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Merge branch 'alpha/origin_2022_JAL-3066_Jalview_212_slivka-integration' into spike...
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
JPredClient.java
diff --git
a/src/jalview/ws/jws1/JPredClient.java
b/src/jalview/ws/jws1/JPredClient.java
index
2b133a7
..
076d71e
100644
(file)
--- a/
src/jalview/ws/jws1/JPredClient.java
+++ b/
src/jalview/ws/jws1/JPredClient.java
@@
-23,6
+23,7
@@
package jalview.ws.jws1;
import java.util.Locale;
import jalview.analysis.AlignSeq;
import java.util.Locale;
import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
@@
-36,6
+37,7
@@
import jalview.util.MessageManager;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Hashtable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Hashtable;
+import java.util.Map;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
@@
-129,8
+131,8
@@
public class JPredClient extends WS1Client
aln[i] = msf[i].getSeq('-');
}
aln[i] = msf[i].getSeq('-');
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Map<String, SequenceInfo> SequenceInfo =
+ jalview.analysis.SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
if (viewonly)
{
// Remove hidden regions from sequence objects.
@@
-163,7
+165,7
@@
public class JPredClient extends WS1Client
+ (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ " from " + title;
String seqname = seq.getName();
+ (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ " from " + title;
String seqname = seq.getName();
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
if (viewonly)
{
.SeqCharacterHash(seq);
if (viewonly)
{
@@
-251,8
+253,8
@@
public class JPredClient extends WS1Client
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Map<String, SequenceInfo> SequenceInfo =
+ jalview.analysis.SeqsetUtils.uniquify(aln, true);
Jpred server = locateWebService();
if (server == null)
Jpred server = locateWebService();
if (server == null)
@@
-280,7
+282,7
@@
public class JPredClient extends WS1Client
String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
.SeqCharacterHash(seq);
Jpred server = locateWebService();
.SeqCharacterHash(seq);
Jpred server = locateWebService();