-/*
-* 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
+import jalview.datamodel.*;\r
+\r
\r
/**\r
* DOCUMENT ME!\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
{\r
\r
while (ids.lastIndexOf(name) > -1)\r
{\r
- name = id.substring(id.indexOf(";") + 1) + "_" + 1;\r
+ name = id.substring(id.indexOf(";") + 1) + "_" + ++i;\r
}\r
\r
ids.addElement(name);\r
}\r
}\r
}\r
-\r
+ /* leave it to the parser user to actually check this.\r
if (noSeqs < 1)\r
{\r
throw new IOException(\r
"JpredFile Parser: No sequence in the prediction!");\r
- }\r
+ }*/\r
\r
maxLength = seq_entries.elementAt(0).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
+ throw new IOException("JPredConcise: "\r
+ +AppletFormatAdapter.INVALID_CHARACTERS +" : "\r
+ +ids.elementAt(i).toString() + ")");\r
}\r
\r
if (maxLength != seq_entries.elementAt(i).toString().length())\r
}\r
}\r
\r
- /**
- * print
- *
- * @return String
+ /**\r
+ * print\r
+ *\r
+ * @return String\r
*/\r
public String print()\r
{\r
e.printStackTrace();\r
}\r
}\r
+ Vector annotSeqs=null;\r
+ /**\r
+ * removeNonSequences\r
+ */\r
+ public void removeNonSequences()\r
+ {\r
+ if (annotSeqs!=null)\r
+ return;\r
+ annotSeqs = new Vector();\r
+ Vector newseqs = new Vector();\r
+ int i=0;\r
+ int j=seqs.size();\r
+ for (; i<QuerySeqPosition; i++)\r
+ annotSeqs.add(seqs.get(i));\r
+ // check that no stray annotations have been added at the end.\r
+ {\r
+ SequenceI sq = (SequenceI) seqs.get(j-1);\r
+ if (sq.getName().toUpperCase().startsWith("JPRED")) {\r
+ annotSeqs.add(sq);\r
+ seqs.remove(--j);\r
+ }\r
+ }\r
+ for (; i<j; i++)\r
+ newseqs.add(seqs.get(i));\r
+\r
+ seqs.clear();\r
+ seqs = newseqs;\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