X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=8163f05ff2b7d98f89b2cc5252ffd6b9cd289222;hb=9ad1e437d5d6366f0b06fbfbdb446a720ca57104;hp=42fbef699cf58028f645a447a6a005de08208e10;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 42fbef6..8163f05 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,25 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
public class DBRefUtils
{
@@ -45,8 +54,8 @@ public class DBRefUtils
{
return dbrefs;
}
- Hashtable srcs = new Hashtable();
- Vector res = new Vector();
+ Map srcs = new HashMap();
+ ArrayList res = new ArrayList();
for (int i = 0; i < sources.length; i++)
{
@@ -56,18 +65,14 @@ public class DBRefUtils
{
if (srcs.containsKey(dbrefs[i].getSource()))
{
- res.addElement(dbrefs[i]);
+ res.add(dbrefs[i]);
}
}
if (res.size() > 0)
{
DBRefEntry[] reply = new DBRefEntry[res.size()];
- for (int i = 0; i < res.size(); i++)
- {
- reply[i] = (DBRefEntry) res.elementAt(i);
- }
- return reply;
+ return res.toArray(reply);
}
res = null;
// there are probable memory leaks in the hashtable!
@@ -166,7 +171,9 @@ public class DBRefUtils
DbRefComp comparator)
{
if (ref == null || entry == null)
+ {
return null;
+ }
Vector rfs = new Vector();
for (int i = 0; i < ref.length; i++)
{
@@ -300,6 +307,7 @@ public class DBRefUtils
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
+ {
if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && refb
@@ -308,6 +316,7 @@ public class DBRefUtils
{
return true;
}
+ }
}
}
return false;
@@ -415,11 +424,15 @@ public class DBRefUtils
// check for chaincode and mapping
// PFAM style stockhom PDB citation
com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
- "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
if (r.search(acn.trim()))
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
+ if (chaincode==null)
+ {
+ chaincode = " ";
+ }
String mapstart = r.stringMatched(3);
String mapend = r.stringMatched(4);
if (chaincode.equals(" "))
@@ -430,7 +443,11 @@ public class DBRefUtils
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setProperty(new Hashtable());
+ pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
+ } else {
+ System.err.println("Malformed PDB DR line:"+acn);
}
}
else