X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=40bedad3bd03352c03f85475b41ece9a5491c963;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=0aa2bd5e359f63e1a4ae4dcf6982ca219bf478df;hpb=ccc0d91abe38690088a6050faba8ef66cde1f271;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 0aa2bd5..40bedad 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,46 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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 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
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
-/**
- *
Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @author not attributable
- * @version 1.0
- */
public class SeqsetUtils
{
/**
* Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
- * @param seq SequenceI
+ * Keys are Name, Start, End, SeqFeatures, PdbId
+ *
+ * @param seq
+ * SequenceI
* @return Hashtable
*/
public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -64,18 +61,22 @@ public class SeqsetUtils
}
sqinfo.put("SeqFeatures", sfeat);
sqinfo.put("PdbId",
- (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector());
sqinfo.put("datasetSequence",
- (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
- new Sequence("THISISAPLACEHOLDER", ""));
+ (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+ : new Sequence("THISISAPLACEHOLDER", ""));
return sqinfo;
}
/**
- * Recover essential properties of a sequence from a hashtable
- * TODO: replace these methods with something more elegant.
- * @param sq SequenceI
- * @param sqinfo Hashtable
+ * Recover essential properties of a sequence from a hashtable TODO: replace
+ * these methods with something more elegant.
+ *
+ * @param sq
+ * SequenceI
+ * @param sqinfo
+ * Hashtable
* @return boolean true if name was not updated from sqinfo Name entry
*/
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
@@ -88,9 +89,8 @@ public class SeqsetUtils
String oldname = (String) sqinfo.get("Name");
Integer start = (Integer) sqinfo.get("Start");
Integer end = (Integer) sqinfo.get("End");
- Vector sfeatures = (Vector) sqinfo.get(
- "SeqFeatures");
- Vector pdbid = (Vector) sqinfo.get("PdbId");
+ Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
+ Vector pdbid = (Vector) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)
@@ -106,17 +106,17 @@ public class SeqsetUtils
sq.setPDBId(pdbid);
}
- if ( (start != null) && (end != null))
+ if ((start != null) && (end != null))
{
sq.setStart(start.intValue());
sq.setEnd(end.intValue());
}
- if ( (sfeatures != null) && (sfeatures.size() > 0))
+ if ((sfeatures != null) && (sfeatures.size() > 0))
{
SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
- for (int is=0,isize=sfeatures.size();is 0 && !quiet)
{
System.err.println("Did not find matches for :");
- for (Enumeration i = unmatched.elements(); i.hasMoreElements();
- System.out.println( ( (SequenceI) i.nextElement()).getName()))
+ for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
+ .println(((SequenceI) i.nextElement()).getName()))
{
;
}
@@ -239,9 +262,11 @@ public class SeqsetUtils
}
/**
- * returns a subset of the sequenceI seuqences,
- * including only those that contain at least one residue.
- * @param sequences SequenceI[]
+ * returns a subset of the sequenceI seuqences, including only those that
+ * contain at least one residue.
+ *
+ * @param sequences
+ * SequenceI[]
* @return SequenceI[]
*/
public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
@@ -252,8 +277,8 @@ public class SeqsetUtils
for (int i = 0, j = sequences.length; i < j; i++)
{
String tempseq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- sequences[i].getSequenceAsString());
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
if (tempseq.length() == 0)
{