/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package MCview;
public void parse() throws IOException
{
- // TODO set the filename sensibly
- id = (inFile == null || inFile.getName()==null || inFile.getName().length()==0) ? "PDBFILE" : inFile.getName();
- try
- {
- chains = new Vector();
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
+
+ chains = new Vector();
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
- String lastID="";
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- String atomnam=null;
+ int index = 0;
+ String atomnam = null;
+ try
+ {
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
{
- if (line.length()>62)
+ if (line.length() > 62)
{
String tid;
- if (line.length()>67) {
+ if (line.length() > 67)
+ {
tid = line.substring(62, 67).trim();
- } else {
- tid=line.substring(62).trim();
}
- if (tid.length()>0)
+ else
+ {
+ tid = line.substring(62).trim();
+ }
+ if (tid.length() > 0)
{
id = tid;
}
{
if (tmpatom.resNumIns.trim().equals(lastID))
{
- // phosphorylated protein - seen both CA and P..
+ // phosphorylated protein - seen both CA and P..
continue;
}
tmpchain.atoms.addElement(tmpatom);
{
entry.setFile(inFile.getAbsolutePath());
}
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
dataset.addPDBId(entry);
SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
- // maintain reference to
- // dataset
+ // maintain reference to
+ // dataset
seqs.addElement(chainseq);
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
throw new IOException("Out of memory loading PDB File");
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
+ }
+ }
+
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int p = 0;
+ while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
+ {
+ dataName = dataName.substring(p + 1);
}
+ return dataName;
}
public void makeResidueList()