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JAL-653 set the warningMessage for the file source to allow the GUI to report problem...
[jalview.git]
/
src
/
jalview
/
analysis
/
SeqsetUtils.java
diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
5c6b99b
..
2ede9ed
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,9
+20,14
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import java.util.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
-import jalview.datamodel.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
public class SeqsetUtils
{
public class SeqsetUtils
{
@@
-56,7
+61,7
@@
public class SeqsetUtils
}
sqinfo.put("SeqFeatures", sfeat);
sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
}
sqinfo.put("SeqFeatures", sfeat);
sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
- : new Vector());
+ : new Vector<PDBEntry>());
sqinfo.put("datasetSequence",
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
sqinfo.put("datasetSequence",
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
@@
-84,7
+89,7
@@
public class SeqsetUtils
Integer start = (Integer) sqinfo.get("Start");
Integer end = (Integer) sqinfo.get("End");
Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
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<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)