catch (java.io.IOException e)
- {
- System.out.println("Exception " + e);
- e.printStackTrace();
- }
- }
- }
-
- /*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
- out.append(s[0].sequence.substring(i, i + 1) + " ");
- out.append(s[1].sequence.substring(i, i + 1) + " ");
- out.append(s[1].score[0].elementAt(i) + " ");
- out.append(s[1].score[1].elementAt(i) + " ");
- out.append(s[1].score[2].elementAt(i) + " ");
- out.append(s[1].score[3].elementAt(i) + " ");
-
- out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
- public static void main(String[] args)
- {
- try
- {
- BLCFile blc = new BLCFile(args[0], "File");
- DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
- for (int i = 0; i < blc.seqs.size(); i++)
- {
- s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
- }
- String out = BLCFile.print(s);
-
- AlignFrame af = new AlignFrame(null, s);
- af.resize(700, 500);
- af.show();
- System.out.println(out);
- }
- catch (java.io.IOException e)
- {
- System.out.println("Exception " + e);
- }
- }
-
- }
- */
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+\r
+/**\r
+ * PredFile.java\r
+ * JalviewX / Vamsas Project\r
+ * JPred.seq.concise reader\r
+ */\r
+package jalview.io;\r
+\r
+import jalview.datamodel.*;\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
+ /**\r
+ * parse a JPred concise file into a sequence-alignment like object.\r
+ */\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) + "_" + ++i;\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
+ /**\r
+ * print\r
+ *\r
+ * @return String\r
+ */\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
+/*\r
+ StringBuffer out = new StringBuffer();\r
+\r
+ out.append("START PRED\n");\r
+ for (int i = 0; i < s[0].sequence.length(); i++)\r
+ {\r
+ out.append(s[0].sequence.substring(i, i + 1) + " ");\r
+ out.append(s[1].sequence.substring(i, i + 1) + " ");\r
+ out.append(s[1].score[0].elementAt(i) + " ");\r
+ out.append(s[1].score[1].elementAt(i) + " ");\r
+ out.append(s[1].score[2].elementAt(i) + " ");\r
+ out.append(s[1].score[3].elementAt(i) + " ");\r
+\r
+ out.append("\n");\r
+ }\r
+ out.append("END PRED\n");\r
+ return out.toString();\r
+ }\r
+\r
+ public static void main(String[] args)\r
+ {\r
+ try\r
+ {\r
+ BLCFile blc = new BLCFile(args[0], "File");\r
+ DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];\r
+ for (int i = 0; i < blc.seqs.size(); i++)\r
+ {\r
+ s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));\r
+ }\r
+ String out = BLCFile.print(s);\r
+\r
+ AlignFrame af = new AlignFrame(null, s);\r
+ af.resize(700, 500);\r
+ af.show();\r
+ System.out.println(out);\r
+ }\r
+ catch (java.io.IOException e)\r
+ {\r
+ System.out.println("Exception " + e);\r
+ }\r
+ }\r
+\r
+ }\r
+ */\r
git://source.jalview.org / jalview.git / blobdiff