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RNAStruct replaced by RNAStructScoreManager. Why does webservice
[jabaws.git]
/
webservices
/
compbio
/
ws
/
client
/
Jws2Client.java
diff --git
a/webservices/compbio/ws/client/Jws2Client.java
b/webservices/compbio/ws/client/Jws2Client.java
index
a06a6fa
..
ce4980d
100644
(file)
--- a/
webservices/compbio/ws/client/Jws2Client.java
+++ b/
webservices/compbio/ws/client/Jws2Client.java
@@
-50,7
+50,7
@@
import compbio.data.msa.RegistryWS;
import compbio.data.msa.SequenceAnnotation;
\r
import compbio.data.sequence.Alignment;
\r
import compbio.data.sequence.FastaSequence;
\r
import compbio.data.msa.SequenceAnnotation;
\r
import compbio.data.sequence.Alignment;
\r
import compbio.data.sequence.FastaSequence;
\r
-import compbio.data.sequence.RNAstruct;
\r
+import compbio.data.sequence.RNAStruct;
\r
import compbio.data.sequence.ScoreManager;
\r
import compbio.data.sequence.ClustalAlignmentUtil;
\r
import compbio.data.sequence.SequenceUtil;
\r
import compbio.data.sequence.ScoreManager;
\r
import compbio.data.sequence.ClustalAlignmentUtil;
\r
import compbio.data.sequence.SequenceUtil;
\r
@@
-150,7
+150,6
@@
public class Jws2Client {
String presetName = CmdHelper.getPresetName(cmd);
\r
\r
Metadata<T> msaws = (Metadata<T>) connect(hostname, service);
\r
String presetName = CmdHelper.getPresetName(cmd);
\r
\r
Metadata<T> msaws = (Metadata<T>) connect(hostname, service);
\r
- Metadata<T> foldws = (Metadata<T>) connect(hostname, service);
\r
Preset<T> preset = null;
\r
if (presetName != null) {
\r
preset = MetadataHelper.getPreset(msaws, presetName);
\r
Preset<T> preset = null;
\r
if (presetName != null) {
\r
preset = MetadataHelper.getPreset(msaws, presetName);
\r
@@
-164,7
+163,6
@@
public class Jws2Client {
// System.out.println("The Options read from the command line: " + customOptions);
\r
\r
Alignment alignment = null;
\r
// System.out.println("The Options read from the command line: " + customOptions);
\r
\r
Alignment alignment = null;
\r
- String rnastruct = null;
\r
if (inputFile != null) {
\r
Writer writer = null;
\r
if (outFile != null) {
\r
if (inputFile != null) {
\r
Writer writer = null;
\r
if (outFile != null) {
\r
@@
-178,17
+176,12
@@
public class Jws2Client {
ScoreManager result = analize(inputFile,
\r
((SequenceAnnotation<T>) msaws), preset, customOptions);
\r
\r
ScoreManager result = analize(inputFile,
\r
((SequenceAnnotation<T>) msaws), preset, customOptions);
\r
\r
+ System.out.println(result\.asRNAStruct().toString());
\r
IOHelper.writeOut(writer, result);
\r
} else if (service.getServiceType() == MsaWS.class) {
\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,
\r
customOptions);
\r
IOHelper.writeOut(writer, alignment);
\r
IOHelper.writeOut(writer, result);
\r
} else if (service.getServiceType() == MsaWS.class) {
\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,
\r
customOptions);
\r
IOHelper.writeOut(writer, alignment);
\r
- } else if (service.getServiceType() == FoldWS.class) {
\r
- rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);
\r
- // No IOHelper method for rnastruct/String yet
\r
- if (writer != null) {
\r
- writer.write(rnastruct);
\r
- }
\r
}
\r
writer.close();
\r
}
\r
}
\r
writer.close();
\r
}
\r