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JAL-3070 pull up sequence anonymisation hash, presets and params list.
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 27 Jul 2018 11:08:13 +0000
(12:08 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 27 Jul 2018 11:08:13 +0000
(12:08 +0100)
src/jalview/ws/AWsJob.java
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src/jalview/ws/jws1/MsaWSThread.java
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src/jalview/ws/jws1/SeqSearchWSThread.java
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src/jalview/ws/jws2/MsaWSThread.java
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diff --git
a/src/jalview/ws/AWsJob.java
b/src/jalview/ws/AWsJob.java
index
f5f9377
..
bb203fc
100644
(file)
--- a/
src/jalview/ws/AWsJob.java
+++ b/
src/jalview/ws/AWsJob.java
@@
-20,6
+20,13
@@
*/
package jalview.ws;
*/
package jalview.ws;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
/**
* Generic properties for an individual job within a Web Service Client thread.
* Derived from jalview web services version 1 statuses, and revised for Jws2.
/**
* Generic properties for an individual job within a Web Service Client thread.
* Derived from jalview web services version 1 statuses, and revised for Jws2.
@@
-145,6
+152,12
@@
public abstract class AWsJob
*/
protected boolean subjobComplete = false;
*/
protected boolean subjobComplete = false;
+ protected WsParamSetI preset = null;
+
+ protected List<ArgumentI> arguments = null;
+
+ protected Hashtable<String, Map> SeqNames = new Hashtable();
+
public AWsJob()
{
}
public AWsJob()
{
}
@@
-227,4
+240,15
@@
public abstract class AWsJob
String state = "";
return state;
}
String state = "";
return state;
}
+
+ public void setPreset(WsParamSetI jobpreset)
+ {
+ preset = jobpreset;
+ }
+
+ public void setArguments(List<ArgumentI> paramset)
+ {
+ arguments = paramset;
+
+ }
}
}
diff --git
a/src/jalview/ws/jws1/MsaWSThread.java
b/src/jalview/ws/jws1/MsaWSThread.java
index
006f014
..
7b3df82
100644
(file)
--- a/
src/jalview/ws/jws1/MsaWSThread.java
+++ b/
src/jalview/ws/jws1/MsaWSThread.java
@@
-36,7
+36,6
@@
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
-import java.util.Hashtable;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
import java.util.Vector;
import vamsas.objects.simple.MsaResult;
@@
-78,8
+77,6
@@
class MsaWSThread extends JWS1Thread implements WSClientI
}
}
- Hashtable SeqNames = new Hashtable();
-
Vector emptySeqs = new Vector();
/**
Vector emptySeqs = new Vector();
/**
diff --git
a/src/jalview/ws/jws1/SeqSearchWSThread.java
b/src/jalview/ws/jws1/SeqSearchWSThread.java
index
761b758
..
2f2bf2c
100644
(file)
--- a/
src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/
src/jalview/ws/jws1/SeqSearchWSThread.java
@@
-37,7
+37,6
@@
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import java.util.HashMap;
import jalview.ws.WSClientI;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
@@
-77,8
+76,6
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
}
}
- Hashtable SeqNames = new Hashtable();
-
Vector emptySeqs = new Vector();
/**
Vector emptySeqs = new Vector();
/**
diff --git
a/src/jalview/ws/jws2/MsaWSThread.java
b/src/jalview/ws/jws2/MsaWSThread.java
index
a0cd0f4
..
b1d6452
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSThread.java
+++ b/
src/jalview/ws/jws2/MsaWSThread.java
@@
-42,9
+42,7
@@
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.List;
-import java.util.Map;
import java.util.Vector;
import javax.swing.JInternalFrame;
import java.util.Vector;
import javax.swing.JInternalFrame;
@@
-69,10
+67,6
@@
class MsaWSThread extends AWS2Thread implements WSClientI
{
long lastChunk = 0;
{
long lastChunk = 0;
- WsParamSetI preset = null;
-
- List<ArgumentI> arguments = null;
-
/**
* input
*/
/**
* input
*/
@@
-107,8
+101,6
@@
class MsaWSThread extends AWS2Thread implements WSClientI
}
}
- Hashtable<String, Map> SeqNames = new Hashtable();
-
Vector<String[]> emptySeqs = new Vector();
/**
Vector<String[]> emptySeqs = new Vector();
/**
@@
-490,7
+482,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
if (conmsa != null)
{
int nvalid = 0, njobs = conmsa.length;
if (conmsa != null)
{
int nvalid = 0, njobs = conmsa.length;
- jobs = new MsaWSJob[njobs];
+ jobs = new AWsJob[njobs];
for (int j = 0; j < njobs; j++)
{
if (j != 0)
for (int j = 0; j < njobs; j++)
{
if (j != 0)
@@
-501,12
+493,12
@@
class MsaWSThread extends AWS2Thread implements WSClientI
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
- if (((MsaWSJob) jobs[j]).hasValidInput())
+ if (jobs[j].hasValidInput())
{
nvalid++;
}
{
nvalid++;
}
- ((MsaWSJob) jobs[j]).preset = preset;
- ((MsaWSJob) jobs[j]).arguments = paramset;
+ jobs[j].setPreset(preset);
+ jobs[j].setArguments(paramset);
((MsaWSJob) jobs[j]).alignmentProgram = wsname;
if (njobs > 0)
{
((MsaWSJob) jobs[j]).alignmentProgram = wsname;
if (njobs > 0)
{