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JAL-1807 explicit imports (jalview.ws.*)
[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
2e000f8
..
1e483e3
100644
(file)
--- a/
src/jalview/ws/jws1/JPredClient.java
+++ b/
src/jalview/ws/jws1/JPredClient.java
@@
-21,6
+21,7
@@
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
@@
-89,7
+90,7
@@
public class JPredClient extends WS1Client
* visible regions
*/
private void startJPredClient(String title, boolean msa,
* visible regions
*/
private void startJPredClient(String title, boolean msa,
- jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+ AlignmentView alview, AlignFrame parentFrame,
boolean viewonly)
{
AlignmentView input = alview;
boolean viewonly)
{
AlignmentView input = alview;
@@
-128,8
+129,7
@@
public class JPredClient extends WS1Client
aln[i] = msf[i].getSeq('-');
}
aln[i] = msf[i].getSeq('-');
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
- true);
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln, true);
if (viewonly)
{
// Remove hidden regions from sequence objects.
if (viewonly)
{
// Remove hidden regions from sequence objects.
@@
-161,8
+161,7
@@
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
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
if (viewonly)
{
// Remove hidden regions from input sequence
if (viewonly)
{
// Remove hidden regions from input sequence
@@
-248,7
+247,7
@@
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,
+ Hashtable SequenceInfo = SeqsetUtils.uniquify(aln,
true);
Jpred server = locateWebService();
true);
Jpred server = locateWebService();
@@
-276,8
+275,7
@@
public class JPredClient extends WS1Client
String altitle = "JNet prediction for sequence " + seq.getName()
+ " from " + title;
String altitle = "JNet prediction for sequence " + seq.getName()
+ " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seq);
+ Hashtable SequenceInfo = SeqsetUtils.SeqCharacterHash(seq);
Jpred server = locateWebService();
if (server == null)
Jpred server = locateWebService();
if (server == null)