git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1933 only create and add occupancy row to alignment view if showOccupancy viewpor...
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
SeqSearchWSThread.java
diff --git
a/src/jalview/ws/jws1/SeqSearchWSThread.java
b/src/jalview/ws/jws1/SeqSearchWSThread.java
index
86c2b9f
..
b14917e
100644
(file)
--- a/
src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/
src/jalview/ws/jws1/SeqSearchWSThread.java
@@
-21,6
+21,7
@@
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-173,7
+174,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
public Object[] getAlignment(AlignmentI dataset,
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
public Object[] getAlignment(AlignmentI dataset,
- Map<String, Object> featureColours)
+ Map<String, FeatureColourI> featureColours)
{
if (result != null && result.isFinished())
{
if (result != null && result.isFinished())
@@
-208,7
+209,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
if (inFile != null && inFile.length() > 0)
{
new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
if (inFile != null && inFile.length() > 0)
{
new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
}
} catch (Exception e)
{
}
} catch (Exception e)
{
@@
-224,7
+225,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
if (inFile != null && inFile.length() > 0)
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
if (inFile != null && inFile.length() > 0)
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
- inFile, jalview.io.AppletFormatAdapter.PASTE);
+ inFile, jalview.io.DataSourceType.PASTE);
ff.parse(al, featureColours, false);
}
} catch (Exception e)
ff.parse(al, featureColours, false);
}
} catch (Exception e)
@@
-241,7
+242,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
if (!nf.isValid())
{
nf.close();
if (!nf.isValid())
{
nf.close();
@@
-623,7
+624,7
@@
class SeqSearchWSThread extends JWS1Thread implements WSClientI
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Map<String, Object> featureColours = new HashMap<String, Object>();
+ Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())