X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=497cd63737158295ce90fd31c0eda41609b97d1c;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=a86775d5c4e44f46eb7fd23ad002ff395cc71fbb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index a86775d..497cd63 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,47 +1,34 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
- * 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
+ * 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
{
@@ -50,7 +37,7 @@ public class SeqsetUtils
* Keys are Name, Start, End, SeqFeatures, PdbId
*
* @param seq
- * SequenceI
+ * SequenceI
* @return Hashtable
*/
public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -72,11 +59,19 @@ public class SeqsetUtils
sfeat.addElement(sfarray[i]);
}
}
- sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
- : new Vector());
- sqinfo.put("datasetSequence", (seq.getDatasetSequence() != null) ? seq
- .getDatasetSequence() : new Sequence("THISISAPLACEHOLDER", ""));
+ if (seq.getDatasetSequence() == null)
+ {
+ sqinfo.put("SeqFeatures", sfeat);
+ sqinfo.put("PdbId",
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector());
+ }
+ else
+ {
+ sqinfo.put("datasetSequence",
+ (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+ : new Sequence("THISISAPLACEHOLDER", ""));
+ }
return sqinfo;
}
@@ -85,9 +80,9 @@ public class SeqsetUtils
* these methods with something more elegant.
*
* @param sq
- * SequenceI
+ * SequenceI
* @param sqinfo
- * Hashtable
+ * Hashtable
* @return boolean true if name was not updated from sqinfo Name entry
*/
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
@@ -101,7 +96,7 @@ public class SeqsetUtils
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 pdbid = (Vector) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)
@@ -140,6 +135,11 @@ public class SeqsetUtils
&& !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
.getLength() == 0))
{
+ if (sfeatures != null)
+ {
+ System.err
+ .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ }
sq.setDatasetSequence(seqds);
}
@@ -151,7 +151,7 @@ public class SeqsetUtils
* ordered vector of sequences.
*
* @param i
- * int
+ * int
* @return String
*/
public static String unique_name(int i)
@@ -165,10 +165,10 @@ public class SeqsetUtils
* name.
*
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @param write_names
- * boolean set this to rename each of the sequences to its
- * unique_name(index) name
+ * boolean set this to rename each of the sequences to its
+ * unique_name(index) name
* @return Hashtable to be passed to
* @see deuniquify to recover original names (and properties) for renamed
* sequences
@@ -201,9 +201,9 @@ public class SeqsetUtils
*
* @see uniquify(sequences,true)
* @param map
- * Hashtable
+ * Hashtable
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @return boolean
*/
public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
@@ -217,12 +217,12 @@ public class SeqsetUtils
*
* @see uniquify(sequences,true)
* @param map
- * Hashtable
+ * Hashtable
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @param quiet
- * when false, don't complain about sequences without any data
- * in the map.
+ * when false, don't complain about sequences without any data in the
+ * map.
* @return boolean
*/
public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
@@ -277,7 +277,7 @@ public class SeqsetUtils
* contain at least one residue.
*
* @param sequences
- * SequenceI[]
+ * SequenceI[]
* @return SequenceI[]
*/
public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
@@ -288,8 +288,8 @@ 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)
{