/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
*
- * 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
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
/**
* PredFile.java
Hashtable Scores; // Hash of names and score vectors
Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
- // vector
+
+ // vector
private int QuerySeqPosition;
* Creates a new JPredFile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public JPredFile(String inFile, String type) throws IOException
{
* DOCUMENT ME!
*
* @param QuerySeqPosition
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setQuerySeqPosition(int QuerySeqPosition)
{
seqs.addElement(newSeq);
}
- if (seqs.size() > 0 && QuerySeqPosition>-1)
+ if (seqs.size() > 0 && QuerySeqPosition > -1)
{
// try to make annotation for a prediction only input (default if no
- // alignment is given and prediction contains a QUERY or align;sequence_id line)
+ // alignment is given and prediction contains a QUERY or align;sequence_id
+ // line)
Alignment tal = new Alignment(this.getSeqsAsArray());
try
{
IOException ex = new IOException(
"Couldn't parse concise annotation for prediction profile.\n"
+ e);
- e.printStackTrace(); // java 1.1 does not have : ex.setStackTrace(e.getStackTrace());
+ e.printStackTrace(); // java 1.1 does not have :
+ // ex.setStackTrace(e.getStackTrace());
throw ex;
}
this.annotations = new Vector();
* DOCUMENT ME!
*
* @param args
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static void main(String[] args)
{
/*
* 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("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) + " ");
*
* 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);
+ * 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); } }
- * }
+ * System.out.println("Exception " + e); } } }
*/