-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+/*\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
-/**
- * PredFile.java
- * JalviewX / Vamsas Project
- * JPred.seq.concise reader
+/**\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 jalview.util.*;\r
-\r
import java.io.*;\r
\r
import java.util.*;\r
\r
\r
-public class JPredFile extends AlignFile {\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
- public JPredFile(String inStr) {\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
- public JPredFile(String inFile, String type) throws IOException {\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
- public void setQuerySeqPosition(int QuerySeqPosition) {\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
- public int getQuerySeqPosition() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getQuerySeqPosition()\r
+ {\r
return QuerySeqPosition;\r
}\r
\r
- public Hashtable getScores() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Hashtable getScores()\r
+ {\r
return Scores;\r
}\r
\r
- public Hashtable getSymscores() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Hashtable getSymscores()\r
+ {\r
return Symscores;\r
}\r
\r
- public void initData() {\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
+ * parse a JPred concise file into a sequence-alignment like object.\r
*/\r
- public void parse() throws IOException {\r
+ public void parse() throws IOException\r
+ {\r
// JBPNote log.System.out.println("all read in ");\r
String line;\r
QuerySeqPosition = -1;\r
Vector ids = new Vector();\r
Hashtable Symscores = new Hashtable();\r
\r
- while ((line = nextLine()) != null) {\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
+ if (!str.hasMoreTokens())\r
+ {\r
continue;\r
}\r
\r
// decide if we have more than just alphanumeric symbols\r
int numSymbols = symbols.countTokens();\r
\r
- if (numSymbols == 0) {\r
+ if (numSymbols == 0)\r
+ {\r
continue;\r
}\r
\r
- if (seqsym.length() != (2 * numSymbols)) {\r
+ if (seqsym.length() != (2 * numSymbols))\r
+ {\r
// Set of scalars for some property\r
- if (Scores.containsKey(id)) {\r
+ if (Scores.containsKey(id))\r
+ {\r
int i = 1;\r
\r
- while (Scores.containsKey(id + "_" + i)) {\r
+ while (Scores.containsKey(id + "_" + i))\r
+ {\r
i++;\r
}\r
\r
int i = 0;\r
String ascore = "dead";\r
\r
- try {\r
+ try\r
+ {\r
// store elements as floats...\r
- while (symbols.hasMoreTokens()) {\r
+ while (symbols.hasMoreTokens())\r
+ {\r
ascore = symbols.nextToken();\r
\r
Float score = new Float(ascore);\r
}\r
\r
Scores.put(id, scores);\r
- } catch (Exception e) {\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
+ 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
+ while (symbols.hasMoreTokens())\r
+ {\r
ascore = symbols.nextToken();\r
scores.addElement((Object) ascore);\r
}\r
\r
Scores.put(id, scores);\r
}\r
- } else if (id.equals("jnetconf")) {\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
+ for (int i = 0; i < numSymbols; i++)\r
+ {\r
conf.set(i, (Object) symbols.nextToken());\r
}\r
- } else {\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
+ for (int i = 0; i < numSymbols; i++)\r
+ {\r
newseq.append(symbols.nextToken());\r
}\r
\r
- if (id.indexOf(";") > -1) {\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
- name = id.substring(id.indexOf(";") + 1) + "_" + 1;\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
- } else {\r
- if (id.equals("JNETPRED")) {\r
+ }\r
+ else\r
+ {\r
+ if (id.equals("JNETPRED"))\r
+ {\r
id = "Predicted Secondary Structure";\r
}\r
\r
}\r
}\r
\r
- if (noSeqs < 1) {\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
+ 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
+ !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
+ 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
+ (QuerySeqPosition == -1))\r
+ {\r
QuerySeqPosition = seqs.size();\r
}\r
\r
}\r
}\r
\r
- /**
- * print
- *
- * @return String
+ /**\r
+ * print\r
+ *\r
+ * @return String\r
*/\r
- public String print() {\r
+ public String print()\r
+ {\r
return "Not Supported";\r
}\r
\r
- public static void main(String[] args) {\r
- try {\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
+ 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
- } catch (java.io.IOException e) {\r
+ }\r
+ catch (java.io.IOException e)\r
+ {\r
System.err.println("Exception " + e);\r
e.printStackTrace();\r
}\r
}\r
\r
\r
-/*
- 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
+ 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